diff --git a/.github/labeler.yml b/.github/labeler.yml index 00e85fd53..5f063c512 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -35,7 +35,7 @@ area:Core: area:Documentation: files: - "Documentation/*" - - "Documentation.rst" + - "Documentation.md" area:Filtering: files: @@ -93,4 +93,4 @@ type:Infrastructure: - "Formatting/*" - "Superbuild/*" - "Utilities/*" - - "index.rst" + - "index.md" diff --git a/.github/workflows/build-test-publish.yml b/.github/workflows/build-test-publish.yml index 055ffcca5..042ea93dc 100644 --- a/.github/workflows/build-test-publish.yml +++ b/.github/workflows/build-test-publish.yml @@ -3,7 +3,7 @@ name: Build, test, publish on: [push,pull_request] env: - itk-git-tag: "v5.4rc03" + itk-git-tag: "v5.4.0" jobs: build-test-cxx: diff --git a/CMakeLists.txt b/CMakeLists.txt index bad72f548..48a023351 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -240,7 +240,7 @@ if(BUILD_DOCUMENTATION) add_custom_target(copy_sources ALL COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/src" "${ITKSphinxExamples_BINARY_DIR}/src" COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Documentation" "${ITKSphinxExamples_BINARY_DIR}/Documentation" - COMMAND ${CMAKE_COMMAND} -E copy "${ITKSphinxExamples_SOURCE_DIR}/index.rst" "${ITKSphinxExamples_BINARY_DIR}/index.rst" + COMMAND ${CMAKE_COMMAND} -E copy "${ITKSphinxExamples_SOURCE_DIR}/index.md" "${ITKSphinxExamples_BINARY_DIR}/index.md" COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Formatting" "${ITKSphinxExamples_BINARY_DIR}/Formatting" COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Utilities" diff --git a/Documentation/Build/index.md b/Documentation/Build/index.md new file mode 100644 index 000000000..d91e6363a --- /dev/null +++ b/Documentation/Build/index.md @@ -0,0 +1,279 @@ +# Build, Run, Visualize + +(run-python-examples)= + +The Python examples do not need to be built. First, install Python from +[python.org](https://www.python.org/), [Anaconda](https://www.anaconda.com/distribution), or a system package manager like +Ubuntu Linux [apt](https://help.ubuntu.com/lts/serverguide/apt.html) +or macOS [Homebrew](https://brew.sh/). + +Next, install the *itk* package: + +``` +python -m pip install --upgrade pip +python -m pip install itk +``` + +:::{figure} DownloadExampleHighlighted.png +:align: center +:alt: Download an example + +Download [an example](https://itk.org/ITKExamples/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.html) +by clicking the *Download* button. +::: + +Download the *\.zip* file from the link on the top +of an example's webpage. Unpack the example. For example, + +``` +unzip ExampleName.zip +``` + +Finally, run the example: + +``` +python ExampleName/Code.py +``` + +(build-individual-examples)= + +## Build individual examples + +Download the *\.zip* file from the link on the top +of the example's webpage. Unpack the example: + +``` +unzip ExampleName.zip +``` + +Set convenience variables: + +``` +ITK_SOURCE=ExampleName +ITK_BUILD=ExampleName/build +``` + +Move to the build directory: + +``` +cd ${ITK_BUILD} +``` + +Run CMake (minimum version 3.10.2) to configure the project. + +- If ITK Version 5.0.0 or above not installed but compiled on your + system, you will need to specify the path to your ITK build: + + ``` + cmake -DITK_DIR=/home/luis/itk_build -S ${ITK_SOURCE} -B ${ITK_BUILD} + ``` + +Build the project, and run the test: + +``` +cmake --build . +ctest -V +``` + +(building-examples)= + +## Build all examples and the documentation + +Set convenience variables: + +``` +ITK_SOURCE=ITKEx +ITK_BUILD=ITKEx-build +``` + +Clone the repository: + +``` +git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git ${ITK_SOURCE} +``` + +Make a build directory: + +``` +mkdir -p ${ITK_BUILD} +cd ${ITK_BUILD} +``` + +Run CMake (minimum version 3.10.2) to configure the project. + +- If ITK is not installed nor compiled, you can then make use of the superbuild functionality: + + ``` + cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE}/Superbuild/ -B ${ITK_BUILD} + ``` + +- If ITK (Version 5.0.0 or above) is installed: + + ``` + cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE} -B ${ITK_BUILD} + ``` + +- If ITK (Version 5.0.0 or above) is not installed but compiled on your + system, you will need to specify the path to your ITK build: + + ``` + ITK_COMPILED_DIR=/usr/opt/itk_build + cmake -DITK_DIR=${ITK_COMPILED_DIR} -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE_DIR} -B ${ITK_BUILD_DIR} + ``` + +The superbuild will download and build all required dependencies. If you are +building the documentation and not using superbuild functionality, then you must +have all the required dependencies installed, which are listed in the +*README.rst* file located at the root of the source tree. If you just want to +build the examples and not their documentation, set *BUILD_DOCUMENTATION* to +*OFF* in your CMake configuration. + +Build the project (this will generate the documentation and all examples): + +``` +cmake --build . +``` + +Run the tests with a superbuild: + +``` +cd ${ITK_BUILD_DIR}/ITKEX-build +ctest -V +``` + +Run the tests without a superbuild: + +``` +cd ${ITK_BUILD_DIR} +ctest -V +``` + +## Run an example + +After building the examples, you can run an example by using `cd` to move to +the example's directory. Then, directly run the executable. + +Alternatively, the `ctest` command line program that comes with [CMake] can be +used to drive the examples as unit test. Running: + +``` +ctest +``` + +in the binary tree will run all unit tests found in the current directory and +below. + +``` +ctest -R Binary +``` + +will run all tests whose name matches the regular expression *Binary*. + +``` +ctest -V +``` + +will run *ctest* in verbose mode, which prints out the command executed and all +of the resulting text output. + +(visualize)= + +## Visualize the results + +ITK is a library limited in scope to image analysis, and it purposely does not +attempt to perform image visualization. Visualizing the results of analysis is +possible with a number of third-party applications. Note that these packages +are specially suited for medical images, which often have anisotropic spacing +and can span three or more dimensions. All applications listed are open source +and cross-platform. + +3DSlicer + +: [3DSlicer] is an open-source software platform for the analysis and + visualization of medical images and for research in image guided therapy. + The platform provides functionality for segmentation, registration and + three-dimensional visualization of multi-modal image data, as well as advanced + image analysis algorithms for diffusion tensor imaging, functional magnetic + resonance imaging and image-guided therapy. Standard image file formats are + supported, and the application integrates interface capabilities to biomedical + research software and image informatics frameworks. + +:::{figure} Slicer.png +:align: center +:alt: 3DSlicer + +[3DSlicer] +::: + +ImageViewer + +: An [FLTK]-based [ImageViewer] was extracted from the [ITKApps] repository. This + simple yet effective slice-based viewer works on 2D and 3D images and supports + probing of data values. + +:::{figure} ImageViewer.png +:align: center +:alt: ITKApps ImageViewer + +ImageViewer +::: + +ITK-SNAP + +: [ITK-SNAP] is segmentation application, but it is also a nice general + resource for visualization of the results of analysis. + +:::{figure} ITK-SNAP.png +:align: center +:alt: ITK-SNAP + +[ITK-SNAP] +::: + +MITK + +: [MITK] is a free open-source software system for development of interactive + medical image processing software. + +:::{figure} MITK.png +:align: center +:alt: MITK + +[MITK] +::: + +Paraview + +: [Paraview] is a full-featured scientific visualizion GUI written with [Qt]/[VTK]. + It has extensive parallel processing capabilities. + +:::{figure} Paraview.png +:align: center +:alt: Paraview + +[Paraview] +::: + +VV + +: [VV] is an image viewer designed for fast and simple visualization of + spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images. + +:::{figure} VV.png +:align: center +:alt: VV + +[VV] +::: + +[3dslicer]: https://www.slicer.org/ +[cmake]: https://cmake.org/ +[fltk]: https://www.fltk.org/index.php +[imageviewer]: https://github.com/KitwareMedical/ImageViewer +[itk-snap]: http://www.itksnap.org/pmwiki/pmwiki.php +[itkapps]: https://github.com/InsightSoftwareConsortium/ITKApps +[mitk]: https://www.mitk.org/wiki/MITK +[paraview]: https://www.paraview.org/ +[qt]: https://www.qt.io/developers/ +[vtk]: https://vtk.org/ +[vv]: https://www.creatis.insa-lyon.fr/rio/vv diff --git a/Documentation/Build/index.rst b/Documentation/Build/index.rst deleted file mode 100644 index 0707a273e..000000000 --- a/Documentation/Build/index.rst +++ /dev/null @@ -1,250 +0,0 @@ -Build, Run, Visualize -================================ - -.. _run-python-examples: - -The Python examples do not need to be built. First, install Python from -`python.org `_, `Anaconda -`_, or a system package manager like -Ubuntu Linux `apt `_ -or macOS `Homebrew `_. - -Next, install the *itk* package:: - - python -m pip install --upgrade pip - python -m pip install itk - -.. figure:: DownloadExampleHighlighted.png - :alt: Download an example - :align: center - - Download `an example - `_ - by clicking the *Download* button. - -Download the *.zip* file from the link on the top -of an example's webpage. Unpack the example. For example, - -:: - - unzip ExampleName.zip - -Finally, run the example:: - - python ExampleName/Code.py - - -.. _build-individual-examples: - -Build individual examples -------------------------- - -Download the *.zip* file from the link on the top -of the example's webpage. Unpack the example:: - - unzip ExampleName.zip - -Set convenience variables:: - - ITK_SOURCE=ExampleName - ITK_BUILD=ExampleName/build - -Move to the build directory:: - - cd ${ITK_BUILD} - -Run CMake (minimum version 3.10.2) to configure the project. - -- If ITK Version 5.0.0 or above not installed but compiled on your - system, you will need to specify the path to your ITK build:: - - cmake -DITK_DIR=/home/luis/itk_build -S ${ITK_SOURCE} -B ${ITK_BUILD} - -Build the project, and run the test:: - - cmake --build . - ctest -V - - -.. _building-examples: - -Build all examples and the documentation ----------------------------------------- - -Set convenience variables:: - - ITK_SOURCE=ITKEx - ITK_BUILD=ITKEx-build - -Clone the repository:: - - git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git ${ITK_SOURCE} - -Make a build directory:: - - mkdir -p ${ITK_BUILD} - cd ${ITK_BUILD} - -Run CMake (minimum version 3.10.2) to configure the project. - -- If ITK is not installed nor compiled, you can then make use of the superbuild functionality:: - - cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE}/Superbuild/ -B ${ITK_BUILD} - -- If ITK (Version 5.0.0 or above) is installed:: - - cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE} -B ${ITK_BUILD} - -- If ITK (Version 5.0.0 or above) is not installed but compiled on your - system, you will need to specify the path to your ITK build:: - - ITK_COMPILED_DIR=/usr/opt/itk_build - cmake -DITK_DIR=${ITK_COMPILED_DIR} -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE_DIR} -B ${ITK_BUILD_DIR} - -The superbuild will download and build all required dependencies. If you are -building the documentation and not using superbuild functionality, then you must -have all the required dependencies installed, which are listed in the -*README.rst* file located at the root of the source tree. If you just want to -build the examples and not their documentation, set *BUILD_DOCUMENTATION* to -*OFF* in your CMake configuration. - -Build the project (this will generate the documentation and all examples):: - - cmake --build . - -Run the tests with a superbuild:: - - cd ${ITK_BUILD_DIR}/ITKEX-build - ctest -V - -Run the tests without a superbuild:: - - cd ${ITK_BUILD_DIR} - ctest -V - -Run an example --------------- - -After building the examples, you can run an example by using `cd` to move to -the example's directory. Then, directly run the executable. - -Alternatively, the `ctest` command line program that comes with CMake_ can be -used to drive the examples as unit test. Running:: - - ctest - -in the binary tree will run all unit tests found in the current directory and -below. - -:: - - ctest -R Binary - -will run all tests whose name matches the regular expression *Binary*. - -:: - - ctest -V - -will run *ctest* in verbose mode, which prints out the command executed and all -of the resulting text output. - - -.. _visualize: - -Visualize the results ---------------------- - -ITK is a library limited in scope to image analysis, and it purposely does not -attempt to perform image visualization. Visualizing the results of analysis is -possible with a number of third-party applications. Note that these packages -are specially suited for medical images, which often have anisotropic spacing -and can span three or more dimensions. All applications listed are open source -and cross-platform. - - -3DSlicer - 3DSlicer_ is an open-source software platform for the analysis and - visualization of medical images and for research in image guided therapy. - The platform provides functionality for segmentation, registration and - three-dimensional visualization of multi-modal image data, as well as advanced - image analysis algorithms for diffusion tensor imaging, functional magnetic - resonance imaging and image-guided therapy. Standard image file formats are - supported, and the application integrates interface capabilities to biomedical - research software and image informatics frameworks. - -.. figure:: Slicer.png - :alt: 3DSlicer - :align: center - - 3DSlicer_ - - -ImageViewer - An FLTK_-based ImageViewer_ was extracted from the ITKApps_ repository. This - simple yet effective slice-based viewer works on 2D and 3D images and supports - probing of data values. - -.. figure:: ImageViewer.png - :alt: ITKApps ImageViewer - :align: center - - ImageViewer - - -ITK-SNAP - ITK-SNAP_ is segmentation application, but it is also a nice general - resource for visualization of the results of analysis. - -.. figure:: ITK-SNAP.png - :alt: ITK-SNAP - :align: center - - ITK-SNAP_ - - -MITK - MITK_ is a free open-source software system for development of interactive - medical image processing software. - -.. figure:: MITK.png - :alt: MITK - :align: center - - MITK_ - - -Paraview - Paraview_ is a full-featured scientific visualizion GUI written with Qt_/VTK_. - It has extensive parallel processing capabilities. - -.. figure:: Paraview.png - :alt: Paraview - :align: center - - Paraview_ - - -VV - VV_ is an image viewer designed for fast and simple visualization of - spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images. - -.. figure:: VV.png - :alt: VV - :align: center - - VV_ - - -.. _3DSlicer: https://www.slicer.org/ -.. _CMake: https://cmake.org/ -.. _FLTK: https://www.fltk.org/index.php -.. _ImageViewer: https://github.com/KitwareMedical/ImageViewer -.. _ITKApps: https://github.com/InsightSoftwareConsortium/ITKApps -.. _ITK-SNAP: http://www.itksnap.org/pmwiki/pmwiki.php -.. _MITK: https://www.mitk.org/wiki/MITK -.. _Paraview: https://www.paraview.org/ -.. _Qt: https://www.qt.io/developers/ -.. _VTK: https://vtk.org/ -.. _VV: https://www.creatis.insa-lyon.fr/rio/vv - diff --git a/Documentation/Contribute/ContributeWithGit.md b/Documentation/Contribute/ContributeWithGit.md new file mode 100644 index 000000000..46f327714 --- /dev/null +++ b/Documentation/Contribute/ContributeWithGit.md @@ -0,0 +1,92 @@ +(text-editor-submission)= + +# Contribute with Git + +## Clone the repository and setup for development + +The entire source tree can be downloaded with [Git]: + +```bash +git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git ITKEx +``` + +:::{note} +Due to path length limitations on Windows, it is recommended to clone into a +short directory like *ITKEx*. +::: + +After cloning the repository, it can be configured for development (confirm +proper Git configuration, setup [Git hooks], configure your [GitHub account]) +with + +```bash +cd ITKEx +./Utilities/SetupForDevelopment.sh +``` + +## Modifying an existing example + +First, create a local branch: + +``` +git checkout -b Modification +``` + +Modify existing example (source code and/or corresponding documentation). +Add files which are missing + +``` +git add missing_files +``` + +Once you are done, commit your changes as follows: + +``` +git commit -a +``` + +To submit your changes to [GitHub]: + +``` +git review-push +``` + +(createnewexample)= + +## Create a new example + +To create a new example, first install [Cookiecutter]: + +``` +python -m pip install cookiecutter titlecase +``` + +and make use of the Python script located in the +binary tree (*/path/to/ITKSphinxExamples-build/Utilities*): + +``` +cd /path/to/ITKSphinxExamples-build/Utilities +python ./CreateNewExample.py +``` + +The script will ask for an *example_name* and a *class_name*. The example_name +would be *ComputeTumorIntensityVariation* for an example that answers the +question "How do I compute tumor intensity variation?" The class_name +indicates the itk class that is the focus of the example, such as +*itk::Statistics::MaskedImageToHistogramFilter*. + +*This script will generate \*.cxx, \*.py, and \*.rst files to be modified.* + +Note that the generated files are then located based on the group, module and +class name to be demonstrated. For instance an example which would demonstrate +the usage of {itkdox}`itk::Image` will be generated in +`src/Core/Common/`. + +Please do not add images directly to the repository. Instead, use the +{ref}`content link system `. + +[cookiecutter]: https://cookiecutter.readthedocs.io/en/latest/ +[git]: https://git-scm.com/ +[git hooks]: https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks +[github]: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples +[github account]: https://github.com/login diff --git a/Documentation/Contribute/ContributeWithGit.rst b/Documentation/Contribute/ContributeWithGit.rst deleted file mode 100644 index d66057dad..000000000 --- a/Documentation/Contribute/ContributeWithGit.rst +++ /dev/null @@ -1,90 +0,0 @@ -.. _text-editor-submission: - -Contribute with Git -=================== - -Clone the repository and setup for development ----------------------------------------------- - -The entire source tree can be downloaded with Git_: - -.. code-block:: bash - - git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git ITKEx - -.. note:: - - Due to path length limitations on Windows, it is recommended to clone into a - short directory like *ITKEx*. - -After cloning the repository, it can be configured for development (confirm -proper Git configuration, setup `Git hooks`_, configure your `GitHub account`_) -with - -.. code-block:: bash - - cd ITKEx - ./Utilities/SetupForDevelopment.sh - - -Modifying an existing example ------------------------------ - -First, create a local branch:: - - git checkout -b Modification - - -Modify existing example (source code and/or corresponding documentation). -Add files which are missing :: - - git add missing_files - - -Once you are done, commit your changes as follows:: - - git commit -a - - -To submit your changes to `GitHub`_:: - - git review-push - - -.. _CreateNewExample: - -Create a new example --------------------- - -To create a new example, first install `Cookiecutter`_:: - - python -m pip install cookiecutter titlecase - -and make use of the Python script located in the -binary tree (*/path/to/ITKSphinxExamples-build/Utilities*):: - - cd /path/to/ITKSphinxExamples-build/Utilities - python ./CreateNewExample.py - -The script will ask for an *example_name* and a *class_name*. The example_name -would be *ComputeTumorIntensityVariation* for an example that answers the -question "How do I compute tumor intensity variation?" The class_name -indicates the itk class that is the focus of the example, such as -*itk::Statistics::MaskedImageToHistogramFilter*. - -*This script will generate *.cxx, *.py, and *.rst files to be modified.* - -Note that the generated files are then located based on the group, module and -class name to be demonstrated. For instance an example which would demonstrate -the usage of :itkdox:`itk::Image` will be generated in -``src/Core/Common/``. - -Please do not add images directly to the repository. Instead, use the -:ref:`content link system `. - - -.. _Git: https://git-scm.com/ -.. _Git hooks: https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks -.. _GitHub account: https://github.com/login -.. _GitHub: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples -.. _Cookiecutter: https://cookiecutter.readthedocs.io/en/latest/ diff --git a/Documentation/Contribute/DashboardSubmission.md b/Documentation/Contribute/DashboardSubmission.md new file mode 100644 index 000000000..aed79fc8d --- /dev/null +++ b/Documentation/Contribute/DashboardSubmission.md @@ -0,0 +1,134 @@ +# Submit results to CDash + +Quality control of the examples is maintained with a dashboard that collects +configuration, build, and testings results in a [CDash] dashboard. Examples are +compiled nightly, executed and compared to baseline images to ensure these +examples remain valid on all supported platforms and to ensure changes in the +development of ITK do not adversely effect these examples. + +## Experimental submission + +To submit test results after {ref}`building all the examples `, simply run: + +``` +ctest -D Experimental +``` + +at the top of the build tree. + +## Nightly submission + +You can volunteer to submit nightly testing results that ensure repository +activity during the day will allow breakage on your system to go unnoticed. + +### Step 1: Setup the build directory + +You will need a directory with sufficient disk space to hold the project source +code, build tree, and testing scripts. This can be placed anywhere on your +system where you have write access: + +``` +mkdir ~/dashboards +cd ~/dashboards +``` + +Copy the testing support script into your dashboard directory. + +``` +cp ~/src/ITKSphinxExamples/Utilities/Dashboard/itkexamples_common.cmake . +``` + +### Step 2: Setup a script describing your system + +We will write a CTest script that will update the repository, configure, build, +and test the project, and then upload the results to the CDash server. Most of +work in this script will be performed by `itkexamples_common.cmake`, but we need +to configure the settings unique to our system. + +Create a file, `itkexamples_dashboard.cmake`, to hold these settings: + +``` +cp ~/src/ITKSphinxExamples/Utilities/Dashboard/itkexamples_dashboard.cmake.example itkexamples_dashboard.cmake +``` + +You *must* edit this file to describe your local system. + +```{literalinclude} ../../Utilities/Dashboard/itkexamples_dashboard.cmake.example +:language: cmake +``` + +### Step 3: Configure your system to run the script on a daily basis + +#### Linux or Mac + +First, test the script to ensure that it runs correctly: + +``` +.. code-block:: bash +``` + +> ctest -S ./itkexamples_dashboard.cmake -V -A + +Did everything work? Do you see your build on the [ITKSphinxExamples dashboard]? +If so, continue to [setup a cronjob] that will run the script daily. Edit your +crontab: + +``` +.. code-block:: bash +``` + +> crontab -e + +The following line will run the script every day at 3 AM: + +``` +.. code-block:: bash +``` + +> 0 3 * * * ctest -S /home/luis/dashboards/itkexamples_dashboard.cmake -A &> /dev/null + +#### Windows + +In windows, the scheduler can be accessed by entering the *Schedule tasks* +program in the Control Panel. + +It may be useful to put all the nightly dashboards in a batch script and run the +batch script daily. When creating the new task, the Action associate with the +task is to *Start a program*. This script could be placed at: + +``` +.. code-block:: bash +``` + +> C:Dashboardsrun_dashboard.bat + +where `run_dashboard.bat` contains: + +``` +.. code-block:: bash +``` + +> call ctest -S C:Dashboardsitkexamples_dashboard.cmake + +To schedule your Windows box to reboot nightly, set up a task that runs: + +``` +.. code-block:: bash +``` + +> C:WindowsSystem32shutdown.exe /r /t 60 /f + +If you're automatically rebooting your computer every night, you also need to +make sure the computer automatically logs in as the dashboard user when it boots +back up. To do this + +1. Enter `control userpasswords2` in the *Start*, *Run...* menu entry or a *cmd.exe* shell. +2. Select the account of the user you want to automatically login. +3. Uncheck the box labelled *Users must enter a user name and password to use this computer* +4. Click OK. + +Thank you for contributing to the quality of the ITK Sphinx Examples! + +[cdash]: https://www.cdash.org/ +[itksphinxexamples dashboard]: https://open.cdash.org/index.php?project=Insight&filtercount=1&showfilters=0&field1=buildname/string&compare1=63&value1=Examples +[setup a cronjob]: https://en.wikipedia.org/wiki/Cron diff --git a/Documentation/Contribute/DashboardSubmission.rst b/Documentation/Contribute/DashboardSubmission.rst deleted file mode 100644 index b1dbb7219..000000000 --- a/Documentation/Contribute/DashboardSubmission.rst +++ /dev/null @@ -1,123 +0,0 @@ -Submit results to CDash -======================= - -Quality control of the examples is maintained with a dashboard that collects -configuration, build, and testings results in a CDash_ dashboard. Examples are -compiled nightly, executed and compared to baseline images to ensure these -examples remain valid on all supported platforms and to ensure changes in the -development of ITK do not adversely effect these examples. - -Experimental submission ------------------------ - -To submit test results after :ref:`building all the examples `, simply run:: - - ctest -D Experimental - -at the top of the build tree. - -Nightly submission ------------------- - -You can volunteer to submit nightly testing results that ensure repository -activity during the day will allow breakage on your system to go unnoticed. - -Step 1: Setup the build directory -................................. - -You will need a directory with sufficient disk space to hold the project source -code, build tree, and testing scripts. This can be placed anywhere on your -system where you have write access:: - - mkdir ~/dashboards - cd ~/dashboards - -Copy the testing support script into your dashboard directory. - -:: - - cp ~/src/ITKSphinxExamples/Utilities/Dashboard/itkexamples_common.cmake . - -Step 2: Setup a script describing your system -............................................. - -We will write a CTest script that will update the repository, configure, build, -and test the project, and then upload the results to the CDash server. Most of -work in this script will be performed by `itkexamples_common.cmake`, but we need -to configure the settings unique to our system. - -Create a file, `itkexamples_dashboard.cmake`, to hold these settings:: - - cp ~/src/ITKSphinxExamples/Utilities/Dashboard/itkexamples_dashboard.cmake.example itkexamples_dashboard.cmake - -You *must* edit this file to describe your local system. - -.. literalinclude:: ../../Utilities/Dashboard/itkexamples_dashboard.cmake.example - :language: cmake - -Step 3: Configure your system to run the script on a daily basis -................................................................ - -Linux or Mac -^^^^^^^^^^^^ - -First, test the script to ensure that it runs correctly:: - -.. code-block:: bash - - ctest -S ./itkexamples_dashboard.cmake -V -A - -Did everything work? Do you see your build on the `ITKSphinxExamples dashboard`_? -If so, continue to `setup a cronjob`_ that will run the script daily. Edit your -crontab:: - -.. code-block:: bash - - crontab -e - -The following line will run the script every day at 3 AM:: - -.. code-block:: bash - - 0 3 * * * ctest -S /home/luis/dashboards/itkexamples_dashboard.cmake -A &> /dev/null - -Windows -^^^^^^^ - -In windows, the scheduler can be accessed by entering the *Schedule tasks* -program in the Control Panel. - -It may be useful to put all the nightly dashboards in a batch script and run the -batch script daily. When creating the new task, the Action associate with the -task is to *Start a program*. This script could be placed at:: - -.. code-block:: bash - - C:\Dashboards\run_dashboard.bat - -where `run_dashboard.bat` contains:: - -.. code-block:: bash - - call ctest -S C:\Dashboards\itkexamples_dashboard.cmake - -To schedule your Windows box to reboot nightly, set up a task that runs:: - -.. code-block:: bash - - C:\Windows\System32\shutdown.exe /r /t 60 /f - -If you're automatically rebooting your computer every night, you also need to -make sure the computer automatically logs in as the dashboard user when it boots -back up. To do this - -1. Enter `control userpasswords2` in the *Start*, *Run...* menu entry or a *cmd.exe* shell. -2. Select the account of the user you want to automatically login. -3. Uncheck the box labelled *Users must enter a user name and password to use this computer* -4. Click OK. - -Thank you for contributing to the quality of the ITK Sphinx Examples! - -.. _CDash: https://www.cdash.org/ -.. _ITKSphinxExamples dashboard: https://open.cdash.org/index.php?project=Insight&filtercount=1&showfilters=0&field1=buildname/string&compare1=63&value1=Examples -.. _setup a cronjob: https://en.wikipedia.org/wiki/Cron diff --git a/Documentation/Contribute/PeerReviewWithGitHub.md b/Documentation/Contribute/PeerReviewWithGitHub.md new file mode 100644 index 000000000..8dca58f49 --- /dev/null +++ b/Documentation/Contribute/PeerReviewWithGitHub.md @@ -0,0 +1,48 @@ +# Peer review with GitHub + +GitHub code reviews are a method to vastly improve the quality of code, train +new community members, and learn from other community members. In this +section, we describe how to perform a pull request review. + +## Peer review duty + +All community members are encouraged to perform reviews. If possible, all code +that is merged should be reviewed and marked *Approved* by at least one other +community member prior to merging. In order for this system to function +smoothly, community members must perform more reviews than submit patches. +Any community member can register for a GitHub account and perform a review. + +Please review any patch of interest open for review on GitHub; it is not +necessary for the author to request your review. + +## Review comments + +To start a review, open the pull request, then click on an individual commit. +Or, view all files changed in the topic branch by clicking *Files changed*. + +When reviewing files, inline comments can be entered by clicking on a the *+* +button that pops up when hovering with a mouse to the right of the source code +line numbers. When creating the first comment, select *Add a single comment*, +which will send an email per comment, or select *Start a review*, which sends +all inline comments along with the summary comment in a single email to the +author. + +After all inline comments have been made, click the *Review changes* button, +optionally enter a summary comment, and optionally mark the pull request with +*Approve* or *Request changes*. If inline comments were entered, please +provide an indication in the overall review comment with a phrase like, "Please see +inline comments." + +## Review ratings + +*Approve* + +: Everything looks good -- ready to merge. + +*Comment* + +: The code was not examined or a neutral remark was made. + +*Request changes* + +: Some issues were identified in the code that should be addressed. diff --git a/Documentation/Contribute/PeerReviewWithGitHub.rst b/Documentation/Contribute/PeerReviewWithGitHub.rst deleted file mode 100644 index f17e6ee30..000000000 --- a/Documentation/Contribute/PeerReviewWithGitHub.rst +++ /dev/null @@ -1,52 +0,0 @@ -Peer review with GitHub -======================= - -GitHub code reviews are a method to vastly improve the quality of code, train -new community members, and learn from other community members. In this -section, we describe how to perform a pull request review. - - -Peer review duty ----------------- - -All community members are encouraged to perform reviews. If possible, all code -that is merged should be reviewed and marked *Approved* by at least one other -community member prior to merging. In order for this system to function -smoothly, community members must perform more reviews than submit patches. -Any community member can register for a GitHub account and perform a review. - -Please review any patch of interest open for review on GitHub; it is not -necessary for the author to request your review. - - -Review comments ---------------- - -To start a review, open the pull request, then click on an individual commit. -Or, view all files changed in the topic branch by clicking *Files changed*. - -When reviewing files, inline comments can be entered by clicking on a the *+* -button that pops up when hovering with a mouse to the right of the source code -line numbers. When creating the first comment, select *Add a single comment*, -which will send an email per comment, or select *Start a review*, which sends -all inline comments along with the summary comment in a single email to the -author. - -After all inline comments have been made, click the *Review changes* button, -optionally enter a summary comment, and optionally mark the pull request with -*Approve* or *Request changes*. If inline comments were entered, please -provide an indication in the overall review comment with a phrase like, "Please see -inline comments." - - -Review ratings --------------- - -*Approve* - Everything looks good -- ready to merge. - -*Comment* - The code was not examined or a neutral remark was made. - -*Request changes* - Some issues were identified in the code that should be addressed. diff --git a/Documentation/Contribute/UploadBinaryData.md b/Documentation/Contribute/UploadBinaryData.md new file mode 100644 index 000000000..b3ce54281 --- /dev/null +++ b/Documentation/Contribute/UploadBinaryData.md @@ -0,0 +1,132 @@ +(upload-binary-data)= + +# Upload Binary Data + +## Motivation + +Since every local [Git] repository contains a copy of the entire project +history, it is important to avoid adding large binary files directly to the +repository. Large binary files added and removed throughout a project's +history will cause the repository to become bloated, take up too much disk +space, require excessive time and bandwidth to download, etc. + +A [solution to this problem] which has been adopted by this project, is to +store binary files such as images in a separate location outside the Git +repository. Then, download the files at build time with [CMake]. + +A "content link" file contains an identifying [Content Identifier (CID)]. The +content link is stored in the [Git] repository at the path where the file would +exist, but with a `` .cid` `` extension appended to the file name. CMake will +find these content link files at *build* time, download them from a list of +server resources, and create symlinks or copies of the original files at the +corresponding location in the *build tree*. + +The [Content Identifier (CID)] is self-describing hash following the +[multiformats] standard created by the Interplanetary Filesystem ([IPFS]) +community. A file with a CID for its filename is content-verifable. Locating +files according to their CID makes content-addressed, as opposed to +location-addressed, data exchange possible. This practice is the foundation of +the decentralized web, also known as the dWeb or Web3. By adopting Web3, we +gain: + +- Permissionless data uploads +- Robust, redundant storage +- Local and peer-to-peer storage +- Scalability +- Sustainability + +Contributors to the examples upload their data through an easy-to-use, +permissionless, free service, [web3.storage]. + +Data used in the examples Git repository is periodically tracked in a +[dedicated Datalad repository] and stored across redundant locations so it +can be retrieved from any of the following: + +- Local [IPFS] nodes +- Peer [IPFS] nodes +- [web3.storage] +- [estuary.tech] +- [pinata.cloud] +- Kitware's HTTP Server + +## Prerequisites + +[web3.storage] is a decentralized IPFS storage provider where any ITK +community member can upload binary data files. There are two methods available +to upload data files: + +1. The CMake ExternalData Web3 upload browser interface. +2. The `w3` command line executable that comes with the + [@web3-storage/w3] Node.js NPM package. + +Once files have been uploaded to your account, they will be publicly available +and accessible since data is content addressed on the IPFS peer-to-peer +network. At release time, the release manager will upload and archive +repository data references in other redundant storage locations. + +## Upload Via the Web Interface + +Use the [CMake ExternalData Web3 Upload] tool to upload your data to the +InterPlanetary Filesystem and download the corresponding CMake content link +file. + +:::{figure} CMakeW3ExternalDataUpload.png +:align: center +:alt: CMake ExternalData Web3 Upload +:target: https://cmake-w3-externaldata-upload.on.fleek.co/ +:width: 500 + +[CMake ExternalData Web3 Upload] +::: + +Add the file to the examples repository in your example's directory. Next time +CMake configuration runs, it will find the new content link. During the next +project build, the data file corresponding to the content link will be +downloaded into the build tree. + +## Upload Via CMake and Node.js CLI + +Install the `w3` CLI with the [@web3-storage/w3] [Node.js] package: + +```shell +$ npm install --location=global @web3-storage/w3 +``` + +Login in and create an API token at [web3.storage] then pass it into `w3 token`: + +```shell +$ w3 token +? Paste your API token for api.web3.storage › + +⁂ API token saved +``` + +Create an `w3externaldata` bash/zsh function: + +```shell +$ function w3externaldata() { w3 put $1 --no-wrap | tail -n 1 | awk -F "/ipfs/" '{print $2}' | tee $1.cid } +``` + +Call the function with the file to be uploaded. This command will generate the +`.cid` content link: + +```shell +$ w3externaldata +# Packed 1 file (0.3MB) +⁂ Stored 1 file +bafkreifpfhcc3gc7zo2ds3ktyyl5qrycwisyaolegp47cl27i4swxpa2ey +``` + +[@web3-storage/w3]: https://www.npmjs.com/package/@web3-storage/w3 +[cmake]: https://cmake.org/ +[cmake externaldata web3 upload]: https://cmake-w3-externaldata-upload.on.fleek.co/ +[content identifier (cid)]: https://proto.school/anatomy-of-a-cid +[dedicated datalad repository]: https://github.com/InsightSoftwareConsortium/ITKSphinxExamplesData +[estuary.tech]: https://estuary.tech +[git]: https://git-scm.com/ +[ipfs]: https://ipfs.io/ +[multiformats]: https://multiformats.io/ +[node.js]: https://nodejs.org/ +[pinata.cloud]: https://pinata.cloud +[solution to this problem]: https://blog.kitware.com/cmake-externaldata-using-large-files-with-distributed-version-control/ +[web3.storage]: https://web3.storage/ diff --git a/Documentation/Contribute/UploadBinaryData.rst b/Documentation/Contribute/UploadBinaryData.rst deleted file mode 100644 index d882f6904..000000000 --- a/Documentation/Contribute/UploadBinaryData.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. _upload-binary-data: - -Upload Binary Data -================== - -Motivation ----------- - -Since every local Git_ repository contains a copy of the entire project -history, it is important to avoid adding large binary files directly to the -repository. Large binary files added and removed throughout a project's -history will cause the repository to become bloated, take up too much disk -space, require excessive time and bandwidth to download, etc. - -A `solution to this problem`_ which has been adopted by this project, is to -store binary files such as images in a separate location outside the Git -repository. Then, download the files at build time with CMake_. - -A "content link" file contains an identifying `Content Identifier (CID)`_. The -content link is stored in the Git_ repository at the path where the file would -exist, but with a `.cid`` extension appended to the file name. CMake will -find these content link files at *build* time, download them from a list of -server resources, and create symlinks or copies of the original files at the -corresponding location in the *build tree*. - -The `Content Identifier (CID)`_ is self-describing hash following the -`multiformats`_ standard created by the Interplanetary Filesystem (`IPFS`_) -community. A file with a CID for its filename is content-verifable. Locating -files according to their CID makes content-addressed, as opposed to -location-addressed, data exchange possible. This practice is the foundation of -the decentralized web, also known as the dWeb or Web3. By adopting Web3, we -gain: - -- Permissionless data uploads -- Robust, redundant storage -- Local and peer-to-peer storage -- Scalability -- Sustainability - -Contributors to the examples upload their data through an easy-to-use, -permissionless, free service, `web3.storage`_. - -Data used in the examples Git repository is periodically tracked in a -`dedicated Datalad repository`_ and stored across redundant locations so it -can be retrieved from any of the following: - -- Local `IPFS`_ nodes -- Peer `IPFS`_ nodes -- `web3.storage`_ -- `estuary.tech`_ -- `pinata.cloud`_ -- Kitware's HTTP Server - -Prerequisites -------------- - -`web3.storage`_ is a decentralized IPFS storage provider where any ITK -community member can upload binary data files. There are two methods available -to upload data files: - -1. The CMake ExternalData Web3 upload browser interface. -2. The `w3` command line executable that comes with the - `@web3-storage/w3`_ Node.js NPM package. - -Once files have been uploaded to your account, they will be publicly available -and accessible since data is content addressed on the IPFS peer-to-peer -network. At release time, the release manager will upload and archive -repository data references in other redundant storage locations. - -Upload Via the Web Interface ----------------------------- - -Use the `CMake ExternalData Web3 Upload`_ tool to upload your data to the -InterPlanetary Filesystem and download the corresponding CMake content link -file. - -.. figure:: CMakeW3ExternalDataUpload.png - :alt: CMake ExternalData Web3 Upload - :align: center - :width: 500 - :target: https://cmake-w3-externaldata-upload.on.fleek.co/ - - `CMake ExternalData Web3 Upload`_ - -Add the file to the examples repository in your example's directory. Next time -CMake configuration runs, it will find the new content link. During the next -project build, the data file corresponding to the content link will be -downloaded into the build tree. - -Upload Via CMake and Node.js CLI --------------------------------- - -Install the `w3` CLI with the `@web3-storage/w3`_ `Node.js`_ package: - -.. code-block:: shell - - $ npm install --location=global @web3-storage/w3 - -Login in and create an API token at `web3.storage`_ then pass it into `w3 token`: - -.. code-block:: shell - - $ w3 token - ? Paste your API token for api.web3.storage › - - ⁂ API token saved - -Create an `w3externaldata` bash/zsh function: - -.. code-block:: shell - - $ function w3externaldata() { w3 put $1 --no-wrap | tail -n 1 | awk -F "/ipfs/" '{print $2}' | tee $1.cid } - -Call the function with the file to be uploaded. This command will generate the -`.cid` content link: - -.. code-block:: shell - - $ w3externaldata - # Packed 1 file (0.3MB) - ⁂ Stored 1 file - bafkreifpfhcc3gc7zo2ds3ktyyl5qrycwisyaolegp47cl27i4swxpa2ey - -.. _CMake: https://cmake.org/ -.. _Git: https://git-scm.com/ -.. _solution to this problem: https://blog.kitware.com/cmake-externaldata-using-large-files-with-distributed-version-control/ -.. _Content Identifier (CID): https://proto.school/anatomy-of-a-cid -.. _multiformats: https://multiformats.io/ -.. _IPFS: https://ipfs.io/ -.. _web3.storage: https://web3.storage/ -.. _dedicated Datalad repository: https://github.com/InsightSoftwareConsortium/ITKSphinxExamplesData -.. _estuary.tech: https://estuary.tech -.. _pinata.cloud: https://pinata.cloud -.. _CMake ExternalData Web3 Upload: https://cmake-w3-externaldata-upload.on.fleek.co/ -.. _@web3-storage/w3: https://www.npmjs.com/package/@web3-storage/w3 -.. _Node.js: https://nodejs.org/ diff --git a/Documentation/Contribute/WriteANewExample.md b/Documentation/Contribute/WriteANewExample.md new file mode 100644 index 000000000..636543b64 --- /dev/null +++ b/Documentation/Contribute/WriteANewExample.md @@ -0,0 +1,209 @@ +# How to write a new example + +In this section we describe how to write an example by walking through the +sections of an example's [reStructuredText] file. The mechanics of submitting an +example via Git are {ref}`covered in other sections `. + +## General guidelines + +All lines should be wrapped to 80 characters or less. This improves readability +in text editors. It is generally ITK's policy to format code lines without +wrapping up to 200 characters, but the 80 character limit keeps code readable in +the PDF output. + +Please remove all trailing whitespace. Use two newlines between section +headings. + +Follow ITK conventions for coding; do not use TABs, and use two spacing for +indentation. + +The characters used to define [reStructuredText] sections are as follows: + +``` +Title +===== + +Section +------- + +Subsection +.......... +``` + +## Directory placement + +The examples live inside the *src* directory of the repository. They +are organized by the dominant class demonstrated in the example. There +are two directories of organization which mirror the directory layout in ITKv4, +*Group* followed by *Module*. Therefore, place the example in the directory +corresponding to the Module of one of the prominant classes used in the example. + +For instance, an examples that demonstrates the *BinaryDilateImageFilter* would +be placed in the *src/Filtering/BinaryMathematicalMorphology/* +directory. + +Note that when adding new examples, both *CMakeLists.txt* and *index.rst* files +for the tree should be updated (to enforce the examples to be compiled, tested +and to appear in the sphinx documentation). For this reason, we recommend to +use the provided python script *CreateNewExample.py* see {ref}`CreateNewExample` + +## Title + +The ITK Sphinx Examples are intended to be a set of cookbook recipes that concisely +demonstrate how to achieve a single objective. In general, they are intended to +provide an answer to the question, "How do I ...?" The title for an example can +be derived by placing the example in the question format; we call this the +Trebek Title Method. + +For instance, an example that answers the question, *"How do I dilate a binary +image?"* would be called *Dilate a binary image*. This determines the title in +the [reStructuredText] file: + +``` +Dilate a binary image +===================== +``` + +and it also determines the name of the directory, file, and test associated with +the example. These names come from a CamelCase conversion of the title. For +instance, in this case, the corresponding CamelCase title is +*DilateABinaryImage*. All files for the examples are placed in a directory +called *DilateABinaryImage*, the C++ code is placed in *DilateABinaryImage.cxx*, +Python code in *DilateABinaryImage.py*, [reStructuredText] documentation in +*DilateABinaryImage.rst*, and the test will be named *DilateABinaryImageTest*. + +## Index entries + +Index entries follow the title entry. They are entered with the [Sphinx index +directive][sphinx index directive]; see that documentation for more information on how to specify index +entries. Important classes for the example or terms associated with the example +should be *single* entries. Term index entries should be lower case to +distinguish them from classes or methods in the index. Terms with sub-terms or +classes with important methods demonstrated should be used as *pair* entries. +Use *seealso* instead of *see* to add a *see also* entry. For instance, with +our dilate a binary image example: + +``` +.. index:: + single: BinaryBallStructuringElement + single: BinaryDilateImageFilter + pair: mathematical morphology; dilation + pair: BinaryBallStructuringElement; SetRadius + +.. seealso:: dilation; erosion +``` + +## Synopsis + +This section contains a short summary of the example. + +## Code + +This section sources the relevant code for inclusion in the documentation with +syntax highlighting care of [Pygments]. The [literalinclude directive] performs +this function. This ensures that all the code that is documented is also +tested. Each program should be included in a subsection corresponding to its +language; one of *C++*, *Python*, or *Java*. For instance: + +``` +C++ +... + +.. literalinclude:: DilateABinaryImage.cxx +``` + +Follow ITK style guidelines when writing code. Keep the example as simple as +possible, and follow the best practices layed out in the rest of the examples. +Do basic argument checking and parsing. Wrap *Update()* calls in a *try / +catch* for C++ code, etc. + +## Results + +Include images or text output here that results from the example. + +### Images + +If there was an input image, display it for reference. The images displayed +here should be rendered in the PNG format for display either by directly outputing +to PNG format or by rendering with your favorite {ref}`visualization application +` and saving a screenshot. Display the image with the [figure +directive][figure directive]. Provide alt text with the *:alt:* option and a brief descriptive +caption. For instance: + +``` +.. figure:: DilateABinaryImageOutputBaseline.png + :scale: 50% + :alt: Dilated output. + + Dilated output. +``` + +### Text + +Text output should be placed in a [literal block] by inserting two colons +followed by indentation. For instance: + +``` +:: + + Registration done ! + Number of iterations = 27 + Translation along X = 25.0966 + Translation along Y = 22.3275 + Optimal metric value = 4597.96 +``` + +### PolyData + +For data structures rendered as a PolyData, such as meshes, a screenshot of the +input and output rendering is insightful and motivating. The screenshot can +be rendered with your favorite visualization, then included like the image +renderings per above. + +As a supplement to the renderings, an interactive 3D WebGL can be included in +HTML output. This can be produced with the `--webgl` flag to the [VTK] Python +script in the repository at `Utilities/Visualization/VTKPolyData.py`. In +recent releases of [Paraview], it can be produced by clicking *File*, *Export +Scene*, *WEBGL files*. In the reStructuredText file, add: + +``` +.. raw:: html + +
+ +

Interactive input mesh

+
+``` + +## Classes demonstrated + +At the end of the example, provide quick reference and a link to the doxygen +documentation for the important classes or structs used in the example. To do this, use +the `breathelink` directive for C++ classes or `breathelinkstruct` directive for C++ structs, as follows: + +``` +.. breathelink:: itk::BinaryDilateImageFilter +.. breathelinkstruct:: itk::Index +``` + +Note that `breathelink` and `breathelinkstruct` are custom directives which make the use of: + +- the [doxygenclass directive] or [doxygenstruct directive] provided by [Breathe] with the *:no-link:* + option. +- the [doxylink] directive which provides a link to the full doxygen + documentation with an [external hyperlink target]. Note that Doxygen URL's + follow a predictable pattern. + +[breathe]: https://github.com/michaeljones/breathe +[doxygenclass directive]: https://breathe.readthedocs.io/en/latest/class.html +[doxygenstruct directive]: https://breathe.readthedocs.io/en/latest/struct.html +[doxylink]: https://pythonhosted.org/sphinxcontrib-doxylink/ +[external hyperlink target]: http://docutils.sourceforge.net/docs/user/rst/quickref.html#external-hyperlink-targets +[figure directive]: http://docutils.sourceforge.net/docs/ref/rst/directives.html#figure +[literal block]: http://docutils.sourceforge.net/docs/user/rst/quickref.html#literal-blocks +[literalinclude directive]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-literalinclude +[paraview]: https://www.paraview.org +[pygments]: https://pygments.org/ +[restructuredtext]: http://docutils.sourceforge.net/rst.html +[sphinx index directive]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#index-generating-markup +[vtk]: https://vtk.org diff --git a/Documentation/Contribute/WriteANewExample.rst b/Documentation/Contribute/WriteANewExample.rst deleted file mode 100644 index f1adfbfa4..000000000 --- a/Documentation/Contribute/WriteANewExample.rst +++ /dev/null @@ -1,211 +0,0 @@ -How to write a new example -========================== - -In this section we describe how to write an example by walking through the -sections of an example's reStructuredText_ file. The mechanics of submitting an -example via Git are :ref:`covered in other sections `. - - -General guidelines ------------------- - -All lines should be wrapped to 80 characters or less. This improves readability -in text editors. It is generally ITK's policy to format code lines without -wrapping up to 200 characters, but the 80 character limit keeps code readable in -the PDF output. - -Please remove all trailing whitespace. Use two newlines between section -headings. - -Follow ITK conventions for coding; do not use TABs, and use two spacing for -indentation. - -The characters used to define reStructuredText_ sections are as follows:: - - Title - ===== - - Section - ------- - - Subsection - .......... - - -Directory placement -------------------- - -The examples live inside the *src* directory of the repository. They -are organized by the dominant class demonstrated in the example. There -are two directories of organization which mirror the directory layout in ITKv4, -*Group* followed by *Module*. Therefore, place the example in the directory -corresponding to the Module of one of the prominant classes used in the example. - -For instance, an examples that demonstrates the *BinaryDilateImageFilter* would -be placed in the *src/Filtering/BinaryMathematicalMorphology/* -directory. - -Note that when adding new examples, both *CMakeLists.txt* and *index.rst* files -for the tree should be updated (to enforce the examples to be compiled, tested -and to appear in the sphinx documentation). For this reason, we recommend to -use the provided python script *CreateNewExample.py* see :ref:`CreateNewExample` - -Title ------ - -The ITK Sphinx Examples are intended to be a set of cookbook recipes that concisely -demonstrate how to achieve a single objective. In general, they are intended to -provide an answer to the question, "How do I ...?" The title for an example can -be derived by placing the example in the question format; we call this the -Trebek Title Method. - -For instance, an example that answers the question, *"How do I dilate a binary -image?"* would be called *Dilate a binary image*. This determines the title in -the reStructuredText_ file:: - - Dilate a binary image - ===================== - -and it also determines the name of the directory, file, and test associated with -the example. These names come from a CamelCase conversion of the title. For -instance, in this case, the corresponding CamelCase title is -*DilateABinaryImage*. All files for the examples are placed in a directory -called *DilateABinaryImage*, the C++ code is placed in *DilateABinaryImage.cxx*, -Python code in *DilateABinaryImage.py*, reStructuredText_ documentation in -*DilateABinaryImage.rst*, and the test will be named *DilateABinaryImageTest*. - - -Index entries -------------- - -Index entries follow the title entry. They are entered with the `Sphinx index -directive`_; see that documentation for more information on how to specify index -entries. Important classes for the example or terms associated with the example -should be *single* entries. Term index entries should be lower case to -distinguish them from classes or methods in the index. Terms with sub-terms or -classes with important methods demonstrated should be used as *pair* entries. -Use *seealso* instead of *see* to add a *see also* entry. For instance, with -our dilate a binary image example:: - - .. index:: - single: BinaryBallStructuringElement - single: BinaryDilateImageFilter - pair: mathematical morphology; dilation - pair: BinaryBallStructuringElement; SetRadius - - .. seealso:: dilation; erosion - - -Synopsis --------- - -This section contains a short summary of the example. - - -Code ----- - -This section sources the relevant code for inclusion in the documentation with -syntax highlighting care of Pygments_. The `literalinclude directive`_ performs -this function. This ensures that all the code that is documented is also -tested. Each program should be included in a subsection corresponding to its -language; one of *C++*, *Python*, or *Java*. For instance:: - - C++ - ... - - .. literalinclude:: DilateABinaryImage.cxx - -Follow ITK style guidelines when writing code. Keep the example as simple as -possible, and follow the best practices layed out in the rest of the examples. -Do basic argument checking and parsing. Wrap *Update()* calls in a *try / -catch* for C++ code, etc. - - -Results -------- - -Include images or text output here that results from the example. - -Images -...... - -If there was an input image, display it for reference. The images displayed -here should be rendered in the PNG format for display either by directly outputing -to PNG format or by rendering with your favorite :ref:`visualization application -` and saving a screenshot. Display the image with the `figure -directive`_. Provide alt text with the *:alt:* option and a brief descriptive -caption. For instance:: - - .. figure:: DilateABinaryImageOutputBaseline.png - :scale: 50% - :alt: Dilated output. - - Dilated output. - -Text -.... - -Text output should be placed in a `literal block`_ by inserting two colons -followed by indentation. For instance:: - - :: - - Registration done ! - Number of iterations = 27 - Translation along X = 25.0966 - Translation along Y = 22.3275 - Optimal metric value = 4597.96 - -PolyData -........ - -For data structures rendered as a PolyData, such as meshes, a screenshot of the -input and output rendering is insightful and motivating. The screenshot can -be rendered with your favorite visualization, then included like the image -renderings per above. - -As a supplement to the renderings, an interactive 3D WebGL can be included in -HTML output. This can be produced with the `--webgl` flag to the VTK_ Python -script in the repository at `Utilities/Visualization/VTKPolyData.py`. In -recent releases of Paraview_, it can be produced by clicking *File*, *Export -Scene*, *WEBGL files*. In the reStructuredText file, add:: - - .. raw:: html - -
- -

Interactive input mesh

-
- -Classes demonstrated --------------------- - -At the end of the example, provide quick reference and a link to the doxygen -documentation for the important classes or structs used in the example. To do this, use -the ``breathelink`` directive for C++ classes or ``breathelinkstruct`` directive for C++ structs, as follows:: - - .. breathelink:: itk::BinaryDilateImageFilter - .. breathelinkstruct:: itk::Index - -Note that ``breathelink`` and ``breathelinkstruct`` are custom directives which make the use of: - -- the `doxygenclass directive`_ or `doxygenstruct directive`_ provided by Breathe_ with the *:no-link:* - option. -- the `doxylink`_ directive which provides a link to the full doxygen - documentation with an `external hyperlink target`_. Note that Doxygen URL's - follow a predictable pattern. - -.. _Breathe: https://github.com/michaeljones/breathe -.. _external hyperlink target: http://docutils.sourceforge.net/docs/user/rst/quickref.html#external-hyperlink-targets -.. _doxygenclass directive: https://breathe.readthedocs.io/en/latest/class.html -.. _doxygenstruct directive: https://breathe.readthedocs.io/en/latest/struct.html -.. _figure directive: http://docutils.sourceforge.net/docs/ref/rst/directives.html#figure -.. _literalinclude directive: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-literalinclude -.. _literal block: http://docutils.sourceforge.net/docs/user/rst/quickref.html#literal-blocks -.. _Pygments: https://pygments.org/ -.. _Sphinx index directive: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#index-generating-markup -.. _reStructuredText: http://docutils.sourceforge.net/rst.html -.. _doxylink: https://pythonhosted.org/sphinxcontrib-doxylink/ -.. _VTK: https://vtk.org -.. _Paraview: https://www.paraview.org diff --git a/Documentation/Contribute/index.md b/Documentation/Contribute/index.md new file mode 100644 index 000000000..40409091f --- /dev/null +++ b/Documentation/Contribute/index.md @@ -0,0 +1,33 @@ +# Contribute + +The ITK Sphinx Examples are stored in the [Git] distributed version control system, and +the mainline repository can be found at [ITK Sphinx Examples repository]. Files in +the repository can be edited via the typical {ref}`text editor / version control workflow +` used when modifying source code. + +Examples code can be written in the C++ or Python programming languages. +Documentation for the examples is writted in [reStructuredText] / [Sphinx]. +Sphinx is a build system that uses the reStructuredText syntax with additional +capabilies, such as multi-document projects and rendering of LaTeX-style +equations. A good reference for the easy-to-learn reStructuredText syntax is +the [Quick reStructuredText] guide. + +There are a variety of ways to take part in the ITK Sphinx Examples project. All +facets are important to the success of the project. + +```{toctree} +:maxdepth: 2 + +ContributeWithGit +WriteANewExample +UploadBinaryData +PeerReviewWithGitHub +DashboardSubmission +``` + +[dashboard]: https://open.cdash.org/index.php?project=Insight&filtercount=1&showfilters=0&field1=buildname/string&compare1=63&value1=Examples +[git]: https://git-scm.com/ +[itk sphinx examples repository]: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples +[quick restructuredtext]: http://docutils.sourceforge.net/docs/user/rst/quickref.html +[restructuredtext]: http://docutils.sourceforge.net/rst.html +[sphinx]: https://www.sphinx-doc.org/en/master/ diff --git a/Documentation/Contribute/index.rst b/Documentation/Contribute/index.rst deleted file mode 100644 index 1d211cc98..000000000 --- a/Documentation/Contribute/index.rst +++ /dev/null @@ -1,34 +0,0 @@ -Contribute -========== - -The ITK Sphinx Examples are stored in the Git_ distributed version control system, and -the mainline repository can be found at `ITK Sphinx Examples repository`_. Files in -the repository can be edited via the typical :ref:`text editor / version control workflow -` used when modifying source code. - -Examples code can be written in the C++ or Python programming languages. -Documentation for the examples is writted in reStructuredText_ / Sphinx_. -Sphinx is a build system that uses the reStructuredText syntax with additional -capabilies, such as multi-document projects and rendering of LaTeX-style -equations. A good reference for the easy-to-learn reStructuredText syntax is -the `Quick reStructuredText`_ guide. - -There are a variety of ways to take part in the ITK Sphinx Examples project. All -facets are important to the success of the project. - -.. toctree:: - :maxdepth: 2 - - ContributeWithGit - WriteANewExample - UploadBinaryData - PeerReviewWithGitHub - DashboardSubmission - - -.. _ITK Sphinx Examples repository: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples -.. _Git: https://git-scm.com/ -.. _reStructuredText: http://docutils.sourceforge.net/rst.html -.. _Sphinx: https://www.sphinx-doc.org/en/master/ -.. _Quick reStructuredText: http://docutils.sourceforge.net/docs/user/rst/quickref.html -.. _Dashboard: https://open.cdash.org/index.php?project=Insight&filtercount=1&showfilters=0&field1=buildname/string&compare1=63&value1=Examples diff --git a/Documentation/Credits.md b/Documentation/Credits.md new file mode 100644 index 000000000..c84a22225 --- /dev/null +++ b/Documentation/Credits.md @@ -0,0 +1,10 @@ +# Credits + +```{eval-rst} +.. contributors:: InsightSoftwareConsortium/ITKSphinxExamples + :contributions: + :avatars: + :exclude: itkrobot + :limit: 100 + :order: DESC +``` diff --git a/Documentation/Credits.rst b/Documentation/Credits.rst deleted file mode 100644 index 4d9bb0ada..000000000 --- a/Documentation/Credits.rst +++ /dev/null @@ -1,9 +0,0 @@ -Credits -========== - -.. contributors:: InsightSoftwareConsortium/ITKSphinxExamples - :contributions: - :avatars: - :exclude: itkrobot - :limit: 100 - :order: DESC \ No newline at end of file diff --git a/Documentation/Download/CMakeLists.txt b/Documentation/Download/CMakeLists.txt index 807c365cb..2404d34be 100644 --- a/Documentation/Download/CMakeLists.txt +++ b/Documentation/Download/CMakeLists.txt @@ -1,3 +1,3 @@ -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/index.rst.in - ${CMAKE_CURRENT_BINARY_DIR}/index.rst +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/index.md.in + ${CMAKE_CURRENT_BINARY_DIR}/index.md ) diff --git a/Documentation/Download/index.md.in b/Documentation/Download/index.md.in new file mode 100644 index 000000000..c6927e09a --- /dev/null +++ b/Documentation/Download/index.md.in @@ -0,0 +1,33 @@ +# Download + +## Archives in various formats + +The complete set of examples can be downloaded in various formats: + +- [HTML (Packed as .tar.gz)](https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/releases/download/v@ITKSphinxExamples_RELEASE_VERSION@/ITKSphinxExamples-@ITKSphinxExamples_RELEASE_VERSION@-html.tar.gz) +- [HTML (Packed as .zip)](https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/releases/download/v@ITKSphinxExamples_RELEASE_VERSION@/ITKSphinxExamples-@ITKSphinxExamples_RELEASE_VERSION@-html.zip) + +## Individual examples + +To download the code, data, and documentation for an individual example, click +the **Download** button in the navbar of an example's webpage. + +:::{figure} DownloadExampleHighlightedForDownload.png +:align: center +:alt: Location of the zip link for an example. + +Links to download individual examples. +::: + +Once an example zip has been downloaded and unpacked, follow the additional +documentation on {ref}`how to build and run an example `. + +## Source repository + +The entire source tree can be downloaded with [Git]: + +```bash +git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git +``` + +[git]: https://git-scm.com/ diff --git a/Documentation/Download/index.rst.in b/Documentation/Download/index.rst.in deleted file mode 100644 index 79ce865d0..000000000 --- a/Documentation/Download/index.rst.in +++ /dev/null @@ -1,36 +0,0 @@ -Download -======== - -Archives in various formats ---------------------------- - -The complete set of examples can be downloaded in various formats: - -- `HTML (Packed as .tar.gz) `_ -- `HTML (Packed as .zip) `_ - -Individual examples -------------------- - -To download the code, data, and documentation for an individual example, click -the **Download** button in the navbar of an example's webpage. - -.. figure:: DownloadExampleHighlightedForDownload.png - :align: center - :alt: Location of the zip link for an example. - - Links to download individual examples. - -Once an example zip has been downloaded and unpacked, follow the additional -documentation on :ref:`how to build and run an example `. - -Source repository ------------------ - -The entire source tree can be downloaded with Git_: - -.. code-block:: bash - - git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git - -.. _Git: https://git-scm.com/ diff --git a/Formatting/conf.py.in b/Formatting/conf.py.in index cc2a36702..7703d159b 100644 --- a/Formatting/conf.py.in +++ b/Formatting/conf.py.in @@ -12,6 +12,7 @@ # serve to show the default. import sys, os +from datetime import date # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the @@ -29,6 +30,8 @@ sys.path.insert(0, os.path.abspath(os.path.join('@ITKSphinxExamples_BINARY_DIR@' import pydata_sphinx_theme +myst_enable_extensions = ['colon_fence', 'deflist', 'substitution'] + # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. @@ -39,7 +42,7 @@ primary_domain = 'cpp' # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', +extensions = ['myst_parser', 'sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.imgconverter', 'breathe', 'doxylink', 'breathelink', 'nbsphinx', 'sphinx_contributors', 'IPython.sphinxext.ipython_console_highlighting',] @@ -48,7 +51,10 @@ extensions = ['sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', templates_path = ['templates'] # The suffix of source filenames. -source_suffix = '.rst' +source_suffix = { + '.rst': 'restructuredtext', + '.md': 'markdown', +} # The encoding of source files. #source_encoding = 'utf-8-sig' @@ -58,7 +64,7 @@ master_doc = 'index' # General information about the project. project = u'' -copyright = u'2020, NumFOCUS' +copyright = f'{date.today().year}, NumFOCUS' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/README.md b/README.md new file mode 100644 index 000000000..846eeab55 --- /dev/null +++ b/README.md @@ -0,0 +1,92 @@ +# ITK Sphinx Examples + +```{image} https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/workflows/Build,%20test,%20publish/badge.svg?branch=master +:target: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/actions?query=workflow%3A%22Build%2C+test%2C+publish%22+branch%3Amaster +``` + +```{image} https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=shield +:target: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/blob/master/LICENSE +``` + +A set of cookbook examples for the Insight Toolkit, [ITK]. + +## Download instructions + +Clone the repository using Git: + +``` +$ git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git +``` + +## Build instructions + +See the [build instructions in the documentation]. + +## Features + +### Implemented + +- Stored and editable in [Git] version control. +- HTML / PDF / EPUB output. +- CTest unit testing. +- CMake ExternalData for binary data storage. +- Individual examples can be downloaded independently, and easily built/executed/hacked. +- Download the entire docs for offline viewing. +- Inline Doxygen class descriptions and links to Doxygen class documentation. +- Nightly generated Gitstats for contributors. +- Software quality dashboard. +- Index of examples that apply to given terms and classes. +- Quick search. +- Script to create a new examples from a template. +- GitHub community development. +- Selectable light/dark colorscheme. +- Online editing via GitHub. + +### Todo + +- See [Github Issues] for a complete list of actions to be performed, bugs, *etc.* + +## Build dependencies + +### Required + +- [CMake] ( >= 3.16.3 ) +- [ITK] ( >= 5.3.0 ) + +### Optional + +If building the documentation: + +- [Python] ( >= 3.7 ) +- [Sphinx] +- [Pandoc] +- [nbsphinx] +- [gnuplot] +- [dvipng] ( for rendered equations ) +- [imagemagick] + +PDF generation requires a TeX distribution like [TeX Live] or [MiKTeX]. + +## Development setup + +Run the bash script `SetupForDevelopment.sh`: + +``` +$ ./Utilities/SetupForDevelopment.sh +``` + +[breathe]: https://github.com/michaeljones/breathe +[build instructions in the documentation]: https://itk.org/ITKExamples/Documentation/Build/index.html +[cmake]: https://cmake.org/ +[dvipng]: https://sourceforge.net/projects/dvipng/ +[git]: https://git-scm.com/ +[github issues]: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/issues +[gnuplot]: https://www.gnuplot.info/ +[imagemagick]: https://www.imagemagick.org/ +[itk]: https://itk.org/ +[miktex]: https://miktex.org/ +[nbsphinx]: https://nbsphinx.readthedocs.io/ +[pandoc]: https://pandoc.org/ +[python]: https://python.org/ +[sphinx]: https://sphinx-doc.org/ +[tex live]: https://www.tug.org/texlive/ diff --git a/README.rst b/README.rst deleted file mode 100644 index f14ee2204..000000000 --- a/README.rst +++ /dev/null @@ -1,98 +0,0 @@ -ITK Sphinx Examples -=================== - -.. image:: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/workflows/Build,%20test,%20publish/badge.svg?branch=master - :target: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/actions?query=workflow%3A%22Build%2C+test%2C+publish%22+branch%3Amaster - -.. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=shield - :target: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/blob/master/LICENSE - - -A set of cookbook examples for the Insight Toolkit, ITK_. - -Download instructions ---------------------- - -Clone the repository using Git:: - - $ git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git - - -Build instructions ------------------- - -See the `build instructions in the documentation`_. - -Features --------- - -Implemented -^^^^^^^^^^^ - -- Stored and editable in Git_ version control. -- HTML / PDF / EPUB output. -- CTest unit testing. -- CMake ExternalData for binary data storage. -- Individual examples can be downloaded independently, and easily built/executed/hacked. -- Download the entire docs for offline viewing. -- Inline Doxygen class descriptions and links to Doxygen class documentation. -- Nightly generated Gitstats for contributors. -- Software quality dashboard. -- Index of examples that apply to given terms and classes. -- Quick search. -- Script to create a new examples from a template. -- GitHub community development. -- Selectable light/dark colorscheme. -- Online editing via GitHub. - -Todo -^^^^ - -- See `Github Issues`_ for a complete list of actions to be performed, bugs, *etc.* - -Build dependencies ------------------- - -Required -^^^^^^^^ - -- CMake_ ( >= 3.16.3 ) -- ITK_ ( >= 5.3.0 ) - -Optional -^^^^^^^^ - -If building the documentation: - -- Python_ ( >= 3.7 ) -- Sphinx_ -- Pandoc_ -- nbsphinx_ -- gnuplot_ -- dvipng_ ( for rendered equations ) -- imagemagick_ - -PDF generation requires a TeX distribution like `TeX Live`_ or MiKTeX_. - -Development setup ------------------- - -Run the bash script ``SetupForDevelopment.sh``:: - - $ ./Utilities/SetupForDevelopment.sh - -.. _Breathe: https://github.com/michaeljones/breathe -.. _build instructions in the documentation: https://itk.org/ITKExamples/Documentation/Build/index.html -.. _CMake: https://cmake.org/ -.. _Git: https://git-scm.com/ -.. _ITK: https://itk.org/ -.. _Sphinx: https://sphinx-doc.org/ -.. _Github Issues: https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/issues -.. _Python: https://python.org/ -.. _gnuplot: https://www.gnuplot.info/ -.. _TeX Live: https://www.tug.org/texlive/ -.. _MiKTeX: https://miktex.org/ -.. _dvipng: https://sourceforge.net/projects/dvipng/ -.. _Pandoc: https://pandoc.org/ -.. _nbsphinx: https://nbsphinx.readthedocs.io/ -.. _imagemagick: https://www.imagemagick.org/ diff --git a/Superbuild/External-ITK.cmake b/Superbuild/External-ITK.cmake index 1be6b3146..a95be612e 100644 --- a/Superbuild/External-ITK.cmake +++ b/Superbuild/External-ITK.cmake @@ -2,8 +2,8 @@ # Get and build itk if(NOT ITK_TAG) - # ITK release 2024-04-09 - set(ITK_TAG "v5.4rc03") + # ITK release 2024-05-22 + set(ITK_TAG "v5.4.0") endif() set(_vtk_args) diff --git a/Superbuild/External-Python.cmake b/Superbuild/External-Python.cmake index 0d3dd544c..35617a6b7 100644 --- a/Superbuild/External-Python.cmake +++ b/Superbuild/External-Python.cmake @@ -17,6 +17,6 @@ ExternalProject_Add(ITKPython DOWNLOAD_COMMAND "" CONFIGURE_COMMAND ${PYTHON_EXECUTABLE} -m venv "${_itk_venv}" BUILD_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --upgrade pip - INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.4rc3 sphinx==7.2.6 six black nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a51 pydata-sphinx-theme + INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.4.0 sphinx==7.2.6 six black nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a51 pydata-sphinx-theme myst-parser COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake ) diff --git a/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.md b/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.md new file mode 100644 index 000000000..78837983c --- /dev/null +++ b/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.md @@ -0,0 +1,50 @@ +--- +name: '{{ cookiecutter.example_name }}' +--- + +# {{ cookiecutter.example_title }} + +```{index} single: {{ cookiecutter.class_name }} +``` + +## Synopsis + +{{ cookiecutter.example_synopsis }} + +## Results + +:::{figure} cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1,16- +``` + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::{{ cookiecutter.class_name }} +``` diff --git a/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.rst b/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.rst deleted file mode 100644 index 039e914b4..000000000 --- a/Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.rst +++ /dev/null @@ -1,54 +0,0 @@ -:name: {{ cookiecutter.example_name }} - -{{ cookiecutter.example_title }} -================================ - -.. index:: - single: {{ cookiecutter.class_name }} - -Synopsis --------- - - -{{ cookiecutter.example_synopsis }} - - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1,16- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - - - -Classes demonstrated --------------------- - -.. breathelink:: itk::{{ cookiecutter.class_name }} diff --git a/index.md b/index.md new file mode 100644 index 000000000..e43c0a05f --- /dev/null +++ b/index.md @@ -0,0 +1,20 @@ +% ITK Sphinx Examples documentation master file, created by +% sphinx-quickstart on Thu Dec 22 23:30:02 2011. + +# Welcome to the ITK Sphinx Examples documentation! + +Contents: + +```{toctree} +:maxdepth: 2 + +Documentation/Build/index +Documentation/Contribute/index +src/index +Documentation/Download/index +Documentation/Credits +``` + +# Index + +- {ref}`genindex` diff --git a/index.rst b/index.rst deleted file mode 100644 index 8ea705e9f..000000000 --- a/index.rst +++ /dev/null @@ -1,21 +0,0 @@ -.. ITK Sphinx Examples documentation master file, created by - sphinx-quickstart on Thu Dec 22 23:30:02 2011. - -Welcome to the ITK Sphinx Examples documentation! -================================================= - -Contents: - -.. toctree:: - :maxdepth: 2 - - Documentation/Build/index - Documentation/Contribute/index - src/index - Documentation/Download/index - Documentation/Credits - -Index -===== - -* :ref:`genindex` diff --git a/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.md b/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.md new file mode 100644 index 000000000..7fd2137bd --- /dev/null +++ b/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.md @@ -0,0 +1,50 @@ +--- +name: ConvertNumPyArrayToitkImage +--- + +# Interface ITK with NumPy Array + +```{index} single: Image +``` + +```{toctree} +:maxdepth: 1 + +ConvertNumPyArrayToitkImage.ipynb +``` + +## Synopsis + +This example illustrates interfacing ITK Image data with NumPy array. +While doing this, there are two key issues to keep in mind. One, the order of +indexes is different between ITK image data class and NumPy array. +Second, there are two ways to access ITK image data as a NumPy array. +i) Get direct access to memory with the data called"View" functions, or +ii) Copy the data using array_from_image function. If the view functions are used, +the data can't be modified. + +## Results + +The size of the ITK image data read from the input file = itkSize2 (\[221, 257\]) + +The size of the NumPy array viewed from itk::Image = (257, 221) +The size of the NumPy array copied from itk::Image = (257, 221) +ITK image data size after convesion from NumPy = itkSize2 (\[221, 257\]) + +ITK image data pixel value at \[2,1\] = 6 +NumPy array pixel value at \[2,1\] = 8 + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.rst b/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.rst deleted file mode 100644 index 07bd91959..000000000 --- a/src/Bridge/NumPy/ConvertNumPyArrayToitkImage/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: ConvertNumPyArrayToitkImage - -Interface ITK with NumPy Array -=============================== - -.. index:: - single: Image - -.. toctree:: - :maxdepth: 1 - - ConvertNumPyArrayToitkImage.ipynb - -Synopsis --------- - -This example illustrates interfacing ITK Image data with NumPy array. -While doing this, there are two key issues to keep in mind. One, the order of -indexes is different between ITK image data class and NumPy array. -Second, there are two ways to access ITK image data as a NumPy array. -i) Get direct access to memory with the data called"View" functions, or -ii) Copy the data using array_from_image function. If the view functions are used, -the data can't be modified. - -Results -------- -The size of the ITK image data read from the input file = itkSize2 ([221, 257]) - -The size of the NumPy array viewed from itk::Image = (257, 221) -The size of the NumPy array copied from itk::Image = (257, 221) -ITK image data size after convesion from NumPy = itkSize2 ([221, 257]) - -ITK image data pixel value at [2,1] = 6 -NumPy array pixel value at [2,1] = 8 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Bridge/NumPy/index.md b/src/Bridge/NumPy/index.md new file mode 100644 index 000000000..9a50517de --- /dev/null +++ b/src/Bridge/NumPy/index.md @@ -0,0 +1,7 @@ +# NumPy + +```{toctree} +:maxdepth: 1 + +ConvertNumPyArrayToitkImage/Documentation.rst +``` diff --git a/src/Bridge/NumPy/index.rst b/src/Bridge/NumPy/index.rst deleted file mode 100644 index 2ccf3ead8..000000000 --- a/src/Bridge/NumPy/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -NumPy -====== - -.. toctree:: - :maxdepth: 1 - - ConvertNumPyArrayToitkImage/Documentation.rst diff --git a/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.md b/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.md new file mode 100644 index 000000000..3120802df --- /dev/null +++ b/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.md @@ -0,0 +1,126 @@ +--- +name: ConvertAnRGBitkImageTovtkImageData +--- + +# Convert an RGB itk::Image to vtkImageData + +```{index} single: ImageToVTKImageFilter +``` + +## Synopsis + +Convert an itk::Image with RGB pixels to vtkImageData. This transfers the image +buffer data along with image size, pixel spacing, and origin. Since +`vtkImageData` does not yet support an orientation matrix, the direction +cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's +CMake configuration. + +## Results + +Output: + +``` +vtkImageData (0x35dc400) + Debug: Off + Modified Time: 242 + Reference Count: 2 + Registered Events: (none) + Information: 0x35dc590 + Data Released: False + Global Release Data: Off + UpdateTime: 243 + Field Data: + Debug: Off + Modified Time: 187 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 0 + Number Of Components: 0 + Number Of Tuples: 0 + Number Of Points: 20574 + Number Of Cells: 20286 + Cell Data: + Debug: Off + Modified Time: 195 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 0 + Number Of Components: 0 + Number Of Tuples: 0 + Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) + Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) + Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) + Scalars: (none) + Vectors: (none) + Normals: (none) + TCoords: (none) + Tensors: (none) + GlobalIds: (none) + PedigreeIds: (none) + EdgeFlag: (none) + Point Data: + Debug: Off + Modified Time: 242 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 1 + Array 0 name = scalars + Number Of Components: 3 + Number Of Tuples: 20574 + Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) + Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) + Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) + Scalars: + Debug: Off + Modified Time: 242 + Reference Count: 1 + Registered Events: (none) + Name: scalars + Data type: unsigned char + Size: 61722 + MaxId: 61721 + NumberOfComponents: 3 + Information: 0 + Name: scalars + Number Of Components: 3 + Number Of Tuples: 20574 + Size: 61722 + MaxId: 61721 + LookupTable: (none) + Array: 0x35c3430 + Vectors: (none) + Normals: (none) + TCoords: (none) + Tensors: (none) + GlobalIds: (none) + PedigreeIds: (none) + EdgeFlag: (none) + Bounds: + Xmin,Xmax: (0, 126) + Ymin,Ymax: (0, 161) + Zmin,Zmax: (0, 0) + Compute Time: 256 + Spacing: (1, 1, 1) + Origin: (0, 0, 0) +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToVTKImageFilter +``` diff --git a/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.rst b/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.rst deleted file mode 100644 index ca7f4c48f..000000000 --- a/src/Bridge/VtkGlue/ConvertAnRGBitkImageTovtkImageData/Documentation.rst +++ /dev/null @@ -1,129 +0,0 @@ -:name: ConvertAnRGBitkImageTovtkImageData - -Convert an RGB itk::Image to vtkImageData -========================================= - -.. index:: - single: ImageToVTKImageFilter - -Synopsis --------- - -Convert an itk::Image with RGB pixels to vtkImageData. This transfers the image -buffer data along with image size, pixel spacing, and origin. Since -`vtkImageData` does not yet support an orientation matrix, the direction -cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's -CMake configuration. - - - -Results -------- - -Output:: - - vtkImageData (0x35dc400) - Debug: Off - Modified Time: 242 - Reference Count: 2 - Registered Events: (none) - Information: 0x35dc590 - Data Released: False - Global Release Data: Off - UpdateTime: 243 - Field Data: - Debug: Off - Modified Time: 187 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 0 - Number Of Components: 0 - Number Of Tuples: 0 - Number Of Points: 20574 - Number Of Cells: 20286 - Cell Data: - Debug: Off - Modified Time: 195 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 0 - Number Of Components: 0 - Number Of Tuples: 0 - Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) - Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) - Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) - Scalars: (none) - Vectors: (none) - Normals: (none) - TCoords: (none) - Tensors: (none) - GlobalIds: (none) - PedigreeIds: (none) - EdgeFlag: (none) - Point Data: - Debug: Off - Modified Time: 242 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 1 - Array 0 name = scalars - Number Of Components: 3 - Number Of Tuples: 20574 - Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) - Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) - Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) - Scalars: - Debug: Off - Modified Time: 242 - Reference Count: 1 - Registered Events: (none) - Name: scalars - Data type: unsigned char - Size: 61722 - MaxId: 61721 - NumberOfComponents: 3 - Information: 0 - Name: scalars - Number Of Components: 3 - Number Of Tuples: 20574 - Size: 61722 - MaxId: 61721 - LookupTable: (none) - Array: 0x35c3430 - Vectors: (none) - Normals: (none) - TCoords: (none) - Tensors: (none) - GlobalIds: (none) - PedigreeIds: (none) - EdgeFlag: (none) - Bounds: - Xmin,Xmax: (0, 126) - Ymin,Ymax: (0, 161) - Zmin,Zmax: (0, 0) - Compute Time: 256 - Spacing: (1, 1, 1) - Origin: (0, 0, 0) - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToVTKImageFilter diff --git a/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.md b/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.md new file mode 100644 index 000000000..282ac139d --- /dev/null +++ b/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.md @@ -0,0 +1,129 @@ +--- +name: ConvertAnitkImageTovtkImageData +--- + +# Convert an itk::Image to vtkImageData + +```{index} single: ImageToVTKImageFilter +``` + +## Synopsis + +Convert an itk::Image to vtkImageData in a pipeline. This transfers the image +buffer data along with image size, pixel spacing, and origin. Since +`vtkImageData` does not yet support an orientation matrix, the direction +cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's +CMake configuration. + +## Results + +Output: + +``` +vtkImageData (0x51828b0) + Debug: Off + Modified Time: 240 + Reference Count: 2 + Registered Events: (none) + Information: 0x35d7810 + Data Released: False + Global Release Data: Off + UpdateTime: 241 + Field Data: + Debug: Off + Modified Time: 186 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 0 + Number Of Components: 0 + Number Of Tuples: 0 + Number Of Points: 39277 + Number Of Cells: 38880 + Cell Data: + Debug: Off + Modified Time: 194 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 0 + Number Of Components: 0 + Number Of Tuples: 0 + Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) + Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) + Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) + Scalars: (none) + Vectors: (none) + Normals: (none) + TCoords: (none) + Tensors: (none) + GlobalIds: (none) + PedigreeIds: (none) + EdgeFlag: (none) + Point Data: + Debug: Off + Modified Time: 240 + Reference Count: 1 + Registered Events: (none) + Number Of Arrays: 1 + Array 0 name = scalars + Number Of Components: 1 + Number Of Tuples: 39277 + Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) + Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) + Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) + Scalars: + Debug: Off + Modified Time: 240 + Reference Count: 1 + Registered Events: (none) + Name: scalars + Data type: unsigned char + Size: 39277 + MaxId: 39276 + NumberOfComponents: 1 + Information: 0 + Name: scalars + Number Of Components: 1 + Number Of Tuples: 39277 + Size: 39277 + MaxId: 39276 + LookupTable: (none) + Array: 0x51a7150 + Vectors: (none) + Normals: (none) + TCoords: (none) + Tensors: (none) + GlobalIds: (none) + PedigreeIds: (none) + EdgeFlag: (none) + Bounds: + Xmin,Xmax: (0, 180) + Ymin,Ymax: (0, 216) + Zmin,Zmax: (0, 0) + Compute Time: 254 + Spacing: (1, 1, 1) + Origin: (0, 0, 0) + Dimensions: (181, 217, 1) + Increments: (0, 0, 0) + Extent: (0, 180, 0, 216, 0, 0) +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToVTKImageFilter +``` diff --git a/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.rst b/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.rst deleted file mode 100644 index 5318e06b2..000000000 --- a/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.rst +++ /dev/null @@ -1,131 +0,0 @@ -:name: ConvertAnitkImageTovtkImageData - -Convert an itk::Image to vtkImageData -===================================== - -.. index:: - single: ImageToVTKImageFilter - -Synopsis --------- - -Convert an itk::Image to vtkImageData in a pipeline. This transfers the image -buffer data along with image size, pixel spacing, and origin. Since -`vtkImageData` does not yet support an orientation matrix, the direction -cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's -CMake configuration. - - -Results -------- - -Output:: - - vtkImageData (0x51828b0) - Debug: Off - Modified Time: 240 - Reference Count: 2 - Registered Events: (none) - Information: 0x35d7810 - Data Released: False - Global Release Data: Off - UpdateTime: 241 - Field Data: - Debug: Off - Modified Time: 186 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 0 - Number Of Components: 0 - Number Of Tuples: 0 - Number Of Points: 39277 - Number Of Cells: 38880 - Cell Data: - Debug: Off - Modified Time: 194 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 0 - Number Of Components: 0 - Number Of Tuples: 0 - Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) - Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) - Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) - Scalars: (none) - Vectors: (none) - Normals: (none) - TCoords: (none) - Tensors: (none) - GlobalIds: (none) - PedigreeIds: (none) - EdgeFlag: (none) - Point Data: - Debug: Off - Modified Time: 240 - Reference Count: 1 - Registered Events: (none) - Number Of Arrays: 1 - Array 0 name = scalars - Number Of Components: 1 - Number Of Tuples: 39277 - Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 ) - Interpolate Flags: ( 1 1 1 1 1 0 0 1 ) - Pass Through Flags: ( 1 1 1 1 1 1 1 1 ) - Scalars: - Debug: Off - Modified Time: 240 - Reference Count: 1 - Registered Events: (none) - Name: scalars - Data type: unsigned char - Size: 39277 - MaxId: 39276 - NumberOfComponents: 1 - Information: 0 - Name: scalars - Number Of Components: 1 - Number Of Tuples: 39277 - Size: 39277 - MaxId: 39276 - LookupTable: (none) - Array: 0x51a7150 - Vectors: (none) - Normals: (none) - TCoords: (none) - Tensors: (none) - GlobalIds: (none) - PedigreeIds: (none) - EdgeFlag: (none) - Bounds: - Xmin,Xmax: (0, 180) - Ymin,Ymax: (0, 216) - Zmin,Zmax: (0, 0) - Compute Time: 254 - Spacing: (1, 1, 1) - Origin: (0, 0, 0) - Dimensions: (181, 217, 1) - Increments: (0, 0, 0) - Extent: (0, 180, 0, 216, 0, 0) - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToVTKImageFilter diff --git a/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.md b/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.md new file mode 100644 index 000000000..fee51355a --- /dev/null +++ b/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.md @@ -0,0 +1,103 @@ +--- +name: ConvertRGBvtkImageDataToAnitkImage +--- + +# Convert RGB vtkImageData to an itk::Image + +```{index} single: VTKImageToImageFilter +``` + +## Synopsis + +Convert RGB vtkImageData to an itk::Image in a processing pipeline. This +transfers the image buffer data along with image size, pixel spacing, and +origin. Since `vtkImageData` does not yet support an orientation matrix, the +direction cosines are lost. This requires `Module_ITKVtkGlue` to be turned on +in ITK's CMake configuration. + +## Results + +Output: + +``` +Image (0x2dc70e0) + RTTI typeinfo: itk::Image, 2u> + Reference Count: 2 + Modified Time: 28 + Debug: Off + Object Name: + Observers: + none + Source: (0x3281a40) + Source output name: Primary + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 23 + UpdateMTime: 29 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 2 + Index: [0, 0] + Size: [127, 162] + BufferedRegion: + Dimension: 2 + Index: [0, 0] + Size: [127, 162] + RequestedRegion: + Dimension: 2 + Index: [0, 0] + Size: [127, 162] + Spacing: [1, 1] + Origin: [0, 0] + Direction: +1 0 +0 1 + + IndexToPointMatrix: +1 0 +0 1 + + PointToIndexMatrix: +1 0 +0 1 + + Inverse Direction: +1 0 +0 1 + + PixelContainer: + ImportImageContainer (0x3282c00) + RTTI typeinfo: itk::ImportImageContainer > + Reference Count: 1 + Modified Time: 27 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x3196130 + Container manages memory: false + Size: 20574 + Capacity: 20574 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VTKImageToImageFilter +``` diff --git a/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.rst b/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.rst deleted file mode 100644 index a977685e0..000000000 --- a/src/Bridge/VtkGlue/ConvertRGBvtkImageDataToAnitkImage/Documentation.rst +++ /dev/null @@ -1,105 +0,0 @@ -:name: ConvertRGBvtkImageDataToAnitkImage - -Convert RGB vtkImageData to an itk::Image -========================================= - -.. index:: - single: VTKImageToImageFilter - -Synopsis --------- - -Convert RGB vtkImageData to an itk::Image in a processing pipeline. This -transfers the image buffer data along with image size, pixel spacing, and -origin. Since `vtkImageData` does not yet support an orientation matrix, the -direction cosines are lost. This requires `Module_ITKVtkGlue` to be turned on -in ITK's CMake configuration. - - -Results -------- - -Output:: - - Image (0x2dc70e0) - RTTI typeinfo: itk::Image, 2u> - Reference Count: 2 - Modified Time: 28 - Debug: Off - Object Name: - Observers: - none - Source: (0x3281a40) - Source output name: Primary - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 23 - UpdateMTime: 29 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 2 - Index: [0, 0] - Size: [127, 162] - BufferedRegion: - Dimension: 2 - Index: [0, 0] - Size: [127, 162] - RequestedRegion: - Dimension: 2 - Index: [0, 0] - Size: [127, 162] - Spacing: [1, 1] - Origin: [0, 0] - Direction: - 1 0 - 0 1 - - IndexToPointMatrix: - 1 0 - 0 1 - - PointToIndexMatrix: - 1 0 - 0 1 - - Inverse Direction: - 1 0 - 0 1 - - PixelContainer: - ImportImageContainer (0x3282c00) - RTTI typeinfo: itk::ImportImageContainer > - Reference Count: 1 - Modified Time: 27 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x3196130 - Container manages memory: false - Size: 20574 - Capacity: 20574 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::VTKImageToImageFilter diff --git a/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.md b/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.md new file mode 100644 index 000000000..686456ee8 --- /dev/null +++ b/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.md @@ -0,0 +1,107 @@ +--- +name: ConvertvtkImageDataToAnitkImage +--- + +# Convert vtkImageData to an itk::Image + +```{index} single: VTKImageToImageFilter +``` + +## Synopsis + +Convert vtkImageData to an itk::Image in a processing pipeline. This transfers +the image buffer data along with image size, pixel spacing, and origin. Since +`vtkImageData` does not yet support an orientation matrix, the direction +cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's +CMake configuration. + +## Results + +Output: + +``` +Image (0x3b9d810) + RTTI typeinfo: itk::Image + Reference Count: 2 + Modified Time: 62 + Debug: Off + Object Name: + Observers: + none + Source: (0x47e5460) + Source output name: Primary + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 57 + UpdateMTime: 63 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [181, 217, 1] + BufferedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [181, 217, 1] + RequestedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [181, 217, 1] + Spacing: [1, 1, 1] + Origin: [0, 0, 0] + Direction: +1 0 0 +0 1 0 +0 0 1 + + IndexToPointMatrix: +1 0 0 +0 1 0 +0 0 1 + + PointToIndexMatrix: +1 0 0 +0 1 0 +0 0 1 + + Inverse Direction: +1 0 0 +0 1 0 +0 0 1 + + PixelContainer: + ImportImageContainer (0x4875620) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 61 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x334e260 + Container manages memory: false + Size: 39277 + Capacity: 39277 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VTKImageToImageFilter +``` diff --git a/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.rst b/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.rst deleted file mode 100644 index 6515b84f1..000000000 --- a/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.rst +++ /dev/null @@ -1,110 +0,0 @@ -:name: ConvertvtkImageDataToAnitkImage - -Convert vtkImageData to an itk::Image -===================================== - -.. index:: - single: VTKImageToImageFilter - -Synopsis --------- - -Convert vtkImageData to an itk::Image in a processing pipeline. This transfers -the image buffer data along with image size, pixel spacing, and origin. Since -`vtkImageData` does not yet support an orientation matrix, the direction -cosines are lost. This requires `Module_ITKVtkGlue` to be turned on in ITK's -CMake configuration. - - - -Results -------- - -Output:: - - Image (0x3b9d810) - RTTI typeinfo: itk::Image - Reference Count: 2 - Modified Time: 62 - Debug: Off - Object Name: - Observers: - none - Source: (0x47e5460) - Source output name: Primary - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 57 - UpdateMTime: 63 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [181, 217, 1] - BufferedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [181, 217, 1] - RequestedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [181, 217, 1] - Spacing: [1, 1, 1] - Origin: [0, 0, 0] - Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - IndexToPointMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - PointToIndexMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - Inverse Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - PixelContainer: - ImportImageContainer (0x4875620) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 61 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x334e260 - Container manages memory: false - Size: 39277 - Capacity: 39277 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::VTKImageToImageFilter diff --git a/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.md b/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.md new file mode 100644 index 000000000..21601510e --- /dev/null +++ b/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: VTKImageToITKImage +--- + +# VTK Image to ITK Image + +```{index} single: VTKImageToImageFilter +``` + +## Synopsis + +Convert a VTK image to an ITK image. + +## Results + +:::{figure} Gourds.png +:alt: Input image. +:scale: 50% + +Input Image +::: + +:::{figure} VTKImageToITKImageQuickview.png +:alt: QuickView output. +:scale: 50% + +Output In QuickView +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VTKImageToImageFilter +``` diff --git a/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.rst b/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.rst deleted file mode 100644 index 592d3e567..000000000 --- a/src/Bridge/VtkGlue/VTKImageToITKImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: VTKImageToITKImage - -VTK Image to ITK Image -====================== -.. index:: - single: VTKImageToImageFilter - -Synopsis --------- - -Convert a VTK image to an ITK image. - - -Results -------- -.. figure:: Gourds.png - :scale: 50% - :alt: Input image. - - Input Image - -.. figure:: VTKImageToITKImageQuickview.png - :scale: 50% - :alt: QuickView output. - - Output In QuickView - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VTKImageToImageFilter diff --git a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.md b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.md new file mode 100644 index 000000000..25122c91d --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.md @@ -0,0 +1,47 @@ +--- +name: VisualizeEvolvingDense2DLevelSetAsElevationMap +--- + +# Visualize an Evolving Dense 2D Level Set as Elevation Map + +```{index} single: VTKVisualize2DLevelSetAsElevationMap single: BinaryImageToLevelSetImageAdaptor single: SinRegularizedHeavisideStepFunction single: LevelSetDenseImage single: LevelSetContainer single: LevelSetEquationChanAndVeseInternalTerm single: LevelSetEquationChanAndVeseExternalTerm single: LevelSetEvolutionNumberOfIterationsStoppingCriterion single: LevelSetEvolution single: LevelSetIterationUpdateCommand +``` + +## Synopsis + +Visualize an evolving dense level-set function 2D rendered as an elevation map. + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.* +:alt: Evolving level-sets rendered as an elevation map +:scale: 100% + +Evolving level-sets +::: + +:::{only} html +```{image} levelsets.gif +:alt: Evolving level-sets animation +:scale: 100% +``` +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualize2DLevelSetAsElevationMap] diff --git a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.rst b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.rst deleted file mode 100644 index cc6ffc63f..000000000 --- a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.rst +++ /dev/null @@ -1,60 +0,0 @@ -:name: VisualizeEvolvingDense2DLevelSetAsElevationMap - -Visualize an Evolving Dense 2D Level Set as Elevation Map -========================================================= - -.. index:: - single: VTKVisualize2DLevelSetAsElevationMap - single: BinaryImageToLevelSetImageAdaptor - single: SinRegularizedHeavisideStepFunction - single: LevelSetDenseImage - single: LevelSetContainer - single: LevelSetEquationChanAndVeseInternalTerm - single: LevelSetEquationChanAndVeseExternalTerm - single: LevelSetEvolutionNumberOfIterationsStoppingCriterion - single: LevelSetEvolution - single: LevelSetIterationUpdateCommand - - -Synopsis --------- - -Visualize an evolving dense level-set function 2D rendered as an elevation map. - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.* - :scale: 100% - :alt: Evolving level-sets rendered as an elevation map - - Evolving level-sets - -.. only:: html - - .. image:: levelsets.gif - :scale: 100% - :alt: Evolving level-sets animation - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualize2DLevelSetAsElevationMap] diff --git a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.md b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.md new file mode 100644 index 000000000..8b7dd093b --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.md @@ -0,0 +1,47 @@ +--- +name: VisualizeEvolvingDense2DLevelSetZeroSet +--- + +# Visualize an Evolving Dense 2D Level-Set Zero-Set + +```{index} single: VTKVisualizeImageLevelSetIsoValues single: BinaryImageToLevelSetImageAdaptor single: SinRegularizedHeavisideStepFunction single: LevelSetDenseImage single: LevelSetContainer single: LevelSetEquationChanAndVeseInternalTerm single: LevelSetEquationChanAndVeseExternalTerm single: LevelSetEvolutionNumberOfIterationsStoppingCriterion single: LevelSetEvolution single: LevelSetIterationUpdateCommand +``` + +## Synopsis + +Visualize the evolving zero-set of a dense level-set function 2D rendered. + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.* +:alt: Evolving level-sets +:scale: 100% + +Evolving level-sets +::: + +:::{only} html +```{image} levelsets.gif +:alt: Evolving level-sets animation +:scale: 100% +``` +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualizeImageLevelSetIsoValues] diff --git a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.rst b/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.rst deleted file mode 100644 index 952c9e4c3..000000000 --- a/src/Bridge/VtkGlue/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.rst +++ /dev/null @@ -1,60 +0,0 @@ -:name: VisualizeEvolvingDense2DLevelSetZeroSet - -Visualize an Evolving Dense 2D Level-Set Zero-Set -================================================= - -.. index:: - single: VTKVisualizeImageLevelSetIsoValues - single: BinaryImageToLevelSetImageAdaptor - single: SinRegularizedHeavisideStepFunction - single: LevelSetDenseImage - single: LevelSetContainer - single: LevelSetEquationChanAndVeseInternalTerm - single: LevelSetEquationChanAndVeseExternalTerm - single: LevelSetEvolutionNumberOfIterationsStoppingCriterion - single: LevelSetEvolution - single: LevelSetIterationUpdateCommand - - -Synopsis --------- - -Visualize the evolving zero-set of a dense level-set function 2D rendered. - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.* - :scale: 100% - :alt: Evolving level-sets - - Evolving level-sets - -.. only:: html - - .. image:: levelsets.gif - :scale: 100% - :alt: Evolving level-sets animation - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualizeImageLevelSetIsoValues] diff --git a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.md b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.md new file mode 100644 index 000000000..25c0dc248 --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.md @@ -0,0 +1,42 @@ +--- +name: VisualizeStaticDense2DLevelSetAsElevationMap +--- + +# Visualize a Static Dense 2D Level Set as Elevation Map + +```{index} single: VTKVisualize2DLevelSetAsElevationMap single: BinaryImageToLevelSetImageAdaptor single: LevelSetDenseImage +``` + +## Synopsis + +Visualize a static dense level-set function 2D rendered as an elevation map. +From the input image, first an otsu thresholding technique is used to get a +binary mask, which is then converted to a dense level-set function. + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.png +:alt: Static level-sets rendered as an elevation map +:scale: 100% + +Static level-sets +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualize2DLevelSetAsElevationMap] diff --git a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.rst b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.rst deleted file mode 100644 index 5b8cf3f60..000000000 --- a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: VisualizeStaticDense2DLevelSetAsElevationMap - -Visualize a Static Dense 2D Level Set as Elevation Map -====================================================== - -.. index:: - single: VTKVisualize2DLevelSetAsElevationMap - single: BinaryImageToLevelSetImageAdaptor - single: LevelSetDenseImage - -Synopsis --------- - -Visualize a static dense level-set function 2D rendered as an elevation map. -From the input image, first an otsu thresholding technique is used to get a -binary mask, which is then converted to a dense level-set function. - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.png - :scale: 100% - :alt: Static level-sets rendered as an elevation map - - Static level-sets - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualize2DLevelSetAsElevationMap] diff --git a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.md b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.md new file mode 100644 index 000000000..28e484a93 --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.md @@ -0,0 +1,42 @@ +--- +name: VisualizeStaticDense2DLevelSetZeroSet +--- + +# Visualize a Static Dense 2D Level-Set Zero-Set + +```{index} single: VTKVisualizeImageLevelSetIsoValues single: BinaryImageToLevelSetImageAdaptor single: LevelSetDenseImage +``` + +## Synopsis + +Visualize a static dense level-set function 2D's zero set. From the input +image, first an otsu thresholding technique is used to get a binary mask, which +is then converted to a dense level-set function. + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.png +:alt: Static level-sets zero-sets +:scale: 100% + +Static level-sets +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualizeImageLevelSetIsoValues] diff --git a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.rst b/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.rst deleted file mode 100644 index 4054d3dc3..000000000 --- a/src/Bridge/VtkGlue/VisualizeStaticDense2DLevelSetZeroSet/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: VisualizeStaticDense2DLevelSetZeroSet - -Visualize a Static Dense 2D Level-Set Zero-Set -============================================== - -.. index:: - single: VTKVisualizeImageLevelSetIsoValues - single: BinaryImageToLevelSetImageAdaptor - single: LevelSetDenseImage - -Synopsis --------- - -Visualize a static dense level-set function 2D's zero set. From the input -image, first an otsu thresholding technique is used to get a binary mask, which -is then converted to a dense level-set function. - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.png - :scale: 100% - :alt: Static level-sets zero-sets - - Static level-sets - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualizeImageLevelSetIsoValues] diff --git a/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.md b/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.md new file mode 100644 index 000000000..929ea282f --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.md @@ -0,0 +1,44 @@ +--- +name: VisualizeStaticMalcolm2DLevelSetLayers +--- + +# Visualize a Static Sparse Malcolm 2D Level-Set Layers + +```{index} single: vtkVisualize2DSparseLevelSetLayers single: BinaryImageToLevelSetImageAdaptor single: MalcolmSparseLevelSetImage +``` + +## Synopsis + +Visualize a static sparse Malcolm level-set function 2D's layers. From the input +image, first an otsu thresholding technique is used to get a binary mask, which +is then converted to a sparse level-set function. + +Note that Malcolm's representation is composed of a single layer (value = \{0}); + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.png +:alt: Static level-sets zero-sets +:scale: 100% + +Static level-sets +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.rst b/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.rst deleted file mode 100644 index 7e4942183..000000000 --- a/src/Bridge/VtkGlue/VisualizeStaticMalcolm2DLevelSetLayers/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: VisualizeStaticMalcolm2DLevelSetLayers - -Visualize a Static Sparse Malcolm 2D Level-Set Layers -===================================================== - -.. index:: - single: vtkVisualize2DSparseLevelSetLayers - single: BinaryImageToLevelSetImageAdaptor - single: MalcolmSparseLevelSetImage - -Synopsis --------- - -Visualize a static sparse Malcolm level-set function 2D's layers. From the input -image, first an otsu thresholding technique is used to get a binary mask, which -is then converted to a sparse level-set function. - -Note that Malcolm's representation is composed of a single layer (value = {0}); - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.png - :scale: 100% - :alt: Static level-sets zero-sets - - Static level-sets - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.md b/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.md new file mode 100644 index 000000000..9d685b8a1 --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.md @@ -0,0 +1,44 @@ +--- +name: VisualizeStaticShi2DLevelSetLayers +--- + +# Visualize a Static Sparse Shi 2D Level-Set Layers + +```{index} single: vtkVisualize2DSparseLevelSetLayers single: BinaryImageToLevelSetImageAdaptor single: ShiSparseLevelSetImage +``` + +## Synopsis + +Visualize a static sparse Shi level-set function 2D's layers. From the input +image, first an otsu thresholding technique is used to get a binary mask, which +is then converted to a sparse level-set function. + +Note that Shi's representation is composed of 4 layers (values = {-3, -1, +1, +3}) + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.png +:alt: Static level-sets zero-sets +:scale: 100% + +Static level-sets +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.rst b/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.rst deleted file mode 100644 index 905ac3709..000000000 --- a/src/Bridge/VtkGlue/VisualizeStaticShi2DLevelSetLayers/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: VisualizeStaticShi2DLevelSetLayers - -Visualize a Static Sparse Shi 2D Level-Set Layers -================================================= - -.. index:: - single: vtkVisualize2DSparseLevelSetLayers - single: BinaryImageToLevelSetImageAdaptor - single: ShiSparseLevelSetImage - -Synopsis --------- - -Visualize a static sparse Shi level-set function 2D's layers. From the input -image, first an otsu thresholding technique is used to get a binary mask, which -is then converted to a sparse level-set function. - -Note that Shi's representation is composed of 4 layers (values = {-3, -1, +1, +3}) - - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.png - :scale: 100% - :alt: Static level-sets zero-sets - - Static level-sets - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.md b/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.md new file mode 100644 index 000000000..7c3f43520 --- /dev/null +++ b/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.md @@ -0,0 +1,44 @@ +--- +name: VisualizeStaticWhitaker2DLevelSetLayers +--- + +# Visualize a Static Sparse Whitaker 2D Level-Set Layers + +```{index} single: vtkVisualize2DSparseLevelSetLayers single: BinaryImageToLevelSetImageAdaptor single: WhitakerSparseLevelSetImage +``` + +## Synopsis + +Visualize a static sparse Whitaker level-set function 2D's layers. From the input +image, first an otsu thresholding technique is used to get a binary mask, which +is then converted to a sparse level-set function. + +Note that Whitaker's representation is composed of 5 layers where values are real. + +## Results + +:::{figure} cells.png +:alt: Input image (cells) +:scale: 100% + +Input image +::: + +:::{figure} levelsets.png +:alt: Static level-sets zero-sets +:scale: 100% + +Static level-sets +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +% [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.rst b/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.rst deleted file mode 100644 index 0a8b5a675..000000000 --- a/src/Bridge/VtkGlue/VisualizeStaticWhitaker2DLevelSetLayers/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: VisualizeStaticWhitaker2DLevelSetLayers - -Visualize a Static Sparse Whitaker 2D Level-Set Layers -====================================================== - -.. index:: - single: vtkVisualize2DSparseLevelSetLayers - single: BinaryImageToLevelSetImageAdaptor - single: WhitakerSparseLevelSetImage - -Synopsis --------- - -Visualize a static sparse Whitaker level-set function 2D's layers. From the input -image, first an otsu thresholding technique is used to get a binary mask, which -is then converted to a sparse level-set function. - -Note that Whitaker's representation is composed of 5 layers where values are real. - -Results -------- - -.. figure:: cells.png - :scale: 100% - :alt: Input image (cells) - - Input image - -.. figure:: levelsets.png - :scale: 100% - :alt: Static level-sets zero-sets - - Static level-sets - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. [breathelink:: itk::VTKVisualize2DSparseLevelSetLayers] diff --git a/src/Bridge/VtkGlue/index.md b/src/Bridge/VtkGlue/index.md new file mode 100644 index 000000000..bdd7cab34 --- /dev/null +++ b/src/Bridge/VtkGlue/index.md @@ -0,0 +1,18 @@ +# VtkGlue + +```{toctree} +:maxdepth: 1 + +ConvertAnitkImageTovtkImageData/Documentation.rst +ConvertAnRGBitkImageTovtkImageData/Documentation.rst +ConvertRGBvtkImageDataToAnitkImage/Documentation.rst +ConvertvtkImageDataToAnitkImage/Documentation.rst +VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.rst +VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.rst +VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.rst +VisualizeStaticDense2DLevelSetZeroSet/Documentation.rst +VisualizeStaticMalcolm2DLevelSetLayers/Documentation.rst +VisualizeStaticShi2DLevelSetLayers/Documentation.rst +VisualizeStaticWhitaker2DLevelSetLayers/Documentation.rst +VTKImageToITKImage/Documentation.rst +``` diff --git a/src/Bridge/VtkGlue/index.rst b/src/Bridge/VtkGlue/index.rst deleted file mode 100644 index 791420dc7..000000000 --- a/src/Bridge/VtkGlue/index.rst +++ /dev/null @@ -1,18 +0,0 @@ -VtkGlue -======= - -.. toctree:: - :maxdepth: 1 - - ConvertAnitkImageTovtkImageData/Documentation.rst - ConvertAnRGBitkImageTovtkImageData/Documentation.rst - ConvertRGBvtkImageDataToAnitkImage/Documentation.rst - ConvertvtkImageDataToAnitkImage/Documentation.rst - VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.rst - VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.rst - VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.rst - VisualizeStaticDense2DLevelSetZeroSet/Documentation.rst - VisualizeStaticMalcolm2DLevelSetLayers/Documentation.rst - VisualizeStaticShi2DLevelSetLayers/Documentation.rst - VisualizeStaticWhitaker2DLevelSetLayers/Documentation.rst - VTKImageToITKImage/Documentation.rst diff --git a/src/Bridge/index.md b/src/Bridge/index.md new file mode 100644 index 000000000..c5cd844bd --- /dev/null +++ b/src/Bridge/index.md @@ -0,0 +1,8 @@ +# Bridge + +```{toctree} +:maxdepth: 2 + +VtkGlue/index.rst +NumPy/index.rst +``` diff --git a/src/Bridge/index.rst b/src/Bridge/index.rst deleted file mode 100644 index 606409cef..000000000 --- a/src/Bridge/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Bridge -====== - -.. toctree:: - :maxdepth: 2 - - VtkGlue/index.rst - NumPy/index.rst diff --git a/src/Core/Common/AddNoiseToBinaryImage/Documentation.md b/src/Core/Common/AddNoiseToBinaryImage/Documentation.md new file mode 100644 index 000000000..2a257e23d --- /dev/null +++ b/src/Core/Common/AddNoiseToBinaryImage/Documentation.md @@ -0,0 +1,48 @@ +--- +name: AddNoiseToBinaryImage +--- + +# Add Noise To Binary Image + +```{index} single: ImageRandomNonRepeatingIteratorWithIndex single: noise pair: binary; image +``` + +## Synopsis + +Add noise to a binary image. + +## Results + +:::{figure} Yinyang.png +:alt: Input.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} AddNoiseToBinaryImage.png +:alt: Output.png +:scale: 70% + +Output.png +::: + +Output: + +``` +Number of random samples: 105062 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRandomNonRepeatingIteratorWithIndex +``` diff --git a/src/Core/Common/AddNoiseToBinaryImage/Documentation.rst b/src/Core/Common/AddNoiseToBinaryImage/Documentation.rst deleted file mode 100644 index 3c28bb8f6..000000000 --- a/src/Core/Common/AddNoiseToBinaryImage/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: AddNoiseToBinaryImage - -Add Noise To Binary Image -========================= - -.. index:: - single: ImageRandomNonRepeatingIteratorWithIndex - single: noise - pair: binary; image - -Synopsis --------- - -Add noise to a binary image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: Input.png - - Yinyang.png - -.. figure:: AddNoiseToBinaryImage.png - :scale: 70% - :alt: Output.png - - Output.png - -Output:: - - Number of random samples: 105062 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRandomNonRepeatingIteratorWithIndex diff --git a/src/Core/Common/AddOffsetToIndex/Documentation.md b/src/Core/Common/AddOffsetToIndex/Documentation.md new file mode 100644 index 000000000..871d51545 --- /dev/null +++ b/src/Core/Common/AddOffsetToIndex/Documentation.md @@ -0,0 +1,48 @@ +--- +name: AddOffsetToIndex +--- + +# Add Offset To Index + +```{index} single: Offset single: Index +``` + +## Synopsis + +Add an offset to a pixel index + +## Results + +Output: +: index: \[5, 5\] + + offset: \[1, 1\] + + index + offset: \[6, 6\] + + index: \[5, 5\] + + offset: \[-1, 1\] + + index + offset: \[4, 6\] + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelinkstruct:: itk::Offset itk::Index +``` diff --git a/src/Core/Common/AddOffsetToIndex/Documentation.rst b/src/Core/Common/AddOffsetToIndex/Documentation.rst deleted file mode 100644 index a0f896a4d..000000000 --- a/src/Core/Common/AddOffsetToIndex/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: AddOffsetToIndex - -Add Offset To Index -=================== - -.. index:: - single: Offset - single: Index - -Synopsis --------- - - -Add an offset to a pixel index - - -Results -------- - -Output: - | index: [5, 5] - | offset: [1, 1] - | index + offset: [6, 6] - - | index: [5, 5] - | offset: [-1, 1] - | index + offset: [4, 6] - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelinkstruct:: itk::Offset itk::Index diff --git a/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.md b/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.md new file mode 100644 index 000000000..110f9733d --- /dev/null +++ b/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.md @@ -0,0 +1,41 @@ +--- +name: ApplyAFilterOnlyToASpecifiedRegionOfAnImage +--- + +# Apply a Filter Only to a Specified Region of an Image + +```{index} single: Image pair: Image; SetRequestedRegion +``` + +## Synopsis + +The key of using SetRequestedRegion to tell a filter to only operate on a specified ImageRegion is to call SetRequestedRegion on the filters GetOutput(). +That is, to tell the DerivativeImageFilter to only operate on a small region, you must do + +``` +derivativeFilter->GetOutput()->SetRequestedRegion(smallRegion); +derivativeFilter->Update(); +``` + +## Results + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.rst b/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.rst deleted file mode 100644 index 9d27bd740..000000000 --- a/src/Core/Common/ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.rst +++ /dev/null @@ -1,45 +0,0 @@ -:name: ApplyAFilterOnlyToASpecifiedRegionOfAnImage - -Apply a Filter Only to a Specified Region of an Image -===================================================== - -.. index:: - single: Image - pair: Image; SetRequestedRegion - -Synopsis --------- - - -The key of using SetRequestedRegion to tell a filter to only operate on a specified ImageRegion is to call SetRequestedRegion on the filters GetOutput(). -That is, to tell the DerivativeImageFilter to only operate on a small region, you must do :: - - derivativeFilter->GetOutput()->SetRequestedRegion(smallRegion); - derivativeFilter->Update(); - - -Results -------- - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.md b/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.md new file mode 100644 index 000000000..7c298740b --- /dev/null +++ b/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ApplyCustomOperationToEachPixelInImage +--- + +# Apply Custom Operation to Each Pixel in Image + +```{index} single: UnaryFunctorImageFilter +``` + +## Synopsis + +Apply a custom operation to each pixel in an image. + +## Results + +Output: + +``` +pixel (1,1) was = [1,0] +pixel (1,1) now = [-4.37144e-08, 1] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::UnaryFunctorImageFilter +``` diff --git a/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.rst b/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.rst deleted file mode 100644 index b456a4368..000000000 --- a/src/Core/Common/ApplyCustomOperationToEachPixelInImage/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: ApplyCustomOperationToEachPixelInImage - -Apply Custom Operation to Each Pixel in Image -============================================= - -.. index:: - single: UnaryFunctorImageFilter - -Synopsis --------- -Apply a custom operation to each pixel in an image. - - -Results -------- -Output:: - - pixel (1,1) was = [1,0] - pixel (1,1) now = [-4.37144e-08, 1] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::UnaryFunctorImageFilter diff --git a/src/Core/Common/BoundingBoxOfAPointSet/Documentation.md b/src/Core/Common/BoundingBoxOfAPointSet/Documentation.md new file mode 100644 index 000000000..d99ea462d --- /dev/null +++ b/src/Core/Common/BoundingBoxOfAPointSet/Documentation.md @@ -0,0 +1,41 @@ +--- +name: BoundingBoxOfAPointSet +--- + +# Bounding Box of a Point Set + +```{index} single: PointSet single: BoundingBox +``` + +## Synopsis + +Get the bounding box of a PointSet + +## Results + +Output:: + +: bounds: \[0, 0.1, 0, 0.1, 0, 0\] + center: \[0.05, 0.05, 0\] + diagonal length squared: 0.02 + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PointSet itk::BoundingBox +``` diff --git a/src/Core/Common/BoundingBoxOfAPointSet/Documentation.rst b/src/Core/Common/BoundingBoxOfAPointSet/Documentation.rst deleted file mode 100644 index 1d02a6a0f..000000000 --- a/src/Core/Common/BoundingBoxOfAPointSet/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: BoundingBoxOfAPointSet - -Bounding Box of a Point Set -=========================== - -.. index:: - single: PointSet - single: BoundingBox - -Synopsis --------- - - -Get the bounding box of a PointSet - - -Results -------- - - -Output:: - bounds: [0, 0.1, 0, 0.1, 0, 0] - center: [0.05, 0.05, 0] - diagonal length squared: 0.02 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PointSet itk::BoundingBox diff --git a/src/Core/Common/BresenhamLine/Documentation.md b/src/Core/Common/BresenhamLine/Documentation.md new file mode 100644 index 000000000..c2a2694a2 --- /dev/null +++ b/src/Core/Common/BresenhamLine/Documentation.md @@ -0,0 +1,44 @@ +--- +name: BresenhamLine +--- + +# Bresenham Line + +```{index} single: BresenhamLine +``` + +## Synopsis + +Get the points on a Bresenham line between two points. + +## Results + +Output: + +``` +[0, 0] +[1, 1] +[2, 2] +[3, 3] +[0, 0] +[1, 1] +[2, 2] +[3, 3] +[4, 4] +[5, 5] +[6, 6] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BresenhamLine +``` diff --git a/src/Core/Common/BresenhamLine/Documentation.rst b/src/Core/Common/BresenhamLine/Documentation.rst deleted file mode 100644 index 032efe0be..000000000 --- a/src/Core/Common/BresenhamLine/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: BresenhamLine - -Bresenham Line -============== - -.. index:: - single: BresenhamLine - -Synopsis --------- - -Get the points on a Bresenham line between two points. - - -Results -------- - -Output:: - - [0, 0] - [1, 1] - [2, 2] - [3, 3] - [0, 0] - [1, 1] - [2, 2] - [3, 3] - [4, 4] - [5, 5] - [6, 6] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BresenhamLine diff --git a/src/Core/Common/BuildAHelloWorldProgram/Documentation.md b/src/Core/Common/BuildAHelloWorldProgram/Documentation.md new file mode 100644 index 000000000..8eeaf488c --- /dev/null +++ b/src/Core/Common/BuildAHelloWorldProgram/Documentation.md @@ -0,0 +1,103 @@ +--- +name: BuildAHelloWorldProgram +--- + +# Build a Hello World Program + +```{index} single: Image, hello world +``` + +## Synopsis + +This demonstrates building a simple Hello World ITK program. We instantiate an +image and print it to stdout. + +## Results + +Output: + +``` +ITK Hello World! +Image (0x19ca6d0) + RTTI typeinfo: itk::Image + Reference Count: 2 + Modified Time: 1 + Debug: Off + Observers: + none + Source: (none) + Source output name: (none) + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 0 + UpdateMTime: 0 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + BufferedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + RequestedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + Spacing: [1, 1, 1] + Origin: [0, 0, 0] + Direction: +1 0 0 +0 1 0 +0 0 1 + + IndexToPointMatrix: + 1 0 0 +0 1 0 +0 0 1 + + PointToIndexMatrix: + 1 0 0 +0 1 0 +0 0 1 + + Inverse Direction: + 1 0 0 +0 1 0 +0 0 1 + + PixelContainer: + ImportImageContainer (0x19ca990) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 2 + Debug: Off + Observers: + none + Pointer: 0 + Container manages memory: true + Size: 0 + Capacity: 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/BuildAHelloWorldProgram/Documentation.rst b/src/Core/Common/BuildAHelloWorldProgram/Documentation.rst deleted file mode 100644 index 263ee5f97..000000000 --- a/src/Core/Common/BuildAHelloWorldProgram/Documentation.rst +++ /dev/null @@ -1,104 +0,0 @@ -:name: BuildAHelloWorldProgram - -Build a Hello World Program -=========================== - -.. index:: - single: Image, hello world - -Synopsis --------- - -This demonstrates building a simple Hello World ITK program. We instantiate an -image and print it to stdout. - - -Results -------- - -Output:: - - ITK Hello World! - Image (0x19ca6d0) - RTTI typeinfo: itk::Image - Reference Count: 2 - Modified Time: 1 - Debug: Off - Observers: - none - Source: (none) - Source output name: (none) - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 0 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - BufferedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - RequestedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - Spacing: [1, 1, 1] - Origin: [0, 0, 0] - Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - IndexToPointMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - PointToIndexMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - Inverse Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - PixelContainer: - ImportImageContainer (0x19ca990) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 2 - Debug: Off - Observers: - none - Pointer: 0 - Container manages memory: true - Size: 0 - Capacity: 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/CastVectorImageToAnotherType/Documentation.md b/src/Core/Common/CastVectorImageToAnotherType/Documentation.md new file mode 100644 index 000000000..77b05594f --- /dev/null +++ b/src/Core/Common/CastVectorImageToAnotherType/Documentation.md @@ -0,0 +1,33 @@ +--- +name: CastVectorImageToAnotherType +--- + +# Cast Vector Image to Another Type + +```{index} single: VectorImage pair: cast; VectorImage +``` + +## Synopsis + +Cast a VectorImage to another type of VectorImage. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorImage +``` diff --git a/src/Core/Common/CastVectorImageToAnotherType/Documentation.rst b/src/Core/Common/CastVectorImageToAnotherType/Documentation.rst deleted file mode 100644 index 3067d542a..000000000 --- a/src/Core/Common/CastVectorImageToAnotherType/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: CastVectorImageToAnotherType - -Cast Vector Image to Another Type -================================= - -.. index:: - single: VectorImage - pair: cast; VectorImage - -Synopsis --------- - -Cast a VectorImage to another type of VectorImage. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorImage diff --git a/src/Core/Common/CheckIfModuleIsPresent/Documentation.md b/src/Core/Common/CheckIfModuleIsPresent/Documentation.md new file mode 100644 index 000000000..8dd667218 --- /dev/null +++ b/src/Core/Common/CheckIfModuleIsPresent/Documentation.md @@ -0,0 +1,26 @@ +--- +name: CheckIfModuleIsPresent +--- + +# Check if Module Is Present + +```{index} single: Image +``` + +## Synopsis + +Check if a specific module is present. + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/CheckIfModuleIsPresent/Documentation.rst b/src/Core/Common/CheckIfModuleIsPresent/Documentation.rst deleted file mode 100644 index c2be3f7a2..000000000 --- a/src/Core/Common/CheckIfModuleIsPresent/Documentation.rst +++ /dev/null @@ -1,27 +0,0 @@ -:name: CheckIfModuleIsPresent - -Check if Module Is Present -========================== - -.. index:: - single: Image - -Synopsis --------- - -Check if a specific module is present. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/ComputeTimeBetweenPoints/Documentation.md b/src/Core/Common/ComputeTimeBetweenPoints/Documentation.md new file mode 100644 index 000000000..e0999dfcc --- /dev/null +++ b/src/Core/Common/ComputeTimeBetweenPoints/Documentation.md @@ -0,0 +1,59 @@ +--- +name: ComputeTimeBetweenPoints +--- + +# Compute Time Between Points + +```{index} single: TimeProbe single: timer single: timing +``` + +## Synopsis + +Compute the time between points in code. The `Report()` method is available in +ITK 4.9.0 or later. + +## Results + +```none +Mean: 0.00756311416626 +Total: 0.00756311416626 +Mean: 0.00671458244324 +Total: 0.0134291648865 +System: clay +Processor: Unknown P6 family + Cache: 15360 + Clock: 2194.87 + Cores: 12 cpus x 12 Cores = 144 + Virtual Memory: Total: 0 Available: 0 + Physical Memory: Total:64294 Available: 36172 +OSName: Linux + Release: 4.1.4-calculate + Version: #2 SMP PREEMPT Sun Aug 9 17:03:44 EDT 2015 + Platform: x86_64 + Operating System is 64 bit +ITK Version: 4.9.0 +Name Of Probe(Time) Iteration Total(s) Min(s) Mean(s) Max(s) Std(s) + 2 0.0134292 0.00586605 0.00671458 0.00756311 0.00120001 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TimeProbe +``` diff --git a/src/Core/Common/ComputeTimeBetweenPoints/Documentation.rst b/src/Core/Common/ComputeTimeBetweenPoints/Documentation.rst deleted file mode 100644 index 2ea15c881..000000000 --- a/src/Core/Common/ComputeTimeBetweenPoints/Documentation.rst +++ /dev/null @@ -1,65 +0,0 @@ -:name: ComputeTimeBetweenPoints - -Compute Time Between Points -=========================== - -.. index:: - single: TimeProbe - single: timer - single: timing - -Synopsis --------- - - -Compute the time between points in code. The `Report()` method is available in -ITK 4.9.0 or later. - - -Results -------- - -.. code-block:: none - - Mean: 0.00756311416626 - Total: 0.00756311416626 - Mean: 0.00671458244324 - Total: 0.0134291648865 - System: clay - Processor: Unknown P6 family - Cache: 15360 - Clock: 2194.87 - Cores: 12 cpus x 12 Cores = 144 - Virtual Memory: Total: 0 Available: 0 - Physical Memory: Total:64294 Available: 36172 - OSName: Linux - Release: 4.1.4-calculate - Version: #2 SMP PREEMPT Sun Aug 9 17:03:44 EDT 2015 - Platform: x86_64 - Operating System is 64 bit - ITK Version: 4.9.0 - Name Of Probe(Time) Iteration Total(s) Min(s) Mean(s) Max(s) Std(s) - 2 0.0134292 0.00586605 0.00671458 0.00756311 0.00120001 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TimeProbe diff --git a/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.md b/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.md new file mode 100644 index 000000000..febc95e3d --- /dev/null +++ b/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.md @@ -0,0 +1,22 @@ +--- +name: ConceptCheckingIsFloatingPoint +--- + +# Concept Checking Is Floating Point + +```{index} pair: ConceptChecking; IsFloatingPoint +``` + +## Synopsis + +Check at compilation time that a given type is floating point. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.rst b/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.rst deleted file mode 100644 index 5e27b4812..000000000 --- a/src/Core/Common/ConceptCheckingIsFloatingPoint/Documentation.rst +++ /dev/null @@ -1,26 +0,0 @@ -:name: ConceptCheckingIsFloatingPoint - -Concept Checking Is Floating Point -================================== - -.. index:: - pair: ConceptChecking; IsFloatingPoint - -Synopsis --------- - -Check at compilation time that a given type is floating point. - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.md b/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.md new file mode 100644 index 000000000..cc829ade5 --- /dev/null +++ b/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.md @@ -0,0 +1,22 @@ +--- +name: ConceptCheckingIsSameDimension +--- + +# Concept Checking Is Same Dimension + +```{index} single: ConceptChecking +``` + +## Synopsis + +Check at compilation time that 2 dimensions are the same. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.rst b/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.rst deleted file mode 100644 index f19cee70d..000000000 --- a/src/Core/Common/ConceptCheckingIsSameDimension/Documentation.rst +++ /dev/null @@ -1,25 +0,0 @@ -:name: ConceptCheckingIsSameDimension - -Concept Checking Is Same Dimension -================================== - -.. index:: - single: ConceptChecking - -Synopsis --------- - -Check at compilation time that 2 dimensions are the same. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Core/Common/ConceptCheckingIsSameType/Documentation.md b/src/Core/Common/ConceptCheckingIsSameType/Documentation.md new file mode 100644 index 000000000..ff34d485c --- /dev/null +++ b/src/Core/Common/ConceptCheckingIsSameType/Documentation.md @@ -0,0 +1,22 @@ +--- +name: ConceptCheckingIsSameType +--- + +# Concept Checking Is Same Type + +```{index} single: ConceptChecking +``` + +## Synopsis + +Check at compilation time that 2 given types are the same. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Core/Common/ConceptCheckingIsSameType/Documentation.rst b/src/Core/Common/ConceptCheckingIsSameType/Documentation.rst deleted file mode 100644 index ba1516bbc..000000000 --- a/src/Core/Common/ConceptCheckingIsSameType/Documentation.rst +++ /dev/null @@ -1,25 +0,0 @@ -:name: ConceptCheckingIsSameType - -Concept Checking Is Same Type -============================= - -.. index:: - single: ConceptChecking - -Synopsis --------- - -Check at compilation time that 2 given types are the same. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Core/Common/ConvertArrayToImage/Documentation.md b/src/Core/Common/ConvertArrayToImage/Documentation.md new file mode 100644 index 000000000..cb758c53a --- /dev/null +++ b/src/Core/Common/ConvertArrayToImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ConvertArrayToImage +--- + +# Convert Array to Image + +```{index} single: ImportImageFilter pair: array; convert pair: array; image +``` + +## Synopsis + +Convert a C-style array to an itkImage. + +## Results + +:::{figure} ConvertArrayToImageOutput.png +:alt: test.png +:scale: 70% + +Output Image. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImportImageFilter +``` diff --git a/src/Core/Common/ConvertArrayToImage/Documentation.rst b/src/Core/Common/ConvertArrayToImage/Documentation.rst deleted file mode 100644 index 2eb5f373d..000000000 --- a/src/Core/Common/ConvertArrayToImage/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: ConvertArrayToImage - -Convert Array to Image -====================== - -.. index:: - single: ImportImageFilter - pair: array; convert - pair: array; image - -Synopsis --------- - -Convert a C-style array to an itkImage. - - -Results -------- -.. figure:: ConvertArrayToImageOutput.png - :scale: 70% - :alt: test.png - - Output Image. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImportImageFilter diff --git a/src/Core/Common/CovariantVectorDotProduct/Documentation.md b/src/Core/Common/CovariantVectorDotProduct/Documentation.md new file mode 100644 index 000000000..fbdebace9 --- /dev/null +++ b/src/Core/Common/CovariantVectorDotProduct/Documentation.md @@ -0,0 +1,37 @@ +--- +name: CovariantVectorDotProduct +--- + +# Covariant Vector Dot Product + +```{index} single: CovariantVector pair: CovariantVector; operator * +``` + +## Synopsis + +Dot product of CovariantVectors + +## Results + +Output: + +``` +u :[-1, 1, -1] +v :[1, 2, 3] +DotProduct( u, v ) = -2 +u - DotProduct( u, v ) * v = [1, 5, 5] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CovariantVector +``` diff --git a/src/Core/Common/CovariantVectorDotProduct/Documentation.rst b/src/Core/Common/CovariantVectorDotProduct/Documentation.rst deleted file mode 100644 index 63840fbdf..000000000 --- a/src/Core/Common/CovariantVectorDotProduct/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: CovariantVectorDotProduct - -Covariant Vector Dot Product -============================ - -.. index:: - single: CovariantVector - pair: CovariantVector; operator * - -Synopsis --------- - -Dot product of CovariantVectors - - -Results -------- - -Output:: - - u :[-1, 1, -1] - v :[1, 2, 3] - DotProduct( u, v ) = -2 - u - DotProduct( u, v ) * v = [1, 5, 5] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CovariantVector diff --git a/src/Core/Common/CovariantVectorNorm/Documentation.md b/src/Core/Common/CovariantVectorNorm/Documentation.md new file mode 100644 index 000000000..9fdfde746 --- /dev/null +++ b/src/Core/Common/CovariantVectorNorm/Documentation.md @@ -0,0 +1,38 @@ +--- +name: CovariantVectorNorm +--- + +# Covariant Vector Norm + +```{index} single: CovariantVector pair: CovariantVector; GetNorm pair: CovariantVector; GetSquaredNorm pair: CovariantVector; Normalize +``` + +## Synopsis + +Compute the norm of a CovariantVector and normalize it. + +## Results + +Output: + +``` +v: [1, 2, 3] +vnorm: 3.74166 +vnorm2: 14 +v: [0.267261, 0.534522, 0.801784] +u: [0.267261, 0.534522, 0.801784] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CovariantVector +``` diff --git a/src/Core/Common/CovariantVectorNorm/Documentation.rst b/src/Core/Common/CovariantVectorNorm/Documentation.rst deleted file mode 100644 index ba3c8c2ac..000000000 --- a/src/Core/Common/CovariantVectorNorm/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: CovariantVectorNorm - -Covariant Vector Norm -===================== - -.. index:: - single: CovariantVector - pair: CovariantVector; GetNorm - pair: CovariantVector; GetSquaredNorm - pair: CovariantVector; Normalize - - -Synopsis --------- - -Compute the norm of a CovariantVector and normalize it. - - -Results -------- - -Output:: - - v: [1, 2, 3] - vnorm: 3.74166 - vnorm2: 14 - v: [0.267261, 0.534522, 0.801784] - u: [0.267261, 0.534522, 0.801784] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CovariantVector diff --git a/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.md b/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.md new file mode 100644 index 000000000..5c04b722f --- /dev/null +++ b/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.md @@ -0,0 +1,48 @@ +--- +name: CreateABackwardDifferenceOperator +--- + +# Create a Backward Difference Operator + +```{index} single: BackwardDifferenceOperator +``` + +## Synopsis + +Create a backward difference operator + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: + Radius:[1, 1] + Size:[3, 3] + DataBuffer:NeighborhoodAllocator { this = 0x7fffb3cae9f8, begin = 0x1dd0e50, size=9 } + +[-1, -1] 0 +[0, -1] 0 +[1, -1] 0 +[-1, 0] -1 +[0, 0] 1 +[1, 0] 0 +[-1, 1] 0 +[0, 1] 0 +[1, 1] 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BackwardDifferenceOperator +``` diff --git a/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.rst b/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.rst deleted file mode 100644 index 63284fbe1..000000000 --- a/src/Core/Common/CreateABackwardDifferenceOperator/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: CreateABackwardDifferenceOperator - -Create a Backward Difference Operator -===================================== - -.. index:: - single: BackwardDifferenceOperator - -Synopsis --------- - - -Create a backward difference operator - - -Results -------- - -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7fffb3cae9f8, begin = 0x1dd0e50, size=9 } - - [-1, -1] 0 - [0, -1] 0 - [1, -1] 0 - [-1, 0] -1 - [0, 0] 1 - [1, 0] 0 - [-1, 1] 0 - [0, 1] 0 - [1, 1] 0 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BackwardDifferenceOperator diff --git a/src/Core/Common/CreateACovariantVector/Documentation.md b/src/Core/Common/CreateACovariantVector/Documentation.md new file mode 100644 index 000000000..5a4a57b42 --- /dev/null +++ b/src/Core/Common/CreateACovariantVector/Documentation.md @@ -0,0 +1,41 @@ +--- +name: CreateACovariantVector +--- + +# Create a CovariantVector + +```{index} single: CovariantVector +``` + +## Synopsis + +Create a CovariantVector + +## Results + +Output: + +``` +v: [1, 2, 3] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CovariantVector +``` diff --git a/src/Core/Common/CreateACovariantVector/Documentation.rst b/src/Core/Common/CreateACovariantVector/Documentation.rst deleted file mode 100644 index 232e04b93..000000000 --- a/src/Core/Common/CreateACovariantVector/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: CreateACovariantVector - -Create a CovariantVector -======================== - -.. index:: - single: CovariantVector - - -Synopsis --------- - -Create a CovariantVector - - -Results -------- - -Output:: - - v: [1, 2, 3] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CovariantVector diff --git a/src/Core/Common/CreateAFixedArray/Documentation.md b/src/Core/Common/CreateAFixedArray/Documentation.md new file mode 100644 index 000000000..1457f9fb2 --- /dev/null +++ b/src/Core/Common/CreateAFixedArray/Documentation.md @@ -0,0 +1,39 @@ +--- +name: CreateAFixedArray +--- + +# Create a Fixed Array + +```{index} single: FixedArray +``` + +## Synopsis + +Create a FixedArray + +## Results + +Output:: + +: \[0, 1\] + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FixedArray +``` diff --git a/src/Core/Common/CreateAFixedArray/Documentation.rst b/src/Core/Common/CreateAFixedArray/Documentation.rst deleted file mode 100644 index f210062cc..000000000 --- a/src/Core/Common/CreateAFixedArray/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: CreateAFixedArray - -Create a Fixed Array -==================== - -.. index:: - single: FixedArray - -Synopsis --------- - - -Create a FixedArray - - -Results -------- - -Output:: - [0, 1] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FixedArray diff --git a/src/Core/Common/CreateAIndex/Documentation.md b/src/Core/Common/CreateAIndex/Documentation.md new file mode 100644 index 000000000..ed93d6ad5 --- /dev/null +++ b/src/Core/Common/CreateAIndex/Documentation.md @@ -0,0 +1,40 @@ +--- +name: CreateAIndex +--- + +# Create a Index + +```{index} single: Index +``` + +## Synopsis + +Create a itk::Index, which represents a pixel location in an itk::Image. + +## Results + +Output:: + +: \[0, 0\] + \[1, 2\] + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelinkstruct:: itk::Index +``` diff --git a/src/Core/Common/CreateAIndex/Documentation.rst b/src/Core/Common/CreateAIndex/Documentation.rst deleted file mode 100644 index a5e884eae..000000000 --- a/src/Core/Common/CreateAIndex/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: CreateAIndex - -Create a Index -============== - -.. index:: - single: Index - -Synopsis --------- - - -Create a itk::Index, which represents a pixel location in an itk::Image. - - -Results -------- - -Output:: - [0, 0] - [1, 2] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelinkstruct:: itk::Index diff --git a/src/Core/Common/CreateAPointSet/Documentation.md b/src/Core/Common/CreateAPointSet/Documentation.md new file mode 100644 index 000000000..717cbd4c0 --- /dev/null +++ b/src/Core/Common/CreateAPointSet/Documentation.md @@ -0,0 +1,33 @@ +--- +name: CreateAPointSet +--- + +# Create a PointSet + +```{index} single: PointSet pair: PointSet; InsertElement +``` + +## Synopsis + +Create a PointSet + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PointSet +``` diff --git a/src/Core/Common/CreateAPointSet/Documentation.rst b/src/Core/Common/CreateAPointSet/Documentation.rst deleted file mode 100644 index a589dada8..000000000 --- a/src/Core/Common/CreateAPointSet/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: CreateAPointSet - -Create a PointSet -================= - -.. index:: single: PointSet - pair: PointSet; InsertElement - - -Synopsis --------- - -Create a PointSet - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PointSet diff --git a/src/Core/Common/CreateASize/Documentation.md b/src/Core/Common/CreateASize/Documentation.md new file mode 100644 index 000000000..87744e052 --- /dev/null +++ b/src/Core/Common/CreateASize/Documentation.md @@ -0,0 +1,42 @@ +--- +name: CreateASize +--- + +# Create a Size + +```{index} single: Size +``` + +## Synopsis + +Create a itk::Size, which represents the size of a region in an itk::Image. + +## Results + +Output: + +``` +[0, 0] +[1, 2] +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelinkstruct:: itk::Size +``` diff --git a/src/Core/Common/CreateASize/Documentation.rst b/src/Core/Common/CreateASize/Documentation.rst deleted file mode 100644 index 9e55d413d..000000000 --- a/src/Core/Common/CreateASize/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: CreateASize - -Create a Size -============= - -.. index:: - single: Size - -Synopsis --------- - -Create a itk::Size, which represents the size of a region in an itk::Image. - -Results -------- - -Output:: - - [0, 0] - [1, 2] - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelinkstruct:: itk::Size diff --git a/src/Core/Common/CreateAVector/Documentation.md b/src/Core/Common/CreateAVector/Documentation.md new file mode 100644 index 000000000..16effbca3 --- /dev/null +++ b/src/Core/Common/CreateAVector/Documentation.md @@ -0,0 +1,41 @@ +--- +name: CreateAVector +--- + +# Create a Vector + +```{index} single: Vector +``` + +## Synopsis + +Create a Vector + +## Results + +Output: + +``` +v: [1, 2, 3] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Vector +``` diff --git a/src/Core/Common/CreateAVector/Documentation.rst b/src/Core/Common/CreateAVector/Documentation.rst deleted file mode 100644 index e4176b9b5..000000000 --- a/src/Core/Common/CreateAVector/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: CreateAVector - -Create a Vector -=============== - -.. index:: - single: Vector - -Synopsis --------- - -Create a Vector - - -Results -------- - -Output:: - - v: [1, 2, 3] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Vector diff --git a/src/Core/Common/CreateAnImage/Documentation.md b/src/Core/Common/CreateAnImage/Documentation.md new file mode 100644 index 000000000..eb22c7159 --- /dev/null +++ b/src/Core/Common/CreateAnImage/Documentation.md @@ -0,0 +1,105 @@ +--- +name: CreateAnImage +--- + +# Create an Image + +```{index} single: Image single: instantiate +``` + +## Synopsis + +This example illustrates how to manually construct Image. + +This example illustrates how to manually construct an *itk::Image* +class. The following is the minimal code needed to instantiate, declare +and create the Image class. + +## Results + +``` +Image (0x1eb5f10) + RTTI typeinfo: itk::Image + Reference Count: 1 + Modified Time: 4 + Debug: Off + Object Name: + Observers: + none + Source: (none) + Source output name: (none) + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 0 + UpdateMTime: 0 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [200, 200, 200] + BufferedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [200, 200, 200] + RequestedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [200, 200, 200] + Spacing: [1, 1, 1] + Origin: [0, 0, 0] + Direction: +1 0 0 +0 1 0 +0 0 1 + + IndexToPointMatrix: +1 0 0 +0 1 0 +0 0 1 + + PointToIndexMatrix: +1 0 0 +0 1 0 +0 0 1 + + Inverse Direction: +1 0 0 +0 1 0 +0 0 1 + + PixelContainer: + ImportImageContainer (0x1a678a0) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 5 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x7facf287d010 + Container manages memory: true + Size: 8000000 + Capacity: 8000000 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/CreateAnImage/Documentation.rst b/src/Core/Common/CreateAnImage/Documentation.rst deleted file mode 100644 index b93710dbc..000000000 --- a/src/Core/Common/CreateAnImage/Documentation.rst +++ /dev/null @@ -1,109 +0,0 @@ -:name: CreateAnImage - -Create an Image -=============== - -.. index:: - single: Image - single: instantiate - -Synopsis --------- - -This example illustrates how to manually construct Image. - -This example illustrates how to manually construct an *itk::Image* -class. The following is the minimal code needed to instantiate, declare -and create the Image class. - -Results -------- - -:: - - Image (0x1eb5f10) - RTTI typeinfo: itk::Image - Reference Count: 1 - Modified Time: 4 - Debug: Off - Object Name: - Observers: - none - Source: (none) - Source output name: (none) - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 0 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [200, 200, 200] - BufferedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [200, 200, 200] - RequestedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [200, 200, 200] - Spacing: [1, 1, 1] - Origin: [0, 0, 0] - Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - IndexToPointMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - PointToIndexMatrix: - 1 0 0 - 0 1 0 - 0 0 1 - - Inverse Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - PixelContainer: - ImportImageContainer (0x1a678a0) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 5 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x7facf287d010 - Container manages memory: true - Size: 8000000 - Capacity: 8000000 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/CreateAnImageOfVectors/Documentation.md b/src/Core/Common/CreateAnImageOfVectors/Documentation.md new file mode 100644 index 000000000..e797dd69a --- /dev/null +++ b/src/Core/Common/CreateAnImageOfVectors/Documentation.md @@ -0,0 +1,49 @@ +--- +name: CreateAnImageOfVectors +--- + +# Create an Image of Vectors + +```{index} single: Vector single: Image +``` + +## Synopsis + +This example illustrates how to instantiate and use an *itk::Image* whose pixels are of *itk::Vector* type. + +## Results + +``` +C++ + +[1.345, 6.841, 3.295] + +Python + +itkVectorF3 ([1.345, 6.841, 3.295]) +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Vector +``` + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/CreateAnImageOfVectors/Documentation.rst b/src/Core/Common/CreateAnImageOfVectors/Documentation.rst deleted file mode 100644 index 9cd5e0902..000000000 --- a/src/Core/Common/CreateAnImageOfVectors/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: CreateAnImageOfVectors - -Create an Image of Vectors -========================== - -.. index:: - single: Vector - single: Image - -Synopsis --------- - -This example illustrates how to instantiate and use an *itk::Image* whose pixels are of *itk::Vector* type. - - -Results -------- -:: - - C++ - - [1.345, 6.841, 3.295] - - Python - - itkVectorF3 ([1.345, 6.841, 3.295]) - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Vector -.. breathelink:: itk::Image diff --git a/src/Core/Common/CreateAnImageRegion/Documentation.md b/src/Core/Common/CreateAnImageRegion/Documentation.md new file mode 100644 index 000000000..a9a1902e6 --- /dev/null +++ b/src/Core/Common/CreateAnImageRegion/Documentation.md @@ -0,0 +1,42 @@ +--- +name: CreateAnImageRegion +--- + +# Create an Image Region + +```{index} single: ImageRegion single: Index single: Size +``` + +## Synopsis + +This class holds an Index (the "bottom left" corner of a region) and a Size (the size of the region). These two items together completely describe a region. + +## Results + +Output:: + +: ImageRegion (0x7fff45dad5c0) + Dimension: 2 + Index: \[1, 1\] + Size: \[3, 3\] + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegion +``` diff --git a/src/Core/Common/CreateAnImageRegion/Documentation.rst b/src/Core/Common/CreateAnImageRegion/Documentation.rst deleted file mode 100644 index c01e13205..000000000 --- a/src/Core/Common/CreateAnImageRegion/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: CreateAnImageRegion - -Create an Image Region -====================== - -.. index:: - single: ImageRegion - single: Index - single: Size - -Synopsis --------- - - -This class holds an Index (the "bottom left" corner of a region) and a Size (the size of the region). These two items together completely describe a region. - - -Results -------- - -Output:: - ImageRegion (0x7fff45dad5c0) - Dimension: 2 - Index: [1, 1] - Size: [3, 3] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegion diff --git a/src/Core/Common/CreateAnRGBImage/Documentation.md b/src/Core/Common/CreateAnRGBImage/Documentation.md new file mode 100644 index 000000000..942ab4323 --- /dev/null +++ b/src/Core/Common/CreateAnRGBImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: CreateAnRGBImage +--- + +# Create an RGB Image + +```{index} single: RGBPixel +``` + +## Synopsis + +Create an RGB Image + +## Results + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RGBPixel +``` diff --git a/src/Core/Common/CreateAnRGBImage/Documentation.rst b/src/Core/Common/CreateAnRGBImage/Documentation.rst deleted file mode 100644 index 63f9613d2..000000000 --- a/src/Core/Common/CreateAnRGBImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: CreateAnRGBImage - -Create an RGB Image -=================== - -.. index:: - single: RGBPixel - -Synopsis --------- - - -Create an RGB Image - - -Results -------- - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::RGBPixel diff --git a/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.md b/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.md new file mode 100644 index 000000000..058f8393f --- /dev/null +++ b/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.md @@ -0,0 +1,34 @@ +--- +name: CreateAnotherInstanceOfAFilter +--- + +# Create Another Instance Of A Filter + +```{index} single: Object +``` + +## Synopsis + +Copy/duplicate a filter + +## Results + +Output: + +``` +2 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Object +``` diff --git a/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.rst b/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.rst deleted file mode 100644 index 49fc3b604..000000000 --- a/src/Core/Common/CreateAnotherInstanceOfAFilter/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: CreateAnotherInstanceOfAFilter - -Create Another Instance Of A Filter -=================================== - -.. index:: - single: Object - -Synopsis --------- - - -Copy/duplicate a filter - - -Results -------- - -Output:: - - 2 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Object diff --git a/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.md b/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.md new file mode 100644 index 000000000..d4a2293a9 --- /dev/null +++ b/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.md @@ -0,0 +1,36 @@ +--- +name: CreateAnotherInstanceOfAnImage +--- + +# Create Another Instance of an Image + +```{index} single: Image sinlge: instance +``` + +## Synopsis + +Create another instance of an image. + +## Results + +Output: + +``` +Image type FloatScalarImageType +Image type FloatScalarImageType +Image type FloatScalarImageType +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.rst b/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.rst deleted file mode 100644 index 470a4a59d..000000000 --- a/src/Core/Common/CreateAnotherInstanceOfAnImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: CreateAnotherInstanceOfAnImage - -Create Another Instance of an Image -=================================== - -.. index:: - single: Image - sinlge: instance - -Synopsis --------- - -Create another instance of an image. - - -Results -------- -Output:: - - Image type FloatScalarImageType - Image type FloatScalarImageType - Image type FloatScalarImageType - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/CreateDerivativeKernel/Documentation.md b/src/Core/Common/CreateDerivativeKernel/Documentation.md new file mode 100644 index 000000000..de2559480 --- /dev/null +++ b/src/Core/Common/CreateDerivativeKernel/Documentation.md @@ -0,0 +1,54 @@ +--- +name: CreateDerivativeKernel +--- + +# Create Derivative Kernel + +```{index} single: DerivativeOperator pair: derivative; kernel +``` + +## Synopsis + +Create a derivative kernel. + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffeec8f19e8, begin = 0x7f822c2a8f00, size=9 } +[-1, -1] 0 +[0, -1] 0 +[1, -1] 0 +[-1, 0] 0.5 +[0, 0] 0 +[1, 0] -0.5 +[-1, 1] 0 +[0, 1] 0 +[1, 1] 0 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DerivativeOperator +``` diff --git a/src/Core/Common/CreateDerivativeKernel/Documentation.rst b/src/Core/Common/CreateDerivativeKernel/Documentation.rst deleted file mode 100644 index e328998b3..000000000 --- a/src/Core/Common/CreateDerivativeKernel/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: CreateDerivativeKernel - -Create Derivative Kernel -======================== - -.. index:: - single: DerivativeOperator - pair: derivative; kernel - -Synopsis --------- - -Create a derivative kernel. - - -Results -------- -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffeec8f19e8, begin = 0x7f822c2a8f00, size=9 } - [-1, -1] 0 - [0, -1] 0 - [1, -1] 0 - [-1, 0] 0.5 - [0, 0] 0 - [1, 0] -0.5 - [-1, 1] 0 - [0, 1] 0 - [1, 1] 0 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::DerivativeOperator diff --git a/src/Core/Common/CreateForwardDifferenceKernel/Documentation.md b/src/Core/Common/CreateForwardDifferenceKernel/Documentation.md new file mode 100644 index 000000000..b0efe5ada --- /dev/null +++ b/src/Core/Common/CreateForwardDifferenceKernel/Documentation.md @@ -0,0 +1,54 @@ +--- +name: CreateForwardDifferenceKernel +--- + +# Create Forward Difference Kernel + +```{index} single: ForwardDifferenceOperator pair: difference; kernel +``` + +## Synopsis + +Create a forward difference kernel. + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffee23339e0, begin = 0x7fd6921a8f60, size=9 } +[-1, -1] 0 +[0, -1] 0 +[1, -1] 0 +[-1, 0] 0 +[0, 0] -1 +[1, 0] 1 +[-1, 1] 0 +[0, 1] 0 +[1, 1] 0 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ForwardDifferenceOperator +``` diff --git a/src/Core/Common/CreateForwardDifferenceKernel/Documentation.rst b/src/Core/Common/CreateForwardDifferenceKernel/Documentation.rst deleted file mode 100644 index e1cfe5736..000000000 --- a/src/Core/Common/CreateForwardDifferenceKernel/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: CreateForwardDifferenceKernel - -Create Forward Difference Kernel -================================ - -.. index:: - single: ForwardDifferenceOperator - pair: difference; kernel - -Synopsis --------- - -Create a forward difference kernel. - - -Results -------- -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffee23339e0, begin = 0x7fd6921a8f60, size=9 } - [-1, -1] 0 - [0, -1] 0 - [1, -1] 0 - [-1, 0] 0 - [0, 0] -1 - [1, 0] 1 - [-1, 1] 0 - [0, 1] 0 - [1, 1] 0 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ForwardDifferenceOperator diff --git a/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.md b/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.md new file mode 100644 index 000000000..c3bd00d16 --- /dev/null +++ b/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.md @@ -0,0 +1,54 @@ +--- +name: CreateGaussianDerivativeKernel +--- + +# Create Gaussian Derivative Kernel + +```{index} single: GaussianDerivativeOperator pair: gaussian; derivative +``` + +## Synopsis + +Create a Gaussian derivative kernel. + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffee86419a8, begin = 0x7fb16bc5cc50, size=9 } +[-1, -1] 0 +[0, -1] 0 +[1, -1] 0 +[-1, 0] 0.208375 +[0, 0] 0 +[1, 0] -0.208375 +[-1, 1] 0 +[0, 1] 0 +[1, 1] 0 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GaussianDerivativeOperator +``` diff --git a/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.rst b/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.rst deleted file mode 100644 index a9553988a..000000000 --- a/src/Core/Common/CreateGaussianDerivativeKernel/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: CreateGaussianDerivativeKernel - -Create Gaussian Derivative Kernel -================================= - -.. index:: - single: GaussianDerivativeOperator - pair: gaussian; derivative - -Synopsis --------- - -Create a Gaussian derivative kernel. - - -Results -------- -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffee86419a8, begin = 0x7fb16bc5cc50, size=9 } - [-1, -1] 0 - [0, -1] 0 - [1, -1] 0 - [-1, 0] 0.208375 - [0, 0] 0 - [1, 0] -0.208375 - [-1, 1] 0 - [0, 1] 0 - [1, 1] 0 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GaussianDerivativeOperator diff --git a/src/Core/Common/CreateGaussianKernel/Documentation.md b/src/Core/Common/CreateGaussianKernel/Documentation.md new file mode 100644 index 000000000..5f7013f2a --- /dev/null +++ b/src/Core/Common/CreateGaussianKernel/Documentation.md @@ -0,0 +1,54 @@ +--- +name: CreateGaussianKernel +--- + +# Create Gaussian Kernel + +```{index} single: GaussianOperator single: kernel +``` + +## Synopsis + +Create a Gaussian kernel. + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffee598a9d8, begin = 0x7f7f502572a0, size=9 } +[-1, -1] 0 +[0, -1] 0 +[1, -1] 0 +[-1, 0] 0.208375 +[0, 0] 0.466801 +[1, 0] 0.208375 +[-1, 1] 0 +[0, 1] 0 +[1, 1] 0 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GaussianOperator +``` diff --git a/src/Core/Common/CreateGaussianKernel/Documentation.rst b/src/Core/Common/CreateGaussianKernel/Documentation.rst deleted file mode 100644 index 4ce770516..000000000 --- a/src/Core/Common/CreateGaussianKernel/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: CreateGaussianKernel - -Create Gaussian Kernel -====================== - -.. index:: - single: GaussianOperator - single: kernel - -Synopsis --------- - -Create a Gaussian kernel. - - -Results -------- -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffee598a9d8, begin = 0x7f7f502572a0, size=9 } - [-1, -1] 0 - [0, -1] 0 - [1, -1] 0 - [-1, 0] 0.208375 - [0, 0] 0.466801 - [1, 0] 0.208375 - [-1, 1] 0 - [0, 1] 0 - [1, 1] 0 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GaussianOperator diff --git a/src/Core/Common/CreateLaplacianKernel/Documentation.md b/src/Core/Common/CreateLaplacianKernel/Documentation.md new file mode 100644 index 000000000..4eb47fc0f --- /dev/null +++ b/src/Core/Common/CreateLaplacianKernel/Documentation.md @@ -0,0 +1,54 @@ +--- +name: CreateLaplacianKernel +--- + +# Create Laplacian Kernel + +```{index} single: LaplacianOperator pair: laplacian; operator +``` + +## Synopsis + +Create a Laplacian kernel. + +## Results + +Output: + +``` +Size: [3, 3] +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffee97e29e0, begin = 0x7f87798a8810, size=9 } +[-1, -1] 0 +[0, -1] 1 +[1, -1] 0 +[-1, 0] 1 +[0, 0] -4 +[1, 0] 1 +[-1, 1] 0 +[0, 1] 1 +[1, 1] 0 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LaplacianOperator +``` diff --git a/src/Core/Common/CreateLaplacianKernel/Documentation.rst b/src/Core/Common/CreateLaplacianKernel/Documentation.rst deleted file mode 100644 index b34055ef1..000000000 --- a/src/Core/Common/CreateLaplacianKernel/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: CreateLaplacianKernel - -Create Laplacian Kernel -======================= - -.. index:: - single: LaplacianOperator - pair: laplacian; operator - -Synopsis --------- - -Create a Laplacian kernel. - - -Results -------- -Output:: - - Size: [3, 3] - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffee97e29e0, begin = 0x7f87798a8810, size=9 } - [-1, -1] 0 - [0, -1] 1 - [1, -1] 0 - [-1, 0] 1 - [0, 0] -4 - [1, 0] 1 - [-1, 1] 0 - [0, 1] 1 - [1, 1] 0 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LaplacianOperator diff --git a/src/Core/Common/CreateSobelKernel/Documentation.md b/src/Core/Common/CreateSobelKernel/Documentation.md new file mode 100644 index 000000000..7374250d0 --- /dev/null +++ b/src/Core/Common/CreateSobelKernel/Documentation.md @@ -0,0 +1,53 @@ +--- +name: CreateSobelKernel +--- + +# Create Sobel Kernel + +```{index} single: SobelOperator pair: sobel; kernel +``` + +## Synopsis + +Create the Sobel kernel. + +## Results + +Output: + +``` +Neighborhood: +Radius:[1, 1] +Size:[3, 3] +DataBuffer:NeighborhoodAllocator { this = 0x7ffee3e84a00, begin = 0x7fca93256b10, size=9 } +-1 +0 +1 +-2 +0 +2 +-1 +0 +1 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SobelOperator +``` diff --git a/src/Core/Common/CreateSobelKernel/Documentation.rst b/src/Core/Common/CreateSobelKernel/Documentation.rst deleted file mode 100644 index 712e27b72..000000000 --- a/src/Core/Common/CreateSobelKernel/Documentation.rst +++ /dev/null @@ -1,54 +0,0 @@ -:name: CreateSobelKernel - -Create Sobel Kernel -=================== - -.. index:: - single: SobelOperator - pair: sobel; kernel - -Synopsis --------- - -Create the Sobel kernel. - - -Results -------- -Output:: - - Neighborhood: - Radius:[1, 1] - Size:[3, 3] - DataBuffer:NeighborhoodAllocator { this = 0x7ffee3e84a00, begin = 0x7fca93256b10, size=9 } - -1 - 0 - 1 - -2 - 0 - 2 - -1 - 0 - 1 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::SobelOperator diff --git a/src/Core/Common/CreateVectorImage/Documentation.md b/src/Core/Common/CreateVectorImage/Documentation.md new file mode 100644 index 000000000..0ae27c74f --- /dev/null +++ b/src/Core/Common/CreateVectorImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: CreateVectorImage +--- + +# Create Vector Image + +```{index} single: VectorImage +``` + +## Synopsis + +Create a vector image. + +## Results + +Output: + +``` +pixel (1,1) = [0, 0] +pixel (1,1) = [1.1, 2.2] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorImage +``` diff --git a/src/Core/Common/CreateVectorImage/Documentation.rst b/src/Core/Common/CreateVectorImage/Documentation.rst deleted file mode 100644 index 9e6a71ee3..000000000 --- a/src/Core/Common/CreateVectorImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: CreateVectorImage - -Create Vector Image -=================== - -.. index:: - single: VectorImage - -Synopsis --------- - -Create a vector image. - - -Results -------- -Output:: - - pixel (1,1) = [0, 0] - pixel (1,1) = [1.1, 2.2] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorImage diff --git a/src/Core/Common/CropImageBySpecifyingRegion/Documentation.md b/src/Core/Common/CropImageBySpecifyingRegion/Documentation.md new file mode 100644 index 000000000..966cc7b2e --- /dev/null +++ b/src/Core/Common/CropImageBySpecifyingRegion/Documentation.md @@ -0,0 +1,50 @@ +--- +name: CropImageBySpecifyingRegion +--- + +# Crop Image by Specifying Region + +```{index} single: ExtractImageFilter pair: crop; region +``` + +## Synopsis + +Crop an image by specifying the region to keep. + +## Results + +Output: + +``` +Image largest region: ImageRegion (0x7f886fc0de00) +Dimension: 2 +Index: [0, 0] +Size: [10, 10] + +desiredRegion: ImageRegion (0x7ffeef707978) +Dimension: 2 +Index: [3, 3] +Size: [4, 4] + +new largest region: ImageRegion (0x7f886fc0eb00) +Dimension: 2 +Index: [3, 3] +Size: [4, 4] + +new: 2 +Original: 5 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ExtractImageFilter +``` diff --git a/src/Core/Common/CropImageBySpecifyingRegion/Documentation.rst b/src/Core/Common/CropImageBySpecifyingRegion/Documentation.rst deleted file mode 100644 index 9e384e005..000000000 --- a/src/Core/Common/CropImageBySpecifyingRegion/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: CropImageBySpecifyingRegion - -Crop Image by Specifying Region -=============================== - -.. index:: - single: ExtractImageFilter - pair: crop; region - -Synopsis --------- - -Crop an image by specifying the region to keep. - - -Results -------- -Output:: - - Image largest region: ImageRegion (0x7f886fc0de00) - Dimension: 2 - Index: [0, 0] - Size: [10, 10] - - desiredRegion: ImageRegion (0x7ffeef707978) - Dimension: 2 - Index: [3, 3] - Size: [4, 4] - - new largest region: ImageRegion (0x7f886fc0eb00) - Dimension: 2 - Index: [3, 3] - Size: [4, 4] - - new: 2 - Original: 5 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ExtractImageFilter diff --git a/src/Core/Common/DeepCopyImage/Documentation.md b/src/Core/Common/DeepCopyImage/Documentation.md new file mode 100644 index 000000000..695f2da0d --- /dev/null +++ b/src/Core/Common/DeepCopyImage/Documentation.md @@ -0,0 +1,32 @@ +--- +name: DeepCopyImage +--- + +# Deep Copy Image + +```{index} single: Image pair: deep; copy +``` + +## Synopsis + +Deep copy an image. + +## Results + +:::{note} +No output is printed, this example simply displays functionality. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/DeepCopyImage/Documentation.rst b/src/Core/Common/DeepCopyImage/Documentation.rst deleted file mode 100644 index 60f61e603..000000000 --- a/src/Core/Common/DeepCopyImage/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: DeepCopyImage - -Deep Copy Image -=============== - -.. index:: - single: Image - pair: deep; copy - -Synopsis --------- - -Deep copy an image. - - -Results -------- -.. note:: - No output is printed, this example simply displays functionality. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/DemonstrateAllOperators/Documentation.md b/src/Core/Common/DemonstrateAllOperators/Documentation.md new file mode 100644 index 000000000..a3a376f43 --- /dev/null +++ b/src/Core/Common/DemonstrateAllOperators/Documentation.md @@ -0,0 +1,40 @@ +--- +name: DemonstrateAllOperators +--- + +# Demonstrate All Operators + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: NeighborhoodOperator +``` + +## Synopsis + +Demonstrate all operators. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NeighborhoodOperator +``` diff --git a/src/Core/Common/DemonstrateAllOperators/Documentation.rst b/src/Core/Common/DemonstrateAllOperators/Documentation.rst deleted file mode 100644 index a363c49fe..000000000 --- a/src/Core/Common/DemonstrateAllOperators/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: DemonstrateAllOperators - -Demonstrate All Operators -========================= -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: NeighborhoodOperator - -Synopsis --------- - -Demonstrate all operators. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NeighborhoodOperator diff --git a/src/Core/Common/DirectWarningToFile/Documentation.md b/src/Core/Common/DirectWarningToFile/Documentation.md new file mode 100644 index 000000000..79c8c0803 --- /dev/null +++ b/src/Core/Common/DirectWarningToFile/Documentation.md @@ -0,0 +1,34 @@ +--- +name: DirectWarningToFile +--- + +# Direct Warning to File + +```{index} single: FileOutputWindow pair: warning; file +``` + +## Synopsis + +Direct itk warnings to a file. + +## Results + +Output: + +``` +Look in itkMessageLog.txt for the output +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FileOutputWindow +``` diff --git a/src/Core/Common/DirectWarningToFile/Documentation.rst b/src/Core/Common/DirectWarningToFile/Documentation.rst deleted file mode 100644 index 11d7ad220..000000000 --- a/src/Core/Common/DirectWarningToFile/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: DirectWarningToFile - -Direct Warning to File -====================== - -.. index:: - single: FileOutputWindow - pair: warning; file - -Synopsis --------- - -Direct itk warnings to a file. - - -Results -------- -Output:: - - Look in itkMessageLog.txt for the output - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::FileOutputWindow diff --git a/src/Core/Common/DisplayImage/Documentation.md b/src/Core/Common/DisplayImage/Documentation.md new file mode 100644 index 000000000..049b0ab03 --- /dev/null +++ b/src/Core/Common/DisplayImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: DisplayImage +--- + +# Display Image + +```{index} single: Image +``` + +## Synopsis + +Display an image. + +## Results + +:::{figure} DisplayImage.png +:scale: 70% + +Displayed Image. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/DisplayImage/Documentation.rst b/src/Core/Common/DisplayImage/Documentation.rst deleted file mode 100644 index 0527f0b0e..000000000 --- a/src/Core/Common/DisplayImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: DisplayImage - -Display Image -============= - -.. index:: - single: Image - -Synopsis --------- - -Display an image. - - -Results -------- -.. figure:: DisplayImage.png - :scale: 70% - - Displayed Image. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/DistanceBetweenIndices/Documentation.md b/src/Core/Common/DistanceBetweenIndices/Documentation.md new file mode 100644 index 000000000..6f2b6b5d0 --- /dev/null +++ b/src/Core/Common/DistanceBetweenIndices/Documentation.md @@ -0,0 +1,38 @@ +--- +name: DistanceBetweenIndices +--- + +# Distance Between Indices + +```{index} single: Point single: Index single: indices pair: Point; SquaredEuclideanDistanceTo pair: Point; EuclideanDistanceTo pair: Indices; SquaredEuclideanDistanceTo pair: Indices; EuclideanDistanceTo +``` + +## Synopsis + +Compute the distance between two Indices. + +## Results + +Output: + +``` +Distance: 2.82843 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Point +``` + +```{eval-rst} +.. breathelinkstruct:: itk::Index +``` diff --git a/src/Core/Common/DistanceBetweenIndices/Documentation.rst b/src/Core/Common/DistanceBetweenIndices/Documentation.rst deleted file mode 100644 index 7cb97b6c5..000000000 --- a/src/Core/Common/DistanceBetweenIndices/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: DistanceBetweenIndices - -Distance Between Indices -======================== - -.. index:: - single: Point - single: Index - single: indices - pair: Point; SquaredEuclideanDistanceTo - pair: Point; EuclideanDistanceTo - pair: Indices; SquaredEuclideanDistanceTo - pair: Indices; EuclideanDistanceTo - -Synopsis --------- - -Compute the distance between two Indices. - - -Results -------- - - -Output:: - - Distance: 2.82843 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Point -.. breathelinkstruct:: itk::Index diff --git a/src/Core/Common/DistanceBetweenPoints/Documentation.md b/src/Core/Common/DistanceBetweenPoints/Documentation.md new file mode 100644 index 000000000..e182f747a --- /dev/null +++ b/src/Core/Common/DistanceBetweenPoints/Documentation.md @@ -0,0 +1,35 @@ +--- +name: DistanceBetweenPoints +--- + +# Distance Between Points + +```{index} single: Point pair: Point; SquaredEuclideanDistanceTo pair: Point; EuclideanDistanceTo +``` + +## Synopsis + +Compute the distance between two 3D points. This can easily be extended to ND by changing the constant Dimension. + +## Results + +Output: + +``` +Dist: 1.73205 +Dist2: 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Point +``` diff --git a/src/Core/Common/DistanceBetweenPoints/Documentation.rst b/src/Core/Common/DistanceBetweenPoints/Documentation.rst deleted file mode 100644 index 1f1fc89b7..000000000 --- a/src/Core/Common/DistanceBetweenPoints/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: DistanceBetweenPoints - -Distance Between Points -======================= - -.. index:: - single: Point - pair: Point; SquaredEuclideanDistanceTo - pair: Point; EuclideanDistanceTo - -Synopsis --------- - -Compute the distance between two 3D points. This can easily be extended to ND by changing the constant Dimension. - - -Results -------- - - -Output:: - - Dist: 1.73205 - Dist2: 3 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Point diff --git a/src/Core/Common/DoDataParallelThreading/Documentation.md b/src/Core/Common/DoDataParallelThreading/Documentation.md new file mode 100644 index 000000000..9c9ed8852 --- /dev/null +++ b/src/Core/Common/DoDataParallelThreading/Documentation.md @@ -0,0 +1,45 @@ +--- +name: DoDataParallelThreading +--- + +# Do Data Parallel Threading + +```{index} single: DomainThreader single: ThreadedIndexedContainerPartitioner +``` + +## Synopsis + +In this example, we show how to do an operation on data across multiple threads to take advantage of multi-core processors. + +In this example we have an `enum` of central nervous system cell types, a +`std::vector< CELL_TYPE >` that contains the cells that we have encountered, and +we want to count how many we have of each `CELL_TYPE`. + +## Results + +Output: + +``` +Result of the multi-threaded cell count: + NEURON: 3 + ASTROCYTE: 5 + OLIGODENDROCYTE: 2 +Result of the single-threaded cell count: + NEURON: 3 + ASTROCYTE: 5 + OLIGODENDROCYTE: 2 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DomainThreader +``` diff --git a/src/Core/Common/DoDataParallelThreading/Documentation.rst b/src/Core/Common/DoDataParallelThreading/Documentation.rst deleted file mode 100644 index 010a813b7..000000000 --- a/src/Core/Common/DoDataParallelThreading/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: DoDataParallelThreading - -Do Data Parallel Threading -========================== - -.. index:: - single: DomainThreader - single: ThreadedIndexedContainerPartitioner - - -Synopsis --------- - -In this example, we show how to do an operation on data across multiple threads to take advantage of multi-core processors. - -In this example we have an `enum` of central nervous system cell types, a -`std::vector< CELL_TYPE >` that contains the cells that we have encountered, and -we want to count how many we have of each `CELL_TYPE`. - - -Results -------- - -Output:: - - Result of the multi-threaded cell count: - NEURON: 3 - ASTROCYTE: 5 - OLIGODENDROCYTE: 2 - Result of the single-threaded cell count: - NEURON: 3 - ASTROCYTE: 5 - OLIGODENDROCYTE: 2 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::DomainThreader diff --git a/src/Core/Common/DuplicateAnImage/Documentation.md b/src/Core/Common/DuplicateAnImage/Documentation.md new file mode 100644 index 000000000..fdf9ad075 --- /dev/null +++ b/src/Core/Common/DuplicateAnImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: DuplicateAnImage +--- + +# Duplicate an Image + +```{index} single: ImageDuplicator +``` + +## Synopsis + +This example demonstrates how to copy/clone/duplicate an image so it can continue down two separate paths of the pipeline. + +## Results + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageDuplicator +``` diff --git a/src/Core/Common/DuplicateAnImage/Documentation.rst b/src/Core/Common/DuplicateAnImage/Documentation.rst deleted file mode 100644 index a3553da41..000000000 --- a/src/Core/Common/DuplicateAnImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: DuplicateAnImage - -Duplicate an Image -================== - -.. index:: - single: ImageDuplicator - -Synopsis --------- - - -This example demonstrates how to copy/clone/duplicate an image so it can continue down two separate paths of the pipeline. - - -Results -------- - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageDuplicator diff --git a/src/Core/Common/EagerModuleLoadingPython/Documentation.md b/src/Core/Common/EagerModuleLoadingPython/Documentation.md new file mode 100644 index 000000000..0930ab141 --- /dev/null +++ b/src/Core/Common/EagerModuleLoadingPython/Documentation.md @@ -0,0 +1,26 @@ +--- +name: EagerModuleLoadingPython +--- + +# Eagerly Load Python Modules + +## Synopsis + +Load all ITK Python modules at once on import. + +## Results + +Output: + +``` +ITK namespace has 4045 symbols +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` diff --git a/src/Core/Common/EagerModuleLoadingPython/Documentation.rst b/src/Core/Common/EagerModuleLoadingPython/Documentation.rst deleted file mode 100644 index 6bedfad7f..000000000 --- a/src/Core/Common/EagerModuleLoadingPython/Documentation.rst +++ /dev/null @@ -1,26 +0,0 @@ -:name: EagerModuleLoadingPython - -Eagerly Load Python Modules -=============================== - -Synopsis --------- - -Load all ITK Python modules at once on import. - - -Results -------- -Output:: - - ITK namespace has 4045 symbols - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- diff --git a/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.md b/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.md new file mode 100644 index 000000000..bbb6b1390 --- /dev/null +++ b/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.md @@ -0,0 +1,43 @@ +--- +name: FilterAndParallelizeImageRegion +--- + +# Filter and ParallelizeImageRegion Comparison + +```{index} single: MultiThreaderBase +``` + +## Synopsis + +This example demonstrates how to take advantage of MultiThreaderBase::ParallelizeImageRegion. +A comparison is made with LogImageFilter for purpose of computing log(1+x), where x is pixel value. + +With ParallelizeImageRegion, we can process an image efficiently and in parallel +with a function that is defined in a flexible way. The entire operation, defined in 10 lines of code, +previously required the definition of an entire class. + +## Results + +Output: + +``` +LogImageFilter and ParallelizeImageRegion generate the same result. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LogImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::MultiThreaderBase +``` diff --git a/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.rst b/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.rst deleted file mode 100644 index c46c3846d..000000000 --- a/src/Core/Common/FilterAndParallelizeImageRegion/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: FilterAndParallelizeImageRegion - -Filter and ParallelizeImageRegion Comparison -============================================ - -.. index:: - single: MultiThreaderBase - -Synopsis --------- - -This example demonstrates how to take advantage of MultiThreaderBase::ParallelizeImageRegion. -A comparison is made with LogImageFilter for purpose of computing log(1+x), where x is pixel value. - -With ParallelizeImageRegion, we can process an image efficiently and in parallel -with a function that is defined in a flexible way. The entire operation, defined in 10 lines of code, -previously required the definition of an entire class. - - -Results -------- - -Output:: - - LogImageFilter and ParallelizeImageRegion generate the same result. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LogImageFilter -.. breathelink:: itk::MultiThreaderBase diff --git a/src/Core/Common/FilterImage/Documentation.md b/src/Core/Common/FilterImage/Documentation.md new file mode 100644 index 000000000..335221763 --- /dev/null +++ b/src/Core/Common/FilterImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: FilterImage +--- + +# Filter Image + +```{index} single: ImageToImageFilter +``` + +## Synopsis + +Filter an image. + +## Results + +Output: + +``` +0 +3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/FilterImage/Documentation.rst b/src/Core/Common/FilterImage/Documentation.rst deleted file mode 100644 index d1fc90e1b..000000000 --- a/src/Core/Common/FilterImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: FilterImage - -Filter Image -============ - -.. index:: - single: ImageToImageFilter - -Synopsis --------- - -Filter an image. - - -Results -------- -Output:: - - 0 - 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.md b/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.md new file mode 100644 index 000000000..f8a8ae3bd --- /dev/null +++ b/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.md @@ -0,0 +1,33 @@ +--- +name: FilterImageUsingMultipleThreads +--- + +# Filter Image Using Multiple Threads + +```{index} single: ImageToImageFilter single: thread +``` + +## Synopsis + +Filter an image using multiple threads. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.rst b/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.rst deleted file mode 100644 index 8c8c1cf49..000000000 --- a/src/Core/Common/FilterImageUsingMultipleThreads/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: FilterImageUsingMultipleThreads - -Filter Image Using Multiple Threads -=================================== - -.. index:: - single: ImageToImageFilter - single: thread - -Synopsis --------- - -Filter an image using multiple threads. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/FilterImageWithoutCopying/Documentation.md b/src/Core/Common/FilterImageWithoutCopying/Documentation.md new file mode 100644 index 000000000..68a899f88 --- /dev/null +++ b/src/Core/Common/FilterImageWithoutCopying/Documentation.md @@ -0,0 +1,34 @@ +--- +name: FilterImageWithoutCopying +--- + +# Filter Image Without Copying Its Data + +```{index} single: InPlaceImageFilter +``` + +## Synopsis + +Filter an image without copying its data. + +## Results + +Output: + +``` +3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::InPlaceImageFilter +``` diff --git a/src/Core/Common/FilterImageWithoutCopying/Documentation.rst b/src/Core/Common/FilterImageWithoutCopying/Documentation.rst deleted file mode 100644 index 9478a5679..000000000 --- a/src/Core/Common/FilterImageWithoutCopying/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: FilterImageWithoutCopying - -Filter Image Without Copying Its Data -===================================== - -.. index:: - single: InPlaceImageFilter - -Synopsis --------- - -Filter an image without copying its data. - - -Results -------- - -Output:: - - 3 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::InPlaceImageFilter diff --git a/src/Core/Common/FindMaxAndMinInImage/Documentation.md b/src/Core/Common/FindMaxAndMinInImage/Documentation.md new file mode 100644 index 000000000..305b49139 --- /dev/null +++ b/src/Core/Common/FindMaxAndMinInImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: FindMaxAndMinInImage +--- + +# Find Max and Min in Image + +```{index} single: MinimumMaximumImageCalculator single: minimum single: maximum +``` + +## Synopsis + +Find the minimum and maximum value (and the position of the value) in an image. + +## Results + +:::{figure} Yinyang.png +:alt: Input Image +:scale: 70% + +Yingyang.png +::: + +:::{figure} FindMaxAndMinInImageOutput.png +:alt: Output Image +:scale: 70% + +Output Image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MinimumMaximumImageCalculator +``` diff --git a/src/Core/Common/FindMaxAndMinInImage/Documentation.rst b/src/Core/Common/FindMaxAndMinInImage/Documentation.rst deleted file mode 100644 index 76a7d4881..000000000 --- a/src/Core/Common/FindMaxAndMinInImage/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: FindMaxAndMinInImage - -Find Max and Min in Image -========================= - -.. index:: - single: MinimumMaximumImageCalculator - single: minimum - single: maximum - -Synopsis --------- - -Find the minimum and maximum value (and the position of the value) in an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: Input Image - - Yingyang.png - -.. figure:: FindMaxAndMinInImageOutput.png - :scale: 70% - :alt: Output Image - - Output Image - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MinimumMaximumImageCalculator diff --git a/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.md b/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.md new file mode 100644 index 000000000..b8b993d4a --- /dev/null +++ b/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.md @@ -0,0 +1,76 @@ +--- +name: GenerateOffsetsShapedImageNeighborhood +--- + +# Generate the Offsets of a Shaped Image Neighborhood + +```{index} single: ConnectedImageNeighborhoodShape single: RectangularImageNeighborhoodShape single: ShapedImageNeighborhoodRange +``` + +## Synopsis + +This example demonstrates various ways to create a container of offsets, to +specify the shape of a neighborhood of pixels: + +> - An arbitrary shape +> - A 4-connected neighborhood shape +> - A rectangular neighborhood shape + +These offsets may be used to specify the shape of a ShapedImageNeighborhoodRange +(as included with this code example), or a ShapedNeighborhoodIterator. + +## Results + +Output: + +``` +Shape of some arbitrary offsets: + + [0, -1] [0, 1] [1, 1] + + 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + 0 0 0 1 0 0 0 + 0 0 0 0 0 0 0 + 0 0 0 2 3 0 0 + 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + +4-connected neighborhood shape (excluding the center pixel) with maximumCityblockDistance = 1: + + [0, -1] [-1, 0] [1, 0] [0, 1] + + 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + 0 0 0 1 0 0 0 + 0 0 2 0 3 0 0 + 0 0 0 4 0 0 0 + 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 + +Rectangular shape of radius [1, 2]: + + [-1, -2] [0, -2] [1, -2] [-1, -1] [0, -1] [1, -1] [-1, 0] [0, 0] [1, 0] [-1, 1] [0, 1] [1, 1] [-1, 2] [0, 2] [1, 2] + + 0 0 0 0 0 0 0 + 0 0 1 2 3 0 0 + 0 0 4 5 6 0 0 + 0 0 7 8 9 0 0 + 0 0 A B C 0 0 + 0 0 D E F 0 0 + 0 0 0 0 0 0 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConnectedImageNeighborhoodShape itk::RectangularImageNeighborhoodShape +``` diff --git a/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.rst b/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.rst deleted file mode 100644 index d398dcf26..000000000 --- a/src/Core/Common/GenerateOffsetsShapedImageNeighborhood/Documentation.rst +++ /dev/null @@ -1,81 +0,0 @@ -:name: GenerateOffsetsShapedImageNeighborhood - -Generate the Offsets of a Shaped Image Neighborhood -=================================================== - -.. index:: - single: ConnectedImageNeighborhoodShape - single: RectangularImageNeighborhoodShape - single: ShapedImageNeighborhoodRange - - -Synopsis --------- - - -This example demonstrates various ways to create a container of offsets, to -specify the shape of a neighborhood of pixels: - - - An arbitrary shape - - A 4-connected neighborhood shape - - A rectangular neighborhood shape - -These offsets may be used to specify the shape of a ShapedImageNeighborhoodRange -(as included with this code example), or a ShapedNeighborhoodIterator. - -Results -------- - -Output:: - - Shape of some arbitrary offsets: - - [0, -1] [0, 1] [1, 1] - - 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 - 0 0 0 1 0 0 0 - 0 0 0 0 0 0 0 - 0 0 0 2 3 0 0 - 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 - - 4-connected neighborhood shape (excluding the center pixel) with maximumCityblockDistance = 1: - - [0, -1] [-1, 0] [1, 0] [0, 1] - - 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 - 0 0 0 1 0 0 0 - 0 0 2 0 3 0 0 - 0 0 0 4 0 0 0 - 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 - - Rectangular shape of radius [1, 2]: - - [-1, -2] [0, -2] [1, -2] [-1, -1] [0, -1] [1, -1] [-1, 0] [0, 0] [1, 0] [-1, 1] [0, 1] [1, 1] [-1, 2] [0, 2] [1, 2] - - 0 0 0 0 0 0 0 - 0 0 1 2 3 0 0 - 0 0 4 5 6 0 0 - 0 0 7 8 9 0 0 - 0 0 A B C 0 0 - 0 0 D E F 0 0 - 0 0 0 0 0 0 0 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConnectedImageNeighborhoodShape itk::RectangularImageNeighborhoodShape diff --git a/src/Core/Common/GetImageSize/Documentation.md b/src/Core/Common/GetImageSize/Documentation.md new file mode 100644 index 000000000..c34563dc4 --- /dev/null +++ b/src/Core/Common/GetImageSize/Documentation.md @@ -0,0 +1,46 @@ +--- +name: GetImageSize +--- + +# Get Image Size + +```{index} single: Size pair: ImageRegion; IsInside +``` + +## Synopsis + +Get the size of a itk::Image + +## Results + +:::{figure} Yinyang.png +:alt: Input yin-yang image. +:scale: 50% + +Input Image +::: + +Output:: + +: \[512, 342\] + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 17- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelinkstruct:: itk::Size +``` diff --git a/src/Core/Common/GetImageSize/Documentation.rst b/src/Core/Common/GetImageSize/Documentation.rst deleted file mode 100644 index 6e5de9df9..000000000 --- a/src/Core/Common/GetImageSize/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: GetImageSize - -Get Image Size -============== - -.. index:: - single: Size - pair: ImageRegion; IsInside - -Synopsis --------- - - -Get the size of a itk::Image - - -Results -------- - -.. figure:: Yinyang.png - :scale: 50% - :alt: Input yin-yang image. - - Input Image - -Output:: - [512, 342] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 17- - - -Classes demonstrated --------------------- - -.. breathelinkstruct:: itk::Size diff --git a/src/Core/Common/GetNameOfClass/Documentation.md b/src/Core/Common/GetNameOfClass/Documentation.md new file mode 100644 index 000000000..825536180 --- /dev/null +++ b/src/Core/Common/GetNameOfClass/Documentation.md @@ -0,0 +1,32 @@ +--- +name: GetNameOfClass +--- + +# Get Name of Class + +```{index} single: LightObject +``` + +## Synopsis + +Get the name of the class of an object. + +## Results + +Output:: + +: image is type: Image + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LightObject +``` diff --git a/src/Core/Common/GetNameOfClass/Documentation.rst b/src/Core/Common/GetNameOfClass/Documentation.rst deleted file mode 100644 index 2e1004eeb..000000000 --- a/src/Core/Common/GetNameOfClass/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: GetNameOfClass - -Get Name of Class -================= - -.. index:: - single: LightObject - -Synopsis --------- - - -Get the name of the class of an object. - - -Results -------- - - -Output:: - image is type: Image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LightObject diff --git a/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.md b/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.md new file mode 100644 index 000000000..cd3fb62a1 --- /dev/null +++ b/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.md @@ -0,0 +1,33 @@ +--- +name: GetOrSetMemberVariableOfITKClass +--- + +# Get or Set Member Variable of ITK Class + +```{index} single: Image +``` + +## Synopsis + +Get or set a member variable of an ITK class. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.rst b/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.rst deleted file mode 100644 index 8cdd7c0fa..000000000 --- a/src/Core/Common/GetOrSetMemberVariableOfITKClass/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: GetOrSetMemberVariableOfITKClass - -Get or Set Member Variable of ITK Class -======================================= - -.. index:: - single: Image - -Synopsis --------- - -Get or set a member variable of an ITK class. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/GetTypeBasicInformation/Documentation.md b/src/Core/Common/GetTypeBasicInformation/Documentation.md new file mode 100644 index 000000000..587706805 --- /dev/null +++ b/src/Core/Common/GetTypeBasicInformation/Documentation.md @@ -0,0 +1,51 @@ +--- +name: GetTypeBasicInformation +--- + +# Get Type Basic Information + +```{index} single: NumericTraits +``` + +## Synopsis + +Get some basic information about a plain old data (POD) type, in this case the +*float* type. + +## Results + +Output: + +``` +Min: 1.17549e-38 +Max: 3.40282e+38 +Zero: 0 +ZeroValue: 0 +Is -1 negative? 1 +Is 1 negative? 0 +One: 1 +Epsilon: 1.19209e-07 +Infinity: inf +Good +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NumericTraits +``` diff --git a/src/Core/Common/GetTypeBasicInformation/Documentation.rst b/src/Core/Common/GetTypeBasicInformation/Documentation.rst deleted file mode 100644 index de0bb8286..000000000 --- a/src/Core/Common/GetTypeBasicInformation/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: GetTypeBasicInformation - -Get Type Basic Information -========================== - -.. index:: - single: NumericTraits - -Synopsis --------- - - -Get some basic information about a plain old data (POD) type, in this case the -*float* type. - - -Results -------- - -Output:: - - Min: 1.17549e-38 - Max: 3.40282e+38 - Zero: 0 - ZeroValue: 0 - Is -1 negative? 1 - Is 1 negative? 0 - One: 1 - Epsilon: 1.19209e-07 - Infinity: inf - Good - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::NumericTraits diff --git a/src/Core/Common/ImageBufferAndIndexRange/Documentation.md b/src/Core/Common/ImageBufferAndIndexRange/Documentation.md new file mode 100644 index 000000000..051fdeaaf --- /dev/null +++ b/src/Core/Common/ImageBufferAndIndexRange/Documentation.md @@ -0,0 +1,57 @@ +--- +name: ImageBufferAndIndexRange +--- + +# Iterate Over an Image Buffer and an Index Range + +```{index} single: ImageBufferRange +``` + +## Synopsis + +This example demonstrates how to iterate over all pixels of the buffered region +of an image, using either an iterator-based algorithm from the C++ Standard +Library, or a range-based for loop. + +## Results + +Output: + +``` +Region index: [100, 200]; Region size: [4, 5] + +Pixel index: [100, 200]; Pixel value: 0 +Pixel index: [101, 200]; Pixel value: 1 +Pixel index: [102, 200]; Pixel value: 2 +Pixel index: [103, 200]; Pixel value: 3 +Pixel index: [100, 201]; Pixel value: 4 +Pixel index: [101, 201]; Pixel value: 5 +Pixel index: [102, 201]; Pixel value: 6 +Pixel index: [103, 201]; Pixel value: 7 +Pixel index: [100, 202]; Pixel value: 8 +Pixel index: [101, 202]; Pixel value: 9 +Pixel index: [102, 202]; Pixel value: 10 +Pixel index: [103, 202]; Pixel value: 11 +Pixel index: [100, 203]; Pixel value: 12 +Pixel index: [101, 203]; Pixel value: 13 +Pixel index: [102, 203]; Pixel value: 14 +Pixel index: [103, 203]; Pixel value: 15 +Pixel index: [100, 204]; Pixel value: 16 +Pixel index: [101, 204]; Pixel value: 17 +Pixel index: [102, 204]; Pixel value: 18 +Pixel index: [103, 204]; Pixel value: 19 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageBufferRange itk::IndexRange +``` diff --git a/src/Core/Common/ImageBufferAndIndexRange/Documentation.rst b/src/Core/Common/ImageBufferAndIndexRange/Documentation.rst deleted file mode 100644 index c33257ee7..000000000 --- a/src/Core/Common/ImageBufferAndIndexRange/Documentation.rst +++ /dev/null @@ -1,59 +0,0 @@ -:name: ImageBufferAndIndexRange - -Iterate Over an Image Buffer and an Index Range -=============================================== - -.. index:: - single: ImageBufferRange - -Synopsis --------- - - -This example demonstrates how to iterate over all pixels of the buffered region -of an image, using either an iterator-based algorithm from the C++ Standard -Library, or a range-based for loop. - - -Results -------- - -Output:: - - Region index: [100, 200]; Region size: [4, 5] - - Pixel index: [100, 200]; Pixel value: 0 - Pixel index: [101, 200]; Pixel value: 1 - Pixel index: [102, 200]; Pixel value: 2 - Pixel index: [103, 200]; Pixel value: 3 - Pixel index: [100, 201]; Pixel value: 4 - Pixel index: [101, 201]; Pixel value: 5 - Pixel index: [102, 201]; Pixel value: 6 - Pixel index: [103, 201]; Pixel value: 7 - Pixel index: [100, 202]; Pixel value: 8 - Pixel index: [101, 202]; Pixel value: 9 - Pixel index: [102, 202]; Pixel value: 10 - Pixel index: [103, 202]; Pixel value: 11 - Pixel index: [100, 203]; Pixel value: 12 - Pixel index: [101, 203]; Pixel value: 13 - Pixel index: [102, 203]; Pixel value: 14 - Pixel index: [103, 203]; Pixel value: 15 - Pixel index: [100, 204]; Pixel value: 16 - Pixel index: [101, 204]; Pixel value: 17 - Pixel index: [102, 204]; Pixel value: 18 - Pixel index: [103, 204]; Pixel value: 19 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageBufferRange itk::IndexRange diff --git a/src/Core/Common/ImageRegionIntersection/Documentation.md b/src/Core/Common/ImageRegionIntersection/Documentation.md new file mode 100644 index 000000000..a9befa1e7 --- /dev/null +++ b/src/Core/Common/ImageRegionIntersection/Documentation.md @@ -0,0 +1,36 @@ +--- +name: ImageRegionIntersection +--- + +# Image Region Intersection + +```{index} single: ImageRegion pair: ImageRegion; IsInside +``` + +## Synopsis + +This example demonstrates how to check if two regions of an image overlap/intersect. + +## Results + +Output: + +``` +Small inside region is 1 +Small outside region is 0 +Small overlap region is 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegion +``` diff --git a/src/Core/Common/ImageRegionIntersection/Documentation.rst b/src/Core/Common/ImageRegionIntersection/Documentation.rst deleted file mode 100644 index e5b85f2d8..000000000 --- a/src/Core/Common/ImageRegionIntersection/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: ImageRegionIntersection - -Image Region Intersection -========================= - -.. index:: - single: ImageRegion - pair: ImageRegion; IsInside - -Synopsis --------- - - -This example demonstrates how to check if two regions of an image overlap/intersect. - - -Results -------- - -Output:: - - Small inside region is 1 - Small outside region is 0 - Small overlap region is 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegion diff --git a/src/Core/Common/ImageRegionOverlap/Documentation.md b/src/Core/Common/ImageRegionOverlap/Documentation.md new file mode 100644 index 000000000..f900055ef --- /dev/null +++ b/src/Core/Common/ImageRegionOverlap/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ImageRegionOverlap +--- + +# Image Region Overlap + +```{index} single: ImageRegion single: RGBPixel single: ImageRegionIterator pair: ImageRegion; Crop pair: ImageRegion; PadByRadius +``` + +## Synopsis + +Determine the overlap of two regions + +## Results + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegion +``` diff --git a/src/Core/Common/ImageRegionOverlap/Documentation.rst b/src/Core/Common/ImageRegionOverlap/Documentation.rst deleted file mode 100644 index 5be60e950..000000000 --- a/src/Core/Common/ImageRegionOverlap/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ImageRegionOverlap - -Image Region Overlap -==================== - -.. index:: - single: ImageRegion - single: RGBPixel - single: ImageRegionIterator - pair: ImageRegion; Crop - pair: ImageRegion; PadByRadius - -Synopsis --------- - - -Determine the overlap of two regions - - -Results -------- - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegion diff --git a/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.md b/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.md new file mode 100644 index 000000000..4ab3dd2ba --- /dev/null +++ b/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.md @@ -0,0 +1,45 @@ +--- +name: ImportPixelBufferIntoAnImage +--- + +# Import Pixel Buffer Into an Image + +```{index} single: ImportImageFilter +``` + +## Synopsis + +This example illustrates how to import data into an `Image` +class. This is particularly useful for interfacing with other software +systems. Many systems use a contiguous block of memory as a buffer +for image pixel data. The current example assumes this is the case and +feeds the buffer into an `ImportImageFilter`, thereby producing an +image as output. + +Here we create a synthetic image with a centered sphere in +a locally allocated buffer and pass this block of memory to the +`ImportImageFilter`. This example is set up so that on execution, the +user must provide the name of an output file as a command-line argument. + +## Results + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImportImageFilter +``` diff --git a/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.rst b/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.rst deleted file mode 100644 index 235c6a0ea..000000000 --- a/src/Core/Common/ImportPixelBufferIntoAnImage/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: ImportPixelBufferIntoAnImage - -Import Pixel Buffer Into an Image -================================= - -.. index:: - single: ImportImageFilter - -Synopsis --------- - -This example illustrates how to import data into an ``Image`` -class. This is particularly useful for interfacing with other software -systems. Many systems use a contiguous block of memory as a buffer -for image pixel data. The current example assumes this is the case and -feeds the buffer into an ``ImportImageFilter``, thereby producing an -image as output. - -Here we create a synthetic image with a centered sphere in -a locally allocated buffer and pass this block of memory to the -``ImportImageFilter``. This example is set up so that on execution, the -user must provide the name of an output file as a command-line argument. - - -Results -------- - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImportImageFilter diff --git a/src/Core/Common/InPlaceFilterOfImage/Documentation.md b/src/Core/Common/InPlaceFilterOfImage/Documentation.md new file mode 100644 index 000000000..1730508d9 --- /dev/null +++ b/src/Core/Common/InPlaceFilterOfImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: InPlaceFilterOfImage +--- + +# In Place Filter of Image + +```{index} single: InPlaceImageFilter +``` + +## Synopsis + +In-place filtering of an image. + +## Results + +:::{figure} Gourds.png +:alt: Input image. +:scale: 50% + +Input Image +::: + +:::{figure} InPlaceFilterOfImageQuickview.png +:alt: QuickView output. +:scale: 50% + +Output In QuickView +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::InPlaceImageFilter +``` diff --git a/src/Core/Common/InPlaceFilterOfImage/Documentation.rst b/src/Core/Common/InPlaceFilterOfImage/Documentation.rst deleted file mode 100644 index f353d972c..000000000 --- a/src/Core/Common/InPlaceFilterOfImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: InPlaceFilterOfImage - -In Place Filter of Image -======================== -.. index:: - single: InPlaceImageFilter - -Synopsis --------- - -In-place filtering of an image. - - -Results -------- -.. figure:: Gourds.png - :scale: 50% - :alt: Input image. - - Input Image - -.. figure:: InPlaceFilterOfImageQuickview.png - :scale: 50% - :alt: QuickView output. - - Output In QuickView - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::InPlaceImageFilter diff --git a/src/Core/Common/IsPixelInsideRegion/Documentation.md b/src/Core/Common/IsPixelInsideRegion/Documentation.md new file mode 100644 index 000000000..3b4b4403f --- /dev/null +++ b/src/Core/Common/IsPixelInsideRegion/Documentation.md @@ -0,0 +1,42 @@ +--- +name: IsPixelInsideRegion +--- + +# Is Pixel Inside Region + +```{index} single: ImageRegion pair: ImageRegion; IsInside single: Index single: Size +``` + +## Synopsis + +Determine if a pixel is inside of a region + +## Results + +Output: + +``` +[1, 1] Inside +[6, 6] Outside +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegion +``` diff --git a/src/Core/Common/IsPixelInsideRegion/Documentation.rst b/src/Core/Common/IsPixelInsideRegion/Documentation.rst deleted file mode 100644 index 8c00d3938..000000000 --- a/src/Core/Common/IsPixelInsideRegion/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: IsPixelInsideRegion - -Is Pixel Inside Region -====================== - -.. index:: - single: ImageRegion - pair: ImageRegion; IsInside - single: Index - single: Size - -Synopsis --------- - - -Determine if a pixel is inside of a region - - -Results -------- - -Output:: - - [1, 1] Inside - [6, 6] Outside - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegion diff --git a/src/Core/Common/IterateImageStartingAtSeed/Documentation.md b/src/Core/Common/IterateImageStartingAtSeed/Documentation.md new file mode 100644 index 000000000..c7b522955 --- /dev/null +++ b/src/Core/Common/IterateImageStartingAtSeed/Documentation.md @@ -0,0 +1,40 @@ +--- +name: IterateImageStartingAtSeed +--- + +# Iterate Image Starting at Seed + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: FloodFilledImageFunctionConditionalIterator +``` + +## Synopsis + +Iterate over an image starting at a seed and following a rule for connectivity decisions. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FloodFilledImageFunctionConditionalIterator +``` diff --git a/src/Core/Common/IterateImageStartingAtSeed/Documentation.rst b/src/Core/Common/IterateImageStartingAtSeed/Documentation.rst deleted file mode 100644 index 258e2c046..000000000 --- a/src/Core/Common/IterateImageStartingAtSeed/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: IterateImageStartingAtSeed - -Iterate Image Starting at Seed -============================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: FloodFilledImageFunctionConditionalIterator - -Synopsis --------- - -Iterate over an image starting at a seed and following a rule for connectivity decisions. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::FloodFilledImageFunctionConditionalIterator diff --git a/src/Core/Common/IterateLineThroughImage/Documentation.md b/src/Core/Common/IterateLineThroughImage/Documentation.md new file mode 100644 index 000000000..b713911c1 --- /dev/null +++ b/src/Core/Common/IterateLineThroughImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: IterateLineThroughImage +--- + +# Iterate Line Through Image + +```{index} single: LineIterator pair: line; image +``` + +## Synopsis + +Iterate over a line through an image. + +## Results + +:::{figure} IterateLineThroughImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LineIterator +``` diff --git a/src/Core/Common/IterateLineThroughImage/Documentation.rst b/src/Core/Common/IterateLineThroughImage/Documentation.rst deleted file mode 100644 index 50b007f13..000000000 --- a/src/Core/Common/IterateLineThroughImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: IterateLineThroughImage - -Iterate Line Through Image -========================== - -.. index:: - single: LineIterator - pair: line; image - -Synopsis --------- - -Iterate over a line through an image. - - -Results -------- -.. figure:: IterateLineThroughImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LineIterator diff --git a/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.md b/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.md new file mode 100644 index 000000000..aca4b9328 --- /dev/null +++ b/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.md @@ -0,0 +1,36 @@ +--- +name: IterateLineThroughImageWithoutWriteAccess +--- + +# Iterate Line Through Image Without Write Access + +```{index} single: LineConstIterator pair: write; access +``` + +## Synopsis + +Iterate over a line through an image without write access. + +## Results + +Output: + +``` +255 +255 +255 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LineConstIterator +``` diff --git a/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.rst b/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.rst deleted file mode 100644 index 0de96ba90..000000000 --- a/src/Core/Common/IterateLineThroughImageWithoutWriteAccess/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: IterateLineThroughImageWithoutWriteAccess - -Iterate Line Through Image Without Write Access -=============================================== - -.. index:: - single: LineConstIterator - pair: write; access - -Synopsis --------- - -Iterate over a line through an image without write access. - - -Results -------- -Output:: - - 255 - 255 - 255 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LineConstIterator diff --git a/src/Core/Common/IterateOnAVectorContainer/Documentation.md b/src/Core/Common/IterateOnAVectorContainer/Documentation.md new file mode 100644 index 000000000..e4c7827f0 --- /dev/null +++ b/src/Core/Common/IterateOnAVectorContainer/Documentation.md @@ -0,0 +1,35 @@ +--- +name: IterateOnAVectorContainer +--- + +# Iterate on a Vector Container + +```{index} single: VectorContainer +``` + +## Synopsis + +basic operation on VectorContainer + +## Results + +Output: + +``` +[1, 2] +[2, 3] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorContainer +``` diff --git a/src/Core/Common/IterateOnAVectorContainer/Documentation.rst b/src/Core/Common/IterateOnAVectorContainer/Documentation.rst deleted file mode 100644 index 9818d872b..000000000 --- a/src/Core/Common/IterateOnAVectorContainer/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: IterateOnAVectorContainer - -Iterate on a Vector Container -============================= - -.. index:: - single: VectorContainer - -Synopsis --------- - - -basic operation on VectorContainer - - -Results -------- - -Output:: - - [1, 2] - [2, 3] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorContainer diff --git a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.md b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.md new file mode 100644 index 000000000..48b906ca5 --- /dev/null +++ b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.md @@ -0,0 +1,69 @@ +--- +name: IterateOverARegionWithAShapedNeighborhoodIterator +--- + +# Iterate Over a Region With a Shaped Neighborhood Iterator + +```{index} single: ShapedNeighborhoodIterator +``` + +## Synopsis + +Iterate over a region of an image with a shaped neighborhood. + +## Results + +Output: + +``` +By default there are 0 active indices. +Now there are 2 active indices. +1 7 +New position: +Centered at [0, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [0, -1] +Centered at [0, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [0, 1] +New position: +Centered at [1, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [1, -1] +Centered at [1, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [1, 1] +New position: +Centered at [2, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [2, -1] +Centered at [2, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [2, 1] + +[...] + +New position: +Centered at [7, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [7, 8] +Centered at [7, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [7, 10] +New position: +Centered at [8, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [8, 8] +Centered at [8, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [8, 10] +New position: +Centered at [9, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [9, 8] +Centered at [9, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [9, 10] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ShapedNeighborhoodIterator +``` diff --git a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.rst b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.rst deleted file mode 100644 index a8b07a90f..000000000 --- a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.rst +++ /dev/null @@ -1,72 +0,0 @@ -:name: IterateOverARegionWithAShapedNeighborhoodIterator - -Iterate Over a Region With a Shaped Neighborhood Iterator -========================================================= - -.. index:: - single: ShapedNeighborhoodIterator - -Synopsis --------- - - -Iterate over a region of an image with a shaped neighborhood. - - -Results -------- - -Output:: - - By default there are 0 active indices. - Now there are 2 active indices. - 1 7 - New position: - Centered at [0, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [0, -1] - Centered at [0, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [0, 1] - New position: - Centered at [1, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [1, -1] - Centered at [1, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [1, 1] - New position: - Centered at [2, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [2, -1] - Centered at [2, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [2, 1] - - [...] - - New position: - Centered at [7, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [7, 8] - Centered at [7, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [7, 10] - New position: - Centered at [8, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [8, 8] - Centered at [8, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [8, 10] - New position: - Centered at [9, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [9, 8] - Centered at [9, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [9, 10] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ShapedNeighborhoodIterator diff --git a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.md b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.md new file mode 100644 index 000000000..8ad24a6bb --- /dev/null +++ b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.md @@ -0,0 +1,69 @@ +--- +name: IterateOverARegionWithAShapedNeighborhoodIteratorManual +--- + +# Iterate Over a Region With a Shaped Neighborhood Iterator Manually + +```{index} single: ShapedNeighborhoodIterator single: manual +``` + +## Synopsis + +Iterate over a region of an image with a shaped neighborhood manually. + +## Results + +Output: + +``` +By default there are 0 active indices. +Now there are 2 active indices. +1 7 +New position: +Centered at [0, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [0, -1] +Centered at [0, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [0, 1] +New position: +Centered at [1, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [1, -1] +Centered at [1, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [1, 1] +New position: +Centered at [2, 0] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [2, -1] +Centered at [2, 0] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [2, 1] + +[...] + +New position: +Centered at [7, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [7, 8] +Centered at [7, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [7, 10] +New position: +Centered at [8, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [8, 8] +Centered at [8, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [8, 10] +New position: +Centered at [9, 9] +Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [9, 8] +Centered at [9, 9] +Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [9, 10] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ShapedNeighborhoodIterator +``` diff --git a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.rst b/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.rst deleted file mode 100644 index 139c9f9f2..000000000 --- a/src/Core/Common/IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.rst +++ /dev/null @@ -1,73 +0,0 @@ -:name: IterateOverARegionWithAShapedNeighborhoodIteratorManual - -Iterate Over a Region With a Shaped Neighborhood Iterator Manually -=================================================================== - -.. index:: - single: ShapedNeighborhoodIterator - single: manual - -Synopsis --------- - - -Iterate over a region of an image with a shaped neighborhood manually. - - -Results -------- - -Output:: - - By default there are 0 active indices. - Now there are 2 active indices. - 1 7 - New position: - Centered at [0, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [0, -1] - Centered at [0, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [0, 1] - New position: - Centered at [1, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [1, -1] - Centered at [1, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [1, 1] - New position: - Centered at [2, 0] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [2, -1] - Centered at [2, 0] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [2, 1] - - [...] - - New position: - Centered at [7, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [7, 8] - Centered at [7, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [7, 10] - New position: - Centered at [8, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [8, 8] - Centered at [8, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [8, 10] - New position: - Centered at [9, 9] - Neighborhood index 1 is offset [0, -1] and has value 0 The real index is [9, 8] - Centered at [9, 9] - Neighborhood index 7 is offset [0, 1] and has value 0 The real index is [9, 10] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ShapedNeighborhoodIterator diff --git a/src/Core/Common/IterateOverSpecificRegion/Documentation.md b/src/Core/Common/IterateOverSpecificRegion/Documentation.md new file mode 100644 index 000000000..10b4a7f78 --- /dev/null +++ b/src/Core/Common/IterateOverSpecificRegion/Documentation.md @@ -0,0 +1,40 @@ +--- +name: IterateOverSpecificRegion +--- + +# Iterate Over Image While Skipping Specific Region + +```{index} single: ImageRegionExclusionConstIteratorWithIndex single: iterator pair: specific; region +``` + +## Synopsis + +Iterator over an image skipping a specified region. + +## Results + +Output: + +``` +0 +0 +0 +0 +0 +0 +Visited 6 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegionExclusionConstIteratorWithIndex +``` diff --git a/src/Core/Common/IterateOverSpecificRegion/Documentation.rst b/src/Core/Common/IterateOverSpecificRegion/Documentation.rst deleted file mode 100644 index eb44c923b..000000000 --- a/src/Core/Common/IterateOverSpecificRegion/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: IterateOverSpecificRegion - -Iterate Over Image While Skipping Specific Region -================================================= - -.. index:: - single: ImageRegionExclusionConstIteratorWithIndex - single: iterator - pair: specific; region - -Synopsis --------- - -Iterator over an image skipping a specified region. - - -Results -------- -Output:: - - 0 - 0 - 0 - 0 - 0 - 0 - Visited 6 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegionExclusionConstIteratorWithIndex diff --git a/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.md b/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.md new file mode 100644 index 000000000..cd1ef47d0 --- /dev/null +++ b/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.md @@ -0,0 +1,66 @@ +--- +name: IterateRegionWithAccessToIndexWithWriteAccess +--- + +# Iterate Region in Image With Access to Current Index With Write Access + +```{index} single: ImageRegionIteratorWithIndex pair: write; access single: index +``` + +## Synopsis + +Iterate over a region of an image with efficient access to the current index (with write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} IterateRegionWithAccessToIndexWithWriteAccess.png +:scale: 70% + +Yinyang.png In VTK Window With Index Access +::: + +Output: + +``` +Indices: +Index: [0, 0] value: ? +Index: [1, 0] value: ? +Index: [2, 0] value: ? +Index: [3, 0] value: ? +Index: [4, 0] value: ? +Index: [0, 1] value: ? +Index: [1, 1] value: ? +Index: [2, 1] value: ? +Index: [3, 1] value: ? +Index: [4, 1] value: ? +Index: [0, 2] value: ? +Index: [1, 2] value: ? +Index: [2, 2] value: ? +Index: [3, 2] value: ? +Index: [4, 2] value: ? +Index: [0, 3] value: ? +Index: [1, 3] value: ? +Index: [2, 3] value: ? +Index: [3, 3] value: ? +Index: [4, 3] value: ? +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegionIteratorWithIndex +``` diff --git a/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.rst b/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.rst deleted file mode 100644 index 69fb8693f..000000000 --- a/src/Core/Common/IterateRegionWithAccessToIndexWithWriteAccess/Documentation.rst +++ /dev/null @@ -1,65 +0,0 @@ -:name: IterateRegionWithAccessToIndexWithWriteAccess - -Iterate Region in Image With Access to Current Index With Write Access -====================================================================== - -.. index:: - single: ImageRegionIteratorWithIndex - pair: write; access - single: index - -Synopsis --------- - -Iterate over a region of an image with efficient access to the current index (with write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png - -.. figure:: IterateRegionWithAccessToIndexWithWriteAccess.png - :scale: 70% - - Yinyang.png In VTK Window With Index Access - -Output:: - - Indices: - Index: [0, 0] value: ? - Index: [1, 0] value: ? - Index: [2, 0] value: ? - Index: [3, 0] value: ? - Index: [4, 0] value: ? - Index: [0, 1] value: ? - Index: [1, 1] value: ? - Index: [2, 1] value: ? - Index: [3, 1] value: ? - Index: [4, 1] value: ? - Index: [0, 2] value: ? - Index: [1, 2] value: ? - Index: [2, 2] value: ? - Index: [3, 2] value: ? - Index: [4, 2] value: ? - Index: [0, 3] value: ? - Index: [1, 3] value: ? - Index: [2, 3] value: ? - Index: [3, 3] value: ? - Index: [4, 3] value: ? - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegionIteratorWithIndex diff --git a/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.md b/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.md new file mode 100644 index 000000000..cff6b3a6b --- /dev/null +++ b/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.md @@ -0,0 +1,46 @@ +--- +name: IterateRegionWithAccessToIndexWithoutWriteAccess +--- + +# Iterate Region in Image With Access to Index Without Write Access + +```{index} single: ImageRegionConstIteratorWithIndex pair: write; access single: index +``` + +## Synopsis + +Iterate over a region of an image with efficient access to the current index (without write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} IterateRegionWithAccessToIndexWithoutWriteAccess.png +:scale: 70% + +Yinyang.png In VTK Window +::: + +Output: + +``` +An extensive list of the neighborhood will be printed to the screen. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegionConstIteratorWithIndex +``` diff --git a/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.rst b/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.rst deleted file mode 100644 index 7b0059e4b..000000000 --- a/src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.rst +++ /dev/null @@ -1,45 +0,0 @@ -:name: IterateRegionWithAccessToIndexWithoutWriteAccess - -Iterate Region in Image With Access to Index Without Write Access -================================================================= - -.. index:: - single: ImageRegionConstIteratorWithIndex - pair: write; access - single: index - -Synopsis --------- - -Iterate over a region of an image with efficient access to the current index (without write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png - -.. figure:: IterateRegionWithAccessToIndexWithoutWriteAccess.png - :scale: 70% - - Yinyang.png In VTK Window - -Output:: - - An extensive list of the neighborhood will be printed to the screen. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegionConstIteratorWithIndex diff --git a/src/Core/Common/IterateRegionWithNeighborhood/Documentation.md b/src/Core/Common/IterateRegionWithNeighborhood/Documentation.md new file mode 100644 index 000000000..8efaedcaf --- /dev/null +++ b/src/Core/Common/IterateRegionWithNeighborhood/Documentation.md @@ -0,0 +1,46 @@ +--- +name: IterateRegionWithNeighborhood +--- + +# Iterate Region in Image With Neighborhood + +```{index} single: NeighborhoodIterator pair: iterate; region +``` + +## Synopsis + +Iterate over a region of an image with a neighborhood (with write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} IterateRegionWithWriteAccess.png +:scale: 70% + +Yinyang.png In VTK Window +::: + +Output: + +``` +An extensive list of the neighborhood will be printed to the screen. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NeighborhoodIterator +``` diff --git a/src/Core/Common/IterateRegionWithNeighborhood/Documentation.rst b/src/Core/Common/IterateRegionWithNeighborhood/Documentation.rst deleted file mode 100644 index 61537cd16..000000000 --- a/src/Core/Common/IterateRegionWithNeighborhood/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: IterateRegionWithNeighborhood - -Iterate Region in Image With Neighborhood -========================================= - -.. index:: - single: NeighborhoodIterator - pair: iterate; region - -Synopsis --------- - -Iterate over a region of an image with a neighborhood (with write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png - -.. figure:: IterateRegionWithWriteAccess.png - :scale: 70% - - Yinyang.png In VTK Window - -Output:: - - An extensive list of the neighborhood will be printed to the screen. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NeighborhoodIterator diff --git a/src/Core/Common/IterateRegionWithWriteAccess/Documentation.md b/src/Core/Common/IterateRegionWithWriteAccess/Documentation.md new file mode 100644 index 000000000..85a23650c --- /dev/null +++ b/src/Core/Common/IterateRegionWithWriteAccess/Documentation.md @@ -0,0 +1,40 @@ +--- +name: IterateRegionWithWriteAccess +--- + +# Iterate Region in Image With Write Access + +```{index} single: ImageRegionIterator pair: iterate; region pair: write; access +``` + +## Synopsis + +Iterate over a region of an image (with write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} IterateRegionWithWriteAccess.png +:scale: 70% + +Yinyang.png In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegionIterator +``` diff --git a/src/Core/Common/IterateRegionWithWriteAccess/Documentation.rst b/src/Core/Common/IterateRegionWithWriteAccess/Documentation.rst deleted file mode 100644 index 39d12065b..000000000 --- a/src/Core/Common/IterateRegionWithWriteAccess/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: IterateRegionWithWriteAccess - -Iterate Region in Image With Write Access -========================================= - -.. index:: - single: ImageRegionIterator - pair: iterate; region - pair: write; access - -Synopsis --------- - -Iterate over a region of an image (with write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png - -.. figure:: IterateRegionWithWriteAccess.png - :scale: 70% - - Yinyang.png In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegionIterator diff --git a/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.md b/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.md new file mode 100644 index 000000000..82619a948 --- /dev/null +++ b/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.md @@ -0,0 +1,59 @@ +--- +name: IterateRegionWithoutWriteAccess +--- + +# Iterate Region in Image Without Write Access + +```{index} single: ImageRegionConstIterator pair: write; access +``` + +## Synopsis + +Iterate over a region of an image (without write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png +::: + +Output: + +``` +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +255 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegionConstIterator +``` diff --git a/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.rst b/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.rst deleted file mode 100644 index ded304949..000000000 --- a/src/Core/Common/IterateRegionWithoutWriteAccess/Documentation.rst +++ /dev/null @@ -1,58 +0,0 @@ -:name: IterateRegionWithoutWriteAccess - -Iterate Region in Image Without Write Access -============================================ - -.. index:: - single: ImageRegionConstIterator - pair: write; access - -Synopsis --------- - -Iterate over a region of an image (without write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png - -Output:: - - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - 255 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegionConstIterator diff --git a/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.md b/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.md new file mode 100644 index 000000000..6073cc409 --- /dev/null +++ b/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.md @@ -0,0 +1,91 @@ +--- +name: IterateWithNeighborhoodWithoutAccess +--- + +# Iterate Region in Image With Neighborhood Without Write Access + +```{index} single: ConstNeighborhoodIterator pair: write; access single: neighborhood +``` + +## Synopsis + +Iterate over a region of an image with a neighborhood (without write access). + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Yinyang.png input image. +::: + +Output: + +``` +-1 -1 +0 -1 +1 -1 +-1 0 +0 0 +1 0 +-1 1 +0 1 +1 1 +0 -1 +1 -1 +2 -1 +0 0 +1 0 +2 0 +0 1 +1 1 +2 1 +1 -1 +2 -1 +3 -1 +1 0 +2 0 +3 0 +1 1 +2 1 +3 1 +2 -1 +3 -1 +4 -1 +2 0 +3 0 +4 0 +2 1 +3 1 +4 1 +3 -1 +4 -1 +5 -1 +3 0 +4 0 +5 0 +3 1 +4 1 +5 1 +4 -1 +5 -1 +6 -1 +4 0 +5 0 +6 0 +... +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConstNeighborhoodIterator +``` diff --git a/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.rst b/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.rst deleted file mode 100644 index e86c460f1..000000000 --- a/src/Core/Common/IterateWithNeighborhoodWithoutAccess/Documentation.rst +++ /dev/null @@ -1,92 +0,0 @@ -:name: IterateWithNeighborhoodWithoutAccess - -Iterate Region in Image With Neighborhood Without Write Access -============================================================== - -.. index:: - single: ConstNeighborhoodIterator - pair: write; access - single: neighborhood - -Synopsis --------- - -Iterate over a region of an image with a neighborhood (without write access). - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Yinyang.png input image. - -Output:: - - -1 -1 - 0 -1 - 1 -1 - -1 0 - 0 0 - 1 0 - -1 1 - 0 1 - 1 1 - 0 -1 - 1 -1 - 2 -1 - 0 0 - 1 0 - 2 0 - 0 1 - 1 1 - 2 1 - 1 -1 - 2 -1 - 3 -1 - 1 0 - 2 0 - 3 0 - 1 1 - 2 1 - 3 1 - 2 -1 - 3 -1 - 4 -1 - 2 0 - 3 0 - 4 0 - 2 1 - 3 1 - 4 1 - 3 -1 - 4 -1 - 5 -1 - 3 0 - 4 0 - 5 0 - 3 1 - 4 1 - 5 1 - 4 -1 - 5 -1 - 6 -1 - 4 0 - 5 0 - 6 0 - ... - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConstNeighborhoodIterator diff --git a/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.md b/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.md new file mode 100644 index 000000000..64e842b4a --- /dev/null +++ b/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.md @@ -0,0 +1,85 @@ +--- +name: MakeOutOfBoundsPixelsReturnConstValue +--- + +# Make Out of Bounds Pixels Return Constant Value + +```{index} single: ConstantBoundaryCondition pair: pixel; constant +``` + +## Synopsis + +Make out of bounds pixels return a constant value. + +## Results + +:::{figure} MakeOutOfBoundsPixelsReturnConstValue.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Index: [-1, -1] Pixel: 0 = 0 +Index: [0, -1] Pixel: 1 = 0 +Index: [1, -1] Pixel: 2 = 0 +Index: [-1, 0] Pixel: 3 = 0 +Index: [0, 0] Pixel: 4 = 255 +Index: [1, 0] Pixel: 5 = 255 +Index: [-1, 1] Pixel: 6 = 0 +Index: [0, 1] Pixel: 7 = 255 +Index: [1, 1] Pixel: 8 = 255 +Index: [0, -1] Pixel: 0 = 0 +Index: [1, -1] Pixel: 1 = 0 +Index: [2, -1] Pixel: 2 = 0 +Index: [0, 0] Pixel: 3 = 255 +Index: [1, 0] Pixel: 4 = 255 +Index: [2, 0] Pixel: 5 = 255 +Index: [0, 1] Pixel: 6 = 255 +Index: [1, 1] Pixel: 7 = 255 +Index: [2, 1] Pixel: 8 = 255 +Index: [1, -1] Pixel: 0 = 0 +Index: [2, -1] Pixel: 1 = 0 +Index: [3, -1] Pixel: 2 = 0 +Index: [1, 0] Pixel: 3 = 255 +Index: [2, 0] Pixel: 4 = 255 +Index: [3, 0] Pixel: 5 = 255 +Index: [1, 1] Pixel: 6 = 255 +Index: [2, 1] Pixel: 7 = 255 +Index: [3, 1] Pixel: 8 = 255 +Index: [2, -1] Pixel: 0 = 0 +Index: [3, -1] Pixel: 1 = 0 +Index: [4, -1] Pixel: 2 = 0 +Index: [2, 0] Pixel: 3 = 255 +Index: [3, 0] Pixel: 4 = 255 +Index: [4, 0] Pixel: 5 = 255 +Index: [2, 1] Pixel: 6 = 255 +Index: [3, 1] Pixel: 7 = 255 +Index: [4, 1] Pixel: 8 = 255 +Index: [3, -1] Pixel: 0 = 0 +Index: [4, -1] Pixel: 1 = 0 +Index: [5, -1] Pixel: 2 = 0 +Index: [3, 0] Pixel: 3 = 255 +Index: [4, 0] Pixel: 4 = 255 +Index: [5, 0] Pixel: 5 = 0 +Index: [3, 1] Pixel: 6 = 255 +Index: [4, 1] Pixel: 7 = 255 +Index: [5, 1] Pixel: 8 = 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConstantBoundaryCondition +``` diff --git a/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.rst b/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.rst deleted file mode 100644 index ef1885fea..000000000 --- a/src/Core/Common/MakeOutOfBoundsPixelsReturnConstValue/Documentation.rst +++ /dev/null @@ -1,84 +0,0 @@ -:name: MakeOutOfBoundsPixelsReturnConstValue - -Make Out of Bounds Pixels Return Constant Value -=============================================== - -.. index:: - single: ConstantBoundaryCondition - pair: pixel; constant - -Synopsis --------- - -Make out of bounds pixels return a constant value. - - -Results -------- -.. figure:: MakeOutOfBoundsPixelsReturnConstValue.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Output:: - - Index: [-1, -1] Pixel: 0 = 0 - Index: [0, -1] Pixel: 1 = 0 - Index: [1, -1] Pixel: 2 = 0 - Index: [-1, 0] Pixel: 3 = 0 - Index: [0, 0] Pixel: 4 = 255 - Index: [1, 0] Pixel: 5 = 255 - Index: [-1, 1] Pixel: 6 = 0 - Index: [0, 1] Pixel: 7 = 255 - Index: [1, 1] Pixel: 8 = 255 - Index: [0, -1] Pixel: 0 = 0 - Index: [1, -1] Pixel: 1 = 0 - Index: [2, -1] Pixel: 2 = 0 - Index: [0, 0] Pixel: 3 = 255 - Index: [1, 0] Pixel: 4 = 255 - Index: [2, 0] Pixel: 5 = 255 - Index: [0, 1] Pixel: 6 = 255 - Index: [1, 1] Pixel: 7 = 255 - Index: [2, 1] Pixel: 8 = 255 - Index: [1, -1] Pixel: 0 = 0 - Index: [2, -1] Pixel: 1 = 0 - Index: [3, -1] Pixel: 2 = 0 - Index: [1, 0] Pixel: 3 = 255 - Index: [2, 0] Pixel: 4 = 255 - Index: [3, 0] Pixel: 5 = 255 - Index: [1, 1] Pixel: 6 = 255 - Index: [2, 1] Pixel: 7 = 255 - Index: [3, 1] Pixel: 8 = 255 - Index: [2, -1] Pixel: 0 = 0 - Index: [3, -1] Pixel: 1 = 0 - Index: [4, -1] Pixel: 2 = 0 - Index: [2, 0] Pixel: 3 = 255 - Index: [3, 0] Pixel: 4 = 255 - Index: [4, 0] Pixel: 5 = 255 - Index: [2, 1] Pixel: 6 = 255 - Index: [3, 1] Pixel: 7 = 255 - Index: [4, 1] Pixel: 8 = 255 - Index: [3, -1] Pixel: 0 = 0 - Index: [4, -1] Pixel: 1 = 0 - Index: [5, -1] Pixel: 2 = 0 - Index: [3, 0] Pixel: 3 = 255 - Index: [4, 0] Pixel: 4 = 255 - Index: [5, 0] Pixel: 5 = 0 - Index: [3, 1] Pixel: 6 = 255 - Index: [4, 1] Pixel: 7 = 255 - Index: [5, 1] Pixel: 8 = 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConstantBoundaryCondition diff --git a/src/Core/Common/MakePartOfImageTransparent/Documentation.md b/src/Core/Common/MakePartOfImageTransparent/Documentation.md new file mode 100644 index 000000000..53949d1d9 --- /dev/null +++ b/src/Core/Common/MakePartOfImageTransparent/Documentation.md @@ -0,0 +1,35 @@ +--- +name: MakePartOfImageTransparent +--- + +# Make Part of an Image Transparent + +```{index} single: RGBAPixel single: transparency +``` + +## Synopsis + +Demonstrates how to assign transparency to pixels in an image, then writing the result to a tif file for inspection and verification. + +## Results + +:::{figure} MakePartOfImageTransparent.png +:alt: test.tif +:scale: 70% + +Output Image. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RGBAPixel +``` diff --git a/src/Core/Common/MakePartOfImageTransparent/Documentation.rst b/src/Core/Common/MakePartOfImageTransparent/Documentation.rst deleted file mode 100644 index de9385d6b..000000000 --- a/src/Core/Common/MakePartOfImageTransparent/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: MakePartOfImageTransparent - -Make Part of an Image Transparent -================================= - -.. index:: - single: RGBAPixel - single: transparency - -Synopsis --------- - -Demonstrates how to assign transparency to pixels in an image, then writing the result to a tif file for inspection and verification. - - -Results -------- -.. figure:: MakePartOfImageTransparent.png - :scale: 70% - :alt: test.tif - - Output Image. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RGBAPixel diff --git a/src/Core/Common/Matrix/Documentation.md b/src/Core/Common/Matrix/Documentation.md new file mode 100644 index 000000000..d5d810a88 --- /dev/null +++ b/src/Core/Common/Matrix/Documentation.md @@ -0,0 +1,43 @@ +--- +name: Matrix +--- + +# Matrix + +```{index} single: Matrix +``` + +## Synopsis + +This will create and display a matrix of NxN dimensions, then multiply it by a vector of N dimension. + +## Results + +Output: + +``` +M: 1 2 3 + 4 5 6 + 7 8 9 + +M: 1 2 3 + 4 5 6 + 7 8 9 + +V: [1, 2, 3] +MV: [14, 32, 50] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Matrix +``` diff --git a/src/Core/Common/Matrix/Documentation.rst b/src/Core/Common/Matrix/Documentation.rst deleted file mode 100644 index 14e16be65..000000000 --- a/src/Core/Common/Matrix/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: Matrix - -Matrix -====== - -.. index:: - single: Matrix - -Synopsis --------- - -This will create and display a matrix of NxN dimensions, then multiply it by a vector of N dimension. - - -Results -------- -Output:: - - M: 1 2 3 - 4 5 6 - 7 8 9 - - M: 1 2 3 - 4 5 6 - 7 8 9 - - V: [1, 2, 3] - MV: [14, 32, 50] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Matrix diff --git a/src/Core/Common/MatrixInverse/Documentation.md b/src/Core/Common/MatrixInverse/Documentation.md new file mode 100644 index 000000000..97bc48b66 --- /dev/null +++ b/src/Core/Common/MatrixInverse/Documentation.md @@ -0,0 +1,37 @@ +--- +name: MatrixInverse +--- + +# Matrix Inverse + +```{index} single: Matrix pair: matrix; inverse +``` + +## Synopsis + +This will compute and display an NxN matrix and its inverse. + +## Results + +Output: + +``` +M: 1 2 + 3 5 +Inverse: -5 2 + 3 -1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Matrix +``` diff --git a/src/Core/Common/MatrixInverse/Documentation.rst b/src/Core/Common/MatrixInverse/Documentation.rst deleted file mode 100644 index 3c4644eea..000000000 --- a/src/Core/Common/MatrixInverse/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: MatrixInverse - -Matrix Inverse -============== - -.. index:: - single: Matrix - pair: matrix; inverse - -Synopsis --------- - -This will compute and display an NxN matrix and its inverse. - - -Results -------- -Output:: - - M: 1 2 - 3 5 - Inverse: -5 2 - 3 -1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Matrix diff --git a/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.md b/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.md new file mode 100644 index 000000000..8505d0809 --- /dev/null +++ b/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.md @@ -0,0 +1,28 @@ +--- +name: MersenneTwisterRandomIntegerGenerator +--- + +# Mersenne Twister Random Integer Generator + +```{index} single: MersenneTwisterRandomVariateGenerator +``` + +## Synopsis + +Random integer generator + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator +``` diff --git a/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.rst b/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.rst deleted file mode 100644 index 30b9933d1..000000000 --- a/src/Core/Common/MersenneTwisterRandomIntegerGenerator/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: MersenneTwisterRandomIntegerGenerator - -Mersenne Twister Random Integer Generator -========================================= - -.. index:: - single: MersenneTwisterRandomVariateGenerator - -Synopsis --------- - - -Random integer generator - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator diff --git a/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.md b/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.md new file mode 100644 index 000000000..9b31ef650 --- /dev/null +++ b/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.md @@ -0,0 +1,28 @@ +--- +name: MersenneTwisterRandomNumberGenerator +--- + +# Mersenne Twister Random Number Generator + +```{index} single: MersenneTwisterRandomVariateGenerator +``` + +## Synopsis + +Generate a random number + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator +``` diff --git a/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.rst b/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.rst deleted file mode 100644 index 3116e9aba..000000000 --- a/src/Core/Common/MersenneTwisterRandomNumberGenerator/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: MersenneTwisterRandomNumberGenerator - -Mersenne Twister Random Number Generator -======================================== - -.. index:: - single: MersenneTwisterRandomVariateGenerator - -Synopsis --------- - - -Generate a random number - - -Results -------- - - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator diff --git a/src/Core/Common/MiniPipeline/Documentation.md b/src/Core/Common/MiniPipeline/Documentation.md new file mode 100644 index 000000000..c96ef58ea --- /dev/null +++ b/src/Core/Common/MiniPipeline/Documentation.md @@ -0,0 +1,51 @@ +--- +name: MiniPipeline +--- + +# Mini Pipeline + +```{index} single: Image +``` + +## Synopsis + +Mini Pipeline. + +## Results + +Output: + +``` +Input: +ImageRegion (0x7fe4c3aaadb0) +Dimension: 2 +Index: [0, 0] +Size: [200, 300] + +Input: +ImageRegion (0x7fe4c3aab920) +Dimension: 2 +Index: [0, 0] +Size: [200, 300] +``` + +:::{figure} MiniPipelineOutput.png +:alt: Output.png +:scale: 70% + +Output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/MiniPipeline/Documentation.rst b/src/Core/Common/MiniPipeline/Documentation.rst deleted file mode 100644 index f3b9d9ec8..000000000 --- a/src/Core/Common/MiniPipeline/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: MiniPipeline - -Mini Pipeline -============= - -.. index:: - single: Image - -Synopsis --------- - -Mini Pipeline. - - -Results -------- -Output:: - - Input: - ImageRegion (0x7fe4c3aaadb0) - Dimension: 2 - Index: [0, 0] - Size: [200, 300] - - Input: - ImageRegion (0x7fe4c3aab920) - Dimension: 2 - Index: [0, 0] - Size: [200, 300] - -.. figure:: MiniPipelineOutput.png - :scale: 70% - :alt: Output.png - - Output.png - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/MultiThreadOilPainting/Documentation.md b/src/Core/Common/MultiThreadOilPainting/Documentation.md new file mode 100644 index 000000000..ccbd0207f --- /dev/null +++ b/src/Core/Common/MultiThreadOilPainting/Documentation.md @@ -0,0 +1,42 @@ +--- +name: MultiThreadOilPainting +--- + +# Multi-thread Oil Painting + +```{index} single: ImageToImageFilter pair: oil; painting +``` + +## Synopsis + +Multi-threaded oil painting image filter. + +## Results + +:::{figure} Yinyang.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} MultiThreadOilPaintingQuickview.png +:alt: Output In QuickView Window +:scale: 70% + +Output In QuickView Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/MultiThreadOilPainting/Documentation.rst b/src/Core/Common/MultiThreadOilPainting/Documentation.rst deleted file mode 100644 index b719b6983..000000000 --- a/src/Core/Common/MultiThreadOilPainting/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: MultiThreadOilPainting - -Multi-thread Oil Painting -========================= - -.. index:: - single: ImageToImageFilter - pair: oil; painting - -Synopsis --------- - -Multi-threaded oil painting image filter. - - -Results -------- -.. figure:: Yinyang.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: MultiThreadOilPaintingQuickview.png - :scale: 70% - :alt: Output In QuickView Window - - Output In QuickView Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/MultipleInputsOfDifferentType/Documentation.md b/src/Core/Common/MultipleInputsOfDifferentType/Documentation.md new file mode 100644 index 000000000..5a412ddd6 --- /dev/null +++ b/src/Core/Common/MultipleInputsOfDifferentType/Documentation.md @@ -0,0 +1,33 @@ +--- +name: MultipleInputsOfDifferentType +--- + +# Multiple Inputs of Different Type + +```{index} single: ImageToImageFilter +``` + +## Synopsis + +Write a filter with multiple inputs of different types. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/MultipleInputsOfDifferentType/Documentation.rst b/src/Core/Common/MultipleInputsOfDifferentType/Documentation.rst deleted file mode 100644 index 1f684e3d2..000000000 --- a/src/Core/Common/MultipleInputsOfDifferentType/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: MultipleInputsOfDifferentType - -Multiple Inputs of Different Type -================================= - -.. index:: - single: ImageToImageFilter - -Synopsis --------- - -Write a filter with multiple inputs of different types. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/MultipleInputsOfSameType/Documentation.md b/src/Core/Common/MultipleInputsOfSameType/Documentation.md new file mode 100644 index 000000000..22cadae36 --- /dev/null +++ b/src/Core/Common/MultipleInputsOfSameType/Documentation.md @@ -0,0 +1,35 @@ +--- +name: MultipleInputsOfSameType +--- + +# Multiple Inputs of Same Type + +```{index} single: ImageToImageFilter +``` + +## Synopsis + +Write a filter with multiple inputs of the same type. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/MultipleInputsOfSameType/Documentation.rst b/src/Core/Common/MultipleInputsOfSameType/Documentation.rst deleted file mode 100644 index 2398ec589..000000000 --- a/src/Core/Common/MultipleInputsOfSameType/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: MultipleInputsOfSameType - -Multiple Inputs of Same Type -============================ - -.. index:: - single: ImageToImageFilter - -Synopsis --------- - -Write a filter with multiple inputs of the same type. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.md b/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.md new file mode 100644 index 000000000..316d2c9cf --- /dev/null +++ b/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.md @@ -0,0 +1,33 @@ +--- +name: MultipleOutputsOfDifferentType +--- + +# Multiple Outputs of Different Type + +```{index} single: ImageToImageFilter +``` + +## Synopsis + +Write a filter with multiple outputs of different types. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.rst b/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.rst deleted file mode 100644 index 520c7e9f8..000000000 --- a/src/Core/Common/MultipleOutputsOfDifferentType/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: MultipleOutputsOfDifferentType - -Multiple Outputs of Different Type -================================== - -.. index:: - single: ImageToImageFilter - -Synopsis --------- - -Write a filter with multiple outputs of different types. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/MultipleOutputsOfSameType/Documentation.md b/src/Core/Common/MultipleOutputsOfSameType/Documentation.md new file mode 100644 index 000000000..df02ad3e2 --- /dev/null +++ b/src/Core/Common/MultipleOutputsOfSameType/Documentation.md @@ -0,0 +1,42 @@ +--- +name: MultipleOutputsOfSameType +--- + +# Multiple Outputs of Same Type + +```{index} single: ImageToImageFilter +``` + +## Synopsis + +Write a filter with multiple outputs of the same type. + +## Results + +:::{figure} TestOutput1.jpg +:alt: TestOutput1.jpg +:scale: 70% + +TestOuput1.jpg +::: + +:::{figure} TestOutput2.jpg +:alt: TestOutput2.jpg +:scale: 70% + +TestOutput2.jpg +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToImageFilter +``` diff --git a/src/Core/Common/MultipleOutputsOfSameType/Documentation.rst b/src/Core/Common/MultipleOutputsOfSameType/Documentation.rst deleted file mode 100644 index 3527a3a2e..000000000 --- a/src/Core/Common/MultipleOutputsOfSameType/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: MultipleOutputsOfSameType - -Multiple Outputs of Same Type -============================= - -.. index:: - single: ImageToImageFilter - -Synopsis --------- - -Write a filter with multiple outputs of the same type. - - -Results -------- -.. figure:: TestOutput1.jpg - :scale: 70% - :alt: TestOutput1.jpg - - TestOuput1.jpg - -.. figure:: TestOutput2.jpg - :scale: 70% - :alt: TestOutput2.jpg - - TestOutput2.jpg - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToImageFilter diff --git a/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.md b/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.md new file mode 100644 index 000000000..4134ba09b --- /dev/null +++ b/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.md @@ -0,0 +1,37 @@ +--- +name: NeighborhoodIteratorOnVectorImage +--- + +# Neighborhood Iterator on Vector Image + +```{index} single: VectorImage single: NeighborhoodIterator +``` + +## Synopsis + +NeighborhoodIterator on a VectorImage. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorImage +``` + +```{eval-rst} +.. breathelink:: itk::NeighborhoodIterator +``` diff --git a/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.rst b/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.rst deleted file mode 100644 index 47d71c8a3..000000000 --- a/src/Core/Common/NeighborhoodIteratorOnVectorImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: NeighborhoodIteratorOnVectorImage - -Neighborhood Iterator on Vector Image -===================================== - -.. index:: - single: VectorImage - single: NeighborhoodIterator - -Synopsis --------- - -NeighborhoodIterator on a VectorImage. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorImage -.. breathelink:: itk::NeighborhoodIterator diff --git a/src/Core/Common/ObserveAnEvent/Documentation.md b/src/Core/Common/ObserveAnEvent/Documentation.md new file mode 100644 index 000000000..33cb6700f --- /dev/null +++ b/src/Core/Common/ObserveAnEvent/Documentation.md @@ -0,0 +1,142 @@ +--- +name: ObserveAnEvent +--- + +# Observe an Event + +```{index} single: Command single: progress +``` + +## Synopsis + +This example demonstrates how to observe and event that is invoked by a filter. + +## Results + +Output: + +``` +Progress: 0 +Progress: 0.00994873 +Progress: 0.0198975 +Progress: 0.0298462 +Progress: 0.0397949 +Progress: 0.0497437 +Progress: 0.0596924 +Progress: 0.0696411 +Progress: 0.0795898 +Progress: 0.0895386 +Progress: 0.0994873 +Progress: 0.109436 +Progress: 0.119385 +Progress: 0.129333 +Progress: 0.139282 +Progress: 0.149231 +Progress: 0.15918 +Progress: 0.169128 +Progress: 0.179077 +Progress: 0.189026 +Progress: 0.198975 +Progress: 0.208923 +Progress: 0.218872 +Progress: 0.228821 +Progress: 0.23877 +Progress: 0.248718 +Progress: 0.258667 +Progress: 0.268616 +Progress: 0.278564 +Progress: 0.288513 +Progress: 0.298462 +Progress: 0.308411 +Progress: 0.318359 +Progress: 0.328308 +Progress: 0.338257 +Progress: 0.348206 +Progress: 0.358154 +Progress: 0.368103 +Progress: 0.378052 +Progress: 0.388 +Progress: 0.397949 +Progress: 0.407898 +Progress: 0.417847 +Progress: 0.427795 +Progress: 0.437744 +Progress: 0.447693 +Progress: 0.457642 +Progress: 0.46759 +Progress: 0.477539 +Progress: 0.487488 +Progress: 0.497437 +Progress: 0.507385 +Progress: 0.517334 +Progress: 0.527283 +Progress: 0.537231 +Progress: 0.54718 +Progress: 0.557129 +Progress: 0.567078 +Progress: 0.577026 +Progress: 0.586975 +Progress: 0.596924 +Progress: 0.606873 +Progress: 0.616821 +Progress: 0.62677 +Progress: 0.636719 +Progress: 0.646667 +Progress: 0.656616 +Progress: 0.666565 +Progress: 0.676514 +Progress: 0.686462 +Progress: 0.696411 +Progress: 0.70636 +Progress: 0.716309 +Progress: 0.726257 +Progress: 0.736206 +Progress: 0.746155 +Progress: 0.756104 +Progress: 0.766052 +Progress: 0.776001 +Progress: 0.78595 +Progress: 0.795898 +Progress: 0.805847 +Progress: 0.815796 +Progress: 0.825745 +Progress: 0.835693 +Progress: 0.845642 +Progress: 0.855591 +Progress: 0.86554 +Progress: 0.875488 +Progress: 0.885437 +Progress: 0.895386 +Progress: 0.905334 +Progress: 0.915283 +Progress: 0.925232 +Progress: 0.935181 +Progress: 0.945129 +Progress: 0.955078 +Progress: 0.965027 +Progress: 0.974976 +Progress: 0.984924 +Progress: 0.994873 +Progress: 1 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Command +``` diff --git a/src/Core/Common/ObserveAnEvent/Documentation.rst b/src/Core/Common/ObserveAnEvent/Documentation.rst deleted file mode 100644 index ed82d071e..000000000 --- a/src/Core/Common/ObserveAnEvent/Documentation.rst +++ /dev/null @@ -1,145 +0,0 @@ -:name: ObserveAnEvent - -Observe an Event -================ - -.. index:: - single: Command - single: progress - -Synopsis --------- - - -This example demonstrates how to observe and event that is invoked by a filter. - - -Results -------- - -Output:: - - Progress: 0 - Progress: 0.00994873 - Progress: 0.0198975 - Progress: 0.0298462 - Progress: 0.0397949 - Progress: 0.0497437 - Progress: 0.0596924 - Progress: 0.0696411 - Progress: 0.0795898 - Progress: 0.0895386 - Progress: 0.0994873 - Progress: 0.109436 - Progress: 0.119385 - Progress: 0.129333 - Progress: 0.139282 - Progress: 0.149231 - Progress: 0.15918 - Progress: 0.169128 - Progress: 0.179077 - Progress: 0.189026 - Progress: 0.198975 - Progress: 0.208923 - Progress: 0.218872 - Progress: 0.228821 - Progress: 0.23877 - Progress: 0.248718 - Progress: 0.258667 - Progress: 0.268616 - Progress: 0.278564 - Progress: 0.288513 - Progress: 0.298462 - Progress: 0.308411 - Progress: 0.318359 - Progress: 0.328308 - Progress: 0.338257 - Progress: 0.348206 - Progress: 0.358154 - Progress: 0.368103 - Progress: 0.378052 - Progress: 0.388 - Progress: 0.397949 - Progress: 0.407898 - Progress: 0.417847 - Progress: 0.427795 - Progress: 0.437744 - Progress: 0.447693 - Progress: 0.457642 - Progress: 0.46759 - Progress: 0.477539 - Progress: 0.487488 - Progress: 0.497437 - Progress: 0.507385 - Progress: 0.517334 - Progress: 0.527283 - Progress: 0.537231 - Progress: 0.54718 - Progress: 0.557129 - Progress: 0.567078 - Progress: 0.577026 - Progress: 0.586975 - Progress: 0.596924 - Progress: 0.606873 - Progress: 0.616821 - Progress: 0.62677 - Progress: 0.636719 - Progress: 0.646667 - Progress: 0.656616 - Progress: 0.666565 - Progress: 0.676514 - Progress: 0.686462 - Progress: 0.696411 - Progress: 0.70636 - Progress: 0.716309 - Progress: 0.726257 - Progress: 0.736206 - Progress: 0.746155 - Progress: 0.756104 - Progress: 0.766052 - Progress: 0.776001 - Progress: 0.78595 - Progress: 0.795898 - Progress: 0.805847 - Progress: 0.815796 - Progress: 0.825745 - Progress: 0.835693 - Progress: 0.845642 - Progress: 0.855591 - Progress: 0.86554 - Progress: 0.875488 - Progress: 0.885437 - Progress: 0.895386 - Progress: 0.905334 - Progress: 0.915283 - Progress: 0.925232 - Progress: 0.935181 - Progress: 0.945129 - Progress: 0.955078 - Progress: 0.965027 - Progress: 0.974976 - Progress: 0.984924 - Progress: 0.994873 - Progress: 1 - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Command diff --git a/src/Core/Common/PassImageToFunction/Documentation.md b/src/Core/Common/PassImageToFunction/Documentation.md new file mode 100644 index 000000000..bafb5c04d --- /dev/null +++ b/src/Core/Common/PassImageToFunction/Documentation.md @@ -0,0 +1,26 @@ +--- +name: PassImageToFunction +--- + +# Pass Image to Function + +```{index} single: Image pair: image; function +``` + +## Synopsis + +Pass an image to a function. + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/PassImageToFunction/Documentation.rst b/src/Core/Common/PassImageToFunction/Documentation.rst deleted file mode 100644 index 245c567e8..000000000 --- a/src/Core/Common/PassImageToFunction/Documentation.rst +++ /dev/null @@ -1,28 +0,0 @@ -:name: PassImageToFunction - -Pass Image to Function -====================== - -.. index:: - single: Image - pair: image; function - -Synopsis --------- - -Pass an image to a function. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/PermuteSequenceOfIndices/Documentation.md b/src/Core/Common/PermuteSequenceOfIndices/Documentation.md new file mode 100644 index 000000000..4606cbcd7 --- /dev/null +++ b/src/Core/Common/PermuteSequenceOfIndices/Documentation.md @@ -0,0 +1,37 @@ +--- +name: PermuteSequenceOfIndices +--- + +# Permute Sequence of Indices + +```{index} single: ImageRandomNonRepeatingConstIteratorWithIndex +``` + +## Synopsis + +Permute a sequence of indices. + +## Results + +Output: + +``` +1 0 4 3 2 + +After shuffle +4 1 0 2 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRandomNonRepeatingConstIteratorWithIndex +``` diff --git a/src/Core/Common/PermuteSequenceOfIndices/Documentation.rst b/src/Core/Common/PermuteSequenceOfIndices/Documentation.rst deleted file mode 100644 index 5b06cb4d0..000000000 --- a/src/Core/Common/PermuteSequenceOfIndices/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: PermuteSequenceOfIndices - -Permute Sequence of Indices -=========================== - -.. index:: - single: ImageRandomNonRepeatingConstIteratorWithIndex - -Synopsis --------- - -Permute a sequence of indices. - - -Results -------- -Output:: - - 1 0 4 3 2 - - After shuffle - 4 1 0 2 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRandomNonRepeatingConstIteratorWithIndex diff --git a/src/Core/Common/PiConstant/Documentation.md b/src/Core/Common/PiConstant/Documentation.md new file mode 100644 index 000000000..9781fc593 --- /dev/null +++ b/src/Core/Common/PiConstant/Documentation.md @@ -0,0 +1,28 @@ +--- +name: PiConstant +--- + +# Pi Constant + +```{index} single: Math single: pi +``` + +## Synopsis + +This will print a float that represents the constant Pi. + +## Results + +Output: + +``` +3.14159 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Core/Common/PiConstant/Documentation.rst b/src/Core/Common/PiConstant/Documentation.rst deleted file mode 100644 index 4187dd611..000000000 --- a/src/Core/Common/PiConstant/Documentation.rst +++ /dev/null @@ -1,30 +0,0 @@ -:name: PiConstant - -Pi Constant -=========== - -.. index:: - single: Math - single: pi - -Synopsis --------- - -This will print a float that represents the constant Pi. - - -Results -------- -Output:: - - 3.14159 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Core/Common/PrintModuleLoadingPython/Documentation.md b/src/Core/Common/PrintModuleLoadingPython/Documentation.md new file mode 100644 index 000000000..e45a53849 --- /dev/null +++ b/src/Core/Common/PrintModuleLoadingPython/Documentation.md @@ -0,0 +1,34 @@ +--- +name: PrintModuleLoadingPython +--- + +# Print ITK Python Module Loading + +## Synopsis + +Print how ITK Python module dependencies are lazily loaded. + +## Results + +Output: + +``` +Loading ITKPyBase... done +Loading ITKCommon... done +Loading ITKStatistics... done +Loading ITKImageFilterBase... done +Loading ITKTransform... done +Loading ITKImageFunction... done +Loading ITKImageGrid... done +Loading ITKFFT... done +Loading ITKPyUtils... done +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` diff --git a/src/Core/Common/PrintModuleLoadingPython/Documentation.rst b/src/Core/Common/PrintModuleLoadingPython/Documentation.rst deleted file mode 100644 index eb79b09af..000000000 --- a/src/Core/Common/PrintModuleLoadingPython/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: PrintModuleLoadingPython - -Print ITK Python Module Loading -================================ - -Synopsis --------- - -Print how ITK Python module dependencies are lazily loaded. - - -Results -------- -Output:: - - Loading ITKPyBase... done - Loading ITKCommon... done - Loading ITKStatistics... done - Loading ITKImageFilterBase... done - Loading ITKTransform... done - Loading ITKImageFunction... done - Loading ITKImageGrid... done - Loading ITKFFT... done - Loading ITKPyUtils... done - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- diff --git a/src/Core/Common/ProduceImageProgrammatically/Documentation.md b/src/Core/Common/ProduceImageProgrammatically/Documentation.md new file mode 100644 index 000000000..b7ba29b71 --- /dev/null +++ b/src/Core/Common/ProduceImageProgrammatically/Documentation.md @@ -0,0 +1,33 @@ +--- +name: ProduceImageProgrammatically +--- + +# Produce Image Programmatically + +```{index} single: ImageSource +``` + +## Synopsis + +Produce an image programmitically. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageSource +``` diff --git a/src/Core/Common/ProduceImageProgrammatically/Documentation.rst b/src/Core/Common/ProduceImageProgrammatically/Documentation.rst deleted file mode 100644 index 9bb33f3cd..000000000 --- a/src/Core/Common/ProduceImageProgrammatically/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: ProduceImageProgrammatically - -Produce Image Programmatically -============================== - -.. index:: - single: ImageSource - -Synopsis --------- - -Produce an image programmitically. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageSource diff --git a/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.md b/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.md new file mode 100644 index 000000000..eedb7d0bf --- /dev/null +++ b/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.md @@ -0,0 +1,233 @@ +--- +name: RandomSelectOfPixelsFromRegion +--- + +# Random Selection of Pixels From Region + +```{index} single: ImageRandomConstIteratorWithIndex pair: random; pixel +``` + +## Synopsis + +Randomly select pixels from a region of an image. + +## Results + +Output: + +``` +[4, 2] +[1, 1] +[1, 3] +[4, 0] +[3, 0] +[4, 3] +[1, 0] +[1, 1] +[4, 2] +[4, 2] +[1, 2] +[2, 1] +[1, 2] +[2, 3] +[2, 3] +[4, 1] +[4, 2] +[3, 1] +[2, 2] +[2, 2] +[1, 1] +[2, 2] +[1, 1] +[1, 1] +[1, 0] +[3, 1] +[2, 1] +[4, 0] +[2, 2] +[4, 1] +[0, 2] +[2, 1] +[0, 2] +[1, 0] +[1, 0] +[2, 3] +[1, 1] +[1, 3] +[0, 1] +[3, 0] +[4, 2] +[4, 0] +[3, 1] +[0, 1] +[0, 3] +[0, 0] +[1, 2] +[3, 2] +[2, 0] +[2, 2] +[1, 1] +[3, 2] +[1, 1] +[2, 1] +[2, 1] +[4, 2] +[1, 3] +[4, 1] +[0, 3] +[1, 2] +[4, 3] +[0, 0] +[2, 1] +[1, 0] +[4, 3] +[4, 3] +[2, 3] +[2, 3] +[0, 3] +[1, 2] +[1, 3] +[2, 0] +[1, 0] +[2, 3] +[3, 3] +[3, 2] +[0, 0] +[3, 3] +[1, 2] +[1, 0] +[3, 0] +[3, 3] +[4, 0] +[1, 2] +[0, 2] +[1, 3] +[3, 3] +[1, 1] +[0, 3] +[0, 0] +[0, 2] +[0, 2] +[2, 2] +[2, 2] +[4, 1] +[2, 2] +[1, 1] +[1, 0] +[4, 1] +[1, 0] +[3, 1] +[4, 3] +[0, 0] +[3, 2] +[1, 2] +[1, 2] +[2, 3] +[4, 2] +[2, 2] +[3, 0] +[0, 3] +[2, 2] +[1, 1] +[2, 3] +[4, 0] +[0, 3] +[4, 2] +[3, 2] +[3, 3] +[1, 2] +[4, 3] +[0, 0] +[1, 3] +[0, 0] +[4, 2] +[0, 2] +[0, 2] +[0, 3] +[4, 2] +[4, 2] +[4, 2] +[3, 2] +[4, 0] +[0, 0] +[0, 1] +[3, 0] +[0, 0] +[0, 0] +[0, 0] +[0, 0] +[4, 2] +[1, 2] +[0, 3] +[3, 3] +[4, 2] +[2, 2] +[2, 2] +[3, 3] +[1, 2] +[2, 1] +[0, 2] +[1, 2] +[4, 0] +[4, 3] +[3, 3] +[1, 2] +[0, 1] +[3, 2] +[0, 2] +[4, 1] +[1, 2] +[3, 0] +[4, 3] +[1, 2] +[2, 2] +[2, 3] +[0, 0] +[2, 3] +[4, 1] +[4, 2] +[4, 2] +[1, 2] +[3, 3] +[1, 3] +[0, 2] +[3, 2] +[3, 0] +[2, 3] +[4, 2] +[2, 3] +[4, 2] +[4, 0] +[2, 0] +[1, 0] +[1, 2] +[1, 0] +[3, 2] +[0, 0] +[3, 1] +[4, 3] +[0, 3] +[0, 2] +[2, 0] +[4, 2] +[3, 2] +[1, 0] +[1, 0] +[4, 0] +[1, 2] +[0, 2] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRandomConstIteratorWithIndex +``` diff --git a/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.rst b/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.rst deleted file mode 100644 index 9c1c333a0..000000000 --- a/src/Core/Common/RandomSelectOfPixelsFromRegion/Documentation.rst +++ /dev/null @@ -1,233 +0,0 @@ -:name: RandomSelectOfPixelsFromRegion - -Random Selection of Pixels From Region -====================================== - -.. index:: - single: ImageRandomConstIteratorWithIndex - pair: random; pixel - -Synopsis --------- - -Randomly select pixels from a region of an image. - - -Results -------- -Output:: - - [4, 2] - [1, 1] - [1, 3] - [4, 0] - [3, 0] - [4, 3] - [1, 0] - [1, 1] - [4, 2] - [4, 2] - [1, 2] - [2, 1] - [1, 2] - [2, 3] - [2, 3] - [4, 1] - [4, 2] - [3, 1] - [2, 2] - [2, 2] - [1, 1] - [2, 2] - [1, 1] - [1, 1] - [1, 0] - [3, 1] - [2, 1] - [4, 0] - [2, 2] - [4, 1] - [0, 2] - [2, 1] - [0, 2] - [1, 0] - [1, 0] - [2, 3] - [1, 1] - [1, 3] - [0, 1] - [3, 0] - [4, 2] - [4, 0] - [3, 1] - [0, 1] - [0, 3] - [0, 0] - [1, 2] - [3, 2] - [2, 0] - [2, 2] - [1, 1] - [3, 2] - [1, 1] - [2, 1] - [2, 1] - [4, 2] - [1, 3] - [4, 1] - [0, 3] - [1, 2] - [4, 3] - [0, 0] - [2, 1] - [1, 0] - [4, 3] - [4, 3] - [2, 3] - [2, 3] - [0, 3] - [1, 2] - [1, 3] - [2, 0] - [1, 0] - [2, 3] - [3, 3] - [3, 2] - [0, 0] - [3, 3] - [1, 2] - [1, 0] - [3, 0] - [3, 3] - [4, 0] - [1, 2] - [0, 2] - [1, 3] - [3, 3] - [1, 1] - [0, 3] - [0, 0] - [0, 2] - [0, 2] - [2, 2] - [2, 2] - [4, 1] - [2, 2] - [1, 1] - [1, 0] - [4, 1] - [1, 0] - [3, 1] - [4, 3] - [0, 0] - [3, 2] - [1, 2] - [1, 2] - [2, 3] - [4, 2] - [2, 2] - [3, 0] - [0, 3] - [2, 2] - [1, 1] - [2, 3] - [4, 0] - [0, 3] - [4, 2] - [3, 2] - [3, 3] - [1, 2] - [4, 3] - [0, 0] - [1, 3] - [0, 0] - [4, 2] - [0, 2] - [0, 2] - [0, 3] - [4, 2] - [4, 2] - [4, 2] - [3, 2] - [4, 0] - [0, 0] - [0, 1] - [3, 0] - [0, 0] - [0, 0] - [0, 0] - [0, 0] - [4, 2] - [1, 2] - [0, 3] - [3, 3] - [4, 2] - [2, 2] - [2, 2] - [3, 3] - [1, 2] - [2, 1] - [0, 2] - [1, 2] - [4, 0] - [4, 3] - [3, 3] - [1, 2] - [0, 1] - [3, 2] - [0, 2] - [4, 1] - [1, 2] - [3, 0] - [4, 3] - [1, 2] - [2, 2] - [2, 3] - [0, 0] - [2, 3] - [4, 1] - [4, 2] - [4, 2] - [1, 2] - [3, 3] - [1, 3] - [0, 2] - [3, 2] - [3, 0] - [2, 3] - [4, 2] - [2, 3] - [4, 2] - [4, 0] - [2, 0] - [1, 0] - [1, 2] - [1, 0] - [3, 2] - [0, 0] - [3, 1] - [4, 3] - [0, 3] - [0, 2] - [2, 0] - [4, 2] - [3, 2] - [1, 0] - [1, 0] - [4, 0] - [1, 2] - [0, 2] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRandomConstIteratorWithIndex diff --git a/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.md b/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.md new file mode 100644 index 000000000..32ea5f32f --- /dev/null +++ b/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.md @@ -0,0 +1,42 @@ +--- +name: RandomSelectPixelFromRegionWithoutReplacee +--- + +# Random Select Pixel From Region Without Replacing + +```{index} single: ImageRandomNonRepeatingConstIteratorWithIndex pair: random; select +``` + +## Synopsis + +Randomly select pixels from a region of an image without replacement. + +## Results + +Output: + +``` +[1, 2] +[1, 1] +[0, 2] +[2, 2] +[2, 1] +[2, 0] +[0, 0] +[0, 1] +[1, 0] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRandomNonRepeatingConstIteratorWithIndex +``` diff --git a/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.rst b/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.rst deleted file mode 100644 index 54089be97..000000000 --- a/src/Core/Common/RandomSelectPixelFromRegionWithoutReplacee/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: RandomSelectPixelFromRegionWithoutReplacee - -Random Select Pixel From Region Without Replacing -================================================= - -.. index:: - single: ImageRandomNonRepeatingConstIteratorWithIndex - pair: random; select - -Synopsis --------- - -Randomly select pixels from a region of an image without replacement. - - -Results -------- -Output:: - - [1, 2] - [1, 1] - [0, 2] - [2, 2] - [2, 1] - [2, 0] - [0, 0] - [0, 1] - [1, 0] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRandomNonRepeatingConstIteratorWithIndex diff --git a/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.md b/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.md new file mode 100644 index 000000000..43981a960 --- /dev/null +++ b/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.md @@ -0,0 +1,65 @@ +--- +name: ReRunPipelineWithChangingLargestPossibleRegion +--- + +# Re-Run Pipeline With Changing Largest Possible Region + +```{index} single: ProcessObject single: ImageSeriesReader single: pipeline +``` + +## Synopsis + +Re-run a pipeline where the LargestPossibleRegion in the pipeline is expected to change on consecutive runs. The pipeline does not detect this condition, and it will throw an exception, + +``` +Requested region is (at least partially) outside the largest possible region. +``` + +In this case, an `UpdateLargestPossibleRegion()` call is required instead of `Update()`. + +## Results + +Output: + +``` +Initial LargestPossibleRegion: ImageRegion (0x7fff11257330) +Dimension: 3 +Index: [0, 0, 0] +Size: [256, 256, 3] + + +Trying to call Update() after shrinking the LargestPossibleRegion... + +Error: +itk::InvalidRequestedRegionError (0x28cd880) +Location: "unknown" +File: /home/matt/bin/ITKSphinxExamples-Clang-RelWithDebInfo/ITK/Modules/Core/Common/src/itkDataObject.cxx +Line: 411 +Description: Requested region is (at least partially) outside the largest possible region. + + +Trying to call UpdateLargestPossibleRegion() after shrinking the LargestPossibleRegion... + +Shrunk LargestPossibleRegion: ImageRegion (0x7fff11257330) + Dimension: 3 + Index: [0, 0, 0] + Size: [256, 256, 2] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ProcessObject +``` + +```{eval-rst} +.. breathelink:: itk::ImageSeriesReader +``` diff --git a/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.rst b/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.rst deleted file mode 100644 index ff93644b2..000000000 --- a/src/Core/Common/ReRunPipelineWithChangingLargestPossibleRegion/Documentation.rst +++ /dev/null @@ -1,66 +0,0 @@ -:name: ReRunPipelineWithChangingLargestPossibleRegion - -Re-Run Pipeline With Changing Largest Possible Region -===================================================== - -.. index:: - single: ProcessObject - single: ImageSeriesReader - single: pipeline - -Synopsis --------- - -Re-run a pipeline where the LargestPossibleRegion in the pipeline is expected to change on consecutive runs. The pipeline does not detect this condition, and it will throw an exception, - -:: - - Requested region is (at least partially) outside the largest possible region. - -In this case, an `UpdateLargestPossibleRegion()` call is required instead of `Update()`. - -Results -------- - -Output:: - - Initial LargestPossibleRegion: ImageRegion (0x7fff11257330) - Dimension: 3 - Index: [0, 0, 0] - Size: [256, 256, 3] - - - Trying to call Update() after shrinking the LargestPossibleRegion... - - Error: - itk::InvalidRequestedRegionError (0x28cd880) - Location: "unknown" - File: /home/matt/bin/ITKSphinxExamples-Clang-RelWithDebInfo/ITK/Modules/Core/Common/src/itkDataObject.cxx - Line: 411 - Description: Requested region is (at least partially) outside the largest possible region. - - - Trying to call UpdateLargestPossibleRegion() after shrinking the LargestPossibleRegion... - - Shrunk LargestPossibleRegion: ImageRegion (0x7fff11257330) - Dimension: 3 - Index: [0, 0, 0] - Size: [256, 256, 2] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ProcessObject - -.. breathelink:: itk::ImageSeriesReader diff --git a/src/Core/Common/ReadAPointSet/Documentation.md b/src/Core/Common/ReadAPointSet/Documentation.md new file mode 100644 index 000000000..d5fa58215 --- /dev/null +++ b/src/Core/Common/ReadAPointSet/Documentation.md @@ -0,0 +1,30 @@ +--- +name: ReadAPointSet +--- + +# Read a PointSet + +```{index} single: PointSet single: Mesh single: VTKPolyDataReader pair: Mesh; GetPoint +``` + +## Synopsis + +Read a PointSet + +## Results + +Print all points + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PointSet +``` diff --git a/src/Core/Common/ReadAPointSet/Documentation.rst b/src/Core/Common/ReadAPointSet/Documentation.rst deleted file mode 100644 index 003cb8966..000000000 --- a/src/Core/Common/ReadAPointSet/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ReadAPointSet - -Read a PointSet -=============== - -.. index:: single: PointSet - single: Mesh - single: VTKPolyDataReader - pair: Mesh; GetPoint - - -Synopsis --------- - -Read a PointSet - - -Results -------- - -Print all points - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PointSet diff --git a/src/Core/Common/ReadWriteVectorImage/Documentation.md b/src/Core/Common/ReadWriteVectorImage/Documentation.md new file mode 100644 index 000000000..f9afe1c6b --- /dev/null +++ b/src/Core/Common/ReadWriteVectorImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ReadWriteVectorImage +--- + +# Read Write Vector Image + +```{index} single: Image single: read single: write +``` + +## Synopsis + +This example illustrates how to read and write an image of pixel type Vector. + +## Results + +:::{figure} image.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} image.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/ReadWriteVectorImage/Documentation.rst b/src/Core/Common/ReadWriteVectorImage/Documentation.rst deleted file mode 100644 index c7663c6f5..000000000 --- a/src/Core/Common/ReadWriteVectorImage/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: ReadWriteVectorImage - -Read Write Vector Image -======================= - -.. index:: - single: Image - single: read - single: write - -Synopsis --------- - -This example illustrates how to read and write an image of pixel type Vector. - - -Results -------- - -.. figure:: image.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: image.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/ReturnObjectFromFunction/Documentation.md b/src/Core/Common/ReturnObjectFromFunction/Documentation.md new file mode 100644 index 000000000..a121b0606 --- /dev/null +++ b/src/Core/Common/ReturnObjectFromFunction/Documentation.md @@ -0,0 +1,37 @@ +--- +name: ReturnObjectFromFunction +--- + +# Return Object From Function + +```{index} single: Image pair: object; function +``` + +## Synopsis + +Return an object from a function. + +## Results + +Output: + +``` +ImageRegion (0x7ff7f950ba70) +Dimension: 2 +Index: [0, 0] +Size: [10, 10] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/ReturnObjectFromFunction/Documentation.rst b/src/Core/Common/ReturnObjectFromFunction/Documentation.rst deleted file mode 100644 index 2348ebc61..000000000 --- a/src/Core/Common/ReturnObjectFromFunction/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ReturnObjectFromFunction - -Return Object From Function -=========================== - -.. index:: - single: Image - pair: object; function - -Synopsis --------- - -Return an object from a function. - - -Results -------- -Output:: - - ImageRegion (0x7ff7f950ba70) - Dimension: 2 - Index: [0, 0] - Size: [10, 10] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/SetDefaultNumberOfThreads/Documentation.md b/src/Core/Common/SetDefaultNumberOfThreads/Documentation.md new file mode 100644 index 000000000..99c1fc3a4 --- /dev/null +++ b/src/Core/Common/SetDefaultNumberOfThreads/Documentation.md @@ -0,0 +1,43 @@ +--- +name: SetDefaultNumberOfThreads +--- + +# Set the Default Number of Threads + +```{index} single: MultiThreaderBase +``` + +## Synopsis + +Set the default number of threads for multi-threading. + +The default number of threads can also be set via the environment variable, +`ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS`. + +## Results + +```none +Filter's default number of threads: 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1,18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MultiThreaderBase +``` diff --git a/src/Core/Common/SetDefaultNumberOfThreads/Documentation.rst b/src/Core/Common/SetDefaultNumberOfThreads/Documentation.rst deleted file mode 100644 index 1ca7074f3..000000000 --- a/src/Core/Common/SetDefaultNumberOfThreads/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: SetDefaultNumberOfThreads - -Set the Default Number of Threads -================================= - -.. index:: - single: MultiThreaderBase - -Synopsis --------- - -Set the default number of threads for multi-threading. - -The default number of threads can also be set via the environment variable, -`ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS`. - - -Results -------- - -.. code-block:: none - - Filter's default number of threads: 3 - - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1,18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MultiThreaderBase diff --git a/src/Core/Common/SetPixelValueInOneImage/Documentation.md b/src/Core/Common/SetPixelValueInOneImage/Documentation.md new file mode 100644 index 000000000..65d46e6a8 --- /dev/null +++ b/src/Core/Common/SetPixelValueInOneImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: SetPixelValueInOneImage +--- + +# Set Pixel Value in One Image + +```{index} single: Image pair: Image; SetPixel +``` + +## Synopsis + +This example demonstrates how to set the value of individual pixels in an image. + +## Results + +:::{figure} OutputBaseline.png +:align: center +:alt: Output image + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 17- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/SetPixelValueInOneImage/Documentation.rst b/src/Core/Common/SetPixelValueInOneImage/Documentation.rst deleted file mode 100644 index 474118cbd..000000000 --- a/src/Core/Common/SetPixelValueInOneImage/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: SetPixelValueInOneImage - -Set Pixel Value in One Image -============================ - -.. index:: - single: Image - pair: Image; SetPixel - -Synopsis --------- - - -This example demonstrates how to set the value of individual pixels in an image. - - -Results -------- - -.. figure:: OutputBaseline.png - :align: center - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 17- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/SortITKIndex/Documentation.md b/src/Core/Common/SortITKIndex/Documentation.md new file mode 100644 index 000000000..d0ae68c12 --- /dev/null +++ b/src/Core/Common/SortITKIndex/Documentation.md @@ -0,0 +1,28 @@ +--- +name: SortITKIndex +--- + +# Sort ITK Index + +```{index} single: Image single: index +``` + +## Synopsis + +Sort itk::Index. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/SortITKIndex/Documentation.rst b/src/Core/Common/SortITKIndex/Documentation.rst deleted file mode 100644 index 4ab9c36fa..000000000 --- a/src/Core/Common/SortITKIndex/Documentation.rst +++ /dev/null @@ -1,31 +0,0 @@ -:name: SortITKIndex - -Sort ITK Index -============== - -.. index:: - single: Image - single: index - -Synopsis --------- - -Sort itk::Index. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/StoreNonPixelDataInImage/Documentation.md b/src/Core/Common/StoreNonPixelDataInImage/Documentation.md new file mode 100644 index 000000000..f2c725347 --- /dev/null +++ b/src/Core/Common/StoreNonPixelDataInImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: StoreNonPixelDataInImage +--- + +# Store Non-Pixel Data In Image + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: MetaDataDictionary +``` + +## Synopsis + +Store non-pixel associated data in an image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MetaDataDictionary +``` diff --git a/src/Core/Common/StoreNonPixelDataInImage/Documentation.rst b/src/Core/Common/StoreNonPixelDataInImage/Documentation.rst deleted file mode 100644 index 4f295607b..000000000 --- a/src/Core/Common/StoreNonPixelDataInImage/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: StoreNonPixelDataInImage - -Store Non-Pixel Data In Image -============================= -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: MetaDataDictionary - -Synopsis --------- - -Store non-pixel associated data in an image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MetaDataDictionary diff --git a/src/Core/Common/StreamAPipeline/Documentation.md b/src/Core/Common/StreamAPipeline/Documentation.md new file mode 100644 index 000000000..a5dbb4727 --- /dev/null +++ b/src/Core/Common/StreamAPipeline/Documentation.md @@ -0,0 +1,66 @@ +--- +name: StreamAPipeline +--- + +# Stream a Pipeline + +```{index} single: StreamingImageFilter single: stream single: PipelineMonitorImageFilter +``` + +## Synopsis + +Stream a pipeline. The PipelineMonitorImageFilter shows how the image is +processed in three sub-regions. Note that the StreamingImageFilter comes at the +end of the pipeline and that no calls to `Update()` occur on any intermediate +filters. + +## Results + +```none +The output LargestPossibleRegion is: ImageRegion (0x8dc420) + Dimension: 2 + Index: [0, 0] + Size: [3, 3] + + +Updated RequestedRegions's: + ImageRegion (0x8dce80) + Dimension: 2 + Index: [0, 0] + Size: [3, 1] + + ImageRegion (0x8dcea8) + Dimension: 2 + Index: [0, 1] + Size: [3, 1] + + ImageRegion (0x8dced0) + Dimension: 2 + Index: [0, 2] + Size: [3, 1] +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::StreamingImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::PipelineMonitorImageFilter +``` diff --git a/src/Core/Common/StreamAPipeline/Documentation.rst b/src/Core/Common/StreamAPipeline/Documentation.rst deleted file mode 100644 index bf4e9d292..000000000 --- a/src/Core/Common/StreamAPipeline/Documentation.rst +++ /dev/null @@ -1,70 +0,0 @@ -:name: StreamAPipeline - -Stream a Pipeline -================= - -.. index:: - single: StreamingImageFilter - single: stream - single: PipelineMonitorImageFilter - -Synopsis --------- - -Stream a pipeline. The PipelineMonitorImageFilter shows how the image is -processed in three sub-regions. Note that the StreamingImageFilter comes at the -end of the pipeline and that no calls to `Update()` occur on any intermediate -filters. - - -Results -------- - -.. code-block:: none - - The output LargestPossibleRegion is: ImageRegion (0x8dc420) - Dimension: 2 - Index: [0, 0] - Size: [3, 3] - - - Updated RequestedRegions's: - ImageRegion (0x8dce80) - Dimension: 2 - Index: [0, 0] - Size: [3, 1] - - ImageRegion (0x8dcea8) - Dimension: 2 - Index: [0, 1] - Size: [3, 1] - - ImageRegion (0x8dced0) - Dimension: 2 - Index: [0, 2] - Size: [3, 1] - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::StreamingImageFilter - -.. breathelink:: itk::PipelineMonitorImageFilter diff --git a/src/Core/Common/ThrowException/Documentation.md b/src/Core/Common/ThrowException/Documentation.md new file mode 100644 index 000000000..a40b6f627 --- /dev/null +++ b/src/Core/Common/ThrowException/Documentation.md @@ -0,0 +1,32 @@ +--- +name: ThrowException +--- + +# Throw Exception + +```{index} single: Image +``` + +## Synopsis + +Throw an exception. + +## Results + +:::{note} +No output is printed, this example simply displays functionality. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Image +``` diff --git a/src/Core/Common/ThrowException/Documentation.rst b/src/Core/Common/ThrowException/Documentation.rst deleted file mode 100644 index 15216f6e0..000000000 --- a/src/Core/Common/ThrowException/Documentation.rst +++ /dev/null @@ -1,32 +0,0 @@ -:name: ThrowException - -Throw Exception -=============== - -.. index:: - single: Image - -Synopsis --------- - -Throw an exception. - - -Results -------- -.. note:: - No output is printed, this example simply displays functionality. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Image diff --git a/src/Core/Common/TraceMemoryBetweenPoints/Documentation.md b/src/Core/Common/TraceMemoryBetweenPoints/Documentation.md new file mode 100644 index 000000000..b73e1166c --- /dev/null +++ b/src/Core/Common/TraceMemoryBetweenPoints/Documentation.md @@ -0,0 +1,47 @@ +--- +name: TraceMemoryBetweenPoints +--- + +# Trace Memory Between Points + +```{index} single: MemoryProbe +``` + +## Synopsis + +Trace the memory charge between the execution of two pieces of code. Note that +the memory must be used for it to be counted. + +## Results + +Results: + +``` +We are measuring Memory in units of kB. + +** Start ** +Mean: 0 +Total: 0 + +** After allocation ** +Mean: 1056 +Total: 2112 + +** After deallocation ** +Mean: 60 +Total: 180 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MemoryProbe +``` diff --git a/src/Core/Common/TraceMemoryBetweenPoints/Documentation.rst b/src/Core/Common/TraceMemoryBetweenPoints/Documentation.rst deleted file mode 100644 index c2b1c44d7..000000000 --- a/src/Core/Common/TraceMemoryBetweenPoints/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: TraceMemoryBetweenPoints - -Trace Memory Between Points -=========================== - -.. index:: - single: MemoryProbe - -Synopsis --------- - -Trace the memory charge between the execution of two pieces of code. Note that -the memory must be used for it to be counted. - - -Results -------- - -Results:: - - We are measuring Memory in units of kB. - - ** Start ** - Mean: 0 - Total: 0 - - ** After allocation ** - Mean: 1056 - Total: 2112 - - ** After deallocation ** - Mean: 60 - Total: 180 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MemoryProbe diff --git a/src/Core/Common/TryCatchException/Documentation.md b/src/Core/Common/TryCatchException/Documentation.md new file mode 100644 index 000000000..380d1d39c --- /dev/null +++ b/src/Core/Common/TryCatchException/Documentation.md @@ -0,0 +1,38 @@ +--- +name: TryCatchException +--- + +# Try Catch Exception + +```{index} single: ExceptionObject +``` + +## Synopsis + +Try and catch an `itk::ExceptionObject`. The exception is printed to console +output. This can provide more information when a program crashes, including +where the exception occurred and its description. Exceptions in ITK are +usually only thrown during calls to `->Update()`, so only the `->Update()` +call is added to the `try` block. + +## Results + +```none +ExceptionObject caught ! + +itk::ImageFileReaderException (0x20cece0) +Location: "void itk::ImageFileReader::GenerateOutputInformation() [with TOutputImage = itk::Image, ConvertPixelTraits = itk::DefaultConvertPixelTraits]" +File: /path/to/ITK/Modules/IO/ImageBase/include/itkImageFileReader.hxx +Line: 143 +Description: Could not create IO object for file nofile.png +The file doesn't exist. +Filename = nofile.png +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Core/Common/TryCatchException/Documentation.rst b/src/Core/Common/TryCatchException/Documentation.rst deleted file mode 100644 index 0f221bc8e..000000000 --- a/src/Core/Common/TryCatchException/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: TryCatchException - -Try Catch Exception -=================== - -.. index:: - single: ExceptionObject - -Synopsis --------- - -Try and catch an `itk::ExceptionObject`. The exception is printed to console -output. This can provide more information when a program crashes, including -where the exception occurred and its description. Exceptions in ITK are -usually only thrown during calls to `->Update()`, so only the `->Update()` -call is added to the `try` block. - - -Results -------- - -.. code-block:: none - - ExceptionObject caught ! - - itk::ImageFileReaderException (0x20cece0) - Location: "void itk::ImageFileReader::GenerateOutputInformation() [with TOutputImage = itk::Image, ConvertPixelTraits = itk::DefaultConvertPixelTraits]" - File: /path/to/ITK/Modules/IO/ImageBase/include/itkImageFileReader.hxx - Line: 143 - Description: Could not create IO object for file nofile.png - The file doesn't exist. - Filename = nofile.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Core/Common/UseParallelizeImageRegion/Documentation.md b/src/Core/Common/UseParallelizeImageRegion/Documentation.md new file mode 100644 index 000000000..0bc24cb60 --- /dev/null +++ b/src/Core/Common/UseParallelizeImageRegion/Documentation.md @@ -0,0 +1,39 @@ +--- +name: UseParallelizeImageRegion +--- + +# Use ParallelizeImageRegion + +```{index} single: MultiThreaderBase +``` + +## Synopsis + +This example demonstrates how to use MultiThreaderBase::ParallelizeImageRegion +to apply a non-trivial operation for all pixels in an image, in parallel. To +perform a multi-threaded operation like this prior ITK 5.0 required the +creation of a class. + +## Results + +:::{figure} CellsFluorescence1.png +:alt: Segmentation and custom colorization. +:scale: 100% + +Segmentation and custom colorization of an image using +MultiThreaderBase::ParallelizeImageRegion. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MultiThreaderBase +``` diff --git a/src/Core/Common/UseParallelizeImageRegion/Documentation.rst b/src/Core/Common/UseParallelizeImageRegion/Documentation.rst deleted file mode 100644 index 54c4c4072..000000000 --- a/src/Core/Common/UseParallelizeImageRegion/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: UseParallelizeImageRegion - -Use ParallelizeImageRegion -========================== - -.. index:: - single: MultiThreaderBase - -Synopsis --------- - -This example demonstrates how to use MultiThreaderBase::ParallelizeImageRegion -to apply a non-trivial operation for all pixels in an image, in parallel. To -perform a multi-threaded operation like this prior ITK 5.0 required the -creation of a class. - - -Results -------- - - -.. figure:: CellsFluorescence1.png - :scale: 100% - :alt: Segmentation and custom colorization. - - Segmentation and custom colorization of an image using - MultiThreaderBase::ParallelizeImageRegion. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MultiThreaderBase diff --git a/src/Core/Common/VariableLengthVector/Documentation.md b/src/Core/Common/VariableLengthVector/Documentation.md new file mode 100644 index 000000000..aebd42f99 --- /dev/null +++ b/src/Core/Common/VariableLengthVector/Documentation.md @@ -0,0 +1,39 @@ +--- +name: VariableLengthVector +--- + +# Variable Length Vector + +```{index} single: VariableLengthVector single: vector +``` + +## Synopsis + +This computes a variable length vector. + +## Results + +Output: + +``` +[1, 2] +1 2 +VectorToVariableLengthVector() +variableLengthVector: [1, 2] +VariableLengthVectorToVector() +fixedLengthVector: [1, 2] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VariableLengthVector +``` diff --git a/src/Core/Common/VariableLengthVector/Documentation.rst b/src/Core/Common/VariableLengthVector/Documentation.rst deleted file mode 100644 index 9341f5d04..000000000 --- a/src/Core/Common/VariableLengthVector/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: VariableLengthVector - -Variable Length Vector -====================== - -.. index:: - single: VariableLengthVector - single: vector - -Synopsis --------- - -This computes a variable length vector. - - -Results -------- -Output:: - - [1, 2] - 1 2 - VectorToVariableLengthVector() - variableLengthVector: [1, 2] - VariableLengthVectorToVector() - fixedLengthVector: [1, 2] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VariableLengthVector diff --git a/src/Core/Common/VectorDotProduct/Documentation.md b/src/Core/Common/VectorDotProduct/Documentation.md new file mode 100644 index 000000000..7ec7f6a0b --- /dev/null +++ b/src/Core/Common/VectorDotProduct/Documentation.md @@ -0,0 +1,44 @@ +--- +name: VectorDotProduct +--- + +# Vector Dot Product + +```{index} single: Vector pair: Vector; operator * +``` + +## Synopsis + +Dot product of Vectors + +## Results + +Output: + +``` +u :[-1, 1, -1] +v :[1, 2, 3] +DotProduct( u, v ) = -2 +u - DotProduct( u, v ) * v = [1, 5, 5] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Vector +``` diff --git a/src/Core/Common/VectorDotProduct/Documentation.rst b/src/Core/Common/VectorDotProduct/Documentation.rst deleted file mode 100644 index 0fd3e62ab..000000000 --- a/src/Core/Common/VectorDotProduct/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: VectorDotProduct - -Vector Dot Product -================== - -.. index:: - single: Vector - pair: Vector; operator * - -Synopsis --------- - -Dot product of Vectors - - -Results -------- - -Output:: - - u :[-1, 1, -1] - v :[1, 2, 3] - DotProduct( u, v ) = -2 - u - DotProduct( u, v ) * v = [1, 5, 5] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Vector diff --git a/src/Core/Common/WatchAFilter/Documentation.md b/src/Core/Common/WatchAFilter/Documentation.md new file mode 100644 index 000000000..e85936d66 --- /dev/null +++ b/src/Core/Common/WatchAFilter/Documentation.md @@ -0,0 +1,28 @@ +--- +name: WatchAFilter +--- + +# Watch a Filter + +```{index} single: SimpleFilterWatcher +``` + +## Synopsis + +This example demonstrates how to watch what is going on inside of a filter. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SimpleFilterWatcher +``` diff --git a/src/Core/Common/WatchAFilter/Documentation.rst b/src/Core/Common/WatchAFilter/Documentation.rst deleted file mode 100644 index 5eba95dba..000000000 --- a/src/Core/Common/WatchAFilter/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: WatchAFilter - -Watch a Filter -============== - -.. index:: - single: SimpleFilterWatcher - -Synopsis --------- - - -This example demonstrates how to watch what is going on inside of a filter. - - -Results -------- - - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::SimpleFilterWatcher diff --git a/src/Core/Common/WriteAPointSet/Documentation.md b/src/Core/Common/WriteAPointSet/Documentation.md new file mode 100644 index 000000000..4b00a0e75 --- /dev/null +++ b/src/Core/Common/WriteAPointSet/Documentation.md @@ -0,0 +1,30 @@ +--- +name: WriteAPointSet +--- + +# Write a PointSet + +```{index} single: PointSet single: Mesh single: VTKPolyDataReader pair: Mesh; GetPoint +``` + +## Synopsis + +Write a PointSet + +## Results + +Stores all points + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PointSet +``` diff --git a/src/Core/Common/WriteAPointSet/Documentation.rst b/src/Core/Common/WriteAPointSet/Documentation.rst deleted file mode 100644 index 21aebafc1..000000000 --- a/src/Core/Common/WriteAPointSet/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: WriteAPointSet - -Write a PointSet -================ - -.. index:: single: PointSet - single: Mesh - single: VTKPolyDataReader - pair: Mesh; GetPoint - - -Synopsis --------- - -Write a PointSet - - -Results -------- - -Stores all points - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PointSet diff --git a/src/Core/Common/index.md b/src/Core/Common/index.md new file mode 100644 index 000000000..93fc1e9b4 --- /dev/null +++ b/src/Core/Common/index.md @@ -0,0 +1,119 @@ +# Common + +```{toctree} +:maxdepth: 1 + +AddNoiseToBinaryImage/Documentation.rst +AddOffsetToIndex/Documentation.rst +ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.rst +ApplyCustomOperationToEachPixelInImage/Documentation.rst +BoundingBoxOfAPointSet/Documentation.rst +BresenhamLine/Documentation.rst +BuildAHelloWorldProgram/Documentation.rst +CastVectorImageToAnotherType/Documentation.rst +CheckIfModuleIsPresent/Documentation.rst +ComputeTimeBetweenPoints/Documentation.rst +ConceptCheckingIsFloatingPoint/Documentation.rst +ConceptCheckingIsSameDimension/Documentation.rst +ConceptCheckingIsSameType/Documentation.rst +ConvertArrayToImage/Documentation.rst +CovariantVectorDotProduct/Documentation.rst +CovariantVectorNorm/Documentation.rst +CreateABackwardDifferenceOperator/Documentation.rst +CreateACovariantVector/Documentation.rst +CreateAFixedArray/Documentation.rst +CreateAIndex/Documentation.rst +CreateAPointSet/Documentation.rst +CreateASize/Documentation.rst +CreateAVector/Documentation.rst +CreateAnImage/Documentation.rst +CreateAnImageRegion/Documentation.rst +CreateAnImageOfVectors/Documentation.rst +CreateAnRGBImage/Documentation.rst +CreateAnotherInstanceOfAFilter/Documentation.rst +CreateAnotherInstanceOfAnImage/Documentation.rst +CreateDerivativeKernel/Documentation.rst +CreateForwardDifferenceKernel/Documentation.rst +CreateGaussianDerivativeKernel/Documentation.rst +CreateGaussianKernel/Documentation.rst +CreateLaplacianKernel/Documentation.rst +CreateSobelKernel/Documentation.rst +CreateVectorImage/Documentation.rst +CropImageBySpecifyingRegion/Documentation.rst +DeepCopyImage/Documentation.rst +DemonstrateAllOperators/Documentation.rst +DirectWarningToFile/Documentation.rst +DisplayImage/Documentation.rst +DistanceBetweenIndices/Documentation.rst +DistanceBetweenPoints/Documentation.rst +DoDataParallelThreading/Documentation.rst +DuplicateAnImage/Documentation.rst +EagerModuleLoadingPython/Documentation.rst +FilterAndParallelizeImageRegion/Documentation.rst +FilterImage/Documentation.rst +FilterImageUsingMultipleThreads/Documentation.rst +FilterImageWithoutCopying/Documentation.rst +FindMaxAndMinInImage/Documentation.rst +GenerateOffsetsShapedImageNeighborhood/Documentation.rst +GetImageSize/Documentation.rst +GetNameOfClass/Documentation.rst +GetOrSetMemberVariableOfITKClass/Documentation.rst +GetTypeBasicInformation/Documentation.rst +ImageBufferAndIndexRange/Documentation.rst +ImageRegionIntersection/Documentation.rst +ImageRegionOverlap/Documentation.rst +ImportPixelBufferIntoAnImage/Documentation.rst +InPlaceFilterOfImage/Documentation.rst +IsPixelInsideRegion/Documentation.rst +IterateImageStartingAtSeed/Documentation.rst +IterateLineThroughImage/Documentation.rst +IterateLineThroughImageWithoutWriteAccess/Documentation.rst +IterateOnAVectorContainer/Documentation.rst +IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.rst +IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.rst +IterateOverSpecificRegion/Documentation.rst +IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.rst +IterateRegionWithAccessToIndexWithWriteAccess/Documentation.rst +IterateRegionWithNeighborhood/Documentation.rst +IterateWithNeighborhoodWithoutAccess/Documentation.rst +IterateRegionWithWriteAccess/Documentation.rst +IterateRegionWithoutWriteAccess/Documentation.rst +MakeOutOfBoundsPixelsReturnConstValue/Documentation.rst +MakePartOfImageTransparent/Documentation.rst +Matrix/Documentation.rst +MatrixInverse/Documentation.rst +MersenneTwisterRandomIntegerGenerator/Documentation.rst +MersenneTwisterRandomNumberGenerator/Documentation.rst +MiniPipeline/Documentation.rst +MultipleInputsOfDifferentType/Documentation.rst +MultipleInputsOfSameType/Documentation.rst +MultipleOutputsOfDifferentType/Documentation.rst +MultipleOutputsOfSameType/Documentation.rst +MultiThreadOilPainting/Documentation.rst +NeighborhoodIteratorOnVectorImage/Documentation.rst +ObserveAnEvent/Documentation.rst +PassImageToFunction/Documentation.rst +PermuteSequenceOfIndices/Documentation.rst +PiConstant/Documentation.rst +PrintModuleLoadingPython/Documentation.rst +ProduceImageProgrammatically/Documentation.rst +RandomSelectOfPixelsFromRegion/Documentation.rst +RandomSelectPixelFromRegionWithoutReplacee/Documentation.rst +ReadAPointSet/Documentation.rst +ReadWriteVectorImage/Documentation.rst +ReRunPipelineWithChangingLargestPossibleRegion/Documentation.rst +ReturnObjectFromFunction/Documentation.rst +SetDefaultNumberOfThreads/Documentation.rst +SetPixelValueInOneImage/Documentation.rst +SortITKIndex/Documentation.rst +StoreNonPixelDataInImage/Documentation.rst +StreamAPipeline/Documentation.rst +ThrowException/Documentation.rst +TraceMemoryBetweenPoints/Documentation.rst +TryCatchException/Documentation.rst +UseParallelizeImageRegion/Documentation.rst +VariableLengthVector/Documentation.rst +VectorDotProduct/Documentation.rst +WatchAFilter/Documentation.rst +WriteAPointSet/Documentation.rst +``` diff --git a/src/Core/Common/index.rst b/src/Core/Common/index.rst deleted file mode 100644 index 55e0818c7..000000000 --- a/src/Core/Common/index.rst +++ /dev/null @@ -1,119 +0,0 @@ -Common -====== - -.. toctree:: - :maxdepth: 1 - - AddNoiseToBinaryImage/Documentation.rst - AddOffsetToIndex/Documentation.rst - ApplyAFilterOnlyToASpecifiedRegionOfAnImage/Documentation.rst - ApplyCustomOperationToEachPixelInImage/Documentation.rst - BoundingBoxOfAPointSet/Documentation.rst - BresenhamLine/Documentation.rst - BuildAHelloWorldProgram/Documentation.rst - CastVectorImageToAnotherType/Documentation.rst - CheckIfModuleIsPresent/Documentation.rst - ComputeTimeBetweenPoints/Documentation.rst - ConceptCheckingIsFloatingPoint/Documentation.rst - ConceptCheckingIsSameDimension/Documentation.rst - ConceptCheckingIsSameType/Documentation.rst - ConvertArrayToImage/Documentation.rst - CovariantVectorDotProduct/Documentation.rst - CovariantVectorNorm/Documentation.rst - CreateABackwardDifferenceOperator/Documentation.rst - CreateACovariantVector/Documentation.rst - CreateAFixedArray/Documentation.rst - CreateAIndex/Documentation.rst - CreateAPointSet/Documentation.rst - CreateASize/Documentation.rst - CreateAVector/Documentation.rst - CreateAnImage/Documentation.rst - CreateAnImageRegion/Documentation.rst - CreateAnImageOfVectors/Documentation.rst - CreateAnRGBImage/Documentation.rst - CreateAnotherInstanceOfAFilter/Documentation.rst - CreateAnotherInstanceOfAnImage/Documentation.rst - CreateDerivativeKernel/Documentation.rst - CreateForwardDifferenceKernel/Documentation.rst - CreateGaussianDerivativeKernel/Documentation.rst - CreateGaussianKernel/Documentation.rst - CreateLaplacianKernel/Documentation.rst - CreateSobelKernel/Documentation.rst - CreateVectorImage/Documentation.rst - CropImageBySpecifyingRegion/Documentation.rst - DeepCopyImage/Documentation.rst - DemonstrateAllOperators/Documentation.rst - DirectWarningToFile/Documentation.rst - DisplayImage/Documentation.rst - DistanceBetweenIndices/Documentation.rst - DistanceBetweenPoints/Documentation.rst - DoDataParallelThreading/Documentation.rst - DuplicateAnImage/Documentation.rst - EagerModuleLoadingPython/Documentation.rst - FilterAndParallelizeImageRegion/Documentation.rst - FilterImage/Documentation.rst - FilterImageUsingMultipleThreads/Documentation.rst - FilterImageWithoutCopying/Documentation.rst - FindMaxAndMinInImage/Documentation.rst - GenerateOffsetsShapedImageNeighborhood/Documentation.rst - GetImageSize/Documentation.rst - GetNameOfClass/Documentation.rst - GetOrSetMemberVariableOfITKClass/Documentation.rst - GetTypeBasicInformation/Documentation.rst - ImageBufferAndIndexRange/Documentation.rst - ImageRegionIntersection/Documentation.rst - ImageRegionOverlap/Documentation.rst - ImportPixelBufferIntoAnImage/Documentation.rst - InPlaceFilterOfImage/Documentation.rst - IsPixelInsideRegion/Documentation.rst - IterateImageStartingAtSeed/Documentation.rst - IterateLineThroughImage/Documentation.rst - IterateLineThroughImageWithoutWriteAccess/Documentation.rst - IterateOnAVectorContainer/Documentation.rst - IterateOverARegionWithAShapedNeighborhoodIterator/Documentation.rst - IterateOverARegionWithAShapedNeighborhoodIteratorManual/Documentation.rst - IterateOverSpecificRegion/Documentation.rst - IterateRegionWithAccessToIndexWithoutWriteAccess/Documentation.rst - IterateRegionWithAccessToIndexWithWriteAccess/Documentation.rst - IterateRegionWithNeighborhood/Documentation.rst - IterateWithNeighborhoodWithoutAccess/Documentation.rst - IterateRegionWithWriteAccess/Documentation.rst - IterateRegionWithoutWriteAccess/Documentation.rst - MakeOutOfBoundsPixelsReturnConstValue/Documentation.rst - MakePartOfImageTransparent/Documentation.rst - Matrix/Documentation.rst - MatrixInverse/Documentation.rst - MersenneTwisterRandomIntegerGenerator/Documentation.rst - MersenneTwisterRandomNumberGenerator/Documentation.rst - MiniPipeline/Documentation.rst - MultipleInputsOfDifferentType/Documentation.rst - MultipleInputsOfSameType/Documentation.rst - MultipleOutputsOfDifferentType/Documentation.rst - MultipleOutputsOfSameType/Documentation.rst - MultiThreadOilPainting/Documentation.rst - NeighborhoodIteratorOnVectorImage/Documentation.rst - ObserveAnEvent/Documentation.rst - PassImageToFunction/Documentation.rst - PermuteSequenceOfIndices/Documentation.rst - PiConstant/Documentation.rst - PrintModuleLoadingPython/Documentation.rst - ProduceImageProgrammatically/Documentation.rst - RandomSelectOfPixelsFromRegion/Documentation.rst - RandomSelectPixelFromRegionWithoutReplacee/Documentation.rst - ReadAPointSet/Documentation.rst - ReadWriteVectorImage/Documentation.rst - ReRunPipelineWithChangingLargestPossibleRegion/Documentation.rst - ReturnObjectFromFunction/Documentation.rst - SetDefaultNumberOfThreads/Documentation.rst - SetPixelValueInOneImage/Documentation.rst - SortITKIndex/Documentation.rst - StoreNonPixelDataInImage/Documentation.rst - StreamAPipeline/Documentation.rst - ThrowException/Documentation.rst - TraceMemoryBetweenPoints/Documentation.rst - TryCatchException/Documentation.rst - UseParallelizeImageRegion/Documentation.rst - VariableLengthVector/Documentation.rst - VectorDotProduct/Documentation.rst - WatchAFilter/Documentation.rst - WriteAPointSet/Documentation.rst diff --git a/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.md b/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.md new file mode 100644 index 000000000..2d1d15eb1 --- /dev/null +++ b/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.md @@ -0,0 +1,37 @@ +--- +name: AddConstantToPixelsWithoutDuplicatingImage +--- + +# Add Constant to Every Pixel Without Duplicating Memory + +```{index} single: AddPixelAccessor +``` + +## Synopsis + +Add a constant to every pixel without duplicating the image in memory (an accessor). + +## Results + +Output: + +``` +addPixelAccessor.SetValue(5) +image->GetPixel[0, 0]: 20 adaptor->GetPixel[0, 0]: 25 +addPixelAccessor.SetValue(100) +image->GetPixel[0, 0]: 20 adaptor->GetPixel[0, 0]: 120 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Accessor::AddPixelAccessor +``` diff --git a/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.rst b/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.rst deleted file mode 100644 index 0f0ad6ed5..000000000 --- a/src/Core/ImageAdaptors/AddConstantToPixelsWithoutDuplicatingImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: AddConstantToPixelsWithoutDuplicatingImage - -Add Constant to Every Pixel Without Duplicating Memory -====================================================== - -.. index:: - single: AddPixelAccessor - -Synopsis --------- - -Add a constant to every pixel without duplicating the image in memory (an accessor). - - -Results -------- -Output:: - - addPixelAccessor.SetValue(5) - image->GetPixel[0, 0]: 20 adaptor->GetPixel[0, 0]: 25 - addPixelAccessor.SetValue(100) - image->GetPixel[0, 0]: 20 adaptor->GetPixel[0, 0]: 120 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Accessor::AddPixelAccessor diff --git a/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.md b/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.md new file mode 100644 index 000000000..a311ef790 --- /dev/null +++ b/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ExtractChannelOfImageWithMultipleComponents +--- + +# Extract Channel of Image With Multiple Components + +```{index} single: NthElementImageAdaptor single: itkimage pair: extract; channel +``` + +## Synopsis + +Extract a component/channel of an itkImage with pixels with multiple components. + +## Results + +Output: + +``` +[1, 2, 3] +1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NthElementImageAdaptor +``` diff --git a/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.rst b/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.rst deleted file mode 100644 index 3cbe31646..000000000 --- a/src/Core/ImageAdaptors/ExtractChannelOfImageWithMultipleComponents/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: ExtractChannelOfImageWithMultipleComponents - -Extract Channel of Image With Multiple Components -================================================= - -.. index:: - single: NthElementImageAdaptor - single: itkimage - pair: extract; channel - -Synopsis --------- - -Extract a component/channel of an itkImage with pixels with multiple components. - - -Results -------- - -Output:: - - [1, 2, 3] - 1 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NthElementImageAdaptor diff --git a/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.md b/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.md new file mode 100644 index 000000000..75aadf32e --- /dev/null +++ b/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.md @@ -0,0 +1,35 @@ +--- +name: PresentImageAfterOperation +--- + +# Present Image After Operation + +```{index} single: ImageAdaptor single: operation +``` + +## Synopsis + +Present an image by first performing an operation. + +## Results + +Output: + +``` +[1, 2, 3] +1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageAdaptor +``` diff --git a/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.rst b/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.rst deleted file mode 100644 index 890b4b245..000000000 --- a/src/Core/ImageAdaptors/PresentImageAfterOperation/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: PresentImageAfterOperation - -Present Image After Operation -============================= - -.. index:: - single: ImageAdaptor - single: operation - -Synopsis --------- - -Present an image by first performing an operation. - - -Results -------- -Output:: - - [1, 2, 3] - 1 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageAdaptor diff --git a/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.md b/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.md new file mode 100644 index 000000000..b6bed6f8e --- /dev/null +++ b/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.md @@ -0,0 +1,28 @@ +--- +name: ProcessNthComponentOfVectorImage +--- + +# Process Nth Component of Vector Image + +```{index} single: NthElementImageAdaptor pair: vector; image +``` + +## Synopsis + +Process the nth component/element/channel of a vector image. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NthElementImageAdaptor +``` diff --git a/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.rst b/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.rst deleted file mode 100644 index c7661dacf..000000000 --- a/src/Core/ImageAdaptors/ProcessNthComponentOfVectorImage/Documentation.rst +++ /dev/null @@ -1,31 +0,0 @@ -:name: ProcessNthComponentOfVectorImage - -Process Nth Component of Vector Image -===================================== - -.. index:: - single: NthElementImageAdaptor - pair: vector; image - -Synopsis --------- - -Process the nth component/element/channel of a vector image. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NthElementImageAdaptor diff --git a/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.md b/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.md new file mode 100644 index 000000000..af958d8bd --- /dev/null +++ b/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ViewComponentVectorImageAsScaleImage +--- + +# View Component Vector Image as Scalar Image + +```{index} single: VectorImageToImageAdaptor +``` + +## Synopsis + +View a component of a vector image as if it were a scalar image + +## Results + +Output: + +``` +1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorImageToImageAdaptor +``` diff --git a/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.rst b/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.rst deleted file mode 100644 index f62a8db12..000000000 --- a/src/Core/ImageAdaptors/ViewComponentVectorImageAsScaleImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: ViewComponentVectorImageAsScaleImage - -View Component Vector Image as Scalar Image -=========================================== - -.. index:: - single: VectorImageToImageAdaptor - - -Synopsis --------- - -View a component of a vector image as if it were a scalar image - - -Results -------- -Output:: - - 1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorImageToImageAdaptor diff --git a/src/Core/ImageAdaptors/index.md b/src/Core/ImageAdaptors/index.md new file mode 100644 index 000000000..459ff6fc7 --- /dev/null +++ b/src/Core/ImageAdaptors/index.md @@ -0,0 +1,11 @@ +# ImageAdaptors + +```{toctree} +:maxdepth: 1 + +AddConstantToPixelsWithoutDuplicatingImage/Documentation.rst +ExtractChannelOfImageWithMultipleComponents/Documentation.rst +PresentImageAfterOperation/Documentation.rst +ProcessNthComponentOfVectorImage/Documentation.rst +ViewComponentVectorImageAsScaleImage/Documentation.rst +``` diff --git a/src/Core/ImageAdaptors/index.rst b/src/Core/ImageAdaptors/index.rst deleted file mode 100644 index c18c644d4..000000000 --- a/src/Core/ImageAdaptors/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -ImageAdaptors -============= - -.. toctree:: - :maxdepth: 1 - - AddConstantToPixelsWithoutDuplicatingImage/Documentation.rst - ExtractChannelOfImageWithMultipleComponents/Documentation.rst - PresentImageAfterOperation/Documentation.rst - ProcessNthComponentOfVectorImage/Documentation.rst - ViewComponentVectorImageAsScaleImage/Documentation.rst diff --git a/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.md b/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.md new file mode 100644 index 000000000..a768ab2c3 --- /dev/null +++ b/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.md @@ -0,0 +1,41 @@ +--- +name: ComputeMedianOfImageAtPixel +--- + +# Compute Median of Image at Pixel + +```{index} single: MedianImageFunction pair: image; median single: function +``` + +## Synopsis + +Computes the median of an image at a pixil(in a regular neighborhood). + +## Results + +:::{figure} ComputeMedianOfImageAtPixel.png +:alt: input.png +:scale: 70% + +input.png +::: + +Output: + +``` +Median at [10, 10] is 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MedianImageFunction +``` diff --git a/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.rst b/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.rst deleted file mode 100644 index 016eee385..000000000 --- a/src/Core/ImageFunction/ComputeMedianOfImageAtPixel/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: ComputeMedianOfImageAtPixel - -Compute Median of Image at Pixel -================================ - -.. index:: - single: MedianImageFunction - pair: image; median - single: function - -Synopsis --------- - -Computes the median of an image at a pixil(in a regular neighborhood). - - -Results -------- -.. figure:: ComputeMedianOfImageAtPixel.png - :scale: 70% - :alt: input.png - - input.png - -Output:: - - Median at [10, 10] is 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MedianImageFunction diff --git a/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.md b/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.md new file mode 100644 index 000000000..88df313ac --- /dev/null +++ b/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: LinearlyInterpolatePositionInImage +--- + +# Linearly Interpolate Position in Image + +```{index} single: LinearInterpolateImageFunction pair: interpolate; position +``` + +## Synopsis + +Linearly interpolate a position in an image. + +## Results + +Output: + +``` +Value at 1.3: 13 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LinearInterpolateImageFunction +``` diff --git a/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.rst b/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.rst deleted file mode 100644 index 063a18fa5..000000000 --- a/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: LinearlyInterpolatePositionInImage - -Linearly Interpolate Position in Image -====================================== - -.. index:: - single: LinearInterpolateImageFunction - pair: interpolate; position - -Synopsis --------- - -Linearly interpolate a position in an image. - - -Results -------- -Output:: - - Value at 1.3: 13 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LinearInterpolateImageFunction diff --git a/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.md b/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.md new file mode 100644 index 000000000..29fe129d5 --- /dev/null +++ b/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.md @@ -0,0 +1,36 @@ +--- +name: MultiplyKernelWithAnImageAtLocation +--- + +# Multiply Kernel With an Image at Location + +```{index} single: NeighborhoodOperatorImageFunction pair: kernel; image single: location +``` + +## Synopsis + +This will multiply a kernel with an image at a particular location. + +## Results + +Output: + +``` +Sum on border: 4 +Sum in center: 9 +Sum outside: 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NeighborhoodOperatorImageFunction +``` diff --git a/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.rst b/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.rst deleted file mode 100644 index debc3ba37..000000000 --- a/src/Core/ImageFunction/MultiplyKernelWithAnImageAtLocation/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: MultiplyKernelWithAnImageAtLocation - -Multiply Kernel With an Image at Location -========================================= - -.. index:: - single: NeighborhoodOperatorImageFunction - pair: kernel; image - single: location - -Synopsis --------- - -This will multiply a kernel with an image at a particular location. - - -Results -------- -Output:: - - Sum on border: 4 - Sum in center: 9 - Sum outside: 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NeighborhoodOperatorImageFunction diff --git a/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.md b/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.md new file mode 100644 index 000000000..6e8db0f10 --- /dev/null +++ b/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.md @@ -0,0 +1,58 @@ +--- +name: ResampleSegmentedImage +--- + +# Resample Segmented Image + +```{index} single: LabelImageGaussianInterpolateImageFunction pair: segmented; image +``` + +## Synopsis + +Resample (stretch or compress) a label image resulting form segmentation. + +For more on why label image interpolation is necessary and how it works, see the [associated Insight Journal article](https://www.insight-journal.org/browse/publication/705). + +## Results + +:::{figure} 2th_cthead1.png +:alt: Input label image. +:scale: 50% + +Input label image +::: + +:::{figure} OutputBaseline.png +:alt: QuickView output. +:scale: 50% + +Resample with label image gaussian interpolation. +::: + +:::{figure} OutputNearestBaseline.png +:alt: QuickView output. +:scale: 50% + +Resample with nearest neighbor interpolation. +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelImageGaussianInterpolateImageFunction +``` diff --git a/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.rst b/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.rst deleted file mode 100644 index 5d785c006..000000000 --- a/src/Core/ImageFunction/ResampleSegmentedImage/Documentation.rst +++ /dev/null @@ -1,58 +0,0 @@ -:name: ResampleSegmentedImage - -Resample Segmented Image -======================== - -.. index:: - single: LabelImageGaussianInterpolateImageFunction - pair: segmented; image - -Synopsis --------- - -Resample (stretch or compress) a label image resulting form segmentation. - -For more on why label image interpolation is necessary and how it works, see the `associated Insight Journal article `_. - - -Results -------- - -.. figure:: 2th_cthead1.png - :scale: 50% - :alt: Input label image. - - Input label image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: QuickView output. - - Resample with label image gaussian interpolation. - -.. figure:: OutputNearestBaseline.png - :scale: 50% - :alt: QuickView output. - - Resample with nearest neighbor interpolation. - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelImageGaussianInterpolateImageFunction diff --git a/src/Core/ImageFunction/index.md b/src/Core/ImageFunction/index.md new file mode 100644 index 000000000..3a1b64b4f --- /dev/null +++ b/src/Core/ImageFunction/index.md @@ -0,0 +1,10 @@ +# ImageFunction + +```{toctree} +:maxdepth: 1 + +ComputeMedianOfImageAtPixel/Documentation.rst +LinearlyInterpolatePositionInImage/Documentation.rst +MultiplyKernelWithAnImageAtLocation/Documentation.rst +ResampleSegmentedImage/Documentation.rst +``` diff --git a/src/Core/ImageFunction/index.rst b/src/Core/ImageFunction/index.rst deleted file mode 100644 index 4b139d312..000000000 --- a/src/Core/ImageFunction/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -ImageFunction -============= - -.. toctree:: - :maxdepth: 1 - - ComputeMedianOfImageAtPixel/Documentation.rst - LinearlyInterpolatePositionInImage/Documentation.rst - MultiplyKernelWithAnImageAtLocation/Documentation.rst - ResampleSegmentedImage/Documentation.rst diff --git a/src/Core/Mesh/AccessDataInCells/Documentation.md b/src/Core/Mesh/AccessDataInCells/Documentation.md new file mode 100644 index 000000000..5110a27ff --- /dev/null +++ b/src/Core/Mesh/AccessDataInCells/Documentation.md @@ -0,0 +1,52 @@ +# Access data in cells + +```{index} single: Mesh +``` + +## Synopsis + +Just as custom data can be associated with points in the mesh, +it is also possible to associate custom data with cells. The type of the +data associated with the cells can be different from the data type +associated with points. By default, however, these two types are the same. +The following example illustrates how to access data associated with cells. +The approach is analogous to the one used to access point data. + +## Results + +``` +Points = 10 +Cells = 9 + +Cell 0 = 0 +Cell 1 = 1 +Cell 2 = 4 +Cell 3 = 9 +Cell 4 = 16 +Cell 5 = 25 +Cell 6 = 36 +Cell 7 = 49 +Cell 8 = 64 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Mesh +``` diff --git a/src/Core/Mesh/AccessDataInCells/Documentation.rst b/src/Core/Mesh/AccessDataInCells/Documentation.rst deleted file mode 100644 index 9c5066091..000000000 --- a/src/Core/Mesh/AccessDataInCells/Documentation.rst +++ /dev/null @@ -1,58 +0,0 @@ -Access data in cells -==================== - -.. index:: - single: Mesh - -Synopsis --------- - -Just as custom data can be associated with points in the mesh, -it is also possible to associate custom data with cells. The type of the -data associated with the cells can be different from the data type -associated with points. By default, however, these two types are the same. -The following example illustrates how to access data associated with cells. -The approach is analogous to the one used to access point data. - - -Results -------- - -:: - - Points = 10 - Cells = 9 - - Cell 0 = 0 - Cell 1 = 1 - Cell 2 = 4 - Cell 3 = 9 - Cell 4 = 16 - Cell 5 = 25 - Cell 6 = 36 - Cell 7 = 49 - Cell 8 = 64 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Mesh diff --git a/src/Core/Mesh/AddPointsAndEdges/Documentation.md b/src/Core/Mesh/AddPointsAndEdges/Documentation.md new file mode 100644 index 000000000..9dba5cf90 --- /dev/null +++ b/src/Core/Mesh/AddPointsAndEdges/Documentation.md @@ -0,0 +1,40 @@ +--- +name: AddPointsAndEdges +--- + +# Add Points and Edges + +```{index} single: Mesh pair: points; edges +``` + +## Synopsis + +How to add points and edges to a mesh. + +## Results + +Output: + +``` +Points = 4 +[-1, -1, 0] +[1, -1, 0] +[1, 1, 0] +[1, 1, 1] +line first point id: 2 +line second point id: 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Mesh +``` diff --git a/src/Core/Mesh/AddPointsAndEdges/Documentation.rst b/src/Core/Mesh/AddPointsAndEdges/Documentation.rst deleted file mode 100644 index 943640d06..000000000 --- a/src/Core/Mesh/AddPointsAndEdges/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: AddPointsAndEdges - -Add Points and Edges -==================== - -.. index:: - single: Mesh - pair: points; edges - -Synopsis --------- - -How to add points and edges to a mesh. - - -Results -------- -Output:: - - Points = 4 - [-1, -1, 0] - [1, -1, 0] - [1, 1, 0] - [1, 1, 1] - line first point id: 2 - line second point id: 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Mesh diff --git a/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.md b/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.md new file mode 100644 index 000000000..8ae3f7f07 --- /dev/null +++ b/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.md @@ -0,0 +1,37 @@ +--- +name: CalculateAreaAndVolumeOfSimplexMesh +--- + +# Calculate Area and Volume of Simplex Mesh + +```{index} single: SimplexMeshVolumeCalculator pair: area; volume +``` + +## Synopsis + +Calculate the area and volume of an itk::SimplexMesh. + +## Results + +Output: + +``` +Ideal Volume: 523.599 +Mesh Volume: 520.812 +Ideal Surface Area: 314.159 +Mesh Surface Area: 313.1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SimplexMeshVolumeCalculator +``` diff --git a/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.rst b/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.rst deleted file mode 100644 index 7f3bdc6a0..000000000 --- a/src/Core/Mesh/CalculateAreaAndVolumeOfSimplexMesh/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: CalculateAreaAndVolumeOfSimplexMesh - -Calculate Area and Volume of Simplex Mesh -========================================= - -.. index:: - single: SimplexMeshVolumeCalculator - pair: area; volume - -Synopsis --------- - -Calculate the area and volume of an itk::SimplexMesh. - - -Results -------- -Output:: - - Ideal Volume: 523.599 - Mesh Volume: 520.812 - Ideal Surface Area: 314.159 - Mesh Surface Area: 313.1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SimplexMeshVolumeCalculator diff --git a/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.md b/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.md new file mode 100644 index 000000000..8b02b1d74 --- /dev/null +++ b/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.md @@ -0,0 +1,36 @@ +--- +name: ConvertMeshToUnstructeredGrid +--- + +# Convert Mesh to Unstructered Grid + +```{index} single: Mesh +``` + +## Synopsis + +Convert an itk::Mesh to a vtkUnstructuredGrid. + +## Results + +An Output.vtu file will be generated alone with the following output. + +Output: + +``` +Unstructered grid has 3 cells. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Mesh +``` diff --git a/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.rst b/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.rst deleted file mode 100644 index f21c54079..000000000 --- a/src/Core/Mesh/ConvertMeshToUnstructeredGrid/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: ConvertMeshToUnstructeredGrid - -Convert Mesh to Unstructered Grid -================================= - -.. index:: - single: Mesh - -Synopsis --------- - -Convert an itk::Mesh to a vtkUnstructuredGrid. - - -Results -------- -An Output.vtu file will be generated alone with the following output. - -Output:: - - Unstructered grid has 3 cells. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Mesh diff --git a/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.md b/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.md new file mode 100644 index 000000000..9434211d9 --- /dev/null +++ b/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ConvertTriangleMeshToBinaryImage +--- + +# Convert Triangle Mesh to Binary Image + +```{index} single: TriangleMeshToBinaryImageFilter +``` + +## Synopsis + +Convert a triangular itk::Mesh to binary itk::Image + +## Results + +:::{figure} ConvertTriangleMeshToBinaryImageInputs.png +:alt: Input image and mesh +:scale: 80% + +Input 3D Image and Mesh +::: + +:::{figure} Output.png +:alt: Output image +:scale: 100% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TriangleMeshToBinaryImageFilter +``` diff --git a/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.rst b/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.rst deleted file mode 100644 index 4c0954934..000000000 --- a/src/Core/Mesh/ConvertTriangleMeshToBinaryImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: ConvertTriangleMeshToBinaryImage - -Convert Triangle Mesh to Binary Image -===================================== - -.. index:: - single: TriangleMeshToBinaryImageFilter - -Synopsis --------- - -Convert a triangular itk::Mesh to binary itk::Image - - -Results -------- - -.. figure:: ConvertTriangleMeshToBinaryImageInputs.png - :scale: 80% - :alt: Input image and mesh - - Input 3D Image and Mesh - -.. figure:: Output.png - :scale: 100% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TriangleMeshToBinaryImageFilter diff --git a/src/Core/Mesh/ExtractIsoSurface/Documentation.md b/src/Core/Mesh/ExtractIsoSurface/Documentation.md new file mode 100644 index 000000000..6b1e1d59b --- /dev/null +++ b/src/Core/Mesh/ExtractIsoSurface/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ExtractIsoSurface +--- + +# Extract Iso Surface + +```{index} single: BinaryMask3DMeshSource +``` + +## Synopsis + +Extract the iso surface as one itk::Mesh from a 3D itk::Image + +## Results + +:::{figure} MeshAndVolume.png +:alt: Input image and resulting mesh +:scale: 50% + +Input 3D image with iso-surface mesh +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryMask3DMeshSource +``` diff --git a/src/Core/Mesh/ExtractIsoSurface/Documentation.rst b/src/Core/Mesh/ExtractIsoSurface/Documentation.rst deleted file mode 100644 index 1c2ef8ac3..000000000 --- a/src/Core/Mesh/ExtractIsoSurface/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ExtractIsoSurface - -Extract Iso Surface -=================== - -.. index:: - single: BinaryMask3DMeshSource - -Synopsis --------- - -Extract the iso surface as one itk::Mesh from a 3D itk::Image - - -Results -------- - -.. figure:: MeshAndVolume.png - :scale: 50% - :alt: Input image and resulting mesh - - Input 3D image with iso-surface mesh - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryMask3DMeshSource diff --git a/src/Core/Mesh/TranslateOneMesh/Documentation.md b/src/Core/Mesh/TranslateOneMesh/Documentation.md new file mode 100644 index 000000000..a7a69ae40 --- /dev/null +++ b/src/Core/Mesh/TranslateOneMesh/Documentation.md @@ -0,0 +1,35 @@ +--- +name: TranslateOneMesh +--- + +# Translate One Mesh + +```{index} single: TransformMeshFilter +``` + +## Synopsis + +translate one itk::Mesh + +## Results + +:::{figure} TranslateOneMesh.png +:alt: Input image +:scale: 50% + +Input Mesh (grey) and Output Mesh (yellow) +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TransformMeshFilter +``` diff --git a/src/Core/Mesh/TranslateOneMesh/Documentation.rst b/src/Core/Mesh/TranslateOneMesh/Documentation.rst deleted file mode 100644 index 839e442ff..000000000 --- a/src/Core/Mesh/TranslateOneMesh/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: TranslateOneMesh - -Translate One Mesh -================== - -.. index:: - single: TransformMeshFilter - -Synopsis --------- - -translate one itk::Mesh - - -Results -------- - -.. figure:: TranslateOneMesh.png - :scale: 50% - :alt: Input image - - Input Mesh (grey) and Output Mesh (yellow) - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TransformMeshFilter diff --git a/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.md b/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.md new file mode 100644 index 000000000..d4ad1bfee --- /dev/null +++ b/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.md @@ -0,0 +1,42 @@ +--- +name: WorkingWithPointAndCellData +--- + +# Working With Point and Cell Data + +```{index} single: Mesh +``` + +## Synopsis + +Associate point and cell data with a mesh. + +## Results + +Output: + +``` +66 +66 +5 + +128 +128 +10 +``` + +mesh.vtk is also created. + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Mesh +``` diff --git a/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.rst b/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.rst deleted file mode 100644 index 4fa1ad916..000000000 --- a/src/Core/Mesh/WorkingWithPointAndCellData/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: WorkingWithPointAndCellData - -Working With Point and Cell Data -================================ - -.. index:: - single: Mesh - -Synopsis --------- - -Associate point and cell data with a mesh. - - -Results -------- -Output:: - - 66 - 66 - 5 - - 128 - 128 - 10 - -mesh.vtk is also created. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Mesh diff --git a/src/Core/Mesh/WriteMeshToVTP/Documentation.md b/src/Core/Mesh/WriteMeshToVTP/Documentation.md new file mode 100644 index 000000000..e619819ef --- /dev/null +++ b/src/Core/Mesh/WriteMeshToVTP/Documentation.md @@ -0,0 +1,43 @@ +--- +name: WriteMeshToVTP +--- + +# Write Mesh to VTP + +```{index} single: VTKPolyDataWriter +``` + +## Synopsis + +Write an itk::Mesh to a vtp (vtkPolyData) file. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +Output: + +``` +Points = 4 +[-1, -1, 0] +[1, -1, 0] +[1, 1, 0] +[1, 1, 1] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VTKPolyDataWriter +``` diff --git a/src/Core/Mesh/WriteMeshToVTP/Documentation.rst b/src/Core/Mesh/WriteMeshToVTP/Documentation.rst deleted file mode 100644 index 5abdd0e4d..000000000 --- a/src/Core/Mesh/WriteMeshToVTP/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: WriteMeshToVTP - -Write Mesh to VTP -================= - -.. index:: - single: VTKPolyDataWriter - -Synopsis --------- - -Write an itk::Mesh to a vtp (vtkPolyData) file. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Output:: - - Points = 4 - [-1, -1, 0] - [1, -1, 0] - [1, 1, 0] - [1, 1, 1] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VTKPolyDataWriter diff --git a/src/Core/Mesh/index.md b/src/Core/Mesh/index.md new file mode 100644 index 000000000..6b4d2fe35 --- /dev/null +++ b/src/Core/Mesh/index.md @@ -0,0 +1,15 @@ +# Mesh + +```{toctree} +:maxdepth: 1 + +AccessDataInCells/Documentation.rst +AddPointsAndEdges/Documentation.rst +CalculateAreaAndVolumeOfSimplexMesh/Documentation.rst +ConvertMeshToUnstructeredGrid/Documentation.rst +ConvertTriangleMeshToBinaryImage/Documentation.rst +ExtractIsoSurface/Documentation.rst +TranslateOneMesh/Documentation.rst +WorkingWithPointAndCellData/Documentation.rst +WriteMeshToVTP/Documentation.rst +``` diff --git a/src/Core/Mesh/index.rst b/src/Core/Mesh/index.rst deleted file mode 100644 index 99ba10d38..000000000 --- a/src/Core/Mesh/index.rst +++ /dev/null @@ -1,15 +0,0 @@ -Mesh -==== - -.. toctree:: - :maxdepth: 1 - - AccessDataInCells/Documentation.rst - AddPointsAndEdges/Documentation.rst - CalculateAreaAndVolumeOfSimplexMesh/Documentation.rst - ConvertMeshToUnstructeredGrid/Documentation.rst - ConvertTriangleMeshToBinaryImage/Documentation.rst - ExtractIsoSurface/Documentation.rst - TranslateOneMesh/Documentation.rst - WorkingWithPointAndCellData/Documentation.rst - WriteMeshToVTP/Documentation.rst diff --git a/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.md b/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.md new file mode 100644 index 000000000..9e7359a6b --- /dev/null +++ b/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.md @@ -0,0 +1,35 @@ +--- +name: CreateTriangularQuadEdgeMesh +--- + +# Create Triangular Quad Edge Mesh + +```{index} single: QuadEdgeMesh +``` + +## Synopsis + +Create a triangular surface mesh using itk::QuadEdgeMesh + +## Results + +:::{figure} OutputMesh.png +:alt: Output mesh +:scale: 50% + +Output mesh +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::QuadEdgeMesh +``` diff --git a/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.rst b/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.rst deleted file mode 100644 index 501473025..000000000 --- a/src/Core/QuadEdgeMesh/CreateTriangularQuadEdgeMesh/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: CreateTriangularQuadEdgeMesh - -Create Triangular Quad Edge Mesh -================================ - -.. index:: - single: QuadEdgeMesh - -Synopsis --------- - -Create a triangular surface mesh using itk::QuadEdgeMesh - - -Results -------- - -.. figure:: OutputMesh.png - :scale: 50% - :alt: Output mesh - - Output mesh - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::QuadEdgeMesh diff --git a/src/Core/QuadEdgeMesh/CutMesh/Documentation.md b/src/Core/QuadEdgeMesh/CutMesh/Documentation.md new file mode 100644 index 000000000..b99b3b13b --- /dev/null +++ b/src/Core/QuadEdgeMesh/CutMesh/Documentation.md @@ -0,0 +1,55 @@ +--- +name: CutMesh +--- + +# Cut Mesh + +```{index} single: QuadEdgeMesh single: QuadEdgeMeshPolygonCell single: MeshFileReader single: MeshFileWriter pair: QuadEdge; GetLnext pair: QuadEdge; GetOnext pair: QuadEdgeMeshPoint; CastFrom pair: QuadEdgeMeshPolygonCell; GetEdgeRingEntry pair: QuadEdgeMesh; AddPoint pair: QuadEdgeMesh; AddFaceTriangle pair: PointSet; GetPoints +``` + +## Synopsis + +Given a bounding box and a mesh, first retrieve all vertices whose coordinates +are in the bounding box; then retrieve all faces connected to these vertices. + +## Results + +:::{figure} inputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +:::{figure} outputMesh.png +:alt: Output mesh +:scale: 50% + +Output mesh (cut) +::: + +```{raw} html +
+ +

Interactive input mesh

+
+ +
+ +

Interactive cut output mesh

+
+``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::QuadEdgeMesh +``` diff --git a/src/Core/QuadEdgeMesh/CutMesh/Documentation.rst b/src/Core/QuadEdgeMesh/CutMesh/Documentation.rst deleted file mode 100644 index dcef06757..000000000 --- a/src/Core/QuadEdgeMesh/CutMesh/Documentation.rst +++ /dev/null @@ -1,65 +0,0 @@ -:name: CutMesh - -Cut Mesh -======== - -.. index:: - single: QuadEdgeMesh - single: QuadEdgeMeshPolygonCell - single: MeshFileReader - single: MeshFileWriter - pair: QuadEdge; GetLnext - pair: QuadEdge; GetOnext - pair: QuadEdgeMeshPoint; CastFrom - pair: QuadEdgeMeshPolygonCell; GetEdgeRingEntry - pair: QuadEdgeMesh; AddPoint - pair: QuadEdgeMesh; AddFaceTriangle - pair: PointSet; GetPoints - -Synopsis --------- - -Given a bounding box and a mesh, first retrieve all vertices whose coordinates -are in the bounding box; then retrieve all faces connected to these vertices. - -Results -------- - -.. figure:: inputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. figure:: outputMesh.png - :scale: 50% - :alt: Output mesh - - Output mesh (cut) - -.. raw:: html - -
- -

Interactive input mesh

-
- -
- -

Interactive cut output mesh

-
- -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::QuadEdgeMesh diff --git a/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.md b/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.md new file mode 100644 index 000000000..615ef4acf --- /dev/null +++ b/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.md @@ -0,0 +1,57 @@ +--- +name: ExtractVertexOnMeshBoundaries +--- + +# Extract Vertex on Mesh Boundaries + +```{index} single: QuadEdgeMeshBoundaryEdgesMeshFunction +``` + +## Synopsis + +Print the vertices in order which lie on each boundary of a given mesh. + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+``` + +Example output: + +``` +There are 1 borders on this mesh +0: 684 -> 3848 -> 955 -> 1643 -> 4340 -> 178 -> 1160 -> 6650 -> 3539 -> 523 -> +6052 -> 9 -> 7619 -> 2876 -> 4010 -> 102 -> 1451 -> 557 -> 5658 -> 3326 -> 4606 +-> 1154 -> 4584 -> 5553 -> 6739 -> 1725 -> 7207 -> 3978 -> 3116 -> 7770 -> 2293 +-> 3285 -> 2215 -> 6505 -> 7128 -> 7973 -> 6479 -> 3292 -> 3719 -> 3111 -> 6566 +-> 1227 -> 3410 -> 3418 -> 7208 -> 5732 -> 7203 -> 645 -> 314 -> 7872 -> 6941 +-> 5076 -> 1965 -> 2017 -> 3235 -> 3801 -> 4754 -> 1348 -> 2390 -> 7367 -> 6319 +-> 5458 -> 7572 -> 151 -> 4095 -> 3873 -> 7336 -> 7260 -> 2112 -> 6373 -> 1664 +-> 7247 -> 7661 -> 5790 -> 1698 -> 572 -> 5783 -> 3042 -> 5259 -> 7802 -> 6192 +-> 894 -> 4545 -> 1298 -> 684 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::QuadEdgeMeshBoundaryEdgesMeshFunction +``` diff --git a/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.rst b/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.rst deleted file mode 100644 index c373fef8e..000000000 --- a/src/Core/QuadEdgeMesh/ExtractVertexOnMeshBoundaries/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: ExtractVertexOnMeshBoundaries - -Extract Vertex on Mesh Boundaries -================================= - -.. index:: - single: QuadEdgeMeshBoundaryEdgesMeshFunction - -Synopsis --------- - -Print the vertices in order which lie on each boundary of a given mesh. - - -Results -------- - -.. figure:: InputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- -Example output:: - - There are 1 borders on this mesh - 0: 684 -> 3848 -> 955 -> 1643 -> 4340 -> 178 -> 1160 -> 6650 -> 3539 -> 523 -> - 6052 -> 9 -> 7619 -> 2876 -> 4010 -> 102 -> 1451 -> 557 -> 5658 -> 3326 -> 4606 - -> 1154 -> 4584 -> 5553 -> 6739 -> 1725 -> 7207 -> 3978 -> 3116 -> 7770 -> 2293 - -> 3285 -> 2215 -> 6505 -> 7128 -> 7973 -> 6479 -> 3292 -> 3719 -> 3111 -> 6566 - -> 1227 -> 3410 -> 3418 -> 7208 -> 5732 -> 7203 -> 645 -> 314 -> 7872 -> 6941 - -> 5076 -> 1965 -> 2017 -> 3235 -> 3801 -> 4754 -> 1348 -> 2390 -> 7367 -> 6319 - -> 5458 -> 7572 -> 151 -> 4095 -> 3873 -> 7336 -> 7260 -> 2112 -> 6373 -> 1664 - -> 7247 -> 7661 -> 5790 -> 1698 -> 572 -> 5783 -> 3042 -> 5259 -> 7802 -> 6192 - -> 894 -> 4545 -> 1298 -> 684 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::QuadEdgeMeshBoundaryEdgesMeshFunction diff --git a/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.md b/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.md new file mode 100644 index 000000000..c8efab232 --- /dev/null +++ b/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.md @@ -0,0 +1,54 @@ +--- +name: GetListOfFacesAroundAGivenVertex +--- + +# Get List of Faces Around a Given Vertex + +```{index} single: QuadEdgeMesh +``` + +## Synopsis + +Get the list of faces around a given vertex. + +## Results + +Results: + +``` +79 +1961 +2036 +1960 +1 +``` + +These faces are visualized in the figures below. + +:::{figure} SelectedFaces.png +:alt: Selected faces. +:scale: 50% + +The selected faces around the given vertex are highlighted in pink. +::: + +```{raw} html +
+ +

Interactive view of the selected faces

+
+``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::QuadEdgeMesh +``` diff --git a/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.rst b/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.rst deleted file mode 100644 index 75bfd08b8..000000000 --- a/src/Core/QuadEdgeMesh/GetListOfFacesAroundAGivenVertex/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: GetListOfFacesAroundAGivenVertex - -Get List of Faces Around a Given Vertex -======================================= - -.. index:: - single: QuadEdgeMesh - -Synopsis --------- - -Get the list of faces around a given vertex. - - -Results -------- - -Results:: - - 79 - 1961 - 2036 - 1960 - 1 - -These faces are visualized in the figures below. - -.. figure:: SelectedFaces.png - :scale: 50% - :alt: Selected faces. - - The selected faces around the given vertex are highlighted in pink. - -.. raw:: html - -
- -

Interactive view of the selected faces

-
- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::QuadEdgeMesh diff --git a/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.md b/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.md new file mode 100644 index 000000000..d50dfa470 --- /dev/null +++ b/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.md @@ -0,0 +1,53 @@ +--- +name: PrintVertexNeighbors +--- + +# Print Vertex Neighbors + +```{index} single: QuadEdgeMesh +``` + +## Synopsis + +Print the neighbors of a given vertex. + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+``` + +Example output: + +``` +3435 +6999 +5422 +2869 +244 +584 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::QuadEdgeMesh +``` diff --git a/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.rst b/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.rst deleted file mode 100644 index 5b5145b13..000000000 --- a/src/Core/QuadEdgeMesh/PrintVertexNeighbors/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: PrintVertexNeighbors - -Print Vertex Neighbors -====================== - -.. index:: - single: QuadEdgeMesh - -Synopsis --------- - -Print the neighbors of a given vertex. - - -Results -------- - -.. figure:: InputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- -Example output:: - - 3435 - 6999 - 5422 - 2869 - 244 - 584 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::QuadEdgeMesh diff --git a/src/Core/QuadEdgeMesh/index.md b/src/Core/QuadEdgeMesh/index.md new file mode 100644 index 000000000..047edf312 --- /dev/null +++ b/src/Core/QuadEdgeMesh/index.md @@ -0,0 +1,11 @@ +# QuadEdgeMesh + +```{toctree} +:maxdepth: 1 + +CreateTriangularQuadEdgeMesh/Documentation.rst +CutMesh/Documentation.rst +ExtractVertexOnMeshBoundaries/Documentation.rst +GetListOfFacesAroundAGivenVertex/Documentation.rst +PrintVertexNeighbors/Documentation.rst +``` diff --git a/src/Core/QuadEdgeMesh/index.rst b/src/Core/QuadEdgeMesh/index.rst deleted file mode 100644 index ff3e447f5..000000000 --- a/src/Core/QuadEdgeMesh/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -QuadEdgeMesh -============ - -.. toctree:: - :maxdepth: 1 - - CreateTriangularQuadEdgeMesh/Documentation.rst - CutMesh/Documentation.rst - ExtractVertexOnMeshBoundaries/Documentation.rst - GetListOfFacesAroundAGivenVertex/Documentation.rst - PrintVertexNeighbors/Documentation.rst diff --git a/src/Core/SpatialObjects/Blob/Documentation.md b/src/Core/SpatialObjects/Blob/Documentation.md new file mode 100644 index 000000000..389b3ce7d --- /dev/null +++ b/src/Core/SpatialObjects/Blob/Documentation.md @@ -0,0 +1,34 @@ +--- +name: Blob +--- + +# Blob + +```{index} single: BlobSpatialObject single: blob +``` + +## Synopsis + +Blob. + +## Results + +Output: + +``` +Bounds: [0, 0, 0, 0] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BlobSpatialObject +``` diff --git a/src/Core/SpatialObjects/Blob/Documentation.rst b/src/Core/SpatialObjects/Blob/Documentation.rst deleted file mode 100644 index 95135726f..000000000 --- a/src/Core/SpatialObjects/Blob/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: Blob - -Blob -==== - -.. index:: - single: BlobSpatialObject - single: blob - -Synopsis --------- - -Blob. - - -Results -------- -Output:: - - Bounds: [0, 0, 0, 0] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BlobSpatialObject diff --git a/src/Core/SpatialObjects/ContourSpatialObject/Documentation.md b/src/Core/SpatialObjects/ContourSpatialObject/Documentation.md new file mode 100644 index 000000000..5a973f33f --- /dev/null +++ b/src/Core/SpatialObjects/ContourSpatialObject/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ContourSpatialObject +--- + +# Contour Spatial Object + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ContourSpatialObject +``` + +## Synopsis + +Contour spatial object. + +## Results + +**Results Coming Soon!** + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ContourSpatialObject +``` diff --git a/src/Core/SpatialObjects/ContourSpatialObject/Documentation.rst b/src/Core/SpatialObjects/ContourSpatialObject/Documentation.rst deleted file mode 100644 index 75f3351c6..000000000 --- a/src/Core/SpatialObjects/ContourSpatialObject/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: ContourSpatialObject - -Contour Spatial Object -====================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ContourSpatialObject - -Synopsis --------- - -Contour spatial object. - - -Results -------- -**Results Coming Soon!** - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ContourSpatialObject diff --git a/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.md b/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.md new file mode 100644 index 000000000..f6aca1e14 --- /dev/null +++ b/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ConvertSpatialObjectToImage +--- + +# Convert Spatial Object to Image + +```{index} single: SpatialObjectToImageFilter +``` + +## Synopsis + +Convert a spatial object to an image. + +## Results + +:::{figure} ConvertSpatialObjectToImage.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SpatialObjectToImageFilter +``` diff --git a/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.rst b/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.rst deleted file mode 100644 index 222fa1753..000000000 --- a/src/Core/SpatialObjects/ConvertSpatialObjectToImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: ConvertSpatialObjectToImage - -Convert Spatial Object to Image -=============================== - -.. index:: - single: SpatialObjectToImageFilter - -Synopsis --------- - -Convert a spatial object to an image. - - -Results -------- -.. figure:: ConvertSpatialObjectToImage.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SpatialObjectToImageFilter diff --git a/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.md b/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.md new file mode 100644 index 000000000..9bad74d10 --- /dev/null +++ b/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.md @@ -0,0 +1,39 @@ +--- +name: CreateALineSpatialObject +--- + +# Create a Line Spatial Object + +```{index} single: LineSpatialObject single: LineSpatialObjectPoint +``` + +## Synopsis + +Specify a piecewise-linear object by specifying points along the line. + +## Results + +:::{figure} line.png +:alt: line.png +:scale: 70% + +line.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LineSpatialObject +``` + +```{eval-rst} +.. breathelink:: itk::LineSpatialObjectPoint +``` diff --git a/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.rst b/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.rst deleted file mode 100644 index d360afeb7..000000000 --- a/src/Core/SpatialObjects/CreateALineSpatialObject/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: CreateALineSpatialObject - -Create a Line Spatial Object -============================ - -.. index:: - single: LineSpatialObject - single: LineSpatialObjectPoint - -Synopsis --------- - -Specify a piecewise-linear object by specifying points along the line. - - -Results -------- -.. figure:: line.png - :scale: 70% - :alt: line.png - - line.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- -.. breathelink:: itk::LineSpatialObject -.. breathelink:: itk::LineSpatialObjectPoint diff --git a/src/Core/SpatialObjects/Ellipse/Documentation.md b/src/Core/SpatialObjects/Ellipse/Documentation.md new file mode 100644 index 000000000..2f6f77cee --- /dev/null +++ b/src/Core/SpatialObjects/Ellipse/Documentation.md @@ -0,0 +1,35 @@ +--- +name: Ellipse +--- + +# Ellipse + +```{index} single: EllipseSpatialObject single: ellipse +``` + +## Synopsis + +Create ellipse. + +## Results + +:::{figure} EllipseOutput.png +:alt: Output.png +:scale: 70% + +Output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::EllipseSpatialObject +``` diff --git a/src/Core/SpatialObjects/Ellipse/Documentation.rst b/src/Core/SpatialObjects/Ellipse/Documentation.rst deleted file mode 100644 index 382727083..000000000 --- a/src/Core/SpatialObjects/Ellipse/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: Ellipse - -Ellipse -======= - -.. index:: - single: EllipseSpatialObject - single: ellipse - -Synopsis --------- - -Create ellipse. - - -Results -------- -.. figure:: EllipseOutput.png - :scale: 70% - :alt: Output.png - - Output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::EllipseSpatialObject diff --git a/src/Core/SpatialObjects/index.md b/src/Core/SpatialObjects/index.md new file mode 100644 index 000000000..6ca1b596b --- /dev/null +++ b/src/Core/SpatialObjects/index.md @@ -0,0 +1,11 @@ +# SpatialObjects + +```{toctree} +:maxdepth: 1 + +Blob/Documentation.rst +ContourSpatialObject/Documentation.rst +ConvertSpatialObjectToImage/Documentation.rst +CreateALineSpatialObject/Documentation.rst +Ellipse/Documentation.rst +``` diff --git a/src/Core/SpatialObjects/index.rst b/src/Core/SpatialObjects/index.rst deleted file mode 100644 index b0bea94e6..000000000 --- a/src/Core/SpatialObjects/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -SpatialObjects -============== - -.. toctree:: - :maxdepth: 1 - - Blob/Documentation.rst - ContourSpatialObject/Documentation.rst - ConvertSpatialObjectToImage/Documentation.rst - CreateALineSpatialObject/Documentation.rst - Ellipse/Documentation.rst diff --git a/src/Core/TestKernel/GenerateRandomImage/Documentation.md b/src/Core/TestKernel/GenerateRandomImage/Documentation.md new file mode 100644 index 000000000..9a51e4d4e --- /dev/null +++ b/src/Core/TestKernel/GenerateRandomImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: GenerateRandomImage +--- + +# Generate Random Image + +```{index} single: RandomImageSource single: random +``` + +## Synopsis + +This example produces an image with random pixel values. + +## Results + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 600% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RandomImageSource +``` diff --git a/src/Core/TestKernel/GenerateRandomImage/Documentation.rst b/src/Core/TestKernel/GenerateRandomImage/Documentation.rst deleted file mode 100644 index 7deb95ccb..000000000 --- a/src/Core/TestKernel/GenerateRandomImage/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: GenerateRandomImage - -Generate Random Image -===================== - -.. index:: - single: RandomImageSource - single: random - -Synopsis --------- - -This example produces an image with random pixel values. - - -Results -------- - -.. figure:: OutputBaseline.png - :scale: 600% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::RandomImageSource diff --git a/src/Core/TestKernel/index.md b/src/Core/TestKernel/index.md new file mode 100644 index 000000000..cbbace79b --- /dev/null +++ b/src/Core/TestKernel/index.md @@ -0,0 +1,7 @@ +# TestKernel + +```{toctree} +:maxdepth: 1 + +GenerateRandomImage/Documentation.rst +``` diff --git a/src/Core/TestKernel/index.rst b/src/Core/TestKernel/index.rst deleted file mode 100644 index b09199286..000000000 --- a/src/Core/TestKernel/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -TestKernel -========== - -.. toctree:: - :maxdepth: 1 - - GenerateRandomImage/Documentation.rst diff --git a/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.md b/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.md new file mode 100644 index 000000000..36bd84d47 --- /dev/null +++ b/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.md @@ -0,0 +1,52 @@ +--- +name: ApplyAffineTransformFromHomogeneousMatrixAndResample +--- + +# Apply Affine Transform From Homogeneous Matrix and Resample + +```{index} single: AffineTransform single: WindowedSincInterpolateImageFunction single: ResampleImageFilter +``` + +## Synopsis + +Given one homogeneous matrix (here a 3x3 matrix), apply the corresponding +transform to a given image and resample using a +WindowedSincInterpolateImageFunction. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AffineTransform +``` + +```{eval-rst} +.. breathelink:: itk::WindowedSincInterpolateImageFunction +``` + +```{eval-rst} +.. breathelink:: itk::ResampleImageFilter +``` diff --git a/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.rst b/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.rst deleted file mode 100644 index 1b36e7c1d..000000000 --- a/src/Core/Transform/ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: ApplyAffineTransformFromHomogeneousMatrixAndResample - -Apply Affine Transform From Homogeneous Matrix and Resample -=========================================================== - -.. index:: - single: AffineTransform - single: WindowedSincInterpolateImageFunction - single: ResampleImageFilter - -Synopsis --------- - -Given one homogeneous matrix (here a 3x3 matrix), apply the corresponding -transform to a given image and resample using a -WindowedSincInterpolateImageFunction. - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AffineTransform -.. breathelink:: itk::WindowedSincInterpolateImageFunction -.. breathelink:: itk::ResampleImageFilter diff --git a/src/Core/Transform/CartesianToAzimuthElevation/Documentation.md b/src/Core/Transform/CartesianToAzimuthElevation/Documentation.md new file mode 100644 index 000000000..3b8469bea --- /dev/null +++ b/src/Core/Transform/CartesianToAzimuthElevation/Documentation.md @@ -0,0 +1,35 @@ +--- +name: CartesianToAzimuthElevation +--- + +# Cartesian to Azimuth Elevation + +```{index} single: AzimuthElevationToCartesianTransform pair: cartesian; azimuth-elevation +``` + +## Synopsis + +Cartesian to AzimuthElevation and vice-versa. + +## Results + +Output: + +``` +spherical: [0, 45, 1] +Cartesian: [0.00611663, 0.713237, 0.700896] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AzimuthElevationToCartesianTransform +``` diff --git a/src/Core/Transform/CartesianToAzimuthElevation/Documentation.rst b/src/Core/Transform/CartesianToAzimuthElevation/Documentation.rst deleted file mode 100644 index a6146ecb1..000000000 --- a/src/Core/Transform/CartesianToAzimuthElevation/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: CartesianToAzimuthElevation - -Cartesian to Azimuth Elevation -============================== - -.. index:: - single: AzimuthElevationToCartesianTransform - pair: cartesian; azimuth-elevation - -Synopsis --------- - -Cartesian to AzimuthElevation and vice-versa. - - -Results -------- -Output:: - - spherical: [0, 45, 1] - Cartesian: [0.00611663, 0.713237, 0.700896] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AzimuthElevationToCartesianTransform diff --git a/src/Core/Transform/CopyACompositeTransform/Documentation.md b/src/Core/Transform/CopyACompositeTransform/Documentation.md new file mode 100644 index 000000000..8e47e9db6 --- /dev/null +++ b/src/Core/Transform/CopyACompositeTransform/Documentation.md @@ -0,0 +1,160 @@ +--- +name: CopyACompositeTransform +--- + +# Copy a CompositeTransform + +```{index} single: Transform pair: copy; Transform pair: clone; Transform +``` + +## Synopsis + +Copy a CompositeTransform. + +## Results + +```none +Original transform: CompositeTransform (0x173cdb0) + RTTI typeinfo: itk::CompositeTransform + Reference Count: 2 + Modified Time: 12 + Debug: Off + Object Name: + Observers: + none + Transforms in queue, from begin to end: + >>>>>>>>> + Euler3DTransform (0x173c880) + RTTI typeinfo: itk::Euler3DTransform + Reference Count: 2 + Modified Time: 5 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.930432 -0.294044 0.218711 + 0.308577 0.950564 -0.0347626 + -0.197677 0.0998334 0.97517 + Offset: [3.63622, 5.66636, 5.62082] + Center: [-3.5, -4.5, -5.5] + Translation: [4, 5, 6] + Inverse: + 0.930432 0.308577 -0.197677 + -0.294044 0.950564 0.0998333 + 0.218711 -0.0347626 0.97517 + Singular: 0 + Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 + m_ComputeZYX = 0 + >>>>>>>>> + ScaleTransform (0x173cb10) + RTTI typeinfo: itk::ScaleTransform + Reference Count: 2 + Modified Time: 9 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.6 0 0 + 0 0.7 0 + 0 0 0.8 + Offset: [0, 0, 0] + Center: [0, 0, 0] + Translation: [0, 0, 0] + Inverse: + 1.66667 0 0 + 0 1.42857 0 + 0 0 1.25 + Singular: 0 + Scale: [0.6, 0.7, 0.8] + Center: [0, 0, 0] + End of MultiTransform. +<<<<<<<<<< + TransformsToOptimizeFlags, begin() to end(): + 1 1 + TransformsToOptimize in queue, from begin to end: + End of TransformsToOptimizeQueue. +<<<<<<<<<< + End of CompositeTransform. +<<<<<<<<<< + +Transform copy: CompositeTransform (0x173da00) + RTTI typeinfo: itk::CompositeTransform + Reference Count: 3 + Modified Time: 26 + Debug: Off + Object Name: + Observers: + none + Transforms in queue, from begin to end: + >>>>>>>>> + Euler3DTransform (0x173e2e0) + RTTI typeinfo: itk::Euler3DTransform + Reference Count: 1 + Modified Time: 18 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.930432 -0.294044 0.218711 + 0.308577 0.950564 -0.0347626 + -0.197677 0.0998334 0.97517 + Offset: [3.63622, 5.66636, 5.62082] + Center: [-3.5, -4.5, -5.5] + Translation: [4, 5, 6] + Inverse: + 0.930432 0.308577 -0.197677 + -0.294044 0.950564 0.0998333 + 0.218711 -0.0347626 0.97517 + Singular: 0 + Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 + m_ComputeZYX = 0 + >>>>>>>>> + ScaleTransform (0x173e470) + RTTI typeinfo: itk::ScaleTransform + Reference Count: 1 + Modified Time: 24 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.6 0 0 + 0 0.7 0 + 0 0 0.8 + Offset: [0, 0, 0] + Center: [0, 0, 0] + Translation: [0, 0, 0] + Inverse: + 1.66667 0 0 + 0 1.42857 0 + 0 0 1.25 + Singular: 0 + Scale: [0.6, 0.7, 0.8] + Center: [0, 0, 0] + End of MultiTransform. +<<<<<<<<<< + TransformsToOptimizeFlags, begin() to end(): + 1 1 + TransformsToOptimize in queue, from begin to end: + End of TransformsToOptimizeQueue. +<<<<<<<<<< + End of CompositeTransform. +<<<<<<<<<< +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Transform +``` diff --git a/src/Core/Transform/CopyACompositeTransform/Documentation.rst b/src/Core/Transform/CopyACompositeTransform/Documentation.rst deleted file mode 100644 index ac94fc2a5..000000000 --- a/src/Core/Transform/CopyACompositeTransform/Documentation.rst +++ /dev/null @@ -1,166 +0,0 @@ -:name: CopyACompositeTransform - -Copy a CompositeTransform -========================= - -.. index:: - single: Transform - pair: copy; Transform - pair: clone; Transform - -Synopsis --------- - -Copy a CompositeTransform. - - -Results -------- - -.. code-block:: none - - Original transform: CompositeTransform (0x173cdb0) - RTTI typeinfo: itk::CompositeTransform - Reference Count: 2 - Modified Time: 12 - Debug: Off - Object Name: - Observers: - none - Transforms in queue, from begin to end: - >>>>>>>>> - Euler3DTransform (0x173c880) - RTTI typeinfo: itk::Euler3DTransform - Reference Count: 2 - Modified Time: 5 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.930432 -0.294044 0.218711 - 0.308577 0.950564 -0.0347626 - -0.197677 0.0998334 0.97517 - Offset: [3.63622, 5.66636, 5.62082] - Center: [-3.5, -4.5, -5.5] - Translation: [4, 5, 6] - Inverse: - 0.930432 0.308577 -0.197677 - -0.294044 0.950564 0.0998333 - 0.218711 -0.0347626 0.97517 - Singular: 0 - Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 - m_ComputeZYX = 0 - >>>>>>>>> - ScaleTransform (0x173cb10) - RTTI typeinfo: itk::ScaleTransform - Reference Count: 2 - Modified Time: 9 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.6 0 0 - 0 0.7 0 - 0 0 0.8 - Offset: [0, 0, 0] - Center: [0, 0, 0] - Translation: [0, 0, 0] - Inverse: - 1.66667 0 0 - 0 1.42857 0 - 0 0 1.25 - Singular: 0 - Scale: [0.6, 0.7, 0.8] - Center: [0, 0, 0] - End of MultiTransform. - <<<<<<<<<< - TransformsToOptimizeFlags, begin() to end(): - 1 1 - TransformsToOptimize in queue, from begin to end: - End of TransformsToOptimizeQueue. - <<<<<<<<<< - End of CompositeTransform. - <<<<<<<<<< - - Transform copy: CompositeTransform (0x173da00) - RTTI typeinfo: itk::CompositeTransform - Reference Count: 3 - Modified Time: 26 - Debug: Off - Object Name: - Observers: - none - Transforms in queue, from begin to end: - >>>>>>>>> - Euler3DTransform (0x173e2e0) - RTTI typeinfo: itk::Euler3DTransform - Reference Count: 1 - Modified Time: 18 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.930432 -0.294044 0.218711 - 0.308577 0.950564 -0.0347626 - -0.197677 0.0998334 0.97517 - Offset: [3.63622, 5.66636, 5.62082] - Center: [-3.5, -4.5, -5.5] - Translation: [4, 5, 6] - Inverse: - 0.930432 0.308577 -0.197677 - -0.294044 0.950564 0.0998333 - 0.218711 -0.0347626 0.97517 - Singular: 0 - Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 - m_ComputeZYX = 0 - >>>>>>>>> - ScaleTransform (0x173e470) - RTTI typeinfo: itk::ScaleTransform - Reference Count: 1 - Modified Time: 24 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.6 0 0 - 0 0.7 0 - 0 0 0.8 - Offset: [0, 0, 0] - Center: [0, 0, 0] - Translation: [0, 0, 0] - Inverse: - 1.66667 0 0 - 0 1.42857 0 - 0 0 1.25 - Singular: 0 - Scale: [0.6, 0.7, 0.8] - Center: [0, 0, 0] - End of MultiTransform. - <<<<<<<<<< - TransformsToOptimizeFlags, begin() to end(): - 1 1 - TransformsToOptimize in queue, from begin to end: - End of TransformsToOptimizeQueue. - <<<<<<<<<< - End of CompositeTransform. - <<<<<<<<<< - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Transform diff --git a/src/Core/Transform/CopyANonCompositeTransform/Documentation.md b/src/Core/Transform/CopyANonCompositeTransform/Documentation.md new file mode 100644 index 000000000..87d454690 --- /dev/null +++ b/src/Core/Transform/CopyANonCompositeTransform/Documentation.md @@ -0,0 +1,80 @@ +--- +name: CopyANonCompositeTransform +--- + +# Copy a Non-CompositeTransform + +```{index} single: Transform pair: copy; Transform pair: clone; Transform +``` + +## Synopsis + +Copy a non-CompositeTransform. + +## Results + +```none +Original transform: Euler3DTransform (0x132e880) + RTTI typeinfo: itk::Euler3DTransform + Reference Count: 2 + Modified Time: 5 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.930432 -0.294044 0.218711 + 0.308577 0.950564 -0.0347626 + -0.197677 0.0998334 0.97517 + Offset: [3.63622, 5.66636, 5.62082] + Center: [-3.5, -4.5, -5.5] + Translation: [4, 5, 6] + Inverse: + 0.930432 0.308577 -0.197677 + -0.294044 0.950564 0.0998333 + 0.218711 -0.0347626 0.97517 + Singular: 0 + Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 + m_ComputeZYX = 0 + +Transform copy: Euler3DTransform (0x132eda0) + RTTI typeinfo: itk::Euler3DTransform + Reference Count: 3 + Modified Time: 10 + Debug: Off + Object Name: + Observers: + none + Matrix: + 0.930432 -0.294044 0.218711 + 0.308577 0.950564 -0.0347626 + -0.197677 0.0998334 0.97517 + Offset: [3.63622, 5.66636, 5.62082] + Center: [-3.5, -4.5, -5.5] + Translation: [4, 5, 6] + Inverse: + 0.930432 0.308577 -0.197677 + -0.294044 0.950564 0.0998333 + 0.218711 -0.0347626 0.97517 + Singular: 0 + Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 + m_ComputeZYX = 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Transform +``` + +```{eval-rst} +.. breathelink:: itk::CompositeTransform +``` diff --git a/src/Core/Transform/CopyANonCompositeTransform/Documentation.rst b/src/Core/Transform/CopyANonCompositeTransform/Documentation.rst deleted file mode 100644 index bf11aa330..000000000 --- a/src/Core/Transform/CopyANonCompositeTransform/Documentation.rst +++ /dev/null @@ -1,84 +0,0 @@ -:name: CopyANonCompositeTransform - -Copy a Non-CompositeTransform -============================= - -.. index:: - single: Transform - pair: copy; Transform - pair: clone; Transform - -Synopsis --------- - -Copy a non-CompositeTransform. - - -Results -------- - -.. code-block:: none - - Original transform: Euler3DTransform (0x132e880) - RTTI typeinfo: itk::Euler3DTransform - Reference Count: 2 - Modified Time: 5 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.930432 -0.294044 0.218711 - 0.308577 0.950564 -0.0347626 - -0.197677 0.0998334 0.97517 - Offset: [3.63622, 5.66636, 5.62082] - Center: [-3.5, -4.5, -5.5] - Translation: [4, 5, 6] - Inverse: - 0.930432 0.308577 -0.197677 - -0.294044 0.950564 0.0998333 - 0.218711 -0.0347626 0.97517 - Singular: 0 - Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 - m_ComputeZYX = 0 - - Transform copy: Euler3DTransform (0x132eda0) - RTTI typeinfo: itk::Euler3DTransform - Reference Count: 3 - Modified Time: 10 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.930432 -0.294044 0.218711 - 0.308577 0.950564 -0.0347626 - -0.197677 0.0998334 0.97517 - Offset: [3.63622, 5.66636, 5.62082] - Center: [-3.5, -4.5, -5.5] - Translation: [4, 5, 6] - Inverse: - 0.930432 0.308577 -0.197677 - -0.294044 0.950564 0.0998333 - 0.218711 -0.0347626 0.97517 - Singular: 0 - Euler's angles: AngleX=0.1 AngleY=0.2 AngleZ=0.3 - m_ComputeZYX = 0 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Transform - -.. breathelink:: itk::CompositeTransform diff --git a/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.md b/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.md new file mode 100644 index 000000000..a6c7c5171 --- /dev/null +++ b/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.md @@ -0,0 +1,57 @@ +--- +name: DeformAVolumeWithAThinPlateSpline +--- + +# Deform a Volume With a Thin Plate Spline + +```{index} single: ThinPlateSplineKernelTransform +``` + +## Synopsis + +This example deforms a 3D volume with the thin plate spline. + +## Results + +:::{figure} InputImage.png +:alt: Input image +:width: 640px + +Input image +::: + +:::{figure} DeformedImage.png +:alt: Deformed image +:width: 640px + +Deformed image +::: + +:::{figure} CheckerBoard.png +:alt: CheckerBoard image +:width: 640px + +CheckerBoard image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1,16- +``` + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ThinPlateSplineKernelTransform +``` diff --git a/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.rst b/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.rst deleted file mode 100644 index 7dca14d76..000000000 --- a/src/Core/Transform/DeformAVolumeWithAThinPlateSpline/Documentation.rst +++ /dev/null @@ -1,59 +0,0 @@ -:name: DeformAVolumeWithAThinPlateSpline - -Deform a Volume With a Thin Plate Spline -======================================== - -.. index:: - single: ThinPlateSplineKernelTransform - -Synopsis --------- - - -This example deforms a 3D volume with the thin plate spline. - - -Results -------- - -.. figure:: InputImage.png - :width: 640px - :alt: Input image - - Input image - -.. figure:: DeformedImage.png - :width: 640px - :alt: Deformed image - - Deformed image - -.. figure:: CheckerBoard.png - :width: 640px - :alt: CheckerBoard image - - CheckerBoard image - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1,16- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ThinPlateSplineKernelTransform diff --git a/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.md b/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.md new file mode 100644 index 000000000..6416af904 --- /dev/null +++ b/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.md @@ -0,0 +1,61 @@ +--- +name: GlobalRegistrationTwoImagesAffine +--- + +# Global Registration Two Images (Affine) + +```{index} single: AffineTransform single: ImageRegistrationMethod single: affine +``` + +## Synopsis + +A basic global registration of two images. + +## Results + +:::{figure} fixed.png +:alt: fixed.png +:scale: 70% + +fixed.png +::: + +:::{figure} moving.png +:alt: moving.png +:scale: 70% + +moving.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +Output: + +``` +Final parameters: [1.1921533496320087, 0.10372902569023787, -0.18132002016416124, 1.1464158834351523, 0.0021451859042650244, -0.003039195975788232] +Result = +Metric value = 1836.41 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AffineTransform +``` + +```{eval-rst} +.. breathelink:: itk::ImageRegistrationMethod +``` diff --git a/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.rst b/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.rst deleted file mode 100644 index 4feb36ba6..000000000 --- a/src/Core/Transform/GlobalRegistrationTwoImagesAffine/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: GlobalRegistrationTwoImagesAffine - -Global Registration Two Images (Affine) -======================================= - -.. index:: - single: AffineTransform - single: ImageRegistrationMethod - single: affine - -Synopsis --------- - -A basic global registration of two images. - - -Results -------- - -.. figure:: fixed.png - :scale: 70% - :alt: fixed.png - - fixed.png - -.. figure:: moving.png - :scale: 70% - :alt: moving.png - - moving.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Output:: - - Final parameters: [1.1921533496320087, 0.10372902569023787, -0.18132002016416124, 1.1464158834351523, 0.0021451859042650244, -0.003039195975788232] - Result = - Metric value = 1836.41 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AffineTransform -.. breathelink:: itk::ImageRegistrationMethod diff --git a/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.md b/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.md new file mode 100644 index 000000000..1fd28db5f --- /dev/null +++ b/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.md @@ -0,0 +1,72 @@ +--- +name: GlobalRegistrationTwoImagesBSpline +--- + +# Global Registration of Two Images (BSpline) + +```{index} single: BSplineDeformableTransform single: ImageRegistrationMethod +``` + +## Synopsis + +A global registration of two images. + +## Results + +Output: + +``` +Intial Parameters = +[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] + +Starting Registration +************************************************* +N=50 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= 5410.08 GNORM= 98.7811 +************************************************* +I NFN FUNC GNORM STEPLENGTH +1 2 5173.917 47.318 0.010 +2 8 1312.526 35.022 67.448 +3 10 1241.036 21.952 0.095 +4 11 1214.603 20.777 0.500 +5 12 1169.045 47.965 0.500 +6 13 1066.160 73.507 0.500 +7 14 750.612 84.979 0.500 +8 16 427.232 44.597 0.235 +9 17 371.768 44.133 0.500 +10 19 320.897 30.003 0.054 +11 20 319.018 23.934 0.500 +12 21 276.782 16.253 0.500 +13 22 190.496 16.864 0.500 +14 23 121.434 17.719 0.500 +15 24 80.920 23.984 0.500 +16 25 50.736 11.243 0.500 +17 26 40.862 5.633 0.500 +THE MINIMIZATION TERMINATED WITHOUT DETECTING ERRORS. +Optimizer stop condition = LBFGSOptimizer: Failure +Last Transform Parameters +[0.000004242652759130258, -0.09801257315348906, -0.3773136074775823, 0.04057356343246512, 0.011460974084144235, 0.046750769129838214, 5.442980649652609, -1.3233672220673571, 10.138325385009857, 1.2593858799352904, 0.1744432989808139, 27.255697794222773, 18.42787109104701, 27.82714519423285, 3.443535460389487, 0.04083243642873029, 5.114318164332667, 0.5697948754499333, 5.4282475197978695, 0.7721289215254623, -0.00001989578361620887, -0.034703497612920686, -0.08550784338556144, 0.006239176991931418, 0.001367593141535802, -4.808966670313369e-7, -0.2187505995413243, -1.8087191436710883, -0.9922884310554664, -0.014742349905146031, 0.003053794283557083, -11.874136737768657, -75.22296974556679, -33.96218955913907, -0.42061613449053764, 0.011561263304423593, -0.7922226379398286, -7.185598670736005, 0.7735213860631797, 0.1316131069607225, 0.0033284552078211094, 10.085406006964824, 56.37568206497135, 25.246189532623205, 0.3387536225030382, 0.000015865649566500348, 0.11028526291334259, 0.6117750781918082, 0.26063979972963747, 0.0029171257653189493] +``` + +:::{figure} GlobalRegistrationTwoImagesBSpline.png +:scale: 70% + +Output Image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BSplineDeformableTransform +``` + +```{eval-rst} +.. breathelink:: itk::ImageRegistrationMethod +``` diff --git a/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.rst b/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.rst deleted file mode 100644 index d4682520c..000000000 --- a/src/Core/Transform/GlobalRegistrationTwoImagesBSpline/Documentation.rst +++ /dev/null @@ -1,68 +0,0 @@ -:name: GlobalRegistrationTwoImagesBSpline - -Global Registration of Two Images (BSpline) -=========================================== - -.. index:: - single: BSplineDeformableTransform - single: ImageRegistrationMethod - -Synopsis --------- - -A global registration of two images. - - -Results -------- -Output:: - - Intial Parameters = - [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] - - Starting Registration - ************************************************* - N=50 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= 5410.08 GNORM= 98.7811 - ************************************************* - I NFN FUNC GNORM STEPLENGTH - 1 2 5173.917 47.318 0.010 - 2 8 1312.526 35.022 67.448 - 3 10 1241.036 21.952 0.095 - 4 11 1214.603 20.777 0.500 - 5 12 1169.045 47.965 0.500 - 6 13 1066.160 73.507 0.500 - 7 14 750.612 84.979 0.500 - 8 16 427.232 44.597 0.235 - 9 17 371.768 44.133 0.500 - 10 19 320.897 30.003 0.054 - 11 20 319.018 23.934 0.500 - 12 21 276.782 16.253 0.500 - 13 22 190.496 16.864 0.500 - 14 23 121.434 17.719 0.500 - 15 24 80.920 23.984 0.500 - 16 25 50.736 11.243 0.500 - 17 26 40.862 5.633 0.500 - THE MINIMIZATION TERMINATED WITHOUT DETECTING ERRORS. - Optimizer stop condition = LBFGSOptimizer: Failure - Last Transform Parameters - [0.000004242652759130258, -0.09801257315348906, -0.3773136074775823, 0.04057356343246512, 0.011460974084144235, 0.046750769129838214, 5.442980649652609, -1.3233672220673571, 10.138325385009857, 1.2593858799352904, 0.1744432989808139, 27.255697794222773, 18.42787109104701, 27.82714519423285, 3.443535460389487, 0.04083243642873029, 5.114318164332667, 0.5697948754499333, 5.4282475197978695, 0.7721289215254623, -0.00001989578361620887, -0.034703497612920686, -0.08550784338556144, 0.006239176991931418, 0.001367593141535802, -4.808966670313369e-7, -0.2187505995413243, -1.8087191436710883, -0.9922884310554664, -0.014742349905146031, 0.003053794283557083, -11.874136737768657, -75.22296974556679, -33.96218955913907, -0.42061613449053764, 0.011561263304423593, -0.7922226379398286, -7.185598670736005, 0.7735213860631797, 0.1316131069607225, 0.0033284552078211094, 10.085406006964824, 56.37568206497135, 25.246189532623205, 0.3387536225030382, 0.000015865649566500348, 0.11028526291334259, 0.6117750781918082, 0.26063979972963747, 0.0029171257653189493] - -.. figure:: GlobalRegistrationTwoImagesBSpline.png - :scale: 70% - - Output Image - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BSplineDeformableTransform -.. breathelink:: itk::ImageRegistrationMethod diff --git a/src/Core/Transform/MutualInformationAffine/Documentation.md b/src/Core/Transform/MutualInformationAffine/Documentation.md new file mode 100644 index 000000000..db94141b5 --- /dev/null +++ b/src/Core/Transform/MutualInformationAffine/Documentation.md @@ -0,0 +1,78 @@ +--- +name: MutualInformationAffine +--- + +# Mutual Information Affine + +```{index} single: AffineTransform single: MutualInformationImageToImageMetric single: GradientDescentOptimizer +``` + +```{toctree} +:maxdepth: 1 + +MutualInformationAffine.ipynb +``` + +## Synopsis + +Global registration by maximizing the mutual information and using an affine transform. + +## Results + +:::{figure} fixed.png +:alt: fixed.png + +Fixed +::: + +:::{figure} moving.png +:alt: moving.png + +Moving +::: + +:::{figure} OutputBaseline.png +:alt: OutputBaseline.png + +Output +::: + +Output: + +``` +Optimizer stop condition: GradientDescentOptimizer: Maximum number of iterations (200) exceeded. +Final Parameters: [1.0028069041777101, -0.009647107048100798, -0.010717116855425006, 1.0029040091646872, 13.26279335943067, 12.226979744206531] + +Result = + Iterations = 200 + Metric value = 0.000971698 + Numb. Samples = 567 +``` + +## Jupyter Notebook + +```{image} https://mybinder.org/badge_logo.svg +:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FCore%2FTransform%2FMutualInformationAffine%2FMutualInformationAffine.ipynb +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AffineTransform +``` + +```{eval-rst} +.. breathelink:: itk::MutualInformationImageToImageMetric +``` + +```{eval-rst} +.. breathelink:: itk::GradientDescentOptimizer +``` diff --git a/src/Core/Transform/MutualInformationAffine/Documentation.rst b/src/Core/Transform/MutualInformationAffine/Documentation.rst deleted file mode 100644 index c13e4b84d..000000000 --- a/src/Core/Transform/MutualInformationAffine/Documentation.rst +++ /dev/null @@ -1,72 +0,0 @@ -:name: MutualInformationAffine - -Mutual Information Affine -========================= - -.. index:: - single: AffineTransform - single: MutualInformationImageToImageMetric - single: GradientDescentOptimizer - -.. toctree:: - :maxdepth: 1 - - MutualInformationAffine.ipynb - -Synopsis --------- - -Global registration by maximizing the mutual information and using an affine transform. - - -Results -------- - -.. figure:: fixed.png - :alt: fixed.png - - Fixed - -.. figure:: moving.png - :alt: moving.png - - Moving - -.. figure:: OutputBaseline.png - :alt: OutputBaseline.png - - Output - -Output:: - - Optimizer stop condition: GradientDescentOptimizer: Maximum number of iterations (200) exceeded. - Final Parameters: [1.0028069041777101, -0.009647107048100798, -0.010717116855425006, 1.0029040091646872, 13.26279335943067, 12.226979744206531] - - Result = - Iterations = 200 - Metric value = 0.000971698 - Numb. Samples = 567 - -Jupyter Notebook ----------------- - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FCore%2FTransform%2FMutualInformationAffine%2FMutualInformationAffine.ipynb - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AffineTransform -.. breathelink:: itk::MutualInformationImageToImageMetric -.. breathelink:: itk::GradientDescentOptimizer diff --git a/src/Core/Transform/ScaleAnImage/Documentation.md b/src/Core/Transform/ScaleAnImage/Documentation.md new file mode 100644 index 000000000..0bcf13b5c --- /dev/null +++ b/src/Core/Transform/ScaleAnImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ScaleAnImage +--- + +# Scale an Image + +```{index} single: ScaleTransform +``` + +## Synopsis + +Scale an image. + +## Results + +:::{figure} ScaleAnImageInput.png +:alt: Generated Input Image +:scale: 70% + +Input Image +::: + +:::{figure} ScaleAnImageOutputBaseline.png +:alt: Generated Output Image +:scale: 70% + +Output Image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +Python +... + +```{literalinclude} Code.py +:lines: 21- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScaleTransform +``` diff --git a/src/Core/Transform/ScaleAnImage/Documentation.rst b/src/Core/Transform/ScaleAnImage/Documentation.rst deleted file mode 100644 index b8d96269a..000000000 --- a/src/Core/Transform/ScaleAnImage/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: ScaleAnImage - -Scale an Image -============== - -.. index:: - single: ScaleTransform - -Synopsis --------- - -Scale an image. - - -Results -------- -.. figure:: ScaleAnImageInput.png - :scale: 70% - :alt: Generated Input Image - - Input Image - -.. figure:: ScaleAnImageOutputBaseline.png - :scale: 70% - :alt: Generated Output Image - - Output Image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -... - -.. literalinclude:: Code.py - :lines: 21- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScaleTransform diff --git a/src/Core/Transform/TranslateAVectorImage/Documentation.md b/src/Core/Transform/TranslateAVectorImage/Documentation.md new file mode 100644 index 000000000..6e15c4a5f --- /dev/null +++ b/src/Core/Transform/TranslateAVectorImage/Documentation.md @@ -0,0 +1,28 @@ +--- +name: TranslateAVectorImage +--- + +# Translate a Vector Image + +```{index} single: TranslationTransform pair: vector; image +``` + +## Synopsis + +Translate a vector image. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TranslationTransform +``` diff --git a/src/Core/Transform/TranslateAVectorImage/Documentation.rst b/src/Core/Transform/TranslateAVectorImage/Documentation.rst deleted file mode 100644 index 902ca5948..000000000 --- a/src/Core/Transform/TranslateAVectorImage/Documentation.rst +++ /dev/null @@ -1,31 +0,0 @@ -:name: TranslateAVectorImage - -Translate a Vector Image -======================== - -.. index:: - single: TranslationTransform - pair: vector; image - -Synopsis --------- - -Translate a vector image. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::TranslationTransform diff --git a/src/Core/Transform/TranslateImage/Documentation.md b/src/Core/Transform/TranslateImage/Documentation.md new file mode 100644 index 000000000..87f1d5116 --- /dev/null +++ b/src/Core/Transform/TranslateImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: TranslateImage +--- + +# Translate Image + +```{index} single: TranslationTransform +``` + +## Synopsis + +Translate one itk::Image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TranslationTransform +``` diff --git a/src/Core/Transform/TranslateImage/Documentation.rst b/src/Core/Transform/TranslateImage/Documentation.rst deleted file mode 100644 index f80b5feac..000000000 --- a/src/Core/Transform/TranslateImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: TranslateImage - -Translate Image -=============== - -.. index:: - single: TranslationTransform - -Synopsis --------- - -Translate one itk::Image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TranslationTransform diff --git a/src/Core/Transform/index.md b/src/Core/Transform/index.md new file mode 100644 index 000000000..64925cd43 --- /dev/null +++ b/src/Core/Transform/index.md @@ -0,0 +1,17 @@ +# Transform + +```{toctree} +:maxdepth: 1 + +ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.rst +CartesianToAzimuthElevation/Documentation.rst +CopyACompositeTransform/Documentation.rst +CopyANonCompositeTransform/Documentation.rst +GlobalRegistrationTwoImagesAffine/Documentation.rst +GlobalRegistrationTwoImagesBSpline/Documentation.rst +MutualInformationAffine/Documentation.rst +ScaleAnImage/Documentation.rst +TranslateAVectorImage/Documentation.rst +TranslateImage/Documentation.rst +DeformAVolumeWithAThinPlateSpline/Documentation.rst +``` diff --git a/src/Core/Transform/index.rst b/src/Core/Transform/index.rst deleted file mode 100644 index 9971259d8..000000000 --- a/src/Core/Transform/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -Transform -========= - -.. toctree:: - :maxdepth: 1 - - ApplyAffineTransformFromHomogeneousMatrixAndResample/Documentation.rst - CartesianToAzimuthElevation/Documentation.rst - CopyACompositeTransform/Documentation.rst - CopyANonCompositeTransform/Documentation.rst - GlobalRegistrationTwoImagesAffine/Documentation.rst - GlobalRegistrationTwoImagesBSpline/Documentation.rst - MutualInformationAffine/Documentation.rst - ScaleAnImage/Documentation.rst - TranslateAVectorImage/Documentation.rst - TranslateImage/Documentation.rst - DeformAVolumeWithAThinPlateSpline/Documentation.rst diff --git a/src/Core/index.md b/src/Core/index.md new file mode 100644 index 000000000..2928e2478 --- /dev/null +++ b/src/Core/index.md @@ -0,0 +1,14 @@ +# Core + +```{toctree} +:maxdepth: 2 + +Common/index.rst +ImageAdaptors/index.rst +ImageFunction/index.rst +Mesh/index.rst +QuadEdgeMesh/index.rst +SpatialObjects/index.rst +TestKernel/index.rst +Transform/index.rst +``` diff --git a/src/Core/index.rst b/src/Core/index.rst deleted file mode 100644 index 55b893c1a..000000000 --- a/src/Core/index.rst +++ /dev/null @@ -1,14 +0,0 @@ -Core -==== - -.. toctree:: - :maxdepth: 2 - - Common/index.rst - ImageAdaptors/index.rst - ImageFunction/index.rst - Mesh/index.rst - QuadEdgeMesh/index.rst - SpatialObjects/index.rst - TestKernel/index.rst - Transform/index.rst diff --git a/src/External/index.md b/src/External/index.md new file mode 100644 index 000000000..6871d98a5 --- /dev/null +++ b/src/External/index.md @@ -0,0 +1,5 @@ +# External + +```{toctree} +:maxdepth: 2 +``` diff --git a/src/External/index.rst b/src/External/index.rst deleted file mode 100644 index b8e4fb9ef..000000000 --- a/src/External/index.rst +++ /dev/null @@ -1,5 +0,0 @@ -External -======== - -.. toctree:: - :maxdepth: 2 diff --git a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.md b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.md new file mode 100644 index 000000000..4f05db830 --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeCurvatureAnisotropicDiffusion +--- + +# Compute Curvature Anisotropic Diffusion + +```{index} single: CurvatureAnisotropicDiffusionImageFilter +``` + +## Synopsis + +Perform anisotropic diffusion on an image. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CurvatureAnisotropicDiffusionImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.rst b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.rst deleted file mode 100644 index 728df2ebf..000000000 --- a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ComputeCurvatureAnisotropicDiffusion - -Compute Curvature Anisotropic Diffusion -======================================= - -.. index:: - single: CurvatureAnisotropicDiffusionImageFilter - -Synopsis --------- - -Perform anisotropic diffusion on an image. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CurvatureAnisotropicDiffusionImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.md b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.md new file mode 100644 index 000000000..b4750ee5b --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeCurvatureFlow +--- + +# Compute Curvature Flow + +```{index} single: CurvatureFlowImageFilter +``` + +## Synopsis + +Denoise an image using curvature driven flow. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CurvatureFlowImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.rst b/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.rst deleted file mode 100644 index 0ee3d4c7c..000000000 --- a/src/Filtering/AnisotropicSmoothing/ComputeCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ComputeCurvatureFlow - -Compute Curvature Flow -====================== - -.. index:: - single: CurvatureFlowImageFilter - -Synopsis --------- - -Denoise an image using curvature driven flow. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CurvatureFlowImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.md b/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.md new file mode 100644 index 000000000..4cc52806a --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeGradientAnisotropicDiffusion +--- + +# Compute Gradient Anisotropic Diffusion + +```{index} single: GradientAnisotropicDiffusionImageFilter +``` + +## Synopsis + +Perform anisotropic diffusion on an image. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientAnisotropicDiffusionImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.rst b/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.rst deleted file mode 100644 index bc3550969..000000000 --- a/src/Filtering/AnisotropicSmoothing/ComputeGradientAnisotropicDiffusion/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ComputeGradientAnisotropicDiffusion - -Compute Gradient Anisotropic Diffusion -====================================== - -.. index:: - single: GradientAnisotropicDiffusionImageFilter - -Synopsis --------- - -Perform anisotropic diffusion on an image. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientAnisotropicDiffusionImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.md b/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.md new file mode 100644 index 000000000..686392388 --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.md @@ -0,0 +1,43 @@ +--- +name: ComputePeronaMalikAnisotropicDiffusion +--- + +# Perona Malik Anisotropic Diffusion on Grayscale Image + +```{index} single: GradientAnisotropicDiffusionImageFilter single: smooth +``` + +## Synopsis + +Perona Malik Anisotropic Diffusion for scalar valued images. + +## Results + +:::{figure} ComputePeronaMalikAnisotropicDiffusionComparison.png +:alt: Anisotropic diffusion comparison. +:scale: 50% + +Before anisotropic diffusion (left) and after anisotropic diffusion +(right). +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientAnisotropicDiffusionImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.rst b/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.rst deleted file mode 100644 index 5cde4b833..000000000 --- a/src/Filtering/AnisotropicSmoothing/ComputePeronaMalikAnisotropicDiffusion/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: ComputePeronaMalikAnisotropicDiffusion - -Perona Malik Anisotropic Diffusion on Grayscale Image -===================================================== - -.. index:: - single: GradientAnisotropicDiffusionImageFilter - single: smooth - -Synopsis --------- - -Perona Malik Anisotropic Diffusion for scalar valued images. - - -Results -------- - -.. figure:: ComputePeronaMalikAnisotropicDiffusionComparison.png - :scale: 50% - :alt: Anisotropic diffusion comparison. - - Before anisotropic diffusion (left) and after anisotropic diffusion - (right). - - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientAnisotropicDiffusionImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.md b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.md new file mode 100644 index 000000000..b91dafaf1 --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SmoothImageWhilePreservingEdges +--- + +# Smooth Image While Preserving Edges + +```{index} single: VectorGradientAnisotropicDiffusionImageFilter single: smooth +``` + +## Synopsis + +Smooth an image while preserving edges. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} SmoothImageWhilePreservingEdges.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorGradientAnisotropicDiffusionImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.rst b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.rst deleted file mode 100644 index 5f2a67824..000000000 --- a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: SmoothImageWhilePreservingEdges - -Smooth Image While Preserving Edges -=================================== - -.. index:: - single: VectorGradientAnisotropicDiffusionImageFilter - single: smooth - -Synopsis --------- - -Smooth an image while preserving edges. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: SmoothImageWhilePreservingEdges.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorGradientAnisotropicDiffusionImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.md b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.md new file mode 100644 index 000000000..4f052e637 --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SmoothImageWhilePreservingEdges2 +--- + +# Smooth Image While Preserving Edges (Curvature) + +```{index} single: VectorCurvatureAnisotropicDiffusionImageFilter single: curvature pair: smooth; image pair: preserve; edges +``` + +## Synopsis + +Smooth an image while preserving edges. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} SmoothImageWhilePreservingEdges2.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorCurvatureAnisotropicDiffusionImageFilter +``` diff --git a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.rst b/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.rst deleted file mode 100644 index 821fa116e..000000000 --- a/src/Filtering/AnisotropicSmoothing/SmoothImageWhilePreservingEdges2/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: SmoothImageWhilePreservingEdges2 - -Smooth Image While Preserving Edges (Curvature) -=============================================== - -.. index:: - single: VectorCurvatureAnisotropicDiffusionImageFilter - single: curvature - pair: smooth; image - pair: preserve; edges - -Synopsis --------- - -Smooth an image while preserving edges. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: SmoothImageWhilePreservingEdges2.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorCurvatureAnisotropicDiffusionImageFilter diff --git a/src/Filtering/AnisotropicSmoothing/index.md b/src/Filtering/AnisotropicSmoothing/index.md new file mode 100644 index 000000000..7fa4fbc43 --- /dev/null +++ b/src/Filtering/AnisotropicSmoothing/index.md @@ -0,0 +1,12 @@ +# AnisotropicSmoothing + +```{toctree} +:maxdepth: 1 + +ComputeCurvatureAnisotropicDiffusion/Documentation.rst +ComputeCurvatureFlow/Documentation.rst +ComputeGradientAnisotropicDiffusion/Documentation.rst +ComputePeronaMalikAnisotropicDiffusion/Documentation.rst +SmoothImageWhilePreservingEdges/Documentation.rst +SmoothImageWhilePreservingEdges2/Documentation.rst +``` diff --git a/src/Filtering/AnisotropicSmoothing/index.rst b/src/Filtering/AnisotropicSmoothing/index.rst deleted file mode 100644 index 29932d415..000000000 --- a/src/Filtering/AnisotropicSmoothing/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -AnisotropicSmoothing -==================== - -.. toctree:: - :maxdepth: 1 - - ComputeCurvatureAnisotropicDiffusion/Documentation.rst - ComputeCurvatureFlow/Documentation.rst - ComputeGradientAnisotropicDiffusion/Documentation.rst - ComputePeronaMalikAnisotropicDiffusion/Documentation.rst - SmoothImageWhilePreservingEdges/Documentation.rst - SmoothImageWhilePreservingEdges2/Documentation.rst diff --git a/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.md b/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.md new file mode 100644 index 000000000..ab3544c92 --- /dev/null +++ b/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.md @@ -0,0 +1,53 @@ +--- +name: SmoothBinaryImageBeforeSurfaceExtraction +--- + +# Smooth Binary Image Before Surface Extraction + +```{index} single: AntiAliasBinaryImageFilter single: smooth +``` + +## Synopsis + +This example introduces the use of the `AntiAliasBinaryImageFilter`. This +filter expects a binary mask as input. With level sets, it smooths the image +by keeping the edge of the structure within a one pixel distance from the +original location. It is usually desirable to run this filter before +extracting an isocontour with surface extraction methods. + +## Results + +:::{figure} VentricleModel.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 100% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AntiAliasBinaryImageFilter +``` diff --git a/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.rst b/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.rst deleted file mode 100644 index fed1282d9..000000000 --- a/src/Filtering/AntiAlias/SmoothBinaryImageBeforeSurfaceExtraction/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: SmoothBinaryImageBeforeSurfaceExtraction - -Smooth Binary Image Before Surface Extraction -============================================= - -.. index:: - single: AntiAliasBinaryImageFilter - single: smooth - -Synopsis --------- - -This example introduces the use of the `AntiAliasBinaryImageFilter`. This -filter expects a binary mask as input. With level sets, it smooths the image -by keeping the edge of the structure within a one pixel distance from the -original location. It is usually desirable to run this filter before -extracting an isocontour with surface extraction methods. - - -Results -------- - -.. figure:: VentricleModel.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 100% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AntiAliasBinaryImageFilter diff --git a/src/Filtering/AntiAlias/index.md b/src/Filtering/AntiAlias/index.md new file mode 100644 index 000000000..469adab18 --- /dev/null +++ b/src/Filtering/AntiAlias/index.md @@ -0,0 +1,7 @@ +# AntiAlias + +```{toctree} +:maxdepth: 1 + +SmoothBinaryImageBeforeSurfaceExtraction/Documentation.rst +``` diff --git a/src/Filtering/AntiAlias/index.rst b/src/Filtering/AntiAlias/index.rst deleted file mode 100644 index eacbe8d6c..000000000 --- a/src/Filtering/AntiAlias/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -AntiAlias -========= - -.. toctree:: - :maxdepth: 1 - - SmoothBinaryImageBeforeSurfaceExtraction/Documentation.rst diff --git a/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.md new file mode 100644 index 000000000..192704977 --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ClosingBinaryImage +--- + +# Closing Binary Image + +```{index} single: BinaryMorphologicalClosingImageFilter pair: binary; image +``` + +## Synopsis + +Closing a binary image. + +## Results + +:::{figure} ClosingBinaryImageQuickView.png +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Radius: 5 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryMorphologicalClosingImageFilter +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.rst deleted file mode 100644 index 3a3cdfd79..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/ClosingBinaryImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: ClosingBinaryImage - -Closing Binary Image -==================== - -.. index:: - single: BinaryMorphologicalClosingImageFilter - pair: binary; image - -Synopsis --------- - -Closing a binary image. - - -Results -------- - -.. figure:: ClosingBinaryImageQuickView.png - :scale: 70% - - Output In VTK Window - -Output:: - - Radius: 5 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryMorphologicalClosingImageFilter diff --git a/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.md new file mode 100644 index 000000000..3bf7bf50a --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.md @@ -0,0 +1,61 @@ +--- +name: DilateABinaryImage +substitutions: + input: |- + ```{image} Yinyang.png + :alt: Input yin-yang image. + :scale: 50% + ``` + input_caption: Input binary image. + output: |- + ```{image} OutputBaseline.png + :alt: Dilated output. + :scale: 50% + ``` + output_caption: Dilated output image. +--- + +# Dilate a Binary Image + +```{index} single: BinaryBallStructuringElement single: BinaryDilateImageFilter pair: mathematical morphology; dilation pair: BinaryBallStructuringElement; SetRadius +``` + +:::{seealso} +dilation; erosion +::: + +## Synopsis + +Dilate regions by using a specified kernel, also known as a structuring element. +In this example, the white regions are enlarged. + +## Results + +```{eval-rst} ++-----------------+------------------+ +| |input| | |output| | ++ + + +| |input_caption| | |output_caption| | ++-----------------+------------------+ +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryDilateImageFilter itk::BinaryBallStructuringElement +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.rst deleted file mode 100644 index d08587b1d..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.rst +++ /dev/null @@ -1,64 +0,0 @@ -:name: DilateABinaryImage - -Dilate a Binary Image -===================== - -.. index:: - single: BinaryBallStructuringElement - single: BinaryDilateImageFilter - pair: mathematical morphology; dilation - pair: BinaryBallStructuringElement; SetRadius - -.. seealso:: dilation; erosion - - -Synopsis --------- - -Dilate regions by using a specified kernel, also known as a structuring element. -In this example, the white regions are enlarged. - - -Results -------- - -.. |input| image:: Yinyang.png - :scale: 50% - :alt: Input yin-yang image. - -.. |output| image:: OutputBaseline.png - :scale: 50% - :alt: Dilated output. - -.. |input_caption| replace:: Input binary image. - -.. |output_caption| replace:: Dilated output image. - -+-----------------+------------------+ -| |input| | |output| | -+ + + -| |input_caption| | |output_caption| | -+-----------------+------------------+ - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryDilateImageFilter itk::BinaryBallStructuringElement diff --git a/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.md new file mode 100644 index 000000000..446eddc26 --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.md @@ -0,0 +1,60 @@ +--- +name: ErodeABinaryImage +substitutions: + input: |- + ```{image} Yinyang.png + :alt: Input yin-yang image. + :scale: 50% + ``` + input_caption: Input binary image. + output: |- + ```{image} OutputBaseline.png + :alt: Eroded output. + :scale: 50% + ``` + output_caption: Eroded output image. +--- + +# Erode a Binary Image + +```{index} single: BinaryBallStructuringElement single: BinaryErodeImageFilter pair: mathematical morphology; erosion pair: BinaryBallStructuringElement; SetRadius +``` + +:::{seealso} +erosion; dilation +::: + +## Synopsis + +Erode regions by using a specified kernel, also known as a structuring element. In this example, the white regions shrink. + +## Results + +```{eval-rst} ++-----------------+------------------+ +| |input| | |output| | ++ + + +| |input_caption| | |output_caption| | ++-----------------+------------------+ +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryErodeImageFilter itk::BinaryBallStructuringElement +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.rst deleted file mode 100644 index f13be6f4c..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/ErodeABinaryImage/Documentation.rst +++ /dev/null @@ -1,62 +0,0 @@ -:name: ErodeABinaryImage - -Erode a Binary Image -==================== - -.. index:: - single: BinaryBallStructuringElement - single: BinaryErodeImageFilter - pair: mathematical morphology; erosion - pair: BinaryBallStructuringElement; SetRadius - -.. seealso:: erosion; dilation - - -Synopsis --------- -Erode regions by using a specified kernel, also known as a structuring element. In this example, the white regions shrink. - - -Results -------- - -.. |input| image:: Yinyang.png - :scale: 50% - :alt: Input yin-yang image. - -.. |output| image:: OutputBaseline.png - :scale: 50% - :alt: Eroded output. - -.. |input_caption| replace:: Input binary image. - -.. |output_caption| replace:: Eroded output image. - -+-----------------+------------------+ -| |input| | |output| | -+ + + -| |input_caption| | |output_caption| | -+-----------------+------------------+ - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryErodeImageFilter itk::BinaryBallStructuringElement diff --git a/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.md new file mode 100644 index 000000000..5ec5f035d --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: OpeningBinaryImage +--- + +# Opening a Binary Image + +```{index} single: BinaryMorphologicalOpeningImageFilter single: binary; image +``` + +## Synopsis + +Opening a binary image. + +## Results + +:::{figure} OpeningBinaryImageQuickView.png +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Radius: 5 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryMorphologicalOpeningImageFilter +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.rst deleted file mode 100644 index b1c8b348d..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/OpeningBinaryImage/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: OpeningBinaryImage - -Opening a Binary Image -====================== - -.. index:: - single: BinaryMorphologicalOpeningImageFilter - single: binary; image - -Synopsis --------- - -Opening a binary image. - - -Results -------- -.. figure:: OpeningBinaryImageQuickView.png - :scale: 70% - - Output In VTK Window - -Output:: - - Radius: 5 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryMorphologicalOpeningImageFilter diff --git a/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.md new file mode 100644 index 000000000..e13d3e978 --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: PruneBinaryImage +--- + +# Prune Binary Image + +```{index} single: BinaryPruningImageFilter pair: prune; image +``` + +## Synopsis + +Prune a binary image. + +## Results + +:::{figure} PruneBinaryImageQuickView.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryPruningImageFilter +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.rst deleted file mode 100644 index e79511b33..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/PruneBinaryImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: PruneBinaryImage - -Prune Binary Image -================== - -.. index:: - single: BinaryPruningImageFilter - pair: prune; image - -Synopsis --------- - -Prune a binary image. - - -Results -------- -.. figure:: PruneBinaryImageQuickView.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryPruningImageFilter diff --git a/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.md b/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.md new file mode 100644 index 000000000..7a06abf70 --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ThinImage +--- + +# Thin Image + +```{index} single: BinaryThinningImageFilter +``` + +## Synopsis + +Skeletonix/thin an image. + +## Results + +:::{figure} Input.png +:alt: Input.png +:scale: 70% + +input.png +::: + +:::{figure} OutputBaseline.png +:alt: OutputBaseline.png +:scale: 70% + +OutputBaseline.png +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryThinningImageFilter +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.rst b/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.rst deleted file mode 100644 index 65577cdac..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/ThinImage/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: ThinImage - -Thin Image -========== - -.. index:: - single: BinaryThinningImageFilter - -Synopsis --------- - -Skeletonix/thin an image. - - -Results -------- -.. figure:: Input.png - :scale: 70% - :alt: Input.png - - input.png - -.. figure:: OutputBaseline.png - :scale: 70% - :alt: OutputBaseline.png - - OutputBaseline.png - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryThinningImageFilter diff --git a/src/Filtering/BinaryMathematicalMorphology/index.md b/src/Filtering/BinaryMathematicalMorphology/index.md new file mode 100644 index 000000000..a78962cc3 --- /dev/null +++ b/src/Filtering/BinaryMathematicalMorphology/index.md @@ -0,0 +1,12 @@ +# Binary Mathematical Morphology + +```{toctree} +:maxdepth: 1 + +ClosingBinaryImage/Documentation.rst +DilateABinaryImage/Documentation.rst +ErodeABinaryImage/Documentation.rst +OpeningBinaryImage/Documentation.rst +PruneBinaryImage/Documentation.rst +ThinImage/Documentation.rst +``` diff --git a/src/Filtering/BinaryMathematicalMorphology/index.rst b/src/Filtering/BinaryMathematicalMorphology/index.rst deleted file mode 100644 index 7b1136de1..000000000 --- a/src/Filtering/BinaryMathematicalMorphology/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -Binary Mathematical Morphology -============================== - -.. toctree:: - :maxdepth: 1 - - ClosingBinaryImage/Documentation.rst - DilateABinaryImage/Documentation.rst - ErodeABinaryImage/Documentation.rst - OpeningBinaryImage/Documentation.rst - PruneBinaryImage/Documentation.rst - ThinImage/Documentation.rst diff --git a/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.md b/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.md new file mode 100644 index 000000000..719b543ae --- /dev/null +++ b/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ApplyAColormapToAnImage +--- + +# Apply a Color Map to an Image + +```{index} single: ScalarToRGBColormapImageFilter +``` + +## Synopsis + +Apply a color map to an image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarToRGBColormapImageFilter +``` diff --git a/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.rst b/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.rst deleted file mode 100644 index 4e759c105..000000000 --- a/src/Filtering/Colormap/ApplyAColormapToAnImage/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: ApplyAColormapToAnImage - -Apply a Color Map to an Image -============================= - -.. index:: - single: ScalarToRGBColormapImageFilter - -Synopsis --------- - - -Apply a color map to an image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarToRGBColormapImageFilter diff --git a/src/Filtering/Colormap/CreateACustomColormap/Documentation.md b/src/Filtering/Colormap/CreateACustomColormap/Documentation.md new file mode 100644 index 000000000..44fbe87b3 --- /dev/null +++ b/src/Filtering/Colormap/CreateACustomColormap/Documentation.md @@ -0,0 +1,59 @@ +--- +name: CreateACustomColormap +--- + +# Create a Custom Color Map + +```{index} single: CustomColormapFunction single: MersenneTwisterRandomVariateGenerator single: ScalarToRGBColormapImageFilter +``` + +## Synopsis + +Create and apply a custom colormap. + +:::{note} +Python wrapping for CustomColormapFunction and the MersenneTwisterRandomVariateGenerator was introduced in ITK 4.8.0. +::: + +## Results + +:::{figure} sf4.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Function::CustomColormapFunction +``` + +```{eval-rst} +.. breathelink:: itk::ScalarToRGBColormapImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator +``` diff --git a/src/Filtering/Colormap/CreateACustomColormap/Documentation.rst b/src/Filtering/Colormap/CreateACustomColormap/Documentation.rst deleted file mode 100644 index abeec56c3..000000000 --- a/src/Filtering/Colormap/CreateACustomColormap/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: CreateACustomColormap - -Create a Custom Color Map -========================= - -.. index:: - single: CustomColormapFunction - single: MersenneTwisterRandomVariateGenerator - single: ScalarToRGBColormapImageFilter - -Synopsis --------- - -Create and apply a custom colormap. - -.. note:: Python wrapping for CustomColormapFunction and the MersenneTwisterRandomVariateGenerator was introduced in ITK 4.8.0. - - -Results -------- - -.. figure:: sf4.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Function::CustomColormapFunction - -.. breathelink:: itk::ScalarToRGBColormapImageFilter - -.. breathelink:: itk::Statistics::MersenneTwisterRandomVariateGenerator diff --git a/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.md b/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.md new file mode 100644 index 000000000..3d6203574 --- /dev/null +++ b/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.md @@ -0,0 +1,36 @@ +--- +name: MapScalarsIntoJetColormap +--- + +# Map Scalars Into Jet Colormap + +```{index} single: JetColormapFunction pair: scalar; map pair: jet; colormap +``` + +## Synopsis + +Map scalars into a jet colormap. + +## Results + +Output: + +``` +0: 0 0 142 +0.5: 134 255 119 +1: 126 0 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Function::JetColormapFunction +``` diff --git a/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.rst b/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.rst deleted file mode 100644 index a7c2d398d..000000000 --- a/src/Filtering/Colormap/MapScalarsIntoJetColormap/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: MapScalarsIntoJetColormap - -Map Scalars Into Jet Colormap -============================= - -.. index:: - single: JetColormapFunction - pair: scalar; map - pair: jet; colormap - -Synopsis --------- - -Map scalars into a jet colormap. - - -Results -------- -Output:: - - 0: 0 0 142 - 0.5: 134 255 119 - 1: 126 0 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Function::JetColormapFunction diff --git a/src/Filtering/Colormap/index.md b/src/Filtering/Colormap/index.md new file mode 100644 index 000000000..24b4b93ec --- /dev/null +++ b/src/Filtering/Colormap/index.md @@ -0,0 +1,9 @@ +# Colormap + +```{toctree} +:maxdepth: 1 + +ApplyAColormapToAnImage/Documentation.rst +CreateACustomColormap/Documentation.rst +MapScalarsIntoJetColormap/Documentation.rst +``` diff --git a/src/Filtering/Colormap/index.rst b/src/Filtering/Colormap/index.rst deleted file mode 100644 index 22b0908e1..000000000 --- a/src/Filtering/Colormap/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -Colormap -======== - -.. toctree:: - :maxdepth: 1 - - ApplyAColormapToAnImage/Documentation.rst - CreateACustomColormap/Documentation.rst - MapScalarsIntoJetColormap/Documentation.rst diff --git a/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.md b/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.md new file mode 100644 index 000000000..0138480f7 --- /dev/null +++ b/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ColorNormalizedCorrelation +--- + +# Color Normalized Correlation + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: NormalizedCorrelationImageFilter +``` + +## Synopsis + +Color normalized correlation. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalizedCorrelationImageFilter +``` diff --git a/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.rst b/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.rst deleted file mode 100644 index d3b13b0a1..000000000 --- a/src/Filtering/Convolution/ColorNormalizedCorrelation/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ColorNormalizedCorrelation - -Color Normalized Correlation -============================ -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: NormalizedCorrelationImageFilter - -Synopsis --------- - -Color normalized correlation. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalizedCorrelationImageFilter diff --git a/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.md b/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.md new file mode 100644 index 000000000..94cdce8eb --- /dev/null +++ b/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.md @@ -0,0 +1,41 @@ +--- +name: ConvolveImageWithKernel +--- + +# Convolve Image With Kernel + +```{index} single: ConvolutionImageFilter single: convolution +``` + +## Synopsis + +Convolve an image with a kernel. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} ConvolveImageWithKernel.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConvolutionImageFilter +``` diff --git a/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.rst b/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.rst deleted file mode 100644 index bbc825b99..000000000 --- a/src/Filtering/Convolution/ConvolveImageWithKernel/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: ConvolveImageWithKernel - -Convolve Image With Kernel -========================== - -.. index:: - single: ConvolutionImageFilter - single: convolution - -Synopsis --------- - -Convolve an image with a kernel. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: ConvolveImageWithKernel.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConvolutionImageFilter diff --git a/src/Filtering/Convolution/NormalizedCorrelation/Documentation.md b/src/Filtering/Convolution/NormalizedCorrelation/Documentation.md new file mode 100644 index 000000000..c3d2f70b3 --- /dev/null +++ b/src/Filtering/Convolution/NormalizedCorrelation/Documentation.md @@ -0,0 +1,33 @@ +--- +name: NormalizedCorrelation +--- + +# Normalized Correlation + +```{index} single: NormalizedCorrelationImageFilter +``` + +## Synopsis + +Normalized correlation. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalizedCorrelationImageFilter +``` diff --git a/src/Filtering/Convolution/NormalizedCorrelation/Documentation.rst b/src/Filtering/Convolution/NormalizedCorrelation/Documentation.rst deleted file mode 100644 index fa136564b..000000000 --- a/src/Filtering/Convolution/NormalizedCorrelation/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: NormalizedCorrelation - -Normalized Correlation -====================== - -.. index:: - single: NormalizedCorrelationImageFilter - -Synopsis --------- - -Normalized correlation. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalizedCorrelationImageFilter diff --git a/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.md b/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.md new file mode 100644 index 000000000..2ac5d3594 --- /dev/null +++ b/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.md @@ -0,0 +1,70 @@ +--- +name: NormalizedCorrelationOfMaskedImage +--- + +# Normalized Correlation of Masked Image + +```{index} single: NormalizedCorrelationImageFilter pair: correlation; masked +``` + +## Synopsis + +Normalized correlation of a masked image. + +## Results + +:::{figure} mask.png +:alt: mask.png +:scale: 70% + +mask.png +::: + +:::{figure} image1.png +:alt: image1.png +:scale: 70% + +image1.png +::: + +:::{figure} image2.png +:alt: image2.png +:scale: 70% + +image2.png +::: + +:::{figure} NormalizedCorrelationOfMaskedImage.png +:alt: correlation.mha +:scale: 70% + +correlation.mha +::: + +:::{figure} correlation.png +:alt: correlation.png +:scale: 70% + +correlation.png +::: + +Output: + +``` +Maximum location fixed: [20, 6] +Maximum value: 1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalizedCorrelationImageFilter +``` diff --git a/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.rst b/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.rst deleted file mode 100644 index bf34dd257..000000000 --- a/src/Filtering/Convolution/NormalizedCorrelationOfMaskedImage/Documentation.rst +++ /dev/null @@ -1,65 +0,0 @@ -:name: NormalizedCorrelationOfMaskedImage - -Normalized Correlation of Masked Image -====================================== - -.. index:: - single: NormalizedCorrelationImageFilter - pair: correlation; masked - -Synopsis --------- - -Normalized correlation of a masked image. - - -Results -------- -.. figure:: mask.png - :scale: 70% - :alt: mask.png - - mask.png - -.. figure:: image1.png - :scale: 70% - :alt: image1.png - - image1.png - -.. figure:: image2.png - :scale: 70% - :alt: image2.png - - image2.png - -.. figure:: NormalizedCorrelationOfMaskedImage.png - :scale: 70% - :alt: correlation.mha - - correlation.mha - -.. figure:: correlation.png - :scale: 70% - :alt: correlation.png - - correlation.png - -Output:: - - Maximum location fixed: [20, 6] - Maximum value: 1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalizedCorrelationImageFilter diff --git a/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.md b/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.md new file mode 100644 index 000000000..a0e656c59 --- /dev/null +++ b/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.md @@ -0,0 +1,64 @@ +--- +name: NormalizedCorrelationUsingFFT +--- + +# Normalized Correlation Using FFT + +```{index} single: FFTNormalizedCorrelationImageFilter +``` + +## Synopsis + +Normalized correlation using the FFT. + +## Results + +:::{figure} fixedImage.png +:alt: fixedImage.png +:scale: 70% + +fixedImage.png +::: + +:::{figure} movingImage.png +:alt: movingImage.png +:scale: 70% + +movingImage.png +::: + +:::{figure} NormalizedCorrelationUsingFFT.png +:alt: correlation.mha +:scale: 70% + +correlation.mha +::: + +:::{figure} correlation.png +:alt: correlation.png +:scale: 70% + +correlation.png +::: + +Output: + +``` +Maximum location: [45, 44] +Maximum location fixed: [5, 6] +Maximum value: 1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FFTNormalizedCorrelationImageFilter +``` diff --git a/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.rst b/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.rst deleted file mode 100644 index 9385c3fae..000000000 --- a/src/Filtering/Convolution/NormalizedCorrelationUsingFFT/Documentation.rst +++ /dev/null @@ -1,60 +0,0 @@ -:name: NormalizedCorrelationUsingFFT - -Normalized Correlation Using FFT -================================ - -.. index:: - single: FFTNormalizedCorrelationImageFilter - -Synopsis --------- - -Normalized correlation using the FFT. - - -Results -------- -.. figure:: fixedImage.png - :scale: 70% - :alt: fixedImage.png - - fixedImage.png - -.. figure:: movingImage.png - :scale: 70% - :alt: movingImage.png - - movingImage.png - -.. figure:: NormalizedCorrelationUsingFFT.png - :scale: 70% - :alt: correlation.mha - - correlation.mha - -.. figure:: correlation.png - :scale: 70% - :alt: correlation.png - - correlation.png - -Output:: - - Maximum location: [45, 44] - Maximum location fixed: [5, 6] - Maximum value: 1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FFTNormalizedCorrelationImageFilter diff --git a/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.md b/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.md new file mode 100644 index 000000000..b17327c78 --- /dev/null +++ b/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.md @@ -0,0 +1,64 @@ +--- +name: NormalizedCorrelationUsingFFTWithMaskImages +--- + +# Normalized Correlation Using FFT With Mask Images for Input Images + +```{index} single: MaskedFFTNormalizedCorrelationImageFilter pair: masked; input single: FFT +``` + +## Synopsis + +Normalized correlation using the FFT with optional mask images for both input images. + +## Results + +:::{figure} fixedImage.png +:alt: fixedImage.png +:scale: 70% + +fixedImage.png +::: + +:::{figure} movingImage.png +:alt: movingImage.png +:scale: 70% + +movingImage.png +::: + +:::{figure} NormalizedCorrelationUsingFFTWithMaskImages.png +:alt: correlation.mha +:scale: 70% + +correlation.mha +::: + +:::{figure} correlation.png +:alt: correlation.png +:scale: 70% + +correlation.png +::: + +Output: + +``` +Maximum location: [45, 44] +Maximum location fixed: [5, 6] +Maximum value: 1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MaskedFFTNormalizedCorrelationImageFilter +``` diff --git a/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.rst b/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.rst deleted file mode 100644 index ad1363932..000000000 --- a/src/Filtering/Convolution/NormalizedCorrelationUsingFFTWithMaskImages/Documentation.rst +++ /dev/null @@ -1,61 +0,0 @@ -:name: NormalizedCorrelationUsingFFTWithMaskImages - -Normalized Correlation Using FFT With Mask Images for Input Images -================================================================== - -.. index:: - single: MaskedFFTNormalizedCorrelationImageFilter - pair: masked; input - single: FFT - -Synopsis --------- - -Normalized correlation using the FFT with optional mask images for both input images. - - -Results -------- -.. figure:: fixedImage.png - :scale: 70% - :alt: fixedImage.png - - fixedImage.png - -.. figure:: movingImage.png - :scale: 70% - :alt: movingImage.png - - movingImage.png - -.. figure:: NormalizedCorrelationUsingFFTWithMaskImages.png - :scale: 70% - :alt: correlation.mha - - correlation.mha - -.. figure:: correlation.png - :scale: 70% - :alt: correlation.png - - correlation.png - -Output:: - - Maximum location: [45, 44] - Maximum location fixed: [5, 6] - Maximum value: 1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MaskedFFTNormalizedCorrelationImageFilter diff --git a/src/Filtering/Convolution/index.md b/src/Filtering/Convolution/index.md new file mode 100644 index 000000000..aefa82c8d --- /dev/null +++ b/src/Filtering/Convolution/index.md @@ -0,0 +1,12 @@ +# Convolution + +```{toctree} +:maxdepth: 1 + +ColorNormalizedCorrelation/Documentation.rst +ConvolveImageWithKernel/Documentation.rst +NormalizedCorrelation/Documentation.rst +NormalizedCorrelationOfMaskedImage/Documentation.rst +NormalizedCorrelationUsingFFT/Documentation.rst +NormalizedCorrelationUsingFFTWithMaskImages/Documentation.rst +``` diff --git a/src/Filtering/Convolution/index.rst b/src/Filtering/Convolution/index.rst deleted file mode 100644 index dd3bf6849..000000000 --- a/src/Filtering/Convolution/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -Convolution -=========== - -.. toctree:: - :maxdepth: 1 - - ColorNormalizedCorrelation/Documentation.rst - ConvolveImageWithKernel/Documentation.rst - NormalizedCorrelation/Documentation.rst - NormalizedCorrelationOfMaskedImage/Documentation.rst - NormalizedCorrelationUsingFFT/Documentation.rst - NormalizedCorrelationUsingFFTWithMaskImages/Documentation.rst diff --git a/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.md b/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.md new file mode 100644 index 000000000..291e0a8ce --- /dev/null +++ b/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.md @@ -0,0 +1,41 @@ +--- +name: BinaryMinMaxCurvatureFlow +--- + +# Binary Min and Max Curvature Flow of Binary Image + +```{index} single: BinaryMinMaxCurvatureFlowImageFilter pair: curvature; flow pair: binary; image +``` + +## Synopsis + +BinaryMinMaxCurvatureFlow a binary image. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} BinaryMinMaxCurvatureFlow.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryMinMaxCurvatureFlowImageFilter +``` diff --git a/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.rst b/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.rst deleted file mode 100644 index 108835b2b..000000000 --- a/src/Filtering/CurvatureFlow/BinaryMinMaxCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: BinaryMinMaxCurvatureFlow - -Binary Min and Max Curvature Flow of Binary Image -================================================= - -.. index:: - single: BinaryMinMaxCurvatureFlowImageFilter - pair: curvature; flow - pair: binary; image - -Synopsis --------- - -BinaryMinMaxCurvatureFlow a binary image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: BinaryMinMaxCurvatureFlow.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryMinMaxCurvatureFlowImageFilter diff --git a/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.md b/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.md new file mode 100644 index 000000000..ca63a9ac9 --- /dev/null +++ b/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.md @@ -0,0 +1,41 @@ +--- +name: SmoothImageUsingCurvatureFlow +--- + +# Smooth Image Using Curvature Flow + +```{index} single: CurvatureFlowImageFilter pair: curvature; flow single: smooth +``` + +## Synopsis + +Smooth an image using curvature flow. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} SmoothImageUsingCurvatureFlow.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CurvatureFlowImageFilter +``` diff --git a/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.rst b/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.rst deleted file mode 100644 index 7fded9e10..000000000 --- a/src/Filtering/CurvatureFlow/SmoothImageUsingCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: SmoothImageUsingCurvatureFlow - -Smooth Image Using Curvature Flow -================================= - -.. index:: - single: CurvatureFlowImageFilter - pair: curvature; flow - single: smooth - -Synopsis --------- - -Smooth an image using curvature flow. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: SmoothImageUsingCurvatureFlow.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CurvatureFlowImageFilter diff --git a/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.md b/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.md new file mode 100644 index 000000000..b24a48c50 --- /dev/null +++ b/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.md @@ -0,0 +1,41 @@ +--- +name: SmoothImageUsingMinMaxCurvatureFlow +--- + +# Smooth Image Using Min Max Curvature Flow + +```{index} single: MinMaxCurvatureFlowImageFilter pair: curvature; flow pair: min; max +``` + +## Synopsis + +Smooth an image using min/max curvature flow. + +## Results + +:::{figure} Gourds.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} SmoothImageUsingMinMaxCurvatureFlow.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MinMaxCurvatureFlowImageFilter +``` diff --git a/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.rst b/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.rst deleted file mode 100644 index a18bf9da9..000000000 --- a/src/Filtering/CurvatureFlow/SmoothImageUsingMinMaxCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: SmoothImageUsingMinMaxCurvatureFlow - -Smooth Image Using Min Max Curvature Flow -========================================= - -.. index:: - single: MinMaxCurvatureFlowImageFilter - pair: curvature; flow - pair: min; max - -Synopsis --------- - -Smooth an image using min/max curvature flow. - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: SmoothImageUsingMinMaxCurvatureFlow.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MinMaxCurvatureFlowImageFilter diff --git a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.md b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.md new file mode 100644 index 000000000..95395ea7d --- /dev/null +++ b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.md @@ -0,0 +1,41 @@ +--- +name: SmoothRGBImageUsingCurvatureFlow +--- + +# Smooth RGB Image Using Curvature Flow + +```{index} single: CurvatureFlowImageFilter pair: curvature; flow single: RGB +``` + +## Synopsis + +Smooth an RGB image using curvature flow. + +## Results + +:::{figure} Gourds.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} SmoothRGBImageUsingCurvatureFlow.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CurvatureFlowImageFilter +``` diff --git a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.rst b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.rst deleted file mode 100644 index 03ba522eb..000000000 --- a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: SmoothRGBImageUsingCurvatureFlow - -Smooth RGB Image Using Curvature Flow -===================================== - -.. index:: - single: CurvatureFlowImageFilter - pair: curvature; flow - single: RGB - -Synopsis --------- - -Smooth an RGB image using curvature flow. - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: SmoothRGBImageUsingCurvatureFlow.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CurvatureFlowImageFilter diff --git a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.md b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.md new file mode 100644 index 000000000..a5e978341 --- /dev/null +++ b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.md @@ -0,0 +1,41 @@ +--- +name: SmoothRGBImageUsingMinMaxCurvatureFlow +--- + +# Smooth RGB Image Using Min Max Curvature Flow + +```{index} single: MinMaxCurvatureFlowImageFilter single: RGB pair: curvature; flow pair: min; max +``` + +## Synopsis + +Smooth an RGB image using min/max curvature flow. + +## Results + +:::{figure} Gourds.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} SmoothRGBImageUsingMinMaxCurvatureFlow.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MinMaxCurvatureFlowImageFilter +``` diff --git a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.rst b/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.rst deleted file mode 100644 index 2925d1e09..000000000 --- a/src/Filtering/CurvatureFlow/SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: SmoothRGBImageUsingMinMaxCurvatureFlow - -Smooth RGB Image Using Min Max Curvature Flow -============================================= - -.. index:: - single: MinMaxCurvatureFlowImageFilter - single: RGB - pair: curvature; flow - pair: min; max - -Synopsis --------- - -Smooth an RGB image using min/max curvature flow. - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: SmoothRGBImageUsingMinMaxCurvatureFlow.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MinMaxCurvatureFlowImageFilter diff --git a/src/Filtering/CurvatureFlow/index.md b/src/Filtering/CurvatureFlow/index.md new file mode 100644 index 000000000..dcc6b61a3 --- /dev/null +++ b/src/Filtering/CurvatureFlow/index.md @@ -0,0 +1,11 @@ +# CurvatureFlow + +```{toctree} +:maxdepth: 1 + +BinaryMinMaxCurvatureFlow/Documentation.rst +SmoothImageUsingCurvatureFlow/Documentation.rst +SmoothImageUsingMinMaxCurvatureFlow/Documentation.rst +SmoothRGBImageUsingCurvatureFlow/Documentation.rst +SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.rst +``` diff --git a/src/Filtering/CurvatureFlow/index.rst b/src/Filtering/CurvatureFlow/index.rst deleted file mode 100644 index 85f4bf929..000000000 --- a/src/Filtering/CurvatureFlow/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -CurvatureFlow -============= - -.. toctree:: - :maxdepth: 1 - - BinaryMinMaxCurvatureFlow/Documentation.rst - SmoothImageUsingCurvatureFlow/Documentation.rst - SmoothImageUsingMinMaxCurvatureFlow/Documentation.rst - SmoothRGBImageUsingCurvatureFlow/Documentation.rst - SmoothRGBImageUsingMinMaxCurvatureFlow/Documentation.rst diff --git a/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.md b/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.md new file mode 100644 index 000000000..d06963770 --- /dev/null +++ b/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ApproxDistanceMapOfBinary +--- + +# Approximate Distance Map of Binary Image + +```{index} single: ApproximateSignedDistanceMapImageFilter single: distance-map +``` + +## Synopsis + +Compute the distance map from objects in a binary image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ApproximateSignedDistanceMapImageFilter +``` diff --git a/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.rst b/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.rst deleted file mode 100644 index fe4aa3e4c..000000000 --- a/src/Filtering/DistanceMap/ApproxDistanceMapOfBinary/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: ApproxDistanceMapOfBinary - -Approximate Distance Map of Binary Image -======================================== - -.. index:: - single: ApproximateSignedDistanceMapImageFilter - single: distance-map - -Synopsis --------- - -Compute the distance map from objects in a binary image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ApproximateSignedDistanceMapImageFilter diff --git a/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.md b/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.md new file mode 100644 index 000000000..0f34388d3 --- /dev/null +++ b/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.md @@ -0,0 +1,35 @@ +--- +name: MaurerDistanceMapOfBinary +--- + +# Maurer Distance Map of Binary Image + +```{index} single: SignedMaurerDistanceMapImageFilter single: maurer sinlge: distance-map pair: danielsson; distance-map +``` + +## Synopsis + +Compute a distance map from objects in a binary image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SignedMaurerDistanceMapImageFilter +``` diff --git a/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.rst b/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.rst deleted file mode 100644 index 4003d003a..000000000 --- a/src/Filtering/DistanceMap/MaurerDistanceMapOfBinary/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: MaurerDistanceMapOfBinary - -Maurer Distance Map of Binary Image -=================================== - -.. index:: - single: SignedMaurerDistanceMapImageFilter - single: maurer - sinlge: distance-map - pair: danielsson; distance-map - - -Synopsis --------- - -Compute a distance map from objects in a binary image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SignedMaurerDistanceMapImageFilter diff --git a/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.md b/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.md new file mode 100644 index 000000000..9c0d8b63d --- /dev/null +++ b/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.md @@ -0,0 +1,36 @@ +--- +name: MeanDistanceBetweenAllPointsOnTwoCurves +--- + +# Mean Distance Between All Points on Two Curves + +```{index} single: ContourMeanDistanceImageFilter single: mean +``` + +## Synopsis + +Compute the mean distance between all points of two curves. + +## Results + +:::{figure} MeanDistanceBetweenAllPointsOnTwoCurves.png +:alt: Output +:scale: 60% + +Output Image +Mean distance: 5 +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ContourMeanDistanceImageFilter +``` diff --git a/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.rst b/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.rst deleted file mode 100644 index f4dda1a64..000000000 --- a/src/Filtering/DistanceMap/MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: MeanDistanceBetweenAllPointsOnTwoCurves - -Mean Distance Between All Points on Two Curves -============================================== - -.. index:: - single: ContourMeanDistanceImageFilter - single: mean - -Synopsis --------- - -Compute the mean distance between all points of two curves. - - -Results -------- -.. figure:: MeanDistanceBetweenAllPointsOnTwoCurves.png - :scale: 60% - :alt: Output - - Output Image - Mean distance: 5 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ContourMeanDistanceImageFilter diff --git a/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.md b/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.md new file mode 100644 index 000000000..de4f50ca9 --- /dev/null +++ b/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.md @@ -0,0 +1,35 @@ +--- +name: SignedDistanceMapOfBinary +--- + +# Signed Distance Map of Binary Image + +```{index} single: SignedDanielssonDistanceMapImageFilter sinlge: distance-map pair: danielsson; distance-map +``` + +## Synopsis + +Compute a distance map from objects in a binary image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SignedDanielssonDistanceMapImageFilter +``` diff --git a/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.rst b/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.rst deleted file mode 100644 index db6eb4099..000000000 --- a/src/Filtering/DistanceMap/SignedDistanceMapOfBinary/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: SignedDistanceMapOfBinary - -Signed Distance Map of Binary Image -=================================== - -.. index:: - single: SignedDanielssonDistanceMapImageFilter - sinlge: distance-map - pair: danielsson; distance-map - -Synopsis --------- - -Compute a distance map from objects in a binary image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::SignedDanielssonDistanceMapImageFilter diff --git a/src/Filtering/DistanceMap/index.md b/src/Filtering/DistanceMap/index.md new file mode 100644 index 000000000..369cb5446 --- /dev/null +++ b/src/Filtering/DistanceMap/index.md @@ -0,0 +1,10 @@ +# DistanceMap + +```{toctree} +:maxdepth: 1 + +ApproxDistanceMapOfBinary/Documentation.rst +MaurerDistanceMapOfBinary/Documentation.rst +MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.rst +SignedDistanceMapOfBinary/Documentation.rst +``` diff --git a/src/Filtering/DistanceMap/index.rst b/src/Filtering/DistanceMap/index.rst deleted file mode 100644 index db5827fce..000000000 --- a/src/Filtering/DistanceMap/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -DistanceMap -=========== - -.. toctree:: - :maxdepth: 1 - - ApproxDistanceMapOfBinary/Documentation.rst - MaurerDistanceMapOfBinary/Documentation.rst - MeanDistanceBetweenAllPointsOnTwoCurves/Documentation.rst - SignedDistanceMapOfBinary/Documentation.rst diff --git a/src/Filtering/FFT/ComputeForwardFFT/Documentation.md b/src/Filtering/FFT/ComputeForwardFFT/Documentation.md new file mode 100644 index 000000000..a034382d4 --- /dev/null +++ b/src/Filtering/FFT/ComputeForwardFFT/Documentation.md @@ -0,0 +1,76 @@ +--- +name: ComputeForwardFFT +--- + +# Compute Forward FFT + +```{index} single: ForwardFFTImageFilter single: ComplexToRealImageFilter single: ComplexToImaginaryImageFilter single: ComplexToModulusImageFilter single: RescaleIntensityImageFilter single: WrapPadImageFilter single: NumericTraits single: ImageFileReader single: ImageFileWriter +``` + +## Synopsis + +Compute forward FFT of an image. + +## Results + +:::{figure} HeadMRVolume.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Real.png +:alt: Real image +:scale: 50% + +Output Real image +::: + +:::{figure} Complex.png +:alt: Imaginary image +:scale: 50% + +Output Imaginary image +::: + +:::{figure} Modulus.png +:alt: Modulus image +:scale: 50% + +Output Modulus image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ForwardFFTImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::ComplexToRealImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::ComplexToImaginaryImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::ComplexToModulusImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::WrapPadImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::RescaleIntensityImageFilter +``` diff --git a/src/Filtering/FFT/ComputeForwardFFT/Documentation.rst b/src/Filtering/FFT/ComputeForwardFFT/Documentation.rst deleted file mode 100644 index 719d39e9a..000000000 --- a/src/Filtering/FFT/ComputeForwardFFT/Documentation.rst +++ /dev/null @@ -1,73 +0,0 @@ -:name: ComputeForwardFFT - -Compute Forward FFT -=================== - -.. index:: - single: ForwardFFTImageFilter - single: ComplexToRealImageFilter - single: ComplexToImaginaryImageFilter - single: ComplexToModulusImageFilter - single: RescaleIntensityImageFilter - single: WrapPadImageFilter - single: NumericTraits - single: ImageFileReader - single: ImageFileWriter - -Synopsis --------- - -Compute forward FFT of an image. - - -Results -------- - -.. figure:: HeadMRVolume.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Real.png - :scale: 50% - :alt: Real image - - Output Real image - -.. figure:: Complex.png - :scale: 50% - :alt: Imaginary image - - Output Imaginary image - -.. figure:: Modulus.png - :scale: 50% - :alt: Modulus image - - Output Modulus image - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ForwardFFTImageFilter - -.. breathelink:: itk::ComplexToRealImageFilter - -.. breathelink:: itk::ComplexToImaginaryImageFilter - -.. breathelink:: itk::ComplexToModulusImageFilter - -.. breathelink:: itk::WrapPadImageFilter - -.. breathelink:: itk::RescaleIntensityImageFilter diff --git a/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.md b/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.md new file mode 100644 index 000000000..5f348658c --- /dev/null +++ b/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.md @@ -0,0 +1,47 @@ +--- +name: ComputeImageSpectralDensity +--- + +# Compute Image Spectral Density + +```{index} single: ComplexToModulusImageFilter single: FFTShiftImageFilter single: ForwardFFTImageFilter single: Fast Fourier Transform single: spectral density +``` + +## Synopsis + +Compute the magnitude of an image's spectral components. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} Output.png +:alt: Output image of spectral density. +:scale: 100% + +Output image of spectral density. The DC component is shifted to the center +of the image. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ComplexToModulusImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::FFTShiftImageFilter +``` diff --git a/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.rst b/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.rst deleted file mode 100644 index 707c717c0..000000000 --- a/src/Filtering/FFT/ComputeImageSpectralDensity/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: ComputeImageSpectralDensity - -Compute Image Spectral Density -============================== - -.. index:: - single: ComplexToModulusImageFilter - single: FFTShiftImageFilter - single: ForwardFFTImageFilter - single: Fast Fourier Transform - single: spectral density - - -Synopsis --------- - -Compute the magnitude of an image\'s spectral components. - - -Results -------- - -.. figure:: Input.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 100% - :alt: Output image of spectral density. - - Output image of spectral density. The DC component is shifted to the center - of the image. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ComplexToModulusImageFilter - -.. breathelink:: itk::FFTShiftImageFilter diff --git a/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.md b/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.md new file mode 100644 index 000000000..495eab1e4 --- /dev/null +++ b/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ComputeInverseFFTOfImage +--- + +# Compute Inverse FFT of Image + +```{index} single: InverseFFTImageFilter single: FFT single: inverse +``` + +## Synopsis + +Compute the inverse FFT of an image. + +## Results + +:::{figure} ComputeInverseFFTOfImage.png +:alt: ifft.png +:scale: 70% + +ifft.png +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::InverseFFTImageFilter +``` diff --git a/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.rst b/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.rst deleted file mode 100644 index 0dfa5316d..000000000 --- a/src/Filtering/FFT/ComputeInverseFFTOfImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: ComputeInverseFFTOfImage - -Compute Inverse FFT of Image -============================ - -.. index:: - single: InverseFFTImageFilter - single: FFT - single: inverse - -Synopsis --------- - -Compute the inverse FFT of an image. - - -Results -------- -.. figure:: ComputeInverseFFTOfImage.png - :scale: 70% - :alt: ifft.png - - ifft.png - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::InverseFFTImageFilter diff --git a/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.md b/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.md new file mode 100644 index 000000000..0f93b2cc4 --- /dev/null +++ b/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.md @@ -0,0 +1,61 @@ +--- +name: FilterImageInFourierDomain +--- + +# Filter Image in Fourier Domain + +```{index} single: FFTShiftImageFilter single: ForwardFFTImageFilter single: InverseFFTImageFilter single: Fast Fourier Transform +``` + +## Synopsis + +Filter an Image in the Fourier Domain +One of the most common image processing operations performed in the Fourier +Domain is the masking of the spectrum in order to modulate a range of +spatial frequencies from the input image. This operation is typically +performed by taking the input image, computing its Fourier transform using +a FFT filter, masking the resulting image in the Fourier domain with a +mask, and finally taking the result of the masking and computing its +inverse Fourier transform. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 100% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ForwardFFTImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::FFTShiftImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::MultiplyImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::InverseFFTImageFilter +``` diff --git a/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.rst b/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.rst deleted file mode 100644 index c4a721f4e..000000000 --- a/src/Filtering/FFT/FilterImageInFourierDomain/Documentation.rst +++ /dev/null @@ -1,61 +0,0 @@ -:name: FilterImageInFourierDomain - -Filter Image in Fourier Domain -============================== - -.. index:: - single: FFTShiftImageFilter - single: ForwardFFTImageFilter - single: InverseFFTImageFilter - single: Fast Fourier Transform - - -Synopsis --------- - -Filter an Image in the Fourier Domain -One of the most common image processing operations performed in the Fourier -Domain is the masking of the spectrum in order to modulate a range of -spatial frequencies from the input image. This operation is typically -performed by taking the input image, computing its Fourier transform using -a FFT filter, masking the resulting image in the Fourier domain with a -mask, and finally taking the result of the masking and computing its -inverse Fourier transform. - - -Results -------- - -.. figure:: Input.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 100% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ForwardFFTImageFilter - -.. breathelink:: itk::FFTShiftImageFilter - -.. breathelink:: itk::MultiplyImageFilter - -.. breathelink:: itk::InverseFFTImageFilter diff --git a/src/Filtering/FFT/index.md b/src/Filtering/FFT/index.md new file mode 100644 index 000000000..bfa8784be --- /dev/null +++ b/src/Filtering/FFT/index.md @@ -0,0 +1,10 @@ +# FFT + +```{toctree} +:maxdepth: 1 + +ComputeForwardFFT/Documentation.rst +ComputeImageSpectralDensity/Documentation.rst +ComputeInverseFFTOfImage/Documentation.rst +FilterImageInFourierDomain/Documentation.rst +``` diff --git a/src/Filtering/FFT/index.rst b/src/Filtering/FFT/index.rst deleted file mode 100644 index b5eb58dc4..000000000 --- a/src/Filtering/FFT/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -FFT -=== - -.. toctree:: - :maxdepth: 1 - - ComputeForwardFFT/Documentation.rst - ComputeImageSpectralDensity/Documentation.rst - ComputeInverseFFTOfImage/Documentation.rst - FilterImageInFourierDomain/Documentation.rst diff --git a/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.md b/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.md new file mode 100644 index 000000000..cb1aad23b --- /dev/null +++ b/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.md @@ -0,0 +1,54 @@ +--- +name: ComputeGeodesicDistanceOnMesh +--- + +# Compute Geodesic Distance on Mesh + +```{index} single: FastMarchingQuadEdgeMeshFilterBase single: FastMarchingThresholdStoppingCriterion +``` + +## Synopsis + +Compute the geodesic distance from a provided seed vertex on a mesh. + +## Results + +:::{figure} Input.png +:alt: Input mesh +:scale: 100% + +Input mesh +::: + +:::{figure} Output.png +:alt: Output mesh +:scale: 100% + +Output mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+ +
+ +

Interactive output mesh

+
+``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FastMarchingQuadEdgeMeshFilterBase +``` diff --git a/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.rst b/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.rst deleted file mode 100644 index 881f9f986..000000000 --- a/src/Filtering/FastMarching/ComputeGeodesicDistanceOnMesh/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: ComputeGeodesicDistanceOnMesh - -Compute Geodesic Distance on Mesh -================================= - -.. index:: - single: FastMarchingQuadEdgeMeshFilterBase - single: FastMarchingThresholdStoppingCriterion - -Synopsis --------- - -Compute the geodesic distance from a provided seed vertex on a mesh. - - -Results -------- - -.. figure:: Input.png - :scale: 100% - :alt: Input mesh - - Input mesh - -.. figure:: Output.png - :scale: 100% - :alt: Output mesh - - Output mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- -
- -

Interactive output mesh

-
- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FastMarchingQuadEdgeMeshFilterBase diff --git a/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.md b/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.md new file mode 100644 index 000000000..a57f5b1b7 --- /dev/null +++ b/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.md @@ -0,0 +1,28 @@ +--- +name: CreateDistanceMapFromSeeds +--- + +# Create Distance Map From Seeds + +```{index} single: FastMarchingImageFilterBase single: FastMarchingImageToNodePairContainerAdaptor single: ImageFileWriter +``` + +## Synopsis + +Create a distance map from given seeds + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FastMarchingImageFilterBase +``` diff --git a/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.rst b/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.rst deleted file mode 100644 index 7d554e563..000000000 --- a/src/Filtering/FastMarching/CreateDistanceMapFromSeeds/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: CreateDistanceMapFromSeeds - -Create Distance Map From Seeds -============================== - -.. index:: - single: FastMarchingImageFilterBase - single: FastMarchingImageToNodePairContainerAdaptor - single: ImageFileWriter - -Synopsis --------- - - -Create a distance map from given seeds - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FastMarchingImageFilterBase diff --git a/src/Filtering/FastMarching/index.md b/src/Filtering/FastMarching/index.md new file mode 100644 index 000000000..592516ed4 --- /dev/null +++ b/src/Filtering/FastMarching/index.md @@ -0,0 +1,8 @@ +# FastMarching + +```{toctree} +:maxdepth: 1 + +ComputeGeodesicDistanceOnMesh/Documentation.rst +CreateDistanceMapFromSeeds/Documentation.rst +``` diff --git a/src/Filtering/FastMarching/index.rst b/src/Filtering/FastMarching/index.rst deleted file mode 100644 index 34cdae406..000000000 --- a/src/Filtering/FastMarching/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -FastMarching -============ - -.. toctree:: - :maxdepth: 1 - - ComputeGeodesicDistanceOnMesh/Documentation.rst - CreateDistanceMapFromSeeds/Documentation.rst diff --git a/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.md b/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.md new file mode 100644 index 000000000..a3694ffc9 --- /dev/null +++ b/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.md @@ -0,0 +1,28 @@ +--- +name: AbsValueOfTwoImages +--- + +# Absolute Value Of Difference Between Two Images + +```{index} single: AbsoluteValueDifferenceImageFilter +``` + +## Synopsis + +Compute the absolute value of the difference of corresponding pixels in two images. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AbsoluteValueDifferenceImageFilter +``` diff --git a/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.rst b/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.rst deleted file mode 100644 index a1caa17f7..000000000 --- a/src/Filtering/ImageCompare/AbsValueOfTwoImages/Documentation.rst +++ /dev/null @@ -1,30 +0,0 @@ -:name: AbsValueOfTwoImages - -Absolute Value Of Difference Between Two Images -=============================================== - -.. index:: - single: AbsoluteValueDifferenceImageFilter - -Synopsis --------- - -Compute the absolute value of the difference of corresponding pixels in two images. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AbsoluteValueDifferenceImageFilter diff --git a/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.md b/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.md new file mode 100644 index 000000000..2ded9a0c1 --- /dev/null +++ b/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.md @@ -0,0 +1,43 @@ +--- +name: CombineTwoImagesWithCheckerBoardPattern +--- + +# Combine Two Images With Checker Board Pattern + +```{index} single: CheckerBoardImageFilter +``` + +## Synopsis + +Combine two images by alternating blocks of a checkerboard pattern. + +In this example the first image is black and the second one is white. + +## Results + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CheckerBoardImageFilter +``` diff --git a/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.rst b/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.rst deleted file mode 100644 index 217f43210..000000000 --- a/src/Filtering/ImageCompare/CombineTwoImagesWithCheckerBoardPattern/Documentation.rst +++ /dev/null @@ -1,46 +0,0 @@ -:name: CombineTwoImagesWithCheckerBoardPattern - -Combine Two Images With Checker Board Pattern -============================================= - -.. index:: - single: CheckerBoardImageFilter - -Synopsis --------- - - -Combine two images by alternating blocks of a checkerboard pattern. - -In this example the first image is black and the second one is white. - -Results -------- - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CheckerBoardImageFilter diff --git a/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.md b/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.md new file mode 100644 index 000000000..af3b51ae6 --- /dev/null +++ b/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.md @@ -0,0 +1,28 @@ +--- +name: SquaredDifferenceOfTwoImages +--- + +# Squared Difference of Two Images + +```{index} single: SquaredDifferenceImageFilter +``` + +## Synopsis + +Compute the squared difference of corresponding pixels in two images. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SquaredDifferenceImageFilter +``` diff --git a/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.rst b/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.rst deleted file mode 100644 index 82ae98411..000000000 --- a/src/Filtering/ImageCompare/SquaredDifferenceOfTwoImages/Documentation.rst +++ /dev/null @@ -1,30 +0,0 @@ -:name: SquaredDifferenceOfTwoImages - -Squared Difference of Two Images -================================ - -.. index:: - single: SquaredDifferenceImageFilter - -Synopsis --------- - -Compute the squared difference of corresponding pixels in two images. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SquaredDifferenceImageFilter diff --git a/src/Filtering/ImageCompare/index.md b/src/Filtering/ImageCompare/index.md new file mode 100644 index 000000000..4e125a97c --- /dev/null +++ b/src/Filtering/ImageCompare/index.md @@ -0,0 +1,9 @@ +# ImageCompare + +```{toctree} +:maxdepth: 1 + +AbsValueOfTwoImages/Documentation.rst +CombineTwoImagesWithCheckerBoardPattern/Documentation.rst +SquaredDifferenceOfTwoImages/Documentation.rst +``` diff --git a/src/Filtering/ImageCompare/index.rst b/src/Filtering/ImageCompare/index.rst deleted file mode 100644 index c79a6f2ae..000000000 --- a/src/Filtering/ImageCompare/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -ImageCompare -============ - -.. toctree:: - :maxdepth: 1 - - AbsValueOfTwoImages/Documentation.rst - CombineTwoImagesWithCheckerBoardPattern/Documentation.rst - SquaredDifferenceOfTwoImages/Documentation.rst diff --git a/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.md b/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.md new file mode 100644 index 000000000..6ecdc7ff4 --- /dev/null +++ b/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ComposeVectorFromThreeScalarImages +--- + +# Compose Vector From Three Scalar Images + +```{index} single: ComposeImageFilter pair: vector; image +``` + +## Synopsis + +Compose a vector image (with 3 components) from three scalar images. + +## Results + +Output: + +``` +1.2 +[1.2, 1.2, 1.2] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ComposeImageFilter +``` diff --git a/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.rst b/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.rst deleted file mode 100644 index 1bff91643..000000000 --- a/src/Filtering/ImageCompose/ComposeVectorFromThreeScalarImages/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: ComposeVectorFromThreeScalarImages - -Compose Vector From Three Scalar Images -======================================= - -.. index:: - single: ComposeImageFilter - pair: vector; image - -Synopsis --------- - -Compose a vector image (with 3 components) from three scalar images. - - -Results -------- -Output:: - - 1.2 - [1.2, 1.2, 1.2] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ComposeImageFilter diff --git a/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.md b/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.md new file mode 100644 index 000000000..e70285b93 --- /dev/null +++ b/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.md @@ -0,0 +1,92 @@ +--- +name: ConvertRealAndImaginaryToComplexImage +--- + +# Convert Real and Imaginary Images to Complex Image + +```{index} single: ComposeImageFilter pair: real; imaginary single: complex +``` + +## Synopsis + +Convert a real image and an imaginary image to a complex image. + +## Results + +Output: + +``` +Image (0x7ff58250cf20) +RTTI typeinfo: itk::Image, 2u> +Reference Count: 1 +Modified Time: 25 +Debug: Off +Object Name: +Observers: + none +Source: (0x7ff58250c590) +Source output name: Primary +Release Data: Off +Data Released: False +Global Release Data: Off +PipelineMTime: 22 +UpdateMTime: 26 +RealTimeStamp: 0 seconds +LargestPossibleRegion: + Dimension: 2 + Index: [0, 0] + Size: [0, 0] +BufferedRegion: + Dimension: 2 + Index: [0, 0] + Size: [0, 0] +RequestedRegion: + Dimension: 2 + Index: [0, 0] + Size: [0, 0] +Spacing: [1, 1] +Origin: [0, 0] +Direction: +1 0 +0 1 + +IndexToPointMatrix: +1 0 +0 1 + +PointToIndexMatrix: +1 0 +0 1 + +Inverse Direction: +1 0 +0 1 + +PixelContainer: + ImportImageContainer (0x7ff58250d0e0) + RTTI typeinfo: itk::ImportImageContainer > + Reference Count: 1 + Modified Time: 24 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x7ff58250c1b0 + Container manages memory: true + Size: 0 + Capacity: 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ComposeImageFilter +``` diff --git a/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.rst b/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.rst deleted file mode 100644 index 51eac16f0..000000000 --- a/src/Filtering/ImageCompose/ConvertRealAndImaginaryToComplexImage/Documentation.rst +++ /dev/null @@ -1,93 +0,0 @@ -:name: ConvertRealAndImaginaryToComplexImage - -Convert Real and Imaginary Images to Complex Image -================================================== - -.. index:: - single: ComposeImageFilter - pair: real; imaginary - single: complex - -Synopsis --------- - -Convert a real image and an imaginary image to a complex image. - - -Results -------- -Output:: - - Image (0x7ff58250cf20) - RTTI typeinfo: itk::Image, 2u> - Reference Count: 1 - Modified Time: 25 - Debug: Off - Object Name: - Observers: - none - Source: (0x7ff58250c590) - Source output name: Primary - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 22 - UpdateMTime: 26 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 2 - Index: [0, 0] - Size: [0, 0] - BufferedRegion: - Dimension: 2 - Index: [0, 0] - Size: [0, 0] - RequestedRegion: - Dimension: 2 - Index: [0, 0] - Size: [0, 0] - Spacing: [1, 1] - Origin: [0, 0] - Direction: - 1 0 - 0 1 - - IndexToPointMatrix: - 1 0 - 0 1 - - PointToIndexMatrix: - 1 0 - 0 1 - - Inverse Direction: - 1 0 - 0 1 - - PixelContainer: - ImportImageContainer (0x7ff58250d0e0) - RTTI typeinfo: itk::ImportImageContainer > - Reference Count: 1 - Modified Time: 24 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x7ff58250c1b0 - Container manages memory: true - Size: 0 - Capacity: 0 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ComposeImageFilter diff --git a/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.md b/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.md new file mode 100644 index 000000000..184e23977 --- /dev/null +++ b/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.md @@ -0,0 +1,28 @@ +--- +name: CreateVectorImageFromScalarImages +--- + +# Create Vector Image From Scalar Images + +```{index} single: ComposeImageFilter pair: scalar; image +``` + +## Synopsis + +Create a vector image from a collection of scalar images. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ComposeImageFilter +``` diff --git a/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.rst b/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.rst deleted file mode 100644 index c57e93e11..000000000 --- a/src/Filtering/ImageCompose/CreateVectorImageFromScalarImages/Documentation.rst +++ /dev/null @@ -1,31 +0,0 @@ -:name: CreateVectorImageFromScalarImages - -Create Vector Image From Scalar Images -====================================== - -.. index:: - single: ComposeImageFilter - pair: scalar; image - -Synopsis --------- - -Create a vector image from a collection of scalar images. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ComposeImageFilter diff --git a/src/Filtering/ImageCompose/JoinImages/Documentation.md b/src/Filtering/ImageCompose/JoinImages/Documentation.md new file mode 100644 index 000000000..c13ddd945 --- /dev/null +++ b/src/Filtering/ImageCompose/JoinImages/Documentation.md @@ -0,0 +1,35 @@ +--- +name: JoinImages +--- + +# Join Images + +```{index} single: JoinImageFilter +``` + +## Synopsis + +Join images, stacking their components + +## Results + +Output: + +``` +0 +10 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::JoinImageFilter +``` diff --git a/src/Filtering/ImageCompose/JoinImages/Documentation.rst b/src/Filtering/ImageCompose/JoinImages/Documentation.rst deleted file mode 100644 index d9bda78a1..000000000 --- a/src/Filtering/ImageCompose/JoinImages/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: JoinImages - -Join Images -=========== - -.. index:: - single: JoinImageFilter - -Synopsis --------- - -Join images, stacking their components - - -Results -------- -Output:: - - 0 - 10 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::JoinImageFilter diff --git a/src/Filtering/ImageCompose/index.md b/src/Filtering/ImageCompose/index.md new file mode 100644 index 000000000..14bfe6c5a --- /dev/null +++ b/src/Filtering/ImageCompose/index.md @@ -0,0 +1,10 @@ +# ImageCompose + +```{toctree} +:maxdepth: 1 + +ComposeVectorFromThreeScalarImages/Documentation.rst +ConvertRealAndImaginaryToComplexImage/Documentation.rst +CreateVectorImageFromScalarImages/Documentation.rst +JoinImages/Documentation.rst +``` diff --git a/src/Filtering/ImageCompose/index.rst b/src/Filtering/ImageCompose/index.rst deleted file mode 100644 index 7a6a0531a..000000000 --- a/src/Filtering/ImageCompose/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -ImageCompose -============ - -.. toctree:: - :maxdepth: 1 - - ComposeVectorFromThreeScalarImages/Documentation.rst - ConvertRealAndImaginaryToComplexImage/Documentation.rst - CreateVectorImageFromScalarImages/Documentation.rst - JoinImages/Documentation.rst diff --git a/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.md b/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.md new file mode 100644 index 000000000..0618e044c --- /dev/null +++ b/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.md @@ -0,0 +1,47 @@ +--- +name: AdditiveGaussianNoiseImageFilter +--- + +# Add Gaussian Noise to an Image + +```{index} single: DerivativeImageFilter pair: image; random +``` + +## Synopsis + +Adds Gaussian Noise to a particular image + +## Results + +:::{figure} Gourds.png +:scale: 70% + +Input Image +::: + +:::{figure} OutputImage.png +:scale: 70% + +Output Image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AdditiveGaussianNoiseImageFilter +``` diff --git a/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.rst b/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.rst deleted file mode 100644 index 31a763cac..000000000 --- a/src/Filtering/ImageFeature/AdditiveGaussianNoiseImageFilter/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: AdditiveGaussianNoiseImageFilter - -Add Gaussian Noise to an Image -===================================================== - -.. index:: - single: DerivativeImageFilter - pair: image; random - -Synopsis --------- - -Adds Gaussian Noise to a particular image - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - - Input Image - -.. figure:: OutputImage.png - :scale: 70% - - Output Image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AdditiveGaussianNoiseImageFilter diff --git a/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.md b/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.md new file mode 100644 index 000000000..b2cc4c6e9 --- /dev/null +++ b/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ApplyAFilterOnlyToASpecifiedImageRegion +--- + +# Apply a Filter Only to a Specified Image Region + +```{index} single: DerivativeImageFilter pair: image; random +``` + +## Synopsis + +To apply a filter to only operate on a specified ImageRegion. + +## Results + +Output: + +``` +Created random image. +Computed derivative. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DerivativeImageFilter +``` diff --git a/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.rst b/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.rst deleted file mode 100644 index ec4001068..000000000 --- a/src/Filtering/ImageFeature/ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: ApplyAFilterOnlyToASpecifiedImageRegion - -Apply a Filter Only to a Specified Image Region -=============================================== - -.. index:: - single: DerivativeImageFilter - pair: image; random - -Synopsis --------- - -To apply a filter to only operate on a specified ImageRegion. - - -Results -------- -Output:: - - Created random image. - Computed derivative. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::DerivativeImageFilter diff --git a/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.md b/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.md new file mode 100644 index 000000000..d387f69ab --- /dev/null +++ b/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ApplyAFilterToASpecifiedRegionOfAnImage +--- + +# Apply a Filter to a Specified Region of an Image + +```{index} single: DerivativeImageFilter pair: derivative; image +``` + +## Synopsis + +Computes the derivative of an image in a particular direction. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} DerivativeImageQuickview.png +:alt: Output in QuickView +:scale: 50% + +Output in QuickView +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DerivativeImageFilter +``` diff --git a/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.rst b/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.rst deleted file mode 100644 index 930f81086..000000000 --- a/src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ApplyAFilterToASpecifiedRegionOfAnImage - -Apply a Filter to a Specified Region of an Image -================================================ - -.. index:: - single: DerivativeImageFilter - pair: derivative; image - -Synopsis --------- - -Computes the derivative of an image in a particular direction. - - -Results -------- -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: DerivativeImageQuickview.png - :scale: 50% - :alt: Output in QuickView - - Output in QuickView - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::DerivativeImageFilter diff --git a/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.md b/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.md new file mode 100644 index 000000000..606877b4a --- /dev/null +++ b/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: BilateralFilterAnImage +--- + +# Bilateral Filter an Image + +```{index} single: BilateralImageFilter pair: bilateral; filter +``` + +## Synopsis + +Bilateral filter an image. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} BilateralFilterAnImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BilateralImageFilter +``` diff --git a/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.rst b/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.rst deleted file mode 100644 index 97a439bcf..000000000 --- a/src/Filtering/ImageFeature/BilateralFilterAnImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: BilateralFilterAnImage - -Bilateral Filter an Image -========================= - -.. index:: - single: BilateralImageFilter - pair: bilateral; filter - -Synopsis --------- - -Bilateral filter an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: BilateralFilterAnImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BilateralImageFilter diff --git a/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.md b/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.md new file mode 100644 index 000000000..5f439cb19 --- /dev/null +++ b/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeLaplacian +--- + +# Compute Laplacian + +```{index} single: LaplacianImageFilter +``` + +## Synopsis + +This filter computes the Laplacian of a scalar-valued image. + +## Results + +:::{figure} cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LaplacianImageFilter +``` diff --git a/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.rst b/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.rst deleted file mode 100644 index fb59591a7..000000000 --- a/src/Filtering/ImageFeature/ComputeLaplacian/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ComputeLaplacian - -Compute Laplacian -================= - -.. index:: - single: LaplacianImageFilter - -Synopsis --------- - -This filter computes the Laplacian of a scalar-valued image. - - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LaplacianImageFilter diff --git a/src/Filtering/ImageFeature/DerivativeImage/Documentation.md b/src/Filtering/ImageFeature/DerivativeImage/Documentation.md new file mode 100644 index 000000000..32c9670ad --- /dev/null +++ b/src/Filtering/ImageFeature/DerivativeImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: DerivativeImage +--- + +# Compute Derivative + +```{index} single: DerivativeImageFilter +``` + +## Synopsis + +This filter computes a n-th Derivative of a scalar-valued image in a specified direction. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 50% + +Output image +::: + +:::{figure} Output_normalized.png +:alt: Output normalized image +:scale: 50% + +Output normalized image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DerivativeImageFilter +``` diff --git a/src/Filtering/ImageFeature/DerivativeImage/Documentation.rst b/src/Filtering/ImageFeature/DerivativeImage/Documentation.rst deleted file mode 100644 index c221389be..000000000 --- a/src/Filtering/ImageFeature/DerivativeImage/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: DerivativeImage - -Compute Derivative -=================== - -.. index:: - single: DerivativeImageFilter - -Synopsis --------- - -This filter computes a n-th Derivative of a scalar-valued image in a specified direction. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 50% - :alt: Output image - - Output image - - -.. figure:: Output_normalized.png - :scale: 50% - :alt: Output normalized image - - Output normalized image - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::DerivativeImageFilter diff --git a/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.md b/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.md new file mode 100644 index 000000000..9a54ee554 --- /dev/null +++ b/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.md @@ -0,0 +1,49 @@ +--- +name: DetectEdgesWithCannyEdgeDetectionFilter +--- + +# Detect Edges With Canny Edge Detection Filter + +```{index} single: CannyEdgeDetectionImageFilter +``` + +## Synopsis + +Apply CannyEdgeDetectionImageFilter to an image + +## Results + +:::{figure} cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Rescaled Output image +:scale: 50% + +Rescaled Output image (values are in \[0, 255\]) +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CannyEdgeDetectionImageFilter +``` diff --git a/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst b/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst deleted file mode 100644 index 458992dcc..000000000 --- a/src/Filtering/ImageFeature/DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: DetectEdgesWithCannyEdgeDetectionFilter - -Detect Edges With Canny Edge Detection Filter -============================================= - -.. index:: - single: CannyEdgeDetectionImageFilter - -Synopsis --------- - -Apply CannyEdgeDetectionImageFilter to an image - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Rescaled Output image - - Rescaled Output image (values are in [0, 255]) - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CannyEdgeDetectionImageFilter diff --git a/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.md b/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.md new file mode 100644 index 000000000..afdaf40f6 --- /dev/null +++ b/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ExtractContoursFromImage +--- + +# Extract Contours From Image + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: SimpleContourExtractorImageFilter +``` + +## Synopsis + +Extract contours from an image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SimpleContourExtractorImageFilter +``` diff --git a/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.rst b/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.rst deleted file mode 100644 index aa01c4893..000000000 --- a/src/Filtering/ImageFeature/ExtractContoursFromImage/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ExtractContoursFromImage - -Extract Contours From Image -=========================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: SimpleContourExtractorImageFilter - -Synopsis --------- - -Extract contours from an image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SimpleContourExtractorImageFilter diff --git a/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.md b/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.md new file mode 100644 index 000000000..0ebef78b4 --- /dev/null +++ b/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.md @@ -0,0 +1,33 @@ +--- +name: FindZeroCrossingsInSignedImage +--- + +# Find Zero Crossings in Signed Image + +```{index} single: ZeroCrossingImageFilter pair: signed; image +``` + +## Synopsis + +Find zero crossings in a signed image. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ZeroCrossingImageFilter +``` diff --git a/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.rst b/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.rst deleted file mode 100644 index 30fb7d767..000000000 --- a/src/Filtering/ImageFeature/FindZeroCrossingsInSignedImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: FindZeroCrossingsInSignedImage - -Find Zero Crossings in Signed Image -=================================== - -.. index:: - single: ZeroCrossingImageFilter - pair: signed; image - -Synopsis --------- - -Find zero crossings in a signed image. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ZeroCrossingImageFilter diff --git a/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.md b/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.md new file mode 100644 index 000000000..dcfc11ef4 --- /dev/null +++ b/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.md @@ -0,0 +1,47 @@ +--- +name: LaplacianRecursiveGaussianImageFilter +--- + +# Laplacian Recursive Gaussian Image Filter + +```{index} single: LaplacianRecursiveGaussianImageFilter +``` + +## Synopsis + +Compute the Laplacian of an image. + +## Results + +:::{figure} cthead1.png +:alt: Input image + +Input image +::: + +:::{figure} LaplacianRecursiveGaussianImageFilterRescaledOutputBaseline.png +:alt: Rescaled Output image + +Rescaled Output image \[0, 255\] +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LaplacianRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.rst b/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.rst deleted file mode 100644 index 857e2a412..000000000 --- a/src/Filtering/ImageFeature/LaplacianRecursiveGaussianImageFilter/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: LaplacianRecursiveGaussianImageFilter - -Laplacian Recursive Gaussian Image Filter -========================================== - -.. index:: - single: LaplacianRecursiveGaussianImageFilter - -Synopsis --------- - -Compute the Laplacian of an image. - -Results -------- - -.. figure:: cthead1.png - :alt: Input image - - Input image - -.. figure:: LaplacianRecursiveGaussianImageFilterRescaledOutputBaseline.png - :alt: Rescaled Output image - - Rescaled Output image [0, 255] - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LaplacianRecursiveGaussianImageFilter diff --git a/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.md b/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.md new file mode 100644 index 000000000..7f643c72f --- /dev/null +++ b/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.md @@ -0,0 +1,68 @@ +--- +name: SegmentBloodVessels +--- + +# Segment Blood Vessels + +```{index} single: Hessian3DToVesselnessMeasureImageFilter pair: segment; vessel pair: segment; tube +``` + +## Synopsis + +The example takes an image (say MRA image), computes the vesselness measure +of the image using the HessianRecursiveGaussianImageFilter and the +Hessian3DToVesselnessMeasureImageFilter. The goal is to detect bright, tubular +structures in the image. + +Note that since the algorithm is based on the [Hessian], it will also identify +black tubular structures. + +An important parameter is the `Sigma` that determines the amount of smoothing +applied during Hessian estimation. A larger `Sigma` will decrease the +identification of noise or small structures as vessels. In this example, the +`Sigma` is large enough only vessels comprising the [Circle of Willis] and +other large vessels are segmented. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 70% + +Input head MRA. +::: + +:::{figure} Output.png +:alt: Output image +:scale: 70% + +Output vessel segmentation. +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Hessian3DToVesselnessMeasureImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::HessianRecursiveGaussianImageFilter +``` + +[circle of willis]: https://en.wikipedia.org/wiki/Circle_of_Willis +[hessian]: https://en.wikipedia.org/wiki/Hessian_matrix diff --git a/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.rst b/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.rst deleted file mode 100644 index e9bce95cd..000000000 --- a/src/Filtering/ImageFeature/SegmentBloodVessels/Documentation.rst +++ /dev/null @@ -1,69 +0,0 @@ -:name: SegmentBloodVessels - -Segment Blood Vessels -===================== - -.. index:: - single: Hessian3DToVesselnessMeasureImageFilter - pair: segment; vessel - pair: segment; tube - -Synopsis --------- - -The example takes an image (say MRA image), computes the vesselness measure -of the image using the HessianRecursiveGaussianImageFilter and the -Hessian3DToVesselnessMeasureImageFilter. The goal is to detect bright, tubular -structures in the image. - -Note that since the algorithm is based on the Hessian_, it will also identify -black tubular structures. - -An important parameter is the `Sigma` that determines the amount of smoothing -applied during Hessian estimation. A larger `Sigma` will decrease the -identification of noise or small structures as vessels. In this example, the -`Sigma` is large enough only vessels comprising the `Circle of Willis`_ and -other large vessels are segmented. - -Results -------- - -.. figure:: Input.png - :scale: 70% - :alt: Input image - - Input head MRA. - -.. figure:: Output.png - :scale: 70% - :alt: Output image - - Output vessel segmentation. - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Hessian3DToVesselnessMeasureImageFilter - -.. breathelink:: itk::HessianRecursiveGaussianImageFilter - -.. _Hessian: https://en.wikipedia.org/wiki/Hessian_matrix -.. _Circle of Willis: https://en.wikipedia.org/wiki/Circle_of_Willis diff --git a/src/Filtering/ImageFeature/SharpenImage/Documentation.md b/src/Filtering/ImageFeature/SharpenImage/Documentation.md new file mode 100644 index 000000000..4e594132b --- /dev/null +++ b/src/Filtering/ImageFeature/SharpenImage/Documentation.md @@ -0,0 +1,33 @@ +--- +name: SharpenImage +--- + +# Sharpen Image + +```{index} single: LaplacianSharpeningImageFilter +``` + +## Synopsis + +Sharpen an image. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LaplacianSharpeningImageFilter +``` diff --git a/src/Filtering/ImageFeature/SharpenImage/Documentation.rst b/src/Filtering/ImageFeature/SharpenImage/Documentation.rst deleted file mode 100644 index df17c7717..000000000 --- a/src/Filtering/ImageFeature/SharpenImage/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: SharpenImage - -Sharpen Image -============= - -.. index:: - single: LaplacianSharpeningImageFilter - -Synopsis --------- - -Sharpen an image. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LaplacianSharpeningImageFilter diff --git a/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.md b/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.md new file mode 100644 index 000000000..9186c3dac --- /dev/null +++ b/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.md @@ -0,0 +1,49 @@ +--- +name: SobelEdgeDetectionImageFilter +--- + +# Sobel Edge Detection Image Filter + +```{index} single: SobelEdgeDetectionImageFilter +``` + +## Synopsis + +Apply SobelEdgeDetectionImageFilter to an image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} SobelEdgeDetectionImageFilterRescaledOutputBaseline.png +:alt: Rescaled Output image +:scale: 50% + +Rescaled Output image (values are in \[0, 255\]) +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SobelEdgeDetectionImageFilter +``` diff --git a/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.rst b/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.rst deleted file mode 100644 index 5802fcdd3..000000000 --- a/src/Filtering/ImageFeature/SobelEdgeDetectionImageFilter/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: SobelEdgeDetectionImageFilter - -Sobel Edge Detection Image Filter -================================== - -.. index:: - single: SobelEdgeDetectionImageFilter - -Synopsis --------- - -Apply SobelEdgeDetectionImageFilter to an image - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: SobelEdgeDetectionImageFilterRescaledOutputBaseline.png - :scale: 50% - :alt: Rescaled Output image - - Rescaled Output image (values are in [0, 255]) - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SobelEdgeDetectionImageFilter diff --git a/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.md b/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.md new file mode 100644 index 000000000..4360f4623 --- /dev/null +++ b/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ZeroCrossingBasedEdgeDecor +--- + +# Zero-crossing Based Edge Decor + +```{index} single: ZeroCrossingBasedEdgeDetectionImageFilter +``` + +## Synopsis + +A zero-crossing based edge detecor + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} ZeroCrossingBasedEdgeDecor.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ZeroCrossingBasedEdgeDetectionImageFilter +``` diff --git a/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.rst b/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.rst deleted file mode 100644 index 16d137bf8..000000000 --- a/src/Filtering/ImageFeature/ZeroCrossingBasedEdgeDecor/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: ZeroCrossingBasedEdgeDecor - -Zero-crossing Based Edge Decor -============================== - -.. index:: - single: ZeroCrossingBasedEdgeDetectionImageFilter - -Synopsis --------- - -A zero-crossing based edge detecor - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: ZeroCrossingBasedEdgeDecor.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ZeroCrossingBasedEdgeDetectionImageFilter diff --git a/src/Filtering/ImageFeature/index.md b/src/Filtering/ImageFeature/index.md new file mode 100644 index 000000000..50c3fa7c8 --- /dev/null +++ b/src/Filtering/ImageFeature/index.md @@ -0,0 +1,20 @@ +# ImageFeature + +```{toctree} +:maxdepth: 1 + +AdditiveGaussianNoiseImageFilter/Documentation.rst +ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.rst +ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.rst +BilateralFilterAnImage/Documentation.rst +ComputeLaplacian/Documentation.rst +DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst +DerivativeImage/Documentation.rst +ExtractContoursFromImage/Documentation.rst +FindZeroCrossingsInSignedImage/Documentation.rst +LaplacianRecursiveGaussianImageFilter/Documentation.rst +SegmentBloodVessels/Documentation.rst +SharpenImage/Documentation.rst +SobelEdgeDetectionImageFilter/Documentation.rst +ZeroCrossingBasedEdgeDecor/Documentation.rst +``` diff --git a/src/Filtering/ImageFeature/index.rst b/src/Filtering/ImageFeature/index.rst deleted file mode 100644 index 2a38966dc..000000000 --- a/src/Filtering/ImageFeature/index.rst +++ /dev/null @@ -1,20 +0,0 @@ -ImageFeature -============ - -.. toctree:: - :maxdepth: 1 - - AdditiveGaussianNoiseImageFilter/Documentation.rst - ApplyAFilterOnlyToASpecifiedImageRegion/Documentation.rst - ApplyAFilterToASpecifiedRegionOfAnImage/Documentation.rst - BilateralFilterAnImage/Documentation.rst - ComputeLaplacian/Documentation.rst - DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst - DerivativeImage/Documentation.rst - ExtractContoursFromImage/Documentation.rst - FindZeroCrossingsInSignedImage/Documentation.rst - LaplacianRecursiveGaussianImageFilter/Documentation.rst - SegmentBloodVessels/Documentation.rst - SharpenImage/Documentation.rst - SobelEdgeDetectionImageFilter/Documentation.rst - ZeroCrossingBasedEdgeDecor/Documentation.rst diff --git a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.md b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.md new file mode 100644 index 000000000..6aaea44c1 --- /dev/null +++ b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ApplyKernelToEveryPixel +--- + +# Apply Kernel to Every Pixel + +```{index} single: NeighborhoodOperatorImageFilter pair: kernel; pixel +``` + +## Synopsis + +Apply a kernel to every pixel in an image. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NeighborhoodOperatorImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.rst b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.rst deleted file mode 100644 index 0797b8bd4..000000000 --- a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixel/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: ApplyKernelToEveryPixel - -Apply Kernel to Every Pixel -=========================== - -.. index:: - single: NeighborhoodOperatorImageFilter - pair: kernel; pixel - -Synopsis --------- - -Apply a kernel to every pixel in an image. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NeighborhoodOperatorImageFilter diff --git a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.md b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.md new file mode 100644 index 000000000..4cb45b5b8 --- /dev/null +++ b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ApplyKernelToEveryPixelInNonZeroImage +--- + +# Apply Kernel to Every Pixel in Non-Zero Image + +```{index} single: MaskNeighborhoodOperatorImageFilter pair: mask; non-zero single: kernel +``` + +## Synopsis + +Apply a kernel to every pixel in an image that is non-zero in a mask. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} mask.png +:alt: mask.png +:scale: 70% + +mask.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MaskNeighborhoodOperatorImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.rst b/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.rst deleted file mode 100644 index 0b02d1b06..000000000 --- a/src/Filtering/ImageFilterBase/ApplyKernelToEveryPixelInNonZeroImage/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: ApplyKernelToEveryPixelInNonZeroImage - -Apply Kernel to Every Pixel in Non-Zero Image -============================================= - -.. index:: - single: MaskNeighborhoodOperatorImageFilter - pair: mask; non-zero - single: kernel - -Synopsis --------- - -Apply a kernel to every pixel in an image that is non-zero in a mask. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: mask.png - :scale: 70% - :alt: mask.png - - mask.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MaskNeighborhoodOperatorImageFilter diff --git a/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.md b/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.md new file mode 100644 index 000000000..2b4624085 --- /dev/null +++ b/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.md @@ -0,0 +1,42 @@ +--- +name: CastAnImageToAnotherType +--- + +# Cast an Image to Another Type + +```{index} single: CastImageFilter +``` + +## Synopsis + +Cast an Image to another type + +## Results + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CastImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.rst b/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.rst deleted file mode 100644 index 8109d260f..000000000 --- a/src/Filtering/ImageFilterBase/CastAnImageToAnotherType/Documentation.rst +++ /dev/null @@ -1,45 +0,0 @@ -:name: CastAnImageToAnotherType - -Cast an Image to Another Type -============================= - -.. index:: - single: CastImageFilter - -Synopsis --------- - - -Cast an Image to another type - - -Results -------- - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CastImageFilter diff --git a/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.md b/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.md new file mode 100644 index 000000000..5e5028fa9 --- /dev/null +++ b/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ComputeLocalNoise +--- + +# Compute Local Noise in Image + +```{index} single: NoiseImageFilter pair: local; noise +``` + +## Synopsis + +Compute the local noise in an image. + +## Results + +:::{figure} input.png +:alt: input.mhd +:scale: 70% + +input.mhd +::: + +:::{figure} output.png +:alt: output.mhd +:scale: 70% + +output.mhd +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NoiseImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.rst b/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.rst deleted file mode 100644 index d0a3742f5..000000000 --- a/src/Filtering/ImageFilterBase/ComputeLocalNoise/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ComputeLocalNoise - -Compute Local Noise in Image -============================ - -.. index:: - single: NoiseImageFilter - pair: local; noise - -Synopsis --------- - -Compute the local noise in an image. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.mhd - - input.mhd - -.. figure:: output.png - :scale: 70% - :alt: output.mhd - - output.mhd - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NoiseImageFilter diff --git a/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.md b/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.md new file mode 100644 index 000000000..0e54313b6 --- /dev/null +++ b/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.md @@ -0,0 +1,36 @@ +--- +name: CustomOperationToCorrespondingPixelsInTwoImages +--- + +# Custom Operation to Corresponding Pixels in Two Images + +```{index} single: BinaryFunctorImageFilter pair: corresponding; pixels pair: custom; operation +``` + +## Synopsis + +Apply a predefined operation to corresponding pixels in two images. + +## Results + +Output: + +``` +pixel1 was = 2 +pixel2 was = 5 +output is = 9 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryFunctorImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.rst b/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.rst deleted file mode 100644 index f7c46b53f..000000000 --- a/src/Filtering/ImageFilterBase/CustomOperationToCorrespondingPixelsInTwoImages/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: CustomOperationToCorrespondingPixelsInTwoImages - -Custom Operation to Corresponding Pixels in Two Images -====================================================== - -.. index:: - single: BinaryFunctorImageFilter - pair: corresponding; pixels - pair: custom; operation - -Synopsis --------- - -Apply a predefined operation to corresponding pixels in two images. - - -Results -------- -Output:: - - pixel1 was = 2 - pixel2 was = 5 - output is = 9 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryFunctorImageFilter diff --git a/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.md b/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.md new file mode 100644 index 000000000..644002117 --- /dev/null +++ b/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.md @@ -0,0 +1,33 @@ +--- +name: PredefinedOperationToCorrespondingPixelsInTwoImages +--- + +# Predefined Operation to Corresponding Pixels in Two Images + +```{index} single: BinaryFunctorImageFilter pair: corresponding; pixels single: operation +``` + +## Synopsis + +Apply a predefined operation to corresponding pixels in two images. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryFunctorImageFilter +``` diff --git a/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.rst b/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.rst deleted file mode 100644 index 84e31bcc0..000000000 --- a/src/Filtering/ImageFilterBase/PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: PredefinedOperationToCorrespondingPixelsInTwoImages - -Predefined Operation to Corresponding Pixels in Two Images -========================================================== - -.. index:: - single: BinaryFunctorImageFilter - pair: corresponding; pixels - single: operation - -Synopsis --------- - -Apply a predefined operation to corresponding pixels in two images. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryFunctorImageFilter diff --git a/src/Filtering/ImageFilterBase/index.md b/src/Filtering/ImageFilterBase/index.md new file mode 100644 index 000000000..48c69a796 --- /dev/null +++ b/src/Filtering/ImageFilterBase/index.md @@ -0,0 +1,12 @@ +# ImageFilterBase + +```{toctree} +:maxdepth: 1 + +ApplyKernelToEveryPixel/Documentation.rst +ApplyKernelToEveryPixelInNonZeroImage/Documentation.rst +CastAnImageToAnotherType/Documentation.rst +ComputeLocalNoise/Documentation.rst +CustomOperationToCorrespondingPixelsInTwoImages/Documentation.rst +PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.rst +``` diff --git a/src/Filtering/ImageFilterBase/index.rst b/src/Filtering/ImageFilterBase/index.rst deleted file mode 100644 index 7a61209f7..000000000 --- a/src/Filtering/ImageFilterBase/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -ImageFilterBase -=============== - -.. toctree:: - :maxdepth: 1 - - ApplyKernelToEveryPixel/Documentation.rst - ApplyKernelToEveryPixelInNonZeroImage/Documentation.rst - CastAnImageToAnotherType/Documentation.rst - ComputeLocalNoise/Documentation.rst - CustomOperationToCorrespondingPixelsInTwoImages/Documentation.rst - PredefinedOperationToCorrespondingPixelsInTwoImages/Documentation.rst diff --git a/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.md b/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.md new file mode 100644 index 000000000..fa60aae41 --- /dev/null +++ b/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ColorBoundariesOfRegions +--- + +# Color Boundaries of Labeled Regions + +```{index} single: LabelMapContourOverlayImageFilter pair: color; boundary pair: color; regions +``` + +## Synopsis + +Color the boundaries of labeled regions in an image. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMapContourOverlayImageFilter +``` diff --git a/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.rst b/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.rst deleted file mode 100644 index d512452fd..000000000 --- a/src/Filtering/ImageFusion/ColorBoundariesOfRegions/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: ColorBoundariesOfRegions - -Color Boundaries of Labeled Regions -=================================== - -.. index:: - single: LabelMapContourOverlayImageFilter - pair: color; boundary - pair: color; regions - -Synopsis --------- - -Color the boundaries of labeled regions in an image. - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMapContourOverlayImageFilter diff --git a/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.md b/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.md new file mode 100644 index 000000000..ada48e341 --- /dev/null +++ b/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ColorLabeledRegions +--- + +# Color Labeled Regions in Image + +```{index} single: LabelMapOverlayImageFilter pair: color; labeled pair: region; image +``` + +## Synopsis + +Color labeled regions in an image. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMapOverlayImageFilter +``` diff --git a/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.rst b/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.rst deleted file mode 100644 index 3189f06cb..000000000 --- a/src/Filtering/ImageFusion/ColorLabeledRegions/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ColorLabeledRegions - -Color Labeled Regions in Image -============================== - -.. index:: - single: LabelMapOverlayImageFilter - pair: color; labeled - pair: region; image - -Synopsis --------- - -Color labeled regions in an image. - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMapOverlayImageFilter diff --git a/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.md b/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.md new file mode 100644 index 000000000..901fee7da --- /dev/null +++ b/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: OverlayLabelMapOnImage +--- + +# Overlay Label Map on Image + +```{index} single: LabelOverlayImageFilter +``` + +## Synopsis + +Overlay a LabelMap on an image. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelOverlayImageFilter +``` diff --git a/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.rst b/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.rst deleted file mode 100644 index ee20bc2e0..000000000 --- a/src/Filtering/ImageFusion/OverlayLabelMapOnImage/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: OverlayLabelMapOnImage - -Overlay Label Map on Image -========================== - -.. index:: - single: LabelOverlayImageFilter - -Synopsis --------- - -Overlay a LabelMap on an image. - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelOverlayImageFilter diff --git a/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.md b/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.md new file mode 100644 index 000000000..4239dc451 --- /dev/null +++ b/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.md @@ -0,0 +1,56 @@ +--- +name: OverlayLabelMapOnTopOfAnImage +--- + +# Overlay Label Map on Top of an Image + +```{index} single: LabelMapOverlayImageFilter +``` + +## Synopsis + +Apply a colormap to a label map and superimpose it on an image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} label.png +:alt: Label map +:scale: 50% + +Label image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMapOverlayImageFilter +``` diff --git a/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.rst b/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.rst deleted file mode 100644 index 001a7714a..000000000 --- a/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: OverlayLabelMapOnTopOfAnImage - -Overlay Label Map on Top of an Image -==================================== - -.. index:: - single: LabelMapOverlayImageFilter - -Synopsis --------- - -Apply a colormap to a label map and superimpose it on an image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: label.png - :scale: 50% - :alt: Label map - - Label image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMapOverlayImageFilter diff --git a/src/Filtering/ImageFusion/index.md b/src/Filtering/ImageFusion/index.md new file mode 100644 index 000000000..fdb270c82 --- /dev/null +++ b/src/Filtering/ImageFusion/index.md @@ -0,0 +1,10 @@ +# ImageFusion + +```{toctree} +:maxdepth: 1 + +ColorBoundariesOfRegions/Documentation.rst +ColorLabeledRegions/Documentation.rst +OverlayLabelMapOnImage/Documentation.rst +OverlayLabelMapOnTopOfAnImage/Documentation.rst +``` diff --git a/src/Filtering/ImageFusion/index.rst b/src/Filtering/ImageFusion/index.rst deleted file mode 100644 index 490023e7e..000000000 --- a/src/Filtering/ImageFusion/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -ImageFusion -=========== - -.. toctree:: - :maxdepth: 1 - - ColorBoundariesOfRegions/Documentation.rst - ColorLabeledRegions/Documentation.rst - OverlayLabelMapOnImage/Documentation.rst - OverlayLabelMapOnTopOfAnImage/Documentation.rst diff --git a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.md b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.md new file mode 100644 index 000000000..602356f0e --- /dev/null +++ b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.md @@ -0,0 +1,69 @@ +--- +name: ApplyGradientRecursiveGaussian +--- + +# Apply GradientRecursiveGaussianImageFilter + +```{index} single: GradientRecursiveGaussianImageFilter single: RescaleIntensityImageFilter single: VectorIndexSelectionCastImageFilter single: VectorMagnitudeImageFilter +``` + +## Synopsis + +Computes the gradient of an image by convolution with the first derivative of a Gaussian. + +The output of the GradientRecursiveGaussianImageFilter is composed of two imagescomponents (gradients along the X and Y directions). In this example, we store these components using an image with CovariantVector pixel type. Covariant vectors are the natural representation for gradients since they are the equivalent of normals to iso-values manifolds. + +This example shows also how to extract the X and Y gradients as images, and how to compute the magnitude of the CovariantVector image. + +Note that the covariant vector types were only added to the VectorIndexSelectionCastImageFilter Python wrapping in ITK 4.7. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} ApplyGradientRecursiveGaussianTestOutputBaselineX.png +:alt: Gradient along X direction +:scale: 50% + +Gradient along X direction +::: + +:::{figure} ApplyGradientRecursiveGaussianTestOutputBaselineY.png +:alt: Gradient along Y direction +:scale: 50% + +Gradient along Y direction +::: + +:::{figure} ApplyGradientRecursiveGaussianTestOutputBaselineMagnitude.png +:alt: Output magnitude +:scale: 50% + +The image of the magnitude of the vector containing the X and Y values. +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.rst b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.rst deleted file mode 100644 index 490ab10ae..000000000 --- a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Documentation.rst +++ /dev/null @@ -1,71 +0,0 @@ -:name: ApplyGradientRecursiveGaussian - -Apply GradientRecursiveGaussianImageFilter -========================================== - -.. index:: - single: GradientRecursiveGaussianImageFilter - single: RescaleIntensityImageFilter - single: VectorIndexSelectionCastImageFilter - single: VectorMagnitudeImageFilter - -Synopsis --------- - -Computes the gradient of an image by convolution with the first derivative of a Gaussian. - -The output of the GradientRecursiveGaussianImageFilter is composed of two imagescomponents (gradients along the X and Y directions). In this example, we store these components using an image with CovariantVector pixel type. Covariant vectors are the natural representation for gradients since they are the equivalent of normals to iso-values manifolds. - -This example shows also how to extract the X and Y gradients as images, and how to compute the magnitude of the CovariantVector image. - -Note that the covariant vector types were only added to the VectorIndexSelectionCastImageFilter Python wrapping in ITK 4.7. - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: ApplyGradientRecursiveGaussianTestOutputBaselineX.png - :scale: 50% - :alt: Gradient along X direction - - Gradient along X direction - -.. figure:: ApplyGradientRecursiveGaussianTestOutputBaselineY.png - :scale: 50% - :alt: Gradient along Y direction - - Gradient along Y direction - -.. figure:: ApplyGradientRecursiveGaussianTestOutputBaselineMagnitude.png - :scale: 50% - :alt: Output magnitude - - The image of the magnitude of the vector containing the X and Y values. - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientRecursiveGaussianImageFilter diff --git a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.md b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.md new file mode 100644 index 000000000..3054ce578 --- /dev/null +++ b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.md @@ -0,0 +1,80 @@ +--- +name: ApplyGradientRecursiveGaussianWithVectorInput +--- + +# Apply GradientRecursiveGaussianImageFilter on Image With Vector type + +```{index} single: GradientRecursiveGaussianImageFilter single: RescaleIntensityImageFilter single: VectorIndexSelectionCastImageFilter single: InvertIntensityImageFilter single: ComposeImageFilter +``` + +## Synopsis + +Computes the gradient of an image by convolution with the first derivative of a Gaussian. + +The output of the GradientRecursiveGaussianImageFilter is composed of two images (gradient along the X and Y directions). In this example, the input +is an image having two values per pixel (vector type). One value is coming +from the inputed image (first image); the second is the inverse of the inputed image (second image). + +The output of GradientRecursiveGaussianImageFilter will then have four values per pixel. These are in the following order: gradient along X axis (first image), gradient along Y axis (first image), gradient along X axis (second image), gradient along Y axis (second image). + +Note that the Python example will only work with ITK 4.8.0 or greater. The ComoposeImagefilter could be used to cast +from unsigned char to double type without explicitely using the CastImageFilter; but in Python this possibilty is +not allowed. This reduces the number of combinations that need to be wrapped, which helps reducing the size of the ITK binaries. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image (first image) +::: + +:::{figure} ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline1X.png +:alt: Gradient along X direction (first image) +:scale: 50% + +Gradient along X direction (first image) +::: + +:::{figure} ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline1Y.png +:alt: Gradient along Y direction (first image) +:scale: 50% + +Gradient along Y direction (first image) +::: + +:::{figure} ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline2X.png +:alt: Gradient along X direction (second image) +:scale: 50% + +Gradient along X direction (second image) +::: + +:::{figure} ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline2Y.png +:alt: Gradient along Y direction (second image) +:scale: 50% + +Gradient along Y direction (second image) +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.rst b/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.rst deleted file mode 100644 index fcf327275..000000000 --- a/src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Documentation.rst +++ /dev/null @@ -1,82 +0,0 @@ -:name: ApplyGradientRecursiveGaussianWithVectorInput - -Apply GradientRecursiveGaussianImageFilter on Image With Vector type -==================================================================== - -.. index:: - single: GradientRecursiveGaussianImageFilter - single: RescaleIntensityImageFilter - single: VectorIndexSelectionCastImageFilter - single: InvertIntensityImageFilter - single: ComposeImageFilter - -Synopsis --------- - -Computes the gradient of an image by convolution with the first derivative of a Gaussian. - -The output of the GradientRecursiveGaussianImageFilter is composed of two images (gradient along the X and Y directions). In this example, the input -is an image having two values per pixel (vector type). One value is coming -from the inputed image (first image); the second is the inverse of the inputed image (second image). - -The output of GradientRecursiveGaussianImageFilter will then have four values per pixel. These are in the following order: gradient along X axis (first image), gradient along Y axis (first image), gradient along X axis (second image), gradient along Y axis (second image). - -Note that the Python example will only work with ITK 4.8.0 or greater. The ComoposeImagefilter could be used to cast -from unsigned char to double type without explicitely using the CastImageFilter; but in Python this possibilty is -not allowed. This reduces the number of combinations that need to be wrapped, which helps reducing the size of the ITK binaries. - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image (first image) - -.. figure:: ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline1X.png - :scale: 50% - :alt: Gradient along X direction (first image) - - Gradient along X direction (first image) - -.. figure:: ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline1Y.png - :scale: 50% - :alt: Gradient along Y direction (first image) - - Gradient along Y direction (first image) - -.. figure:: ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline2X.png - :scale: 50% - :alt: Gradient along X direction (second image) - - Gradient along X direction (second image) - -.. figure:: ApplyGradientRecursiveGaussianWithVectorInputTestOutputBaseline2Y.png - :scale: 50% - :alt: Gradient along Y direction (second image) - - Gradient along Y direction (second image) - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientRecursiveGaussianImageFilter diff --git a/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.md b/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.md new file mode 100644 index 000000000..98e57f82e --- /dev/null +++ b/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ComputeAndDisplayGradient +--- + +# Compute and Display Gradient of Image + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: GradientImageFilter +``` + +## Synopsis + +Compute and display the gradient of an image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientImageFilter +``` diff --git a/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.rst b/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.rst deleted file mode 100644 index a93f7d853..000000000 --- a/src/Filtering/ImageGradient/ComputeAndDisplayGradient/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ComputeAndDisplayGradient - -Compute and Display Gradient of Image -===================================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: GradientImageFilter - -Synopsis --------- - -Compute and display the gradient of an image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientImageFilter diff --git a/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.md b/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.md new file mode 100644 index 000000000..5e5ab4e0a --- /dev/null +++ b/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ComputeGradientMagnitude +--- + +# Compute Gradient Magnitude of Grayscale Image + +```{index} single: GradientMagnitudeImageFilter, gradient +``` + +## Synopsis + +This example demonstrates how to compute the magnitude of the gradient of an image. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} ComputeGradientMagnitudeTestOutput.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientMagnitudeImageFilter +``` diff --git a/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.rst b/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.rst deleted file mode 100644 index 6c4ede723..000000000 --- a/src/Filtering/ImageGradient/ComputeGradientMagnitude/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: ComputeGradientMagnitude - -Compute Gradient Magnitude of Grayscale Image -============================================= - -.. index:: - single: GradientMagnitudeImageFilter, gradient - -Synopsis --------- - -This example demonstrates how to compute the magnitude of the gradient of an image. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: ComputeGradientMagnitudeTestOutput.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientMagnitudeImageFilter diff --git a/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.md b/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.md new file mode 100644 index 000000000..1ec126daf --- /dev/null +++ b/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeGradientMagnitudeRecursiveGaussian +--- + +# Compute Gradient Magnitude Recursive Gaussian of Grayscale Image + +```{index} single: GradientMagnitudeRecursiveGaussianImageFilter, Gaussian, gradient +``` + +## Synopsis + +Compute the gradient magnitude of the image after first smoothing with a Gaussian kernel. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} ComputeGradientMagnitudeRecursiveGaussianTestOutput.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientMagnitudeRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.rst b/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.rst deleted file mode 100644 index 001a6f4e4..000000000 --- a/src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ComputeGradientMagnitudeRecursiveGaussian - -Compute Gradient Magnitude Recursive Gaussian of Grayscale Image -================================================================ - -.. index:: - single: GradientMagnitudeRecursiveGaussianImageFilter, Gaussian, gradient - -Synopsis --------- - -Compute the gradient magnitude of the image after first smoothing with a Gaussian kernel. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: ComputeGradientMagnitudeRecursiveGaussianTestOutput.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientMagnitudeRecursiveGaussianImageFilter diff --git a/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.md b/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.md new file mode 100644 index 000000000..776574378 --- /dev/null +++ b/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: GradientOfVectorImage +--- + +# Gradient of Vector Image + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: GradientImageFilter +``` + +## Synopsis + +Compute the gradient of a vector image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientImageFilter +``` diff --git a/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.rst b/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.rst deleted file mode 100644 index 1a16604f7..000000000 --- a/src/Filtering/ImageGradient/GradientOfVectorImage/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: GradientOfVectorImage - -Gradient of Vector Image -======================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: GradientImageFilter - -Synopsis --------- - -Compute the gradient of a vector image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientImageFilter diff --git a/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.md b/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.md new file mode 100644 index 000000000..32f219e26 --- /dev/null +++ b/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ImplementationOfSnakes +--- + +# Implementation of Snakes + +```{index} single: GradientRecursiveGaussianImageFilter single: snakes +``` + +## Synopsis + +Simple implementation of Snakes. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GradientRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.rst b/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.rst deleted file mode 100644 index 47d4b3de2..000000000 --- a/src/Filtering/ImageGradient/ImplementationOfSnakes/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: ImplementationOfSnakes - -Implementation of Snakes -======================== - -.. index:: - single: GradientRecursiveGaussianImageFilter - single: snakes - -Synopsis --------- - -Simple implementation of Snakes. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GradientRecursiveGaussianImageFilter diff --git a/src/Filtering/ImageGradient/index.md b/src/Filtering/ImageGradient/index.md new file mode 100644 index 000000000..a9d24e4fb --- /dev/null +++ b/src/Filtering/ImageGradient/index.md @@ -0,0 +1,13 @@ +# ImageGradient + +```{toctree} +:maxdepth: 1 + +ApplyGradientRecursiveGaussian/Documentation.rst +ApplyGradientRecursiveGaussianWithVectorInput/Documentation.rst +ComputeAndDisplayGradient/Documentation.rst +ComputeGradientMagnitude/Documentation.rst +ComputeGradientMagnitudeRecursiveGaussian/Documentation.rst +GradientOfVectorImage/Documentation.rst +ImplementationOfSnakes/Documentation.rst +``` diff --git a/src/Filtering/ImageGradient/index.rst b/src/Filtering/ImageGradient/index.rst deleted file mode 100644 index 8df8eb116..000000000 --- a/src/Filtering/ImageGradient/index.rst +++ /dev/null @@ -1,13 +0,0 @@ -ImageGradient -============= - -.. toctree:: - :maxdepth: 1 - - ApplyGradientRecursiveGaussian/Documentation.rst - ApplyGradientRecursiveGaussianWithVectorInput/Documentation.rst - ComputeAndDisplayGradient/Documentation.rst - ComputeGradientMagnitude/Documentation.rst - ComputeGradientMagnitudeRecursiveGaussian/Documentation.rst - GradientOfVectorImage/Documentation.rst - ImplementationOfSnakes/Documentation.rst diff --git a/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.md b/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.md new file mode 100644 index 000000000..6e6c14c6a --- /dev/null +++ b/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.md @@ -0,0 +1,42 @@ +--- +name: AppendTwo3DVolumes +--- + +# Append Two 3D Volumes + +```{index} single: TileImageFilter single: append single: tile single: concatenate +``` + +## Synopsis + +Append two 3D volumes in the Z-direction. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 70% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 70% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TileImageFilter +``` diff --git a/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.rst b/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.rst deleted file mode 100644 index b52ae6fd6..000000000 --- a/src/Filtering/ImageGrid/AppendTwo3DVolumes/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: AppendTwo3DVolumes - -Append Two 3D Volumes -===================== - -.. index:: - single: TileImageFilter - single: append - single: tile - single: concatenate - -Synopsis --------- - -Append two 3D volumes in the Z-direction. - - -Results -------- - -.. figure:: Input.png - :scale: 70% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 70% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TileImageFilter diff --git a/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.md b/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.md new file mode 100644 index 000000000..53cd1097c --- /dev/null +++ b/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.md @@ -0,0 +1,166 @@ +--- +name: ChangeImageOriginSpacingOrDirection +--- + +# Change Image Origin Spacing or Direction + +```{index} single: ChangeInformationImageFilter +``` + +## Synopsis + +Change an Image's Origin, Spacing, or Direction. + +The `ChangeInformationImageFilter` is commonly used to modify image metadata +such as *Origin*, *Spacing*, and *Orientation*. This filter leaves intact the +pixel data of the image. This filter should be used with extreme caution, since +it can easily change information that is critical for the safety of many medical +image analysis tasks, such as measurement the volume of a tumor, or providing +guidance for surgery. + +## Results + +``` +Original image: Image (0x3131ce0) + RTTI typeinfo: itk::Image + Reference Count: 3 + Modified Time: 195 + Debug: Off + Object Name: + Observers: + none + Source: (0x312d620) + Source output name: Primary + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 47 + UpdateMTime: 0 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [48, 62, 42] + BufferedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + RequestedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + Spacing: [4, 4, 4] + Origin: [0, 0, 0] + Direction: +1 0 0 +0 1 0 +0 0 1 + + IndexToPointMatrix: +4 0 0 +0 4 0 +0 0 4 + + PointToIndexMatrix: +0.25 0 0 +0 0.25 0 +0 0 0.25 + + Inverse Direction: +1 0 0 +0 1 0 +0 0 1 + + PixelContainer: + ImportImageContainer (0x3131fa0) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 34 + Debug: Off + Object Name: + Observers: + none + Pointer: 0 + Container manages memory: true + Size: 0 + Capacity: 0 + +************************************** +Changed image: Image (0x3137100) + RTTI typeinfo: itk::Image + Reference Count: 3 + Modified Time: 222 + Debug: Off + Object Name: + Observers: + none + Source: (0x3132240) + Source output name: Primary + Release Data: Off + Data Released: False + Global Release Data: Off + PipelineMTime: 215 + UpdateMTime: 0 + RealTimeStamp: 0 seconds + LargestPossibleRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [48, 62, 42] + BufferedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + RequestedRegion: + Dimension: 3 + Index: [0, 0, 0] + Size: [0, 0, 0] + Spacing: [8.4, 8.4, 8.4] + Origin: [8.4, 2.9, 4.4] + Direction: +0.866025 -0.5 0 +0.5 0.866025 0 +0 0 1 + + IndexToPointMatrix: +7.27461 -4.2 0 +4.2 7.27461 0 +0 0 8.4 + + PointToIndexMatrix: +0.103098 0.0595238 0 +-0.0595238 0.103098 0 +0 0 0.119048 + + Inverse Direction: +0.866025 0.5 0 +-0.5 0.866025 0 +0 0 1 + + PixelContainer: + ImportImageContainer (0x3137520) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 200 + Debug: Off + Object Name: + Observers: + none + Pointer: 0 + Container manages memory: true + Size: 0 + Capacity: 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ChangeInformationImageFilter +``` diff --git a/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.rst b/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.rst deleted file mode 100644 index eaf75fcf5..000000000 --- a/src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Documentation.rst +++ /dev/null @@ -1,170 +0,0 @@ -:name: ChangeImageOriginSpacingOrDirection - -Change Image Origin Spacing or Direction -======================================== - -.. index:: - single: ChangeInformationImageFilter - -Synopsis --------- - -Change an Image's Origin, Spacing, or Direction. - -The `ChangeInformationImageFilter` is commonly used to modify image metadata -such as *Origin*, *Spacing*, and *Orientation*. This filter leaves intact the -pixel data of the image. This filter should be used with extreme caution, since -it can easily change information that is critical for the safety of many medical -image analysis tasks, such as measurement the volume of a tumor, or providing -guidance for surgery. - - -Results -------- - -:: - - Original image: Image (0x3131ce0) - RTTI typeinfo: itk::Image - Reference Count: 3 - Modified Time: 195 - Debug: Off - Object Name: - Observers: - none - Source: (0x312d620) - Source output name: Primary - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 47 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [48, 62, 42] - BufferedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - RequestedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - Spacing: [4, 4, 4] - Origin: [0, 0, 0] - Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - IndexToPointMatrix: - 4 0 0 - 0 4 0 - 0 0 4 - - PointToIndexMatrix: - 0.25 0 0 - 0 0.25 0 - 0 0 0.25 - - Inverse Direction: - 1 0 0 - 0 1 0 - 0 0 1 - - PixelContainer: - ImportImageContainer (0x3131fa0) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 34 - Debug: Off - Object Name: - Observers: - none - Pointer: 0 - Container manages memory: true - Size: 0 - Capacity: 0 - - ************************************** - Changed image: Image (0x3137100) - RTTI typeinfo: itk::Image - Reference Count: 3 - Modified Time: 222 - Debug: Off - Object Name: - Observers: - none - Source: (0x3132240) - Source output name: Primary - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 215 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [48, 62, 42] - BufferedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - RequestedRegion: - Dimension: 3 - Index: [0, 0, 0] - Size: [0, 0, 0] - Spacing: [8.4, 8.4, 8.4] - Origin: [8.4, 2.9, 4.4] - Direction: - 0.866025 -0.5 0 - 0.5 0.866025 0 - 0 0 1 - - IndexToPointMatrix: - 7.27461 -4.2 0 - 4.2 7.27461 0 - 0 0 8.4 - - PointToIndexMatrix: - 0.103098 0.0595238 0 - -0.0595238 0.103098 0 - 0 0 0.119048 - - Inverse Direction: - 0.866025 0.5 0 - -0.5 0.866025 0 - 0 0 1 - - PixelContainer: - ImportImageContainer (0x3137520) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 200 - Debug: Off - Object Name: - Observers: - none - Pointer: 0 - Container manages memory: true - Size: 0 - Capacity: 0 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ChangeInformationImageFilter diff --git a/src/Filtering/ImageGrid/Create3DVolume/Documentation.md b/src/Filtering/ImageGrid/Create3DVolume/Documentation.md new file mode 100644 index 000000000..869c80879 --- /dev/null +++ b/src/Filtering/ImageGrid/Create3DVolume/Documentation.md @@ -0,0 +1,49 @@ +--- +name: Create3DVolume +--- + +# Create 3D Volume + +```{index} single: TileImageFilter single: append single: tile single: concatenate +``` + +## Synopsis + +This example reads in a series of 2D images and stacks them to create a 3D image. + +## Results + +:::{figure} Input.png +:alt: Input 2D images +:scale: 50% + +Input 2D images +::: + +:::{figure} Output.png +:alt: Output 3D image +:scale: 80% + +Single output 3D image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TileImageFilter +``` diff --git a/src/Filtering/ImageGrid/Create3DVolume/Documentation.rst b/src/Filtering/ImageGrid/Create3DVolume/Documentation.rst deleted file mode 100644 index 6db09b293..000000000 --- a/src/Filtering/ImageGrid/Create3DVolume/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: Create3DVolume - -Create 3D Volume -================ - -.. index:: - single: TileImageFilter - single: append - single: tile - single: concatenate - -Synopsis --------- - -This example reads in a series of 2D images and stacks them to create a 3D image. - -Results -------- - -.. figure:: Input.png - :scale: 50% - :alt: Input 2D images - - Input 2D images - -.. figure:: Output.png - :scale: 80% - :alt: Output 3D image - - Single output 3D image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TileImageFilter diff --git a/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.md b/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.md new file mode 100644 index 000000000..ea078f01f --- /dev/null +++ b/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.md @@ -0,0 +1,34 @@ +--- +name: CropImageBySpecifyingRegion2 +--- + +# Crop Image by Specifying Region + +```{index} single: CropImageFilter pair: crop; region +``` + +## Synopsis + +Crop an image by specifying the region to throw away. + +## Results + +:::{figure} CropImageBySpecifyingRegion2.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CropImageFilter +``` diff --git a/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.rst b/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.rst deleted file mode 100644 index 3923ae1fc..000000000 --- a/src/Filtering/ImageGrid/CropImageBySpecifyingRegion2/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: CropImageBySpecifyingRegion2 - -Crop Image by Specifying Region -=============================== - -.. index:: - single: CropImageFilter - pair: crop; region - -Synopsis --------- - -Crop an image by specifying the region to throw away. - - -Results -------- -.. figure:: CropImageBySpecifyingRegion2.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::CropImageFilter diff --git a/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.md b/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.md new file mode 100644 index 000000000..159a003d2 --- /dev/null +++ b/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ExtractRegionOfInterestInOneImage +--- + +# Extract Region of Interest in One Image + +```{index} single: RegionOfInterestImageFilter +``` + +## Synopsis + +Extract a given Region Of Interest (ROI) in a given image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RegionOfInterestImageFilter +``` diff --git a/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.rst b/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.rst deleted file mode 100644 index 25ac133a5..000000000 --- a/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: ExtractRegionOfInterestInOneImage - -Extract Region of Interest in One Image -======================================= - -.. index:: - single: RegionOfInterestImageFilter - -Synopsis --------- - -Extract a given Region Of Interest (ROI) in a given image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::RegionOfInterestImageFilter diff --git a/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.md b/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.md new file mode 100644 index 000000000..d20931eeb --- /dev/null +++ b/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.md @@ -0,0 +1,40 @@ +--- +name: FitSplineIntoPointSet +--- + +# Fit Spline Into Point Set + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: BSplineScatteredDataPointSetToImageFilter +``` + +## Synopsis + +Fit a spline to a point set. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BSplineScatteredDataPointSetToImageFilter +``` diff --git a/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.rst b/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.rst deleted file mode 100644 index 001cd24a5..000000000 --- a/src/Filtering/ImageGrid/FitSplineIntoPointSet/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: FitSplineIntoPointSet - -Fit Spline Into Point Set -========================= -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: BSplineScatteredDataPointSetToImageFilter - -Synopsis --------- - -Fit a spline to a point set. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BSplineScatteredDataPointSetToImageFilter diff --git a/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.md b/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.md new file mode 100644 index 000000000..4ccdb6720 --- /dev/null +++ b/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.md @@ -0,0 +1,49 @@ +--- +name: FlipAnImageOverSpecifiedAxes +--- + +# Flip an Image Over Specified Axes + +```{index} single: FlipImageFilter single: flip +``` + +## Synopsis + +Flip an image over the specified axes. Pixels are swapped over the given axis. + +## Results + +:::{figure} Yinyang.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FlipImageFilter +``` diff --git a/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.rst b/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.rst deleted file mode 100644 index b96d7a590..000000000 --- a/src/Filtering/ImageGrid/FlipAnImageOverSpecifiedAxes/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: FlipAnImageOverSpecifiedAxes - -Flip an Image Over Specified Axes -================================= - -.. index:: - single: FlipImageFilter - single: flip - - -Synopsis --------- - -Flip an image over the specified axes. Pixels are swapped over the given axis. - - -Results -------- - -.. figure:: Yinyang.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FlipImageFilter diff --git a/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.md b/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.md new file mode 100644 index 000000000..b8e80e11c --- /dev/null +++ b/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.md @@ -0,0 +1,36 @@ +--- +name: PadAnImageByMirroring +--- + +# Pad an Image by Mirroring + +```{index} single: MirrorPadImageFilter +``` + +## Synopsis + +Pad an image using mirroring over the boundaries + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.rst b/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.rst deleted file mode 100644 index 6e971ca75..000000000 --- a/src/Filtering/ImageGrid/PadAnImageByMirroring/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: PadAnImageByMirroring - -Pad an Image by Mirroring -========================= - -.. index:: - single: MirrorPadImageFilter - -Synopsis --------- - -Pad an image using mirroring over the boundaries - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.md b/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.md new file mode 100644 index 000000000..926b2cede --- /dev/null +++ b/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.md @@ -0,0 +1,36 @@ +--- +name: PadAnImageWithAConstant +--- + +# Pad an Image With a Constant + +```{index} single: ConstantPadImageFilter +``` + +## Synopsis + +Pad an itk::Image with a given constant + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` diff --git a/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.rst b/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.rst deleted file mode 100644 index a546ba38a..000000000 --- a/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: PadAnImageWithAConstant - -Pad an Image With a Constant -============================ - -.. index:: - single: ConstantPadImageFilter - -Synopsis --------- - - -Pad an itk::Image with a given constant - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- diff --git a/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.md b/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.md new file mode 100644 index 000000000..34960c19e --- /dev/null +++ b/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.md @@ -0,0 +1,35 @@ +--- +name: PadImageByWrapping +--- + +# Pad Image by Wrapping + +```{index} single: WrapPadImageFilter single: wrapping pair: pad; image +``` + +## Synopsis + +Pad an image by wrapping. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::WrapPadImageFilter +``` diff --git a/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.rst b/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.rst deleted file mode 100644 index 1479c700e..000000000 --- a/src/Filtering/ImageGrid/PadImageByWrapping/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: PadImageByWrapping - -Pad Image by Wrapping -===================== - -.. index:: - single: WrapPadImageFilter - single: wrapping - pair: pad; image - -Synopsis --------- - -Pad an image by wrapping. - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::WrapPadImageFilter diff --git a/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.md b/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.md new file mode 100644 index 000000000..cacd2f4dc --- /dev/null +++ b/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.md @@ -0,0 +1,49 @@ +--- +name: PasteImageIntoAnotherOne +--- + +# Paste Image Into Another One + +```{index} single: PasteImageFilter +``` + +## Synopsis + +Paste one itk::Image into another one + +## Results + +:::{figure} Yinyang.png +:alt: Source image +:scale: 50% + +Source image +::: + +:::{figure} Gourds.png +:alt: Destination image +:scale: 50% + +Destination image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PasteImageFilter +``` diff --git a/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.rst b/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.rst deleted file mode 100644 index c4627733d..000000000 --- a/src/Filtering/ImageGrid/PasteImageIntoAnotherOne/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: PasteImageIntoAnotherOne - -Paste Image Into Another One -============================ - -.. index:: - single: PasteImageFilter - -Synopsis --------- - -Paste one itk::Image into another one - - -Results -------- - -.. figure:: Yinyang.png - :scale: 50% - :alt: Source image - - Source image - -.. figure:: Gourds.png - :scale: 50% - :alt: Destination image - - Destination image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PasteImageFilter diff --git a/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.md b/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.md new file mode 100644 index 000000000..f6ec48038 --- /dev/null +++ b/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: PermuteAxesOfAnImage +--- + +# Permute Axes of an Image + +```{index} single: PermuteAxesImageFilter +``` + +## Synopsis + +switch the axes of an image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PermuteAxesImageFilter +``` diff --git a/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.rst b/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.rst deleted file mode 100644 index 124514f7f..000000000 --- a/src/Filtering/ImageGrid/PermuteAxesOfAnImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: PermuteAxesOfAnImage - -Permute Axes of an Image -======================== - -.. index:: - single: PermuteAxesImageFilter - -Synopsis --------- - -switch the axes of an image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::PermuteAxesImageFilter diff --git a/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.md b/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.md new file mode 100644 index 000000000..6ad68c9c9 --- /dev/null +++ b/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.md @@ -0,0 +1,57 @@ +--- +name: ProcessA2DSliceOfA3DImage +--- + +# Process a 2D Slice of a 3D Image + +```{index} single: ExtractImageFilter +``` + +## Synopsis + +This example illustrates the common task of extracting a 2D slice from a +3D volume. Perform some processing on that slice and then paste it on an +output volume of the same size as the volume from the input. + +## Results + +% figure::Input232.png +% :scale: 50% +% :alt: Slice of input +% +% Slice of input + +% figure::Output232.png +% :scale: 50% +% :alt: Slice of output +% +% Slice of output + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ExtractImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::PasteImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::MedianImageFilter +``` diff --git a/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.rst b/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.rst deleted file mode 100644 index 05350feab..000000000 --- a/src/Filtering/ImageGrid/ProcessA2DSliceOfA3DImage/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: ProcessA2DSliceOfA3DImage - -Process a 2D Slice of a 3D Image -================================ - -.. index:: - single: ExtractImageFilter - -Synopsis --------- - -This example illustrates the common task of extracting a 2D slice from a -3D volume. Perform some processing on that slice and then paste it on an -output volume of the same size as the volume from the input. - - -Results -------- - -.. figure::Input232.png - :scale: 50% - :alt: Slice of input - - Slice of input - -.. figure::Output232.png - :scale: 50% - :alt: Slice of output - - Slice of output - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ExtractImageFilter -.. breathelink:: itk::PasteImageFilter -.. breathelink:: itk::MedianImageFilter diff --git a/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.md b/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.md new file mode 100644 index 000000000..4e2868ffe --- /dev/null +++ b/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ResampleAScalarImage +--- + +# Resample a Scalar Image + +```{index} single: ResampleImageFilter +``` + +## Synopsis + +Resample a scalar image. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ResampleImageFilter +``` diff --git a/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.rst b/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.rst deleted file mode 100644 index 942d42f9d..000000000 --- a/src/Filtering/ImageGrid/ResampleAScalarImage/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ResampleAScalarImage - -Resample a Scalar Image -======================= - -.. index:: - single: ResampleImageFilter - -Synopsis --------- - -Resample a scalar image. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ResampleImageFilter diff --git a/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.md b/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.md new file mode 100644 index 000000000..7563b4c95 --- /dev/null +++ b/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.md @@ -0,0 +1,51 @@ +--- +name: ResampleAVectorImage +--- + +# Resample a Vector Image + +```{index} single: ResampleImageFilter single: IdentityTransform single: LinearInterpolateImageFunction single: RGBPixel +``` + +## Synopsis + +Linearly interpolate a vector image. + +The Python wrapping for the LinearInterpolateImageFunction using vector images was added in ITK 4.7.0. + +## Results + +:::{figure} VisibleWomanHeadSlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ResampleImageFilter +``` diff --git a/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.rst b/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.rst deleted file mode 100644 index efcc0991d..000000000 --- a/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: ResampleAVectorImage - -Resample a Vector Image -======================= - -.. index:: - single: ResampleImageFilter - single: IdentityTransform - single: LinearInterpolateImageFunction - single: RGBPixel - -Synopsis --------- - -Linearly interpolate a vector image. - -The Python wrapping for the LinearInterpolateImageFunction using vector images was added in ITK 4.7.0. - - -Results -------- - -.. figure:: VisibleWomanHeadSlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ResampleImageFilter diff --git a/src/Filtering/ImageGrid/ResampleAnImage/Documentation.md b/src/Filtering/ImageGrid/ResampleAnImage/Documentation.md new file mode 100644 index 000000000..7efa3241a --- /dev/null +++ b/src/Filtering/ImageGrid/ResampleAnImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ResampleAnImage +--- + +# Resample an Image + +```{index} single: ResampleImageFilter single: LinearInterpolateImageFunction single: ScaleTransform +``` + +## Synopsis + +Resample an image. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ResampleImageFilter +``` diff --git a/src/Filtering/ImageGrid/ResampleAnImage/Documentation.rst b/src/Filtering/ImageGrid/ResampleAnImage/Documentation.rst deleted file mode 100644 index b1b643a53..000000000 --- a/src/Filtering/ImageGrid/ResampleAnImage/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: ResampleAnImage - -Resample an Image -======================================= - -.. index:: - single: ResampleImageFilter - single: LinearInterpolateImageFunction - single: ScaleTransform - -Synopsis --------- - -Resample an image. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ResampleImageFilter diff --git a/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.md b/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.md new file mode 100644 index 000000000..faed8ceea --- /dev/null +++ b/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: RunImageFilterOnRegionOfImage +--- + +# Run Image Filter on Region of Image + +```{index} single: PasteImageFilter pair: filter; region +``` + +## Synopsis + +Run an image filter on a region of an image. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image +::: + +:::{figure} RunImageFilterOnRegionOfImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PasteImageFilter +``` diff --git a/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.rst b/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.rst deleted file mode 100644 index c077be727..000000000 --- a/src/Filtering/ImageGrid/RunImageFilterOnRegionOfImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: RunImageFilterOnRegionOfImage - -Run Image Filter on Region of Image -=================================== - -.. index:: - single: PasteImageFilter - pair: filter; region - -Synopsis --------- - -Run an image filter on a region of an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image - -.. figure:: RunImageFilterOnRegionOfImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::PasteImageFilter diff --git a/src/Filtering/ImageGrid/ShrinkImage/Documentation.md b/src/Filtering/ImageGrid/ShrinkImage/Documentation.md new file mode 100644 index 000000000..69071e415 --- /dev/null +++ b/src/Filtering/ImageGrid/ShrinkImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ShrinkImage +--- + +# Shrink Image + +```{index} single: ShrinkImageFilter +``` + +## Synopsis + +Shrink an image. + +## Results + +Output: + +``` +Original size: [100, 100] +New size: [50, 33] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ShrinkImageFilter +``` diff --git a/src/Filtering/ImageGrid/ShrinkImage/Documentation.rst b/src/Filtering/ImageGrid/ShrinkImage/Documentation.rst deleted file mode 100644 index d1fdb996b..000000000 --- a/src/Filtering/ImageGrid/ShrinkImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: ShrinkImage - -Shrink Image -============ - -.. index:: - single: ShrinkImageFilter - -Synopsis --------- - -Shrink an image. - - -Results -------- -Output:: - - Original size: [100, 100] - New size: [50, 33] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ShrinkImageFilter diff --git a/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.md b/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.md new file mode 100644 index 000000000..78e5f107f --- /dev/null +++ b/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: Stack2DImagesInto3DImage +--- + +# Stack 2D Images Into 3D Image + +```{index} single: TileImageFilter pair: 3D; 2D +``` + +## Synopsis + +TileImageFilter + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TileImageFilter +``` diff --git a/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.rst b/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.rst deleted file mode 100644 index 870ae81d0..000000000 --- a/src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: Stack2DImagesInto3DImage - -Stack 2D Images Into 3D Image -============================= - -.. index:: - single: TileImageFilter - pair: 3D; 2D - -Synopsis --------- - -TileImageFilter - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::TileImageFilter diff --git a/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.md b/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.md new file mode 100644 index 000000000..76630e064 --- /dev/null +++ b/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.md @@ -0,0 +1,42 @@ +--- +name: TileImagesSideBySide +--- + +# Tile Images Side by Side + +```{index} single: TileImageFilter +``` + +## Synopsis + +Tile multiple images side by side. + +## Results + +:::{figure} Gourds.png +:alt: Gourds.png +:scale: 70% + +Gourds.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TileImageFilter +``` diff --git a/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.rst b/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.rst deleted file mode 100644 index 95b4f23cd..000000000 --- a/src/Filtering/ImageGrid/TileImagesSideBySide/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: TileImagesSideBySide - -Tile Images Side by Side -======================== - -.. index:: - single: TileImageFilter - -Synopsis --------- - -Tile multiple images side by side. - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - :alt: Gourds.png - - Gourds.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::TileImageFilter diff --git a/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.md b/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.md new file mode 100644 index 000000000..1bd03b633 --- /dev/null +++ b/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.md @@ -0,0 +1,46 @@ +--- +name: UpsampleAnImage +--- + +# Upsample an Image + +```{index} single: ResampleImageFilter single: LinearInterpolateImageFunction single: ScaleTransform single: BSplineInterpolateImageFunction single: Upsampling +``` + +## Synopsis + +Upsample an image. + +## Results + +:::{figure} OutputBaseline.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} BrainProtonDensitySlice.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ResampleImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::BSplineInterpolateImageFunction +``` diff --git a/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.rst b/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.rst deleted file mode 100644 index f46ad54f5..000000000 --- a/src/Filtering/ImageGrid/UpsampleAnImage/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: UpsampleAnImage - -Upsample an Image -======================================= - -.. index:: - single: ResampleImageFilter - single: LinearInterpolateImageFunction - single: ScaleTransform - single: BSplineInterpolateImageFunction - single: Upsampling - -Synopsis --------- - -Upsample an image. - - -Results -------- - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ResampleImageFilter -.. breathelink:: itk::BSplineInterpolateImageFunction diff --git a/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.md b/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.md new file mode 100644 index 000000000..c5cd362a0 --- /dev/null +++ b/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.md @@ -0,0 +1,47 @@ +--- +name: WarpAnImageUsingADeformationField +--- + +# Warp an Image Using a Deformation Field + +```{index} single: WarpImageFilter +``` + +## Synopsis + +Use WarpImageFilter and a deformation field for resampling an image. + +## Results + +:::{figure} WarpImageFilterInput.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::WarpImageFilter +``` diff --git a/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.rst b/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.rst deleted file mode 100644 index 331b00220..000000000 --- a/src/Filtering/ImageGrid/WarpAnImageUsingADeformationField/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: WarpAnImageUsingADeformationField - -Warp an Image Using a Deformation Field -======================================= - -.. index:: - single: WarpImageFilter - -Synopsis --------- - -Use WarpImageFilter and a deformation field for resampling an image. - - -Results -------- - -.. figure:: WarpImageFilterInput.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::WarpImageFilter diff --git a/src/Filtering/ImageGrid/index.md b/src/Filtering/ImageGrid/index.md new file mode 100644 index 000000000..249bc0fff --- /dev/null +++ b/src/Filtering/ImageGrid/index.md @@ -0,0 +1,28 @@ +# ImageGrid + +```{toctree} +:maxdepth: 1 + +AppendTwo3DVolumes/Documentation.rst +ChangeImageOriginSpacingOrDirection/Documentation.rst +Create3DVolume/Documentation.rst +CropImageBySpecifyingRegion2/Documentation.rst +ExtractRegionOfInterestInOneImage/Documentation.rst +FitSplineIntoPointSet/Documentation.rst +FlipAnImageOverSpecifiedAxes/Documentation.rst +PadAnImageByMirroring/Documentation.rst +PadAnImageWithAConstant/Documentation.rst +PadImageByWrapping/Documentation.rst +PasteImageIntoAnotherOne/Documentation.rst +PermuteAxesOfAnImage/Documentation.rst +ProcessA2DSliceOfA3DImage/Documentation.rst +ResampleAnImage/Documentation.rst +ResampleAScalarImage/Documentation.rst +ResampleAVectorImage/Documentation.rst +RunImageFilterOnRegionOfImage/Documentation.rst +ShrinkImage/Documentation.rst +Stack2DImagesInto3DImage/Documentation.rst +TileImagesSideBySide/Documentation.rst +UpsampleAnImage/Documentation.rst +WarpAnImageUsingADeformationField/Documentation.rst +``` diff --git a/src/Filtering/ImageGrid/index.rst b/src/Filtering/ImageGrid/index.rst deleted file mode 100644 index 7a6fcca36..000000000 --- a/src/Filtering/ImageGrid/index.rst +++ /dev/null @@ -1,28 +0,0 @@ -ImageGrid -========= - -.. toctree:: - :maxdepth: 1 - - AppendTwo3DVolumes/Documentation.rst - ChangeImageOriginSpacingOrDirection/Documentation.rst - Create3DVolume/Documentation.rst - CropImageBySpecifyingRegion2/Documentation.rst - ExtractRegionOfInterestInOneImage/Documentation.rst - FitSplineIntoPointSet/Documentation.rst - FlipAnImageOverSpecifiedAxes/Documentation.rst - PadAnImageByMirroring/Documentation.rst - PadAnImageWithAConstant/Documentation.rst - PadImageByWrapping/Documentation.rst - PasteImageIntoAnotherOne/Documentation.rst - PermuteAxesOfAnImage/Documentation.rst - ProcessA2DSliceOfA3DImage/Documentation.rst - ResampleAnImage/Documentation.rst - ResampleAScalarImage/Documentation.rst - ResampleAVectorImage/Documentation.rst - RunImageFilterOnRegionOfImage/Documentation.rst - ShrinkImage/Documentation.rst - Stack2DImagesInto3DImage/Documentation.rst - TileImagesSideBySide/Documentation.rst - UpsampleAnImage/Documentation.rst - WarpAnImageUsingADeformationField/Documentation.rst diff --git a/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.md b/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.md new file mode 100644 index 000000000..63e71aa4f --- /dev/null +++ b/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: AbsValueOfImage +--- + +# Absolute Value of Image + +```{index} single: AbsImageFilter single: absolute +``` + +## Synopsis + +Compute the absolute value of an image. + +## Results + +:::{figure} AbsValueOfImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AbsImageFilter +``` diff --git a/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.rst b/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.rst deleted file mode 100644 index cafd4da83..000000000 --- a/src/Filtering/ImageIntensity/AbsValueOfImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: AbsValueOfImage - -Absolute Value of Image -======================= - -.. index:: - single: AbsImageFilter - single: absolute - -Synopsis --------- - -Compute the absolute value of an image. - -Results -------- -.. figure:: AbsValueOfImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AbsImageFilter diff --git a/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.md b/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.md new file mode 100644 index 000000000..6509b6496 --- /dev/null +++ b/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.md @@ -0,0 +1,42 @@ +--- +name: AddConstantToEveryPixel +--- + +# Add Constant to Every Pixel + +```{index} single: AddImageFilter +``` + +## Synopsis + +Add a constant to every pixel in an image. + +## Results + +:::{figure} Yinyang.png +:alt: Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AddImageFilter +``` diff --git a/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.rst b/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.rst deleted file mode 100644 index e8ad80c82..000000000 --- a/src/Filtering/ImageIntensity/AddConstantToEveryPixel/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: AddConstantToEveryPixel - -Add Constant to Every Pixel -=========================== - -.. index:: - single: AddImageFilter - -Synopsis --------- - -Add a constant to every pixel in an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: Yinyang.png - - Yinyang.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AddImageFilter diff --git a/src/Filtering/ImageIntensity/AddTwoImages/Documentation.md b/src/Filtering/ImageIntensity/AddTwoImages/Documentation.md new file mode 100644 index 000000000..3271691a8 --- /dev/null +++ b/src/Filtering/ImageIntensity/AddTwoImages/Documentation.md @@ -0,0 +1,34 @@ +--- +name: AddTwoImages +--- + +# Add Two Images Together + +```{index} single: AddImageFilter +``` + +## Synopsis + +Add two images together. + +## Results + +:::{figure} AddTwoImages.png +:scale: 70% + +Output In VTK Image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AddImageFilter +``` diff --git a/src/Filtering/ImageIntensity/AddTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/AddTwoImages/Documentation.rst deleted file mode 100644 index 8081e7dfa..000000000 --- a/src/Filtering/ImageIntensity/AddTwoImages/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: AddTwoImages - -Add Two Images Together -======================= - -.. index:: - single: AddImageFilter - -Synopsis --------- - -Add two images together. - - -Results -------- -.. figure:: AddTwoImages.png - :scale: 70% - - Output In VTK Image - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AddImageFilter diff --git a/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.md b/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.md new file mode 100644 index 000000000..2eb2abc76 --- /dev/null +++ b/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.md @@ -0,0 +1,28 @@ +--- +name: ApplyAtanImageFilter +--- + +# Apply Atan Image Filter + +```{index} single: AtanImageFilter +``` + +## Synopsis + +Compute the arctangent of each pixel. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AtanImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.rst b/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.rst deleted file mode 100644 index 982e4bfe4..000000000 --- a/src/Filtering/ImageIntensity/ApplyAtanImageFilter/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: ApplyAtanImageFilter - -Apply Atan Image Filter -======================= - -.. index:: - single: AtanImageFilter - -Synopsis --------- - - -Compute the arctangent of each pixel. - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AtanImageFilter diff --git a/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.md b/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.md new file mode 100644 index 000000000..66a73861d --- /dev/null +++ b/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ApplyCosImageFilter +--- + +# Apply Cos Image Filter + +```{index} single: CosImageFilter +``` + +## Synopsis + +Compute the cosine of each pixel + +## Results + +:::{figure} InputRescaled.png +:alt: Input image + +Rescaled Input image \[0, 255\] +::: + +:::{figure} OutputBaselineRescaled.png +:alt: Output image + +Rescaled Output image \[0, 255\] +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CosImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.rst b/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.rst deleted file mode 100644 index ea0f509ad..000000000 --- a/src/Filtering/ImageIntensity/ApplyCosImageFilter/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: ApplyCosImageFilter - -Apply Cos Image Filter -====================== - -.. index:: - single: CosImageFilter - -Synopsis --------- - - -Compute the cosine of each pixel - - -Results -------- - -.. figure:: InputRescaled.png - :alt: Input image - - Rescaled Input image [0, 255] - -.. figure:: OutputBaselineRescaled.png - :alt: Output image - - Rescaled Output image [0, 255] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CosImageFilter diff --git a/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.md b/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.md new file mode 100644 index 000000000..8ff0ca366 --- /dev/null +++ b/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ApplyExpNegativeImageFilter +--- + +# Apply Exp Negative Image Filter + +```{index} single: ExpNegativeImageFilter +``` + +## Synopsis + +Compute $exp(-K x)$ of each pixel. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ExpNegativeImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.rst b/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.rst deleted file mode 100644 index 1e73ce739..000000000 --- a/src/Filtering/ImageIntensity/ApplyExpNegativeImageFilter/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: ApplyExpNegativeImageFilter - -Apply Exp Negative Image Filter -=============================== - -.. index:: - single: ExpNegativeImageFilter - -Synopsis --------- - -Compute :math:`exp(-K x)` of each pixel. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ExpNegativeImageFilter diff --git a/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.md b/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.md new file mode 100644 index 000000000..5c301e209 --- /dev/null +++ b/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ApplySinImageFilter +--- + +# Apply Sin Image Filter + +```{index} single: SinImageFilter +``` + +## Synopsis + +Compute the sine of each pixel + +## Results + +:::{figure} InputRescaled.png +:alt: Input image + +Rescaled Input image \[0, 255\] +::: + +:::{figure} OutputBaselineRescaled.png +:alt: Output image + +Rescaled Output image \[0, 255\] +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SinImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.rst b/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.rst deleted file mode 100644 index 1cdbdede3..000000000 --- a/src/Filtering/ImageIntensity/ApplySinImageFilter/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: ApplySinImageFilter - -Apply Sin Image Filter -====================== - -.. index:: - single: SinImageFilter - -Synopsis --------- - - -Compute the sine of each pixel - - -Results -------- - -.. figure:: InputRescaled.png - :alt: Input image - - Rescaled Input image [0, 255] - -.. figure:: OutputBaselineRescaled.png - :alt: Output image - - Rescaled Output image [0, 255] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::SinImageFilter diff --git a/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.md b/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.md new file mode 100644 index 000000000..df1128946 --- /dev/null +++ b/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.md @@ -0,0 +1,49 @@ +--- +name: BinaryANDTwoImages +--- + +# Binary AND Two Images + +```{index} single: AndImageFilter single: AND +``` + +## Synopsis + +Binary AND two images. + +## Results + +:::{figure} input1.png +:alt: input1.png +:scale: 70% + +input1.png +::: + +:::{figure} input2.png +:alt: input2.png +:scale: 70% + +input2.png +::: + +:::{figure} BinaryANDTwoImages.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AndImageFilter +``` diff --git a/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.rst deleted file mode 100644 index 3899d4193..000000000 --- a/src/Filtering/ImageIntensity/BinaryANDTwoImages/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: BinaryANDTwoImages - -Binary AND Two Images -===================== - -.. index:: - single: AndImageFilter - single: AND - -Synopsis --------- - -Binary AND two images. - - -Results -------- -.. figure:: input1.png - :scale: 70% - :alt: input1.png - - input1.png - -.. figure:: input2.png - :scale: 70% - :alt: input2.png - - input2.png - -.. figure:: BinaryANDTwoImages.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::AndImageFilter diff --git a/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.md b/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.md new file mode 100644 index 000000000..891b8cfe0 --- /dev/null +++ b/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.md @@ -0,0 +1,49 @@ +--- +name: BinaryORTwoImages +--- + +# Binary OR Two Images + +```{index} single: OrImageFilter single: OR +``` + +## Synopsis + +Binary OR two images. + +## Results + +:::{figure} input1.png +:alt: input1.png +:scale: 70% + +input1.png +::: + +:::{figure} input2.png +:alt: input2.png +:scale: 70% + +input2.png +::: + +:::{figure} BinaryORTwoImages.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::OrImageFilter +``` diff --git a/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.rst deleted file mode 100644 index 5c7d7effa..000000000 --- a/src/Filtering/ImageIntensity/BinaryORTwoImages/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: BinaryORTwoImages - -Binary OR Two Images -==================== - -.. index:: - single: OrImageFilter - single: OR - -Synopsis --------- - -Binary OR two images. - - -Results -------- -.. figure:: input1.png - :scale: 70% - :alt: input1.png - - input1.png - -.. figure:: input2.png - :scale: 70% - :alt: input2.png - - input2.png - -.. figure:: BinaryORTwoImages.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::OrImageFilter diff --git a/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.md b/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.md new file mode 100644 index 000000000..e8cde02e8 --- /dev/null +++ b/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.md @@ -0,0 +1,49 @@ +--- +name: BinaryXORTwoImages +--- + +# Binary XOR Two Images + +```{index} single: XorImageFilter +``` + +## Synopsis + +Binary XOR (exclusive OR) two images. + +## Results + +:::{figure} input1.png +:alt: input1.png +:scale: 70% + +input1.png +::: + +:::{figure} input2.png +:alt: input2.png +:scale: 70% + +input2.png +::: + +:::{figure} BinaryXORTwoImages.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::XorImageFilter +``` diff --git a/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.rst deleted file mode 100644 index 872dcab7b..000000000 --- a/src/Filtering/ImageIntensity/BinaryXORTwoImages/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: BinaryXORTwoImages - -Binary XOR Two Images -===================== - -.. index:: - single: XorImageFilter - -Synopsis --------- - -Binary XOR (exclusive OR) two images. - - -Results -------- -.. figure:: input1.png - :scale: 70% - :alt: input1.png - - input1.png - -.. figure:: input2.png - :scale: 70% - :alt: input2.png - - input2.png - -.. figure:: BinaryXORTwoImages.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::XorImageFilter diff --git a/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.md b/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.md new file mode 100644 index 000000000..5e9b01c8d --- /dev/null +++ b/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.md @@ -0,0 +1,28 @@ +--- +name: CastImageToAnotherTypeButClampToOutput +--- + +# Cast Image to Another Type but Clamp to Output Range + +```{index} single: ClampImageFilter pair: clamp; range +``` + +## Synopsis + +Cast an image from one type to another but clamp to the output value range. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ClampImageFilter +``` diff --git a/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.rst b/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.rst deleted file mode 100644 index 9510c8c2c..000000000 --- a/src/Filtering/ImageIntensity/CastImageToAnotherTypeButClampToOutput/Documentation.rst +++ /dev/null @@ -1,31 +0,0 @@ -:name: CastImageToAnotherTypeButClampToOutput - -Cast Image to Another Type but Clamp to Output Range -==================================================== - -.. index:: - single: ClampImageFilter - pair: clamp; range - -Synopsis --------- - -Cast an image from one type to another but clamp to the output value range. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ClampImageFilter diff --git a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.md b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.md new file mode 100644 index 000000000..61fc4a478 --- /dev/null +++ b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.md @@ -0,0 +1,32 @@ +--- +name: CompareTwoImagesAndSetOutputPixelToMax +--- + +# Compare Two Images and Set Output Pixel to Max + +```{index} single: MaximumImageFilter single: maximum +``` + +## Synopsis + +Pixel wise compare two input images and set the output pixel to their max. + +## Results + +:::{note} +No output is printed, this example simply displays functionality. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MaximumImageFilter +``` diff --git a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.rst b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.rst deleted file mode 100644 index cf5d41c43..000000000 --- a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMax/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: CompareTwoImagesAndSetOutputPixelToMax - -Compare Two Images and Set Output Pixel to Max -============================================== - -.. index:: - single: MaximumImageFilter - single: maximum - -Synopsis --------- - -Pixel wise compare two input images and set the output pixel to their max. - - -Results -------- -.. note:: - No output is printed, this example simply displays functionality. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MaximumImageFilter diff --git a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.md b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.md new file mode 100644 index 000000000..5dd7df976 --- /dev/null +++ b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.md @@ -0,0 +1,32 @@ +--- +name: CompareTwoImagesAndSetOutputPixelToMin +--- + +# Compare Two Images and Set Output Pixel to Min + +```{index} single: MinimumImageFilter single: minimum +``` + +## Synopsis + +Pixel wise compare two input images and set the output pixel to their min. + +## Results + +:::{note} +No output is printed, this example simply displays functionality. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MinimumImageFilter +``` diff --git a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.rst b/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.rst deleted file mode 100644 index dc1aff288..000000000 --- a/src/Filtering/ImageIntensity/CompareTwoImagesAndSetOutputPixelToMin/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: CompareTwoImagesAndSetOutputPixelToMin - -Compare Two Images and Set Output Pixel to Min -============================================== - -.. index:: - single: MinimumImageFilter - single: minimum - -Synopsis --------- - -Pixel wise compare two input images and set the output pixel to their min. - - -Results -------- -.. note:: - No output is printed, this example simply displays functionality. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MinimumImageFilter diff --git a/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.md b/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.md new file mode 100644 index 000000000..14035fbfd --- /dev/null +++ b/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ComputeEdgePotential +--- + +# Compute Edge Potential + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: EdgePotentialImageFilter +``` + +## Synopsis + +Compute edge potential. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::EdgePotentialImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.rst b/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.rst deleted file mode 100644 index 33c31021b..000000000 --- a/src/Filtering/ImageIntensity/ComputeEdgePotential/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ComputeEdgePotential - -Compute Edge Potential -====================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: EdgePotentialImageFilter - -Synopsis --------- - -Compute edge potential. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::EdgePotentialImageFilter diff --git a/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.md b/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.md new file mode 100644 index 000000000..6a41378d1 --- /dev/null +++ b/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ComputeSigmoid +--- + +# Compute Sigmoid + +```{index} single: SigmoidImageFilter +``` + +## Synopsis + +Computes the sigmoid function pixel-wise. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SigmoidImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.rst b/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.rst deleted file mode 100644 index 8899d1796..000000000 --- a/src/Filtering/ImageIntensity/ComputeSigmoid/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: ComputeSigmoid - -Compute Sigmoid -=============== - -.. index:: - single: SigmoidImageFilter - -Synopsis --------- - -Computes the sigmoid function pixel-wise. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::SigmoidImageFilter diff --git a/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.md b/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.md new file mode 100644 index 000000000..6e2f0d279 --- /dev/null +++ b/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ComputerMagInVectorImageToMakeMagImage +--- + +# Computer Magnitude in Vector Image to Make Magnitude Image + +```{index} single: VectorMagnitudeImageFilter pair: magnitude; image pair: vector; image +``` + +## Synopsis + +Compute the magnitude of each pixel in a vector image to produce a magnitude image + +## Results + +:::{figure} Yinyang.png +:alt: Yinyang.png +:scale: 70% + +Yinyang.png +::: + +:::{figure} ComputerMagInVectorImageToMakeMagImage.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorMagnitudeImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.rst b/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.rst deleted file mode 100644 index c3e3aff0b..000000000 --- a/src/Filtering/ImageIntensity/ComputerMagInVectorImageToMakeMagImage/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: ComputerMagInVectorImageToMakeMagImage - -Computer Magnitude in Vector Image to Make Magnitude Image -========================================================== - -.. index:: - single: VectorMagnitudeImageFilter - pair: magnitude; image - pair: vector; image - -Synopsis --------- - -Compute the magnitude of each pixel in a vector image to produce a magnitude image - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: Yinyang.png - - Yinyang.png - -.. figure:: ComputerMagInVectorImageToMakeMagImage.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorMagnitudeImageFilter diff --git a/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.md b/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.md new file mode 100644 index 000000000..443437a2a --- /dev/null +++ b/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.md @@ -0,0 +1,47 @@ +--- +name: ConvertRGBImageToGrayscaleImage +--- + +# Convert RGB Image to Grayscale Image + +```{index} single: RGBToLuminanceImageFilter +``` + +## Synopsis + +Convert a RGB Image to its luminance image (grayscale one). + +## Results + +:::{figure} itk_eg_logo.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RGBToLuminanceImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.rst b/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.rst deleted file mode 100644 index 9a2ddddc0..000000000 --- a/src/Filtering/ImageIntensity/ConvertRGBImageToGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ConvertRGBImageToGrayscaleImage - -Convert RGB Image to Grayscale Image -==================================== - -.. index:: - single: RGBToLuminanceImageFilter - -Synopsis --------- - - -Convert a RGB Image to its luminance image (grayscale one). - - -Results -------- - -.. figure:: itk_eg_logo.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::RGBToLuminanceImageFilter diff --git a/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.md b/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.md new file mode 100644 index 000000000..f4563f56d --- /dev/null +++ b/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.md @@ -0,0 +1,28 @@ +--- +name: ExtractComponentOfVectorImage +--- + +# Extract Component of Vector Image + +```{index} single: VectorIndexSelectionCastImageFilter +``` + +## Synopsis + +Extract a component/channel of a vector image. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorIndexSelectionCastImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.rst b/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.rst deleted file mode 100644 index 7ecd4e974..000000000 --- a/src/Filtering/ImageIntensity/ExtractComponentOfVectorImage/Documentation.rst +++ /dev/null @@ -1,30 +0,0 @@ -:name: ExtractComponentOfVectorImage - -Extract Component of Vector Image -================================= - -.. index:: - single: VectorIndexSelectionCastImageFilter - -Synopsis --------- - -Extract a component/channel of a vector image. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorIndexSelectionCastImageFilter diff --git a/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.md b/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.md new file mode 100644 index 000000000..9d08f93b7 --- /dev/null +++ b/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.md @@ -0,0 +1,35 @@ +--- +name: IntensityWindowing +--- + +# Intensity Windowing + +```{index} single: IntensityWindowingImageFilter +``` + +## Synopsis + +Apply a linear intensity transform from a specified input range to a specified output range. + +## Results + +:::{figure} IntensityWindowing.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::IntensityWindowingImageFilter +``` diff --git a/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.rst b/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.rst deleted file mode 100644 index 25430e0ed..000000000 --- a/src/Filtering/ImageIntensity/IntensityWindowing/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: IntensityWindowing - -Intensity Windowing -=================== - -.. index:: - single: IntensityWindowingImageFilter - -Synopsis --------- - -Apply a linear intensity transform from a specified input range to a specified output range. - - -Results -------- -.. figure:: IntensityWindowing.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::IntensityWindowingImageFilter diff --git a/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.md b/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.md new file mode 100644 index 000000000..2e3132555 --- /dev/null +++ b/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: InverseOfMaskToImage +--- + +# Inverse of Mask to Image + +```{index} single: MaskNegatedImageFilter pair: mask; inverse +``` + +## Synopsis + +Apply the inverse of a mask to an image. + +## Results + +:::{figure} InverseOfMaskToImage.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MaskNegatedImageFilter +``` diff --git a/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.rst b/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.rst deleted file mode 100644 index f9ac96718..000000000 --- a/src/Filtering/ImageIntensity/InverseOfMaskToImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: InverseOfMaskToImage - -Inverse of Mask to Image -======================== - -.. index:: - single: MaskNegatedImageFilter - pair: mask; inverse - -Synopsis --------- - -Apply the inverse of a mask to an image. - - -Results -------- -.. figure:: InverseOfMaskToImage.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MaskNegatedImageFilter diff --git a/src/Filtering/ImageIntensity/InvertImage/Documentation.md b/src/Filtering/ImageIntensity/InvertImage/Documentation.md new file mode 100644 index 000000000..789bf393a --- /dev/null +++ b/src/Filtering/ImageIntensity/InvertImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: InvertImage +--- + +# Invert Image + +```{index} single: InvertIntensityImageFilter single: invert +``` + +## Synopsis + +Invert an image. + +## Results + +:::{figure} InvertImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::InvertIntensityImageFilter +``` diff --git a/src/Filtering/ImageIntensity/InvertImage/Documentation.rst b/src/Filtering/ImageIntensity/InvertImage/Documentation.rst deleted file mode 100644 index dbe128b86..000000000 --- a/src/Filtering/ImageIntensity/InvertImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: InvertImage - -Invert Image -============ - -.. index:: - single: InvertIntensityImageFilter - single: invert - -Synopsis --------- - -Invert an image. - - -Results -------- -.. figure:: InvertImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::InvertIntensityImageFilter diff --git a/src/Filtering/ImageIntensity/MaskImage/Documentation.md b/src/Filtering/ImageIntensity/MaskImage/Documentation.md new file mode 100644 index 000000000..bf1152e2b --- /dev/null +++ b/src/Filtering/ImageIntensity/MaskImage/Documentation.md @@ -0,0 +1,106 @@ +--- +name: MaskImage +--- + +# Mask Image + +```{index} single: MaskImageFilter pair: mask; image +``` + +## Synopsis + +Apply a mask to an image. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input Image +::: + +:::{figure} MaskImage.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Image (0x7f9d9c95ccc0) +RTTI typeinfo: itk::Image +Reference Count: 2 +Modified Time: 235 +Debug: Off +Object Name: +Observers: + none +Source: (none) +Source output name: (none) +Release Data: Off +Data Released: False +Global Release Data: Off +PipelineMTime: 0 +UpdateMTime: 0 +RealTimeStamp: 0 seconds +LargestPossibleRegion: + Dimension: 2 + Index: [0, 0] + Size: [512, 342] +BufferedRegion: + Dimension: 2 + Index: [0, 0] + Size: [512, 342] +RequestedRegion: + Dimension: 2 + Index: [0, 0] + Size: [512, 342] +Spacing: [1, 1] +Origin: [0, 0] +Direction: +1 0 +0 1 + +IndexToPointMatrix: +1 0 +0 1 + +PointToIndexMatrix: +1 0 +0 1 + +Inverse Direction: +1 0 +0 1 + +PixelContainer: + ImportImageContainer (0x7f9d9c95d000) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 236 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x7f9d90050000 + Container manages memory: true + Size: 175104 + Capacity: 175104 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MaskImageFilter +``` diff --git a/src/Filtering/ImageIntensity/MaskImage/Documentation.rst b/src/Filtering/ImageIntensity/MaskImage/Documentation.rst deleted file mode 100644 index 21d2127bd..000000000 --- a/src/Filtering/ImageIntensity/MaskImage/Documentation.rst +++ /dev/null @@ -1,105 +0,0 @@ -:name: MaskImage - -Mask Image -========== - -.. index:: - single: MaskImageFilter - pair: mask; image - -Synopsis --------- - -Apply a mask to an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input Image - -.. figure:: MaskImage.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Output:: - - Image (0x7f9d9c95ccc0) - RTTI typeinfo: itk::Image - Reference Count: 2 - Modified Time: 235 - Debug: Off - Object Name: - Observers: - none - Source: (none) - Source output name: (none) - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 0 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 2 - Index: [0, 0] - Size: [512, 342] - BufferedRegion: - Dimension: 2 - Index: [0, 0] - Size: [512, 342] - RequestedRegion: - Dimension: 2 - Index: [0, 0] - Size: [512, 342] - Spacing: [1, 1] - Origin: [0, 0] - Direction: - 1 0 - 0 1 - - IndexToPointMatrix: - 1 0 - 0 1 - - PointToIndexMatrix: - 1 0 - 0 1 - - Inverse Direction: - 1 0 - 0 1 - - PixelContainer: - ImportImageContainer (0x7f9d9c95d000) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 236 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x7f9d90050000 - Container manages memory: true - Size: 175104 - Capacity: 175104 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MaskImageFilter diff --git a/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.md b/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.md new file mode 100644 index 000000000..866b3aa4d --- /dev/null +++ b/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.md @@ -0,0 +1,42 @@ +--- +name: MultiplyImageByScalar +--- + +# Multiply Image by Scalar + +```{index} single: MultiplyImageFilter +``` + +## Synopsis + +Multiply one image by a given scalar value. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Output.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MultiplyImageFilter +``` diff --git a/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.rst b/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.rst deleted file mode 100644 index c62d872a1..000000000 --- a/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: MultiplyImageByScalar - -Multiply Image by Scalar -======================== - -.. index:: - single: MultiplyImageFilter - -Synopsis --------- - -Multiply one image by a given scalar value. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Output.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MultiplyImageFilter diff --git a/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.md b/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.md new file mode 100644 index 000000000..0de27a16e --- /dev/null +++ b/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.md @@ -0,0 +1,49 @@ +--- +name: MultiplyTwoImages +--- + +# Multiply Two Images + +```{index} single: MultiplyImageFilter +``` + +## Synopsis + +Multiply two images + +## Results + +:::{figure} Gourds.png +:alt: Input image 1 +:scale: 50% + +Input image 1 +::: + +:::{figure} mask.png +:alt: Input image 2 +:scale: 50% + +Input image 2 +::: + +:::{figure} OutputMultiply.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MultiplyImageFilter +``` diff --git a/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.rst deleted file mode 100644 index d70a807c8..000000000 --- a/src/Filtering/ImageIntensity/MultiplyTwoImages/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: MultiplyTwoImages - -Multiply Two Images -=================== - -.. index:: - single: MultiplyImageFilter - -Synopsis --------- - -Multiply two images - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image 1 - - Input image 1 - -.. figure:: mask.png - :scale: 50% - :alt: Input image 2 - - Input image 2 - -.. figure:: OutputMultiply.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MultiplyImageFilter diff --git a/src/Filtering/ImageIntensity/NormalizeImage/Documentation.md b/src/Filtering/ImageIntensity/NormalizeImage/Documentation.md new file mode 100644 index 000000000..97ec2bc10 --- /dev/null +++ b/src/Filtering/ImageIntensity/NormalizeImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: NormalizeImage +--- + +# Normalize Image + +```{index} single: NormalizeImageFilter single: normalize +``` + +## Synopsis + +Normalize an image. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input Image +::: + +:::{figure} NormalizeImage.png +:scale: 50% + +Input And Output Image With Data +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalizeImageFilter +``` diff --git a/src/Filtering/ImageIntensity/NormalizeImage/Documentation.rst b/src/Filtering/ImageIntensity/NormalizeImage/Documentation.rst deleted file mode 100644 index 46208c3c1..000000000 --- a/src/Filtering/ImageIntensity/NormalizeImage/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: NormalizeImage - -Normalize Image -=============== - -.. index:: - single: NormalizeImageFilter - single: normalize - -Synopsis --------- - -Normalize an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input Image - -.. figure:: NormalizeImage.png - :scale: 50% - - Input And Output Image With Data - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalizeImageFilter diff --git a/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.md b/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.md new file mode 100644 index 000000000..9cec59f7d --- /dev/null +++ b/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.md @@ -0,0 +1,35 @@ +--- +name: PixelDivisionOfTwoImages +--- + +# Pixel Division of Two Images + +```{index} single: DivideImageFilter pair: division; image +``` + +## Synopsis + +Pixel-wise division of two images. + +## Results + +:::{figure} PixelDivisionOfTwoImages.png +:alt: PixelDivisionOfTwoImages.png +:scale: 70% + +PixelDivisionOfTwoImages.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DivideImageFilter +``` diff --git a/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.rst deleted file mode 100644 index 6d2ad6ae6..000000000 --- a/src/Filtering/ImageIntensity/PixelDivisionOfTwoImages/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: PixelDivisionOfTwoImages - -Pixel Division of Two Images -============================ - -.. index:: - single: DivideImageFilter - pair: division; image - -Synopsis --------- - -Pixel-wise division of two images. - - -Results -------- -.. figure:: PixelDivisionOfTwoImages.png - :scale: 70% - :alt: PixelDivisionOfTwoImages.png - - PixelDivisionOfTwoImages.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::DivideImageFilter diff --git a/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.md b/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.md new file mode 100644 index 000000000..a7aa20926 --- /dev/null +++ b/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.md @@ -0,0 +1,49 @@ +--- +name: RescaleIntensity +--- + +# Rescale an Image + +```{index} single: RescaleIntensityImageFilter +``` + +## Synopsis + +Rescale a grayscale image + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RescaleIntensityImageFilter +``` diff --git a/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.rst b/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.rst deleted file mode 100644 index 95720f028..000000000 --- a/src/Filtering/ImageIntensity/RescaleIntensity/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: RescaleIntensity - -Rescale an Image -================ - -.. index:: - single: RescaleIntensityImageFilter - -Synopsis --------- - - -Rescale a grayscale image - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::RescaleIntensityImageFilter diff --git a/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.md b/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.md new file mode 100644 index 000000000..ead494737 --- /dev/null +++ b/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ScalePixelSumToConstant +--- + +# Scale All Pixel's Sum to Constant + +```{index} single: NormalizeToConstantImageFilter pair: pixel; constant +``` + +## Synopsis + +Scale all pixels so that their sum is a specified constant. + +## Results + +Output: + +``` +0.111111 +0.111111 +0.111111 +0.111111 +0.111111 +0.111111 +0.111111 +0.111111 +0.111111 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalizeToConstantImageFilter +``` diff --git a/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.rst b/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.rst deleted file mode 100644 index 4e245157c..000000000 --- a/src/Filtering/ImageIntensity/ScalePixelSumToConstant/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: ScalePixelSumToConstant - -Scale All Pixel's Sum to Constant -================================= - -.. index:: - single: NormalizeToConstantImageFilter - pair: pixel; constant - -Synopsis --------- - -Scale all pixels so that their sum is a specified constant. - - -Results -------- -Output:: - - 0.111111 - 0.111111 - 0.111111 - 0.111111 - 0.111111 - 0.111111 - 0.111111 - 0.111111 - 0.111111 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalizeToConstantImageFilter diff --git a/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.md b/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.md new file mode 100644 index 000000000..9237837e1 --- /dev/null +++ b/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.md @@ -0,0 +1,35 @@ +--- +name: SquareEveryPixel +--- + +# Square Every Pixel + +```{index} single: SquareImageFilter +``` + +## Synopsis + +Square every pixel in an image. + +## Results + +:::{figure} SquareEveryPixel.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SquareImageFilter +``` diff --git a/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.rst b/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.rst deleted file mode 100644 index 8abb5aec6..000000000 --- a/src/Filtering/ImageIntensity/SquareEveryPixel/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: SquareEveryPixel - -Square Every Pixel -================== - -.. index:: - single: SquareImageFilter - -Synopsis --------- - -Square every pixel in an image. - - -Results -------- -.. figure:: SquareEveryPixel.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SquareImageFilter diff --git a/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.md b/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.md new file mode 100644 index 000000000..9e87109f2 --- /dev/null +++ b/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.md @@ -0,0 +1,35 @@ +--- +name: SubtractConstantFromEveryPixel +--- + +# Subtract Constant From Every Pixel + +```{index} single: SubtractImageFilter +``` + +## Synopsis + +Subtract a constant from every pixel in an image. + +## Results + +:::{figure} SubtractConstantFromEveryPixel.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SubtractImageFilter +``` diff --git a/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.rst b/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.rst deleted file mode 100644 index 7c88502b5..000000000 --- a/src/Filtering/ImageIntensity/SubtractConstantFromEveryPixel/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: SubtractConstantFromEveryPixel - -Subtract Constant From Every Pixel -================================== - -.. index:: - single: SubtractImageFilter - -Synopsis --------- - -Subtract a constant from every pixel in an image. - - -Results -------- -.. figure:: SubtractConstantFromEveryPixel.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SubtractImageFilter diff --git a/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.md b/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.md new file mode 100644 index 000000000..442d14db3 --- /dev/null +++ b/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.md @@ -0,0 +1,35 @@ +--- +name: SubtractTwoImages +--- + +# Subtract Two Images + +```{index} single: SubtractImageFilter +``` + +## Synopsis + +Subtract two images from one another. + +## Results + +:::{figure} SubtractTwoImages.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SubtractImageFilter +``` diff --git a/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.rst b/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.rst deleted file mode 100644 index 23eb7f7b0..000000000 --- a/src/Filtering/ImageIntensity/SubtractTwoImages/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: SubtractTwoImages - -Subtract Two Images -=================== - -.. index:: - single: SubtractImageFilter - -Synopsis --------- - -Subtract two images from one another. - - -Results -------- -.. figure:: SubtractTwoImages.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SubtractImageFilter diff --git a/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.md b/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.md new file mode 100644 index 000000000..ae02d7f01 --- /dev/null +++ b/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.md @@ -0,0 +1,42 @@ +--- +name: TransformVectorValuedImagePixels +--- + +# Transform Magnitude of Vector Valued Image Pixels + +```{index} single: VectorRescaleIntensityImageFilter +``` + +## Synopsis + +Apply a transformation to the magnitude of vector valued image pixels. + +## Results + +:::{figure} Gourds.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} TransformVectorValuedImagePixels.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorRescaleIntensityImageFilter +``` diff --git a/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.rst b/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.rst deleted file mode 100644 index 6bc327d43..000000000 --- a/src/Filtering/ImageIntensity/TransformVectorValuedImagePixels/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: TransformVectorValuedImagePixels - -Transform Magnitude of Vector Valued Image Pixels -================================================= - -.. index:: - single: VectorRescaleIntensityImageFilter - -Synopsis --------- - -Apply a transformation to the magnitude of vector valued image pixels. - - -Results -------- -.. figure:: Gourds.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: TransformVectorValuedImagePixels.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorRescaleIntensityImageFilter diff --git a/src/Filtering/ImageIntensity/index.md b/src/Filtering/ImageIntensity/index.md new file mode 100644 index 000000000..ae0e13995 --- /dev/null +++ b/src/Filtering/ImageIntensity/index.md @@ -0,0 +1,38 @@ +# ImageIntensity + +```{toctree} +:maxdepth: 1 + +AbsValueOfImage/Documentation.rst +AddConstantToEveryPixel/Documentation.rst +AddTwoImages/Documentation.rst +ApplyAtanImageFilter/Documentation.rst +ApplyCosImageFilter/Documentation.rst +ApplyExpNegativeImageFilter/Documentation.rst +ApplySinImageFilter/Documentation.rst +BinaryANDTwoImages/Documentation.rst +BinaryORTwoImages/Documentation.rst +BinaryXORTwoImages/Documentation.rst +CastImageToAnotherTypeButClampToOutput/Documentation.rst +CompareTwoImagesAndSetOutputPixelToMax/Documentation.rst +CompareTwoImagesAndSetOutputPixelToMin/Documentation.rst +ComputeEdgePotential/Documentation.rst +ComputeSigmoid/Documentation.rst +ComputerMagInVectorImageToMakeMagImage/Documentation.rst +ConvertRGBImageToGrayscaleImage/Documentation.rst +ExtractComponentOfVectorImage/Documentation.rst +IntensityWindowing/Documentation.rst +InverseOfMaskToImage/Documentation.rst +InvertImage/Documentation.rst +MaskImage/Documentation.rst +MultiplyImageByScalar/Documentation.rst +MultiplyTwoImages/Documentation.rst +NormalizeImage/Documentation.rst +PixelDivisionOfTwoImages/Documentation.rst +RescaleIntensity/Documentation.rst +ScalePixelSumToConstant/Documentation.rst +SquareEveryPixel/Documentation.rst +SubtractConstantFromEveryPixel/Documentation.rst +SubtractTwoImages/Documentation.rst +TransformVectorValuedImagePixels/Documentation.rst +``` diff --git a/src/Filtering/ImageIntensity/index.rst b/src/Filtering/ImageIntensity/index.rst deleted file mode 100644 index 9f2688d88..000000000 --- a/src/Filtering/ImageIntensity/index.rst +++ /dev/null @@ -1,38 +0,0 @@ -ImageIntensity -============== - -.. toctree:: - :maxdepth: 1 - - AbsValueOfImage/Documentation.rst - AddConstantToEveryPixel/Documentation.rst - AddTwoImages/Documentation.rst - ApplyAtanImageFilter/Documentation.rst - ApplyCosImageFilter/Documentation.rst - ApplyExpNegativeImageFilter/Documentation.rst - ApplySinImageFilter/Documentation.rst - BinaryANDTwoImages/Documentation.rst - BinaryORTwoImages/Documentation.rst - BinaryXORTwoImages/Documentation.rst - CastImageToAnotherTypeButClampToOutput/Documentation.rst - CompareTwoImagesAndSetOutputPixelToMax/Documentation.rst - CompareTwoImagesAndSetOutputPixelToMin/Documentation.rst - ComputeEdgePotential/Documentation.rst - ComputeSigmoid/Documentation.rst - ComputerMagInVectorImageToMakeMagImage/Documentation.rst - ConvertRGBImageToGrayscaleImage/Documentation.rst - ExtractComponentOfVectorImage/Documentation.rst - IntensityWindowing/Documentation.rst - InverseOfMaskToImage/Documentation.rst - InvertImage/Documentation.rst - MaskImage/Documentation.rst - MultiplyImageByScalar/Documentation.rst - MultiplyTwoImages/Documentation.rst - NormalizeImage/Documentation.rst - PixelDivisionOfTwoImages/Documentation.rst - RescaleIntensity/Documentation.rst - ScalePixelSumToConstant/Documentation.rst - SquareEveryPixel/Documentation.rst - SubtractConstantFromEveryPixel/Documentation.rst - SubtractTwoImages/Documentation.rst - TransformVectorValuedImagePixels/Documentation.rst diff --git a/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.md b/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.md new file mode 100644 index 000000000..501d3dbd9 --- /dev/null +++ b/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ExtractBoundariesOfConnectedRegionsInBinaryImage +--- + +# Extract Boundaries of Connected Regions in Binary Image + +```{index} single: BinaryContourImageFilter +``` + +## Synopsis + +Extract the boundaries of connected regions in a binary image. + +## Results + +:::{figure} ExtractBoundariesOfConnectedRegionsInBinaryImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryContourImageFilter +``` diff --git a/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.rst b/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.rst deleted file mode 100644 index 067a11995..000000000 --- a/src/Filtering/ImageLabel/ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: ExtractBoundariesOfConnectedRegionsInBinaryImage - -Extract Boundaries of Connected Regions in Binary Image -======================================================= - -.. index:: - single: BinaryContourImageFilter - -Synopsis --------- - -Extract the boundaries of connected regions in a binary image. - - -Results -------- -.. figure:: ExtractBoundariesOfConnectedRegionsInBinaryImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryContourImageFilter diff --git a/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.md b/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.md new file mode 100644 index 000000000..56277e304 --- /dev/null +++ b/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage +--- + +# Extract Inner and Outer Boundaries of Blobs in Binary Image + +```{index} single: BinaryContourImageFilter single: blob pair: inner; outer +``` + +## Synopsis + +Extract the inner and outer boundaries of blobs in a binary image. + +## Results + +:::{figure} ExtractBoundariesOfBlobsInBinaryImage.png +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryContourImageFilter +``` diff --git a/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.rst b/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.rst deleted file mode 100644 index b1ba06775..000000000 --- a/src/Filtering/ImageLabel/ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage - -Extract Inner and Outer Boundaries of Blobs in Binary Image -=========================================================== - -.. index:: - single: BinaryContourImageFilter - single: blob - pair: inner; outer - -Synopsis --------- - -Extract the inner and outer boundaries of blobs in a binary image. - - -Results -------- -.. figure:: ExtractBoundariesOfBlobsInBinaryImage.png - :scale: 70% - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryContourImageFilter diff --git a/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.md b/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.md new file mode 100644 index 000000000..fa4cb6f7b --- /dev/null +++ b/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.md @@ -0,0 +1,34 @@ +--- +name: LabelContoursOfConnectComponent +--- + +# Label Contours of Connect Components + +```{index} single: LabelContourImageFilter +``` + +## Synopsis + +Label the contours of connected components. + +## Results + +:::{figure} LabelContoursOfConnectComponents.png +:scale: 70% +::: + +Generated Output. + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelContourImageFilter +``` diff --git a/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.rst b/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.rst deleted file mode 100644 index cf98f96c8..000000000 --- a/src/Filtering/ImageLabel/LabelContoursOfConnectComponent/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: LabelContoursOfConnectComponent - -Label Contours of Connect Components -==================================== - -.. index:: - single: LabelContourImageFilter - -Synopsis --------- - -Label the contours of connected components. - - -Results -------- -.. figure:: LabelContoursOfConnectComponents.png - :scale: 70% - -Generated Output. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelContourImageFilter diff --git a/src/Filtering/ImageLabel/index.md b/src/Filtering/ImageLabel/index.md new file mode 100644 index 000000000..a96660890 --- /dev/null +++ b/src/Filtering/ImageLabel/index.md @@ -0,0 +1,9 @@ +# ImageLabel + +```{toctree} +:maxdepth: 1 + +ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.rst +ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.rst +LabelContoursOfConnectComponent/Documentation.rst +``` diff --git a/src/Filtering/ImageLabel/index.rst b/src/Filtering/ImageLabel/index.rst deleted file mode 100644 index b0378841d..000000000 --- a/src/Filtering/ImageLabel/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -ImageLabel -========== - -.. toctree:: - :maxdepth: 1 - - ExtractInnerAndOuterBoundariesOfBlobsInBinaryImage/Documentation.rst - ExtractBoundariesOfConnectedRegionsInBinaryImage/Documentation.rst - LabelContoursOfConnectComponent/Documentation.rst diff --git a/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.md b/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.md new file mode 100644 index 000000000..3128b63a8 --- /dev/null +++ b/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.md @@ -0,0 +1,87 @@ +--- +name: AdaptiveHistogramEqualizationImageFilter +substitutions: + input_image: |- + ```{image} sf4.png + :align: middle + :alt: Input image + ``` + input_image_caption: Input image. + input_image_histogram: |- + ```{image} sf4_histogram.png + :align: middle + :alt: Input image histogram + ``` + input_image_histogram_caption: Input image histogram. + output_image: |- + ```{image} AdaptiveHistogramEqualizationImageFilter06Baseline.png + :align: middle + :alt: Output image + ``` + output_image_caption: Output image. + output_image_histogram: |- + ```{image} AdaptiveHistogramEqualizationImageFilter06Baseline_histogram.png + :align: middle + :alt: Output image histogram + ``` + output_image_histogram_caption: Output image histogram. +--- + +# Adaptive Histogram Equalization Image Filter + +```{index} single: AdaptiveHistogramEqualizationImageFilter single: smooth +``` + +## Synopsis + +Apply a power law adaptive histogram equalization controlled by the parameters +alpha and beta. + +The parameter `alpha` controls how much the filter acts like the classical +histogram equalization method (`alpha = 0`) to how much the filter acts like +an unsharp mask (`alpha = 1`). + +The parameter `beta` controls how much the filter acts like an unsharp mask +(`beta = 0`) to much the filter acts like pass through (`beta = 1, with +alpha = 1`). + +The parameter window (or radius) controls the size of the region +over which local statistics are calculated. + +## Results + +```{eval-rst} +.. tabularcolumns:: |c|c| +``` + +```{eval-rst} +=================================== ==================================== + |input_image| |output_image| + |input_image_caption| |output_image_caption| +----------------------------------- ------------------------------------ + |input_image_histogram| |output_image_histogram| + |input_image_histogram_caption| |output_image_histogram_caption| +=================================== ==================================== +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AdaptiveHistogramEqualizationImageFilter +``` diff --git a/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.rst b/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.rst deleted file mode 100644 index c3898983a..000000000 --- a/src/Filtering/ImageStatistics/AdaptiveHistogramEqualizationImageFilter/Documentation.rst +++ /dev/null @@ -1,83 +0,0 @@ -:name: AdaptiveHistogramEqualizationImageFilter - -Adaptive Histogram Equalization Image Filter -============================================ - -.. index:: - single: AdaptiveHistogramEqualizationImageFilter - single: smooth - -Synopsis --------- - -Apply a power law adaptive histogram equalization controlled by the parameters -alpha and beta. - -The parameter ``alpha`` controls how much the filter acts like the classical -histogram equalization method (``alpha = 0``) to how much the filter acts like -an unsharp mask (``alpha = 1``). - -The parameter ``beta`` controls how much the filter acts like an unsharp mask -(``beta = 0``) to much the filter acts like pass through (``beta = 1, with -alpha = 1``). - -The parameter window (or radius) controls the size of the region -over which local statistics are calculated. - -Results -------- - -.. |input_image| image:: sf4.png - :align: middle - :alt: Input image - -.. |input_image_histogram| image:: sf4_histogram.png - :align: middle - :alt: Input image histogram - -.. |output_image| image:: AdaptiveHistogramEqualizationImageFilter06Baseline.png - :align: middle - :alt: Output image - -.. |output_image_histogram| image:: AdaptiveHistogramEqualizationImageFilter06Baseline_histogram.png - :align: middle - :alt: Output image histogram - -.. |input_image_caption| replace:: Input image. -.. |input_image_histogram_caption| replace:: Input image histogram. -.. |output_image_caption| replace:: Output image. -.. |output_image_histogram_caption| replace:: Output image histogram. - -.. tabularcolumns:: |c|c| - -=================================== ==================================== - |input_image| |output_image| - |input_image_caption| |output_image_caption| ------------------------------------ ------------------------------------ - |input_image_histogram| |output_image_histogram| - |input_image_histogram_caption| |output_image_histogram_caption| -=================================== ==================================== - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AdaptiveHistogramEqualizationImageFilter diff --git a/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.md b/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.md new file mode 100644 index 000000000..900faebec --- /dev/null +++ b/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.md @@ -0,0 +1,56 @@ +--- +name: ApplyAccumulateImageFilter +--- + +# Apply Accumulate Image Filter + +```{index} single: AccumulateImageFilter +``` + +## Synopsis + +Accumulate pixels of an image along a selected direction. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} Output0.png +:alt: Output image 0 +:scale: 100% + +Output image accumulated along direction 0 +::: + +:::{figure} Output1.png +:alt: Output image 1 +:scale: 100% + +Output image accumulated along direction 1 +::: + +:::{figure} Output2.png +:alt: Output image 2 +:scale: 100% + +Output image accumulated along direction 2 +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AccumulateImageFilter +``` diff --git a/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.rst b/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.rst deleted file mode 100644 index 185040a5a..000000000 --- a/src/Filtering/ImageStatistics/ApplyAccumulateImageFilter/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: ApplyAccumulateImageFilter - -Apply Accumulate Image Filter -============================= - -.. index:: - single: AccumulateImageFilter - -Synopsis --------- - -Accumulate pixels of an image along a selected direction. - - -Results -------- - -.. figure:: Input.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: Output0.png - :scale: 100% - :alt: Output image 0 - - Output image accumulated along direction 0 - -.. figure:: Output1.png - :scale: 100% - :alt: Output image 1 - - Output image accumulated along direction 1 - -.. figure:: Output2.png - :scale: 100% - :alt: Output image 2 - - Output image accumulated along direction 2 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AccumulateImageFilter diff --git a/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.md b/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.md new file mode 100644 index 000000000..8fc2e7e45 --- /dev/null +++ b/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.md @@ -0,0 +1,80 @@ +--- +name: CalculateImageMoments +--- + +# Calculate Image Moments + +```{index} single: ImageMomentsCalculator +``` + +```{toctree} +:maxdepth: 1 + +CalculateEllipseMoments.ipynb +``` + +## Synopsis + +Calculate image moments from binary images and an interactive ellipse. + +## Results + +Input Image + +:::{figure} ellipse.png +:alt: Input image +::: + +``` +Output + ImageMomentsCalculator (000002037138BE90) + RTTI typeinfo: class itk::ImageMomentsCalculator > + Reference Count: 1 + Modified Time: 249 + Debug: Off + Object Name: + Observers: + none + Image: 000002037138FDD0 + Valid: 1 + Zeroth Moment about origin: 153 + First Moment about origin: [30, 50] + Second Moment about origin: 15.0458 -8.8366 + -8.8366 15.0458 + + Center of Gravity: [30, 50] + Second central moments: 15.0458 -8.8366 + -8.8366 15.0458 + + Principal Moments: [950, 3654] + Principal axes: 0.707107 0.707107 + -0.707107 0.707107 +``` + +## Jupyter Notebook + +```{image} https://mybinder.org/badge_logo.svg +:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKExamples/master?filepath=src%2FFiltering%2FImageStatistics%2FImageMomentsCalculator%2FCalculateEllipseMoments.ipynb +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1,16- +``` + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageMomentsCalculator +``` diff --git a/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst b/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst deleted file mode 100644 index 733835242..000000000 --- a/src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst +++ /dev/null @@ -1,85 +0,0 @@ -:name: CalculateImageMoments - -Calculate Image Moments -================================ - -.. index:: - single: ImageMomentsCalculator - -.. toctree:: - :maxdepth: 1 - - CalculateEllipseMoments.ipynb - -Synopsis --------- - - -Calculate image moments from binary images and an interactive ellipse. - -Results -------- - -Input Image - -.. figure:: ellipse.png - :alt: Input image - - -:: - - Output - ImageMomentsCalculator (000002037138BE90) - RTTI typeinfo: class itk::ImageMomentsCalculator > - Reference Count: 1 - Modified Time: 249 - Debug: Off - Object Name: - Observers: - none - Image: 000002037138FDD0 - Valid: 1 - Zeroth Moment about origin: 153 - First Moment about origin: [30, 50] - Second Moment about origin: 15.0458 -8.8366 - -8.8366 15.0458 - - Center of Gravity: [30, 50] - Second central moments: 15.0458 -8.8366 - -8.8366 15.0458 - - Principal Moments: [950, 3654] - Principal axes: 0.707107 0.707107 - -0.707107 0.707107 - - -Jupyter Notebook ------------------ - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKExamples/master?filepath=src%2FFiltering%2FImageStatistics%2FImageMomentsCalculator%2FCalculateEllipseMoments.ipynb - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1,16- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - - - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageMomentsCalculator diff --git a/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.md b/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.md new file mode 100644 index 000000000..716b4ec00 --- /dev/null +++ b/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.md @@ -0,0 +1,33 @@ +--- +name: ComputeMinMaxVarianceMeanOfImage +--- + +# Compute Min, Max, Variance and Mean of Image + +```{index} single: StatisticsImageFilter single: min single: max single: variance single: mean +``` + +## Synopsis + +Compute min, max, variance and mean of an Image. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::StatisticsImageFilter +``` diff --git a/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.rst b/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.rst deleted file mode 100644 index d2c806225..000000000 --- a/src/Filtering/ImageStatistics/ComputeMinMaxVarianceMeanOfImage/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: ComputeMinMaxVarianceMeanOfImage - -Compute Min, Max, Variance and Mean of Image -============================================ - -.. index:: - single: StatisticsImageFilter - single: min - single: max - single: variance - single: mean - -Synopsis --------- - -Compute min, max, variance and mean of an Image. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::StatisticsImageFilter diff --git a/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.md b/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.md new file mode 100644 index 000000000..d5f5d5f15 --- /dev/null +++ b/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ComputePCAShapeFromSample +--- + +# Compute PCA Shape From Training Sample + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ImagePCAShapeModelEstimator +``` + +## Synopsis + +Compute a PCA shape model from a training sample. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImagePCAShapeModelEstimator +``` diff --git a/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.rst b/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.rst deleted file mode 100644 index 0fd9ed8cd..000000000 --- a/src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ComputePCAShapeFromSample - -Compute PCA Shape From Training Sample -====================================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ImagePCAShapeModelEstimator - -Synopsis --------- - -Compute a PCA shape model from a training sample. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImagePCAShapeModelEstimator diff --git a/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.md b/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.md new file mode 100644 index 000000000..7ff253bf5 --- /dev/null +++ b/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.md @@ -0,0 +1,67 @@ +--- +name: StatisticalPropertiesOfRegions +--- + +# Statistical Properties of Labeled Regions + +```{index} single: LabelStatisticsImageFilter pair: label; regions pair: statistics; regions +``` + +## Synopsis + +Get statistical properties of labeled regions in an image. + +## Results + +:::{figure} StatisticalPropertiesOfRegions.png +:alt: image.png +:scale: 70% + +image.png +::: + +Output: + +``` +Number of labels: 2 + +min: 255 +max: 255 +median: 0 +mean: 255 +sigma: 0 +variance: 0 +sum: 4080 +count: 16 +region: ImageRegion (0x7ffedfd04a28) +Dimension: 2 +Index: [6, 6] +Size: [4, 4] + +min: 0 +max: 0 +median: 0 +mean: 0 +sigma: 0 +variance: 0 +sum: 0 +count: 384 +region: ImageRegion (0x7ffedfd04a28) +Dimension: 2 +Index: [0, 0] +Size: [20, 20] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelStatisticsImageFilter +``` diff --git a/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.rst b/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.rst deleted file mode 100644 index f1ad563ab..000000000 --- a/src/Filtering/ImageStatistics/StatisticalPropertiesOfRegions/Documentation.rst +++ /dev/null @@ -1,67 +0,0 @@ -:name: StatisticalPropertiesOfRegions - -Statistical Properties of Labeled Regions -========================================= - -.. index:: - single: LabelStatisticsImageFilter - pair: label; regions - pair: statistics; regions - -Synopsis --------- - -Get statistical properties of labeled regions in an image. - - -Results -------- -.. figure:: StatisticalPropertiesOfRegions.png - :scale: 70% - :alt: image.png - - image.png - -Output:: - - Number of labels: 2 - - min: 255 - max: 255 - median: 0 - mean: 255 - sigma: 0 - variance: 0 - sum: 4080 - count: 16 - region: ImageRegion (0x7ffedfd04a28) - Dimension: 2 - Index: [6, 6] - Size: [4, 4] - - min: 0 - max: 0 - median: 0 - mean: 0 - sigma: 0 - variance: 0 - sum: 0 - count: 384 - region: ImageRegion (0x7ffedfd04a28) - Dimension: 2 - Index: [0, 0] - Size: [20, 20] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelStatisticsImageFilter diff --git a/src/Filtering/ImageStatistics/index.md b/src/Filtering/ImageStatistics/index.md new file mode 100644 index 000000000..0ffedca77 --- /dev/null +++ b/src/Filtering/ImageStatistics/index.md @@ -0,0 +1,12 @@ +# ImageStatistics + +```{toctree} +:maxdepth: 1 + +AdaptiveHistogramEqualizationImageFilter/Documentation.rst +ApplyAccumulateImageFilter/Documentation.rst +ComputeMinMaxVarianceMeanOfImage/Documentation.rst +ComputePCAShapeFromSample/Documentation.rst +StatisticalPropertiesOfRegions/Documentation.rst +CalculateImageMoments/Documentation.rst +``` diff --git a/src/Filtering/ImageStatistics/index.rst b/src/Filtering/ImageStatistics/index.rst deleted file mode 100644 index bd8541eb4..000000000 --- a/src/Filtering/ImageStatistics/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -ImageStatistics -=============== - -.. toctree:: - :maxdepth: 1 - - AdaptiveHistogramEqualizationImageFilter/Documentation.rst - ApplyAccumulateImageFilter/Documentation.rst - ComputeMinMaxVarianceMeanOfImage/Documentation.rst - ComputePCAShapeFromSample/Documentation.rst - StatisticalPropertiesOfRegions/Documentation.rst - CalculateImageMoments/Documentation.rst diff --git a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.md b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.md new file mode 100644 index 000000000..4e9f450cc --- /dev/null +++ b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.md @@ -0,0 +1,54 @@ +--- +name: ApplyMorphologicalClosingOnAllLabelObjects +--- + +# Apply Morphological Closing on All Label Objects + +```{index} single: ObjectByObjectLabelMapFilter single: LabelUniqueLabelMapFilter +``` + +## Synopsis + +Apply morphological closing operation on all LabelObjects of a given LabelMap. + +In details: + +- read image is converted to LabelMap +- apply morphological closing operation on all LabelObjects of the LabelMap +- make sure there is no overlapping LabelObject with using LabelUniqueLabelMapFilter +- convert the LabelMap to LabelImage +- write the corresponding LabelImage + +## Results + +:::{figure} 2th_cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ObjectByObjectLabelMapFilter +``` + +```{eval-rst} +.. breathelink:: itk::LabelUniqueLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.rst b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.rst deleted file mode 100644 index f75d80a74..000000000 --- a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnAllLabelObjects/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: ApplyMorphologicalClosingOnAllLabelObjects - -Apply Morphological Closing on All Label Objects -================================================ - -.. index:: - single: ObjectByObjectLabelMapFilter - single: LabelUniqueLabelMapFilter - -Synopsis --------- - -Apply morphological closing operation on all LabelObjects of a given LabelMap. - -In details: - -* read image is converted to LabelMap -* apply morphological closing operation on all LabelObjects of the LabelMap -* make sure there is no overlapping LabelObject with using LabelUniqueLabelMapFilter -* convert the LabelMap to LabelImage -* write the corresponding LabelImage - - -Results -------- - -.. figure:: 2th_cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ObjectByObjectLabelMapFilter - -.. breathelink:: itk::LabelUniqueLabelMapFilter diff --git a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.md b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.md new file mode 100644 index 000000000..8381e2613 --- /dev/null +++ b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.md @@ -0,0 +1,53 @@ +--- +name: ApplyMorphologicalClosingOnSpecificLabelObject +--- + +# Apply Morphological Closing on Specific Label Object + +```{index} single: LabelSelectionLabelMapFilter single: ObjectByObjectLabelMapFilter single MergeLabelMapFilter single: LabelUniqueLabelMapFilter +``` + +## Synopsis + +Apply BinaryMorphologicalClosingFilter on one LabelObject of given LabelMap. + +In details: + +- read one Image +- convert the LabelImage into one LabelMap +- extract the LabelObject of interest using LabelSelectionLabelMapFilter +- apply morphological closing operation on the LabelObject of interest +- merge the processed LabelObject with remaining LabelObjects from LabelSelectionLabelMapFilter +- make sure there is no overlapping LabelObject with using LabelUniqueLabelMapFilter +- convert the LabelMap to LabelImage +- write the corresponding LabelImage + +## Results + +:::{figure} 2th_cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ObjectByObjectLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.rst b/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.rst deleted file mode 100644 index 05b3f28d6..000000000 --- a/src/Filtering/LabelMap/ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: ApplyMorphologicalClosingOnSpecificLabelObject - -Apply Morphological Closing on Specific Label Object -==================================================== - -.. index:: - single: LabelSelectionLabelMapFilter - single: ObjectByObjectLabelMapFilter - single MergeLabelMapFilter - single: LabelUniqueLabelMapFilter - -Synopsis --------- - -Apply BinaryMorphologicalClosingFilter on one LabelObject of given LabelMap. - -In details: - -* read one Image -* convert the LabelImage into one LabelMap -* extract the LabelObject of interest using LabelSelectionLabelMapFilter -* apply morphological closing operation on the LabelObject of interest -* merge the processed LabelObject with remaining LabelObjects from LabelSelectionLabelMapFilter -* make sure there is no overlapping LabelObject with using LabelUniqueLabelMapFilter -* convert the LabelMap to LabelImage -* write the corresponding LabelImage - -Results -------- - -.. figure:: 2th_cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ObjectByObjectLabelMapFilter diff --git a/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.md b/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.md new file mode 100644 index 000000000..fb038f8db --- /dev/null +++ b/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ConvertImageToLabelMap +--- + +# Convert itk::Image With Labels to Label Map + +```{index} single: LabelImageToLabelMapFilter +``` + +## Synopsis + +Convert an itk::Image consisting of labeled regions to a LabelMap. + +## Results + +Output: + +``` +There are 2 objects. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelImageToLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.rst b/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.rst deleted file mode 100644 index ade8eef14..000000000 --- a/src/Filtering/LabelMap/ConvertImageToLabelMap/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: ConvertImageToLabelMap - -Convert itk::Image With Labels to Label Map -=========================================== - -.. index:: - single: LabelImageToLabelMapFilter - -Synopsis --------- - -Convert an itk::Image consisting of labeled regions to a LabelMap. - - -Results -------- -Output:: - - There are 2 objects. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelImageToLabelMapFilter diff --git a/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.md b/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.md new file mode 100644 index 000000000..c5a454bb2 --- /dev/null +++ b/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.md @@ -0,0 +1,34 @@ +--- +name: ConvertImageWithLabelsToShapeLabelMap +--- + +# Convert Image With Labeled Regions to ShapeLabelMap + +```{index} single: LabelImageToShapeLabelMapFilter single: ShapeLabelMap +``` + +## Synopsis + +Convert an itk::Image consisting of labeled regions to a ShapeLabelMap. + +## Results + +Output: + +``` +There are 2 objects. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelImageToShapeLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.rst b/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.rst deleted file mode 100644 index daa7b77ac..000000000 --- a/src/Filtering/LabelMap/ConvertImageWithLabelsToShapeLabelMap/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: ConvertImageWithLabelsToShapeLabelMap - -Convert Image With Labeled Regions to ShapeLabelMap -=================================================== - -.. index:: - single: LabelImageToShapeLabelMapFilter - single: ShapeLabelMap - -Synopsis --------- - -Convert an itk::Image consisting of labeled regions to a ShapeLabelMap. - - -Results -------- -Output:: - - There are 2 objects. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelImageToShapeLabelMapFilter diff --git a/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.md b/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.md new file mode 100644 index 000000000..a951533b1 --- /dev/null +++ b/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ConvertLabelMapToImage +--- + +# Convert Label Map to Normal Image + +```{index} single: LabelMapToLabelImageFilter pair: label; normal +``` + +## Synopsis + +Convert a LabelMap to a normal image with different values representing each region + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMapToLabelImageFilter +``` diff --git a/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.rst b/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.rst deleted file mode 100644 index a906a823f..000000000 --- a/src/Filtering/LabelMap/ConvertLabelMapToImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: ConvertLabelMapToImage - -Convert Label Map to Normal Image -================================= - -.. index:: - single: LabelMapToLabelImageFilter - pair: label; normal - -Synopsis --------- - -Convert a LabelMap to a normal image with different values representing each region - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMapToLabelImageFilter diff --git a/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.md b/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.md new file mode 100644 index 000000000..e1b32c027 --- /dev/null +++ b/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ExtractGivenLabelObject +--- + +# Extract Given Label Object + +```{index} single: LabelSelectionLabelMapFilter +``` + +## Synopsis + +Extract one given LabelObject from one LabelMap into a new LabelMap and remaining ones into another one. + +## Results + +:::{figure} 2th_cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Output1Baseline.png +:alt: Output1 image +:scale: 50% + +first output (i.e. LabelMap with the LabelObject of interest) +::: + +:::{figure} Output2Baseline.png +:alt: Output2 image +:scale: 50% + +second output (i.e. LabelMap with remaining LabelObjects) +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelSelectionLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.rst b/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.rst deleted file mode 100644 index 5fc54a0b9..000000000 --- a/src/Filtering/LabelMap/ExtractGivenLabelObject/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: ExtractGivenLabelObject - -Extract Given Label Object -========================== - -.. index:: - single: LabelSelectionLabelMapFilter - -Synopsis --------- - -Extract one given LabelObject from one LabelMap into a new LabelMap and remaining ones into another one. - - -Results -------- - -.. figure:: 2th_cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Output1Baseline.png - :scale: 50% - :alt: Output1 image - - first output (i.e. LabelMap with the LabelObject of interest) - -.. figure:: Output2Baseline.png - :scale: 50% - :alt: Output2 image - - second output (i.e. LabelMap with remaining LabelObjects) - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelSelectionLabelMapFilter diff --git a/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.md b/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.md new file mode 100644 index 000000000..7cee4556b --- /dev/null +++ b/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.md @@ -0,0 +1,40 @@ +--- +name: InvertImageUsingBinaryNot +--- + +# Invert Image Using Binary Not Operation + +```{index} single: BinaryNotImageFilter pair: binary; not single: invert +``` + +## Synopsis + +Invert an image using the Binary Not operation. + +## Results + +:::{figure} Input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryNotImageFilter +``` diff --git a/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.rst b/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.rst deleted file mode 100644 index 6b5e597b9..000000000 --- a/src/Filtering/LabelMap/InvertImageUsingBinaryNot/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: InvertImageUsingBinaryNot - -Invert Image Using Binary Not Operation -======================================= - -.. index:: - single: BinaryNotImageFilter - pair: binary; not - single: invert - -Synopsis --------- - -Invert an image using the Binary Not operation. - - -Results -------- -.. figure:: Input.png - :scale: 70% - - input.png - -.. figure:: output.png - :scale: 70% - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryNotImageFilter diff --git a/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.md b/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.md new file mode 100644 index 000000000..3f3a78446 --- /dev/null +++ b/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.md @@ -0,0 +1,42 @@ +--- +name: KeepBinaryRegionsThatMeetSpecific +--- + +# Keep Binary Regions That Meet Specific Properties + +```{index} single: BinaryStatisticsOpeningImageFilter single: binary pair: binary; property pair: threshold; property +``` + +## Synopsis + +Keep only regions that meet a specified threshold of a specified property. + +## Results + +:::{figure} input.png +:alt: input.mhd +:scale: 70% + +input.mhd +::: + +:::{figure} output.png +:alt: output.mhd +:scale: 70% + +output.mhd +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryStatisticsOpeningImageFilter +``` diff --git a/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.rst b/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.rst deleted file mode 100644 index b37159365..000000000 --- a/src/Filtering/LabelMap/KeepBinaryRegionsThatMeetSpecific/Documentation.rst +++ /dev/null @@ -1,45 +0,0 @@ -:name: KeepBinaryRegionsThatMeetSpecific - -Keep Binary Regions That Meet Specific Properties -================================================= - -.. index:: - single: BinaryStatisticsOpeningImageFilter - single: binary - pair: binary; property - pair: threshold; property - -Synopsis --------- - -Keep only regions that meet a specified threshold of a specified property. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.mhd - - input.mhd - -.. figure:: output.png - :scale: 70% - :alt: output.mhd - - output.mhd - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryStatisticsOpeningImageFilter diff --git a/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.md b/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.md new file mode 100644 index 000000000..4d4b87b5d --- /dev/null +++ b/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.md @@ -0,0 +1,42 @@ +--- +name: KeepRegionsAboveLevel +--- + +# Keep Regions Above Certain Level + +```{index} single: LabelShapeKeepNObjectsImageFilter single: region pair: level; property +``` + +## Synopsis + +Keep only regions that rank above a certain level of a particular property. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelShapeKeepNObjectsImageFilter +``` diff --git a/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.rst b/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.rst deleted file mode 100644 index 426d69385..000000000 --- a/src/Filtering/LabelMap/KeepRegionsAboveLevel/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: KeepRegionsAboveLevel - -Keep Regions Above Certain Level -================================ - -.. index:: - single: LabelShapeKeepNObjectsImageFilter - single: region - pair: level; property - -Synopsis --------- - -Keep only regions that rank above a certain level of a particular property. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelShapeKeepNObjectsImageFilter diff --git a/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.md b/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.md new file mode 100644 index 000000000..cf2700f65 --- /dev/null +++ b/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.md @@ -0,0 +1,42 @@ +--- +name: KeepRegionsThatMeetSpecific +--- + +# Keep Regions That Meet Specific Properties + +```{index} single: ShapeOpeningLabelMapFilter single: region pair: threshold; property +``` + +## Synopsis + +Keep only regions that meet a specified threshold of a specified property. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ShapeOpeningLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.rst b/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.rst deleted file mode 100644 index 2126f80ea..000000000 --- a/src/Filtering/LabelMap/KeepRegionsThatMeetSpecific/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: KeepRegionsThatMeetSpecific - -Keep Regions That Meet Specific Properties -========================================== - -.. index:: - single: ShapeOpeningLabelMapFilter - single: region - pair: threshold; property - -Synopsis --------- - -Keep only regions that meet a specified threshold of a specified property. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ShapeOpeningLabelMapFilter diff --git a/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.md b/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.md new file mode 100644 index 000000000..f369a3dfd --- /dev/null +++ b/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.md @@ -0,0 +1,45 @@ +--- +name: LabelBinaryRegionsAndGetProperties +--- + +# Label Binary Regions and Get Properties + +```{index} single: BinaryImageToShapeLabelMapFilter pair: binary; regions pair: label; binary pair: label; properties +``` + +## Synopsis + +Label binary regions in an image and get their properties. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +Output: + +``` +There are 1 objects. +Object 0 has bounding box ImageRegion (0x7ff924a4e558) +Dimension: 2 +Index: [6, 6] +Size: [4, 4] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryImageToShapeLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.rst b/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.rst deleted file mode 100644 index ca948d852..000000000 --- a/src/Filtering/LabelMap/LabelBinaryRegionsAndGetProperties/Documentation.rst +++ /dev/null @@ -1,46 +0,0 @@ -:name: LabelBinaryRegionsAndGetProperties - -Label Binary Regions and Get Properties -======================================= - -.. index:: - single: BinaryImageToShapeLabelMapFilter - pair: binary; regions - pair: label; binary - pair: label; properties - -Synopsis --------- - -Label binary regions in an image and get their properties. - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -Output:: - - There are 1 objects. - Object 0 has bounding box ImageRegion (0x7ff924a4e558) - Dimension: 2 - Index: [6, 6] - Size: [4, 4] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryImageToShapeLabelMapFilter diff --git a/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.md b/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.md new file mode 100644 index 000000000..64c33e8df --- /dev/null +++ b/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.md @@ -0,0 +1,57 @@ +--- +name: LabelBinaryRegionsInImage +--- + +# Label Binary Regions in Image + +```{index} single: BinaryImageToLabelMapFilter pair: label; binary +``` + +## Synopsis + +Label binary regions in an image. + +## Results + +:::{figure} image.png +:alt: image.png +:scale: 70% + +image.png +::: + +Output: + +``` +There are 1 objects. +Object 0 contains pixel [6, 6] +Object 0 contains pixel [7, 6] +Object 0 contains pixel [8, 6] +Object 0 contains pixel [9, 6] +Object 0 contains pixel [6, 7] +Object 0 contains pixel [7, 7] +Object 0 contains pixel [8, 7] +Object 0 contains pixel [9, 7] +Object 0 contains pixel [6, 8] +Object 0 contains pixel [7, 8] +Object 0 contains pixel [8, 8] +Object 0 contains pixel [9, 8] +Object 0 contains pixel [6, 9] +Object 0 contains pixel [7, 9] +Object 0 contains pixel [8, 9] +Object 0 contains pixel [9, 9] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryImageToLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.rst b/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.rst deleted file mode 100644 index c7020553f..000000000 --- a/src/Filtering/LabelMap/LabelBinaryRegionsInImage/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: LabelBinaryRegionsInImage - -Label Binary Regions in Image -============================= - -.. index:: - single: BinaryImageToLabelMapFilter - pair: label; binary - -Synopsis --------- - -Label binary regions in an image. - - -Results -------- -.. figure:: image.png - :scale: 70% - :alt: image.png - - image.png - -Output:: - - There are 1 objects. - Object 0 contains pixel [6, 6] - Object 0 contains pixel [7, 6] - Object 0 contains pixel [8, 6] - Object 0 contains pixel [9, 6] - Object 0 contains pixel [6, 7] - Object 0 contains pixel [7, 7] - Object 0 contains pixel [8, 7] - Object 0 contains pixel [9, 7] - Object 0 contains pixel [6, 8] - Object 0 contains pixel [7, 8] - Object 0 contains pixel [8, 8] - Object 0 contains pixel [9, 8] - Object 0 contains pixel [6, 9] - Object 0 contains pixel [7, 9] - Object 0 contains pixel [8, 9] - Object 0 contains pixel [9, 9] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryImageToLabelMapFilter diff --git a/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.md b/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.md new file mode 100644 index 000000000..3b0d6b704 --- /dev/null +++ b/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.md @@ -0,0 +1,57 @@ +--- +name: MaskOneImageGivenLabelMap +--- + +# Mask One Image Given Label Map + +```{index} single: LabelMapMaskImageFilter +``` + +## Synopsis + +Mask the content of one input itk::Image according to one input itk::LabelMap + +## Results + +:::{figure} cthead1.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} 2th_cthead1.png +:alt: Input label image +:scale: 100% + +Input label image +::: + +:::{figure} Output1Baseline.png +:alt: Masked output 1 +:scale: 100% + +Masked output with label 100, background 0. +::: + +:::{figure} Output2Baseline.png +:alt: Masked output 2 +:scale: 100% + +Masked output with label 0, background 0, negated, cropped, and border size +10\. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMapMaskImageFilter +``` diff --git a/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.rst b/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.rst deleted file mode 100644 index f7af98d2c..000000000 --- a/src/Filtering/LabelMap/MaskOneImageGivenLabelMap/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: MaskOneImageGivenLabelMap - -Mask One Image Given Label Map -============================== - -.. index:: - single: LabelMapMaskImageFilter - -Synopsis --------- - -Mask the content of one input itk::Image according to one input itk::LabelMap - - -Results -------- - -.. figure:: cthead1.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: 2th_cthead1.png - :scale: 100% - :alt: Input label image - - Input label image - -.. figure:: Output1Baseline.png - :scale: 100% - :alt: Masked output 1 - - Masked output with label 100, background 0. - -.. figure:: Output2Baseline.png - :scale: 100% - :alt: Masked output 2 - - Masked output with label 0, background 0, negated, cropped, and border size - 10. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMapMaskImageFilter diff --git a/src/Filtering/LabelMap/MergeLabelMaps/Documentation.md b/src/Filtering/LabelMap/MergeLabelMaps/Documentation.md new file mode 100644 index 000000000..e6bd37120 --- /dev/null +++ b/src/Filtering/LabelMap/MergeLabelMaps/Documentation.md @@ -0,0 +1,35 @@ +--- +name: MergeLabelMaps +--- + +# Merge LabelMaps + +```{index} single: MergeLabelMapFilter +``` + +## Synopsis + +Merges several labelmaps. + +## Results + +Output: + +``` +number of objects: 4 +number of expected objects: 4 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MergeLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/MergeLabelMaps/Documentation.rst b/src/Filtering/LabelMap/MergeLabelMaps/Documentation.rst deleted file mode 100644 index c4656e5f9..000000000 --- a/src/Filtering/LabelMap/MergeLabelMaps/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: MergeLabelMaps - -Merge LabelMaps -================ - -.. index:: - single: MergeLabelMapFilter - -Synopsis --------- - -Merges several labelmaps. - - -Results -------- -Output:: - - number of objects: 4 - number of expected objects: 4 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MergeLabelMapFilter diff --git a/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.md b/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.md new file mode 100644 index 000000000..248217d8b --- /dev/null +++ b/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.md @@ -0,0 +1,51 @@ +--- +name: RemoveHolesNotConnectedToImageBoundaries +--- + +# Remove Holes Not Connected to Image Boundaries + +```{index} single: BinaryFillholeImageFilter +``` + +## Synopsis + +Remove holes in one binary image not connected to its boundary. In this case +the foreground value for the image is taken to be zero (black), and everything +is filled in within the black boundary. + +## Results + +:::{figure} Yinyang.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryFillholeImageFilter +``` diff --git a/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.rst b/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.rst deleted file mode 100644 index 1bd0a920b..000000000 --- a/src/Filtering/LabelMap/RemoveHolesNotConnectedToImageBoundaries/Documentation.rst +++ /dev/null @@ -1,53 +0,0 @@ -:name: RemoveHolesNotConnectedToImageBoundaries - -Remove Holes Not Connected to Image Boundaries -============================================== - -.. index:: - single: BinaryFillholeImageFilter - -Synopsis --------- - -Remove holes in one binary image not connected to its boundary. In this case -the foreground value for the image is taken to be zero (black), and everything -is filled in within the black boundary. - - -Results -------- - -.. figure:: Yinyang.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryFillholeImageFilter diff --git a/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.md b/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.md new file mode 100644 index 000000000..8c2f26278 --- /dev/null +++ b/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.md @@ -0,0 +1,37 @@ +--- +name: RemoveLabelsFromLabelMap +--- + +# Remove Labels From Label Map + +```{index} single: LabelMap pair: remove; labels +``` + +## Synopsis + +Remove the labels from a LabelMap. + +## Results + +Output: + +``` +There are 10 objects. +There are originally 10 objects. +Removing 5 objects. +There are 5 objects remaining. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelMap +``` diff --git a/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.rst b/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.rst deleted file mode 100644 index 2f8827c7e..000000000 --- a/src/Filtering/LabelMap/RemoveLabelsFromLabelMap/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: RemoveLabelsFromLabelMap - -Remove Labels From Label Map -============================ - -.. index:: - single: LabelMap - pair: remove; labels - -Synopsis --------- - -Remove the labels from a LabelMap. - - -Results -------- - -Output:: - - There are 10 objects. - There are originally 10 objects. - Removing 5 objects. - There are 5 objects remaining. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelMap diff --git a/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.md b/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.md new file mode 100644 index 000000000..c4b2181bf --- /dev/null +++ b/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.md @@ -0,0 +1,82 @@ +--- +name: ShapeAttributesForBinaryImage +--- + +# Shape Attributes for Binary Image + +```{index} single: LabelImageToShapeLabelMapFilter +``` + +## Synopsis + +Compute shape attributes for a binary image. + +## Results + +Output: + +``` +File "Generated image" has 2 labels. +Label: 1 +BoundingBox: ImageRegion (0x7fab2f0003b8) +Dimension: 2 +Index: [20, 30] +Size: [60, 70] + + NumberOfPixels: 4200 + PhysicalSize: 4200 + Centroid: [49.5, 64.5] + NumberOfPixelsOnBorder: 0 + PerimeterOnBorder: 0 + FeretDiameter: 0 + PrincipalMoments: [299.917, 408.25] + PrincipalAxes: 1 0 + 0 1 + + Elongation: 1.16671 + Perimeter: 245.385 + Roundness: 0.936229 + EquivalentSphericalRadius: 36.5637 + EquivalentSphericalPerimeter: 229.736 + EquivalentEllipsoidDiameter: [67.7015, 78.988] + Flatness: 1.16671 + PerimeterOnBorderRatio: 0 +Label: 2 +BoundingBox: ImageRegion (0x7fab2ef00308) +Dimension: 2 +Index: [100, 115] +Size: [30, 45] + + NumberOfPixels: 1350 + PhysicalSize: 1350 + Centroid: [114.5, 137] + NumberOfPixelsOnBorder: 0 + PerimeterOnBorder: 0 + FeretDiameter: 0 + PrincipalMoments: [74.9167, 168.667] + PrincipalAxes: 1 0 + 0 1 + + Elongation: 1.50046 + Perimeter: 141.098 + Roundness: 0.923103 + EquivalentSphericalRadius: 20.7296 + EquivalentSphericalPerimeter: 130.248 + EquivalentEllipsoidDiameter: [33.8461, 50.7849] + Flatness: 1.50046 + PerimeterOnBorderRatio: 0 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelImageToShapeLabelMapFilter +``` diff --git a/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.rst b/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.rst deleted file mode 100644 index bc6e021bc..000000000 --- a/src/Filtering/LabelMap/ShapeAttributesForBinaryImage/Documentation.rst +++ /dev/null @@ -1,82 +0,0 @@ -:name: ShapeAttributesForBinaryImage - -Shape Attributes for Binary Image -================================= - -.. index:: - single: LabelImageToShapeLabelMapFilter - -Synopsis --------- - -Compute shape attributes for a binary image. - - -Results -------- -Output:: - - File "Generated image" has 2 labels. - Label: 1 - BoundingBox: ImageRegion (0x7fab2f0003b8) - Dimension: 2 - Index: [20, 30] - Size: [60, 70] - - NumberOfPixels: 4200 - PhysicalSize: 4200 - Centroid: [49.5, 64.5] - NumberOfPixelsOnBorder: 0 - PerimeterOnBorder: 0 - FeretDiameter: 0 - PrincipalMoments: [299.917, 408.25] - PrincipalAxes: 1 0 - 0 1 - - Elongation: 1.16671 - Perimeter: 245.385 - Roundness: 0.936229 - EquivalentSphericalRadius: 36.5637 - EquivalentSphericalPerimeter: 229.736 - EquivalentEllipsoidDiameter: [67.7015, 78.988] - Flatness: 1.16671 - PerimeterOnBorderRatio: 0 - Label: 2 - BoundingBox: ImageRegion (0x7fab2ef00308) - Dimension: 2 - Index: [100, 115] - Size: [30, 45] - - NumberOfPixels: 1350 - PhysicalSize: 1350 - Centroid: [114.5, 137] - NumberOfPixelsOnBorder: 0 - PerimeterOnBorder: 0 - FeretDiameter: 0 - PrincipalMoments: [74.9167, 168.667] - PrincipalAxes: 1 0 - 0 1 - - Elongation: 1.50046 - Perimeter: 141.098 - Roundness: 0.923103 - EquivalentSphericalRadius: 20.7296 - EquivalentSphericalPerimeter: 130.248 - EquivalentEllipsoidDiameter: [33.8461, 50.7849] - Flatness: 1.50046 - PerimeterOnBorderRatio: 0 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelImageToShapeLabelMapFilter diff --git a/src/Filtering/LabelMap/index.md b/src/Filtering/LabelMap/index.md new file mode 100644 index 000000000..037eb94c0 --- /dev/null +++ b/src/Filtering/LabelMap/index.md @@ -0,0 +1,33 @@ +# LabelMap + +```{toctree} +:maxdepth: 1 + +ApplyMorphologicalClosingOnAllLabelObjects/Documentation.rst +ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.rst +ConvertImageToLabelMap/Documentation.rst +ConvertImageWithLabelsToShapeLabelMap/Documentation.rst +ConvertLabelMapToImage/Documentation.rst +ExtractGivenLabelObject/Documentation.rst +InvertImageUsingBinaryNot/Documentation.rst +KeepBinaryRegionsThatMeetSpecific/Documentation.rst +KeepRegionsAboveLevel/Documentation.rst +KeepRegionsThatMeetSpecific/Documentation.rst +LabelBinaryRegionsAndGetProperties/Documentation.rst +LabelBinaryRegionsInImage/Documentation.rst +MaskOneImageGivenLabelMap/Documentation.rst +MergeLabelMaps/Documentation.rst +RemoveHolesNotConnectedToImageBoundaries/Documentation.rst +RemoveLabelsFromLabelMap/Documentation.rst +ShapeAttributesForBinaryImage/Documentation.rst +``` + +## Note about this module: + +This module contains the infrastructure to store the label images in an efficient and convenient way, including label images with overlapping objects. +All the objects contained in the LabelMap can be associated to values called attributes. +Some filters are available to compute the usual attributes values related to the shape of the objects or the pixels values in the objects and to manipulate the objects based on these values. + +Implementations were taken from the [Insight Journal paper]. + +[insight journal paper]: https://www.insight-journal.org/browse/publication/176RemoveLabelsFromLabelMap/Documentation.rstKeepRegionsThatMeetSpecific/Documentation.rstKeepRegionsAboveLevel/Documentation.rstKeepBinaryRegionsThatMeetSpecific/Documentation.rstLabelBinaryRegionsInImage/Documentation.rstLabelBinaryRegionsAndGetProperties/Documentation.rstConvertLabelMapToImage/Documentation.rstMergeLabelMaps/Documentation.rstConvertImageWithLabelsToShapeLabelMap/Documentation.rstShapeAttributesForBinaryImage/Documentation.rstInvertImageUsingBinaryNot/Documentation.rstConvertImageToLabelMap/Documentation.rst diff --git a/src/Filtering/LabelMap/index.rst b/src/Filtering/LabelMap/index.rst deleted file mode 100644 index e887aac15..000000000 --- a/src/Filtering/LabelMap/index.rst +++ /dev/null @@ -1,48 +0,0 @@ -LabelMap -======== - -.. toctree:: - :maxdepth: 1 - - ApplyMorphologicalClosingOnAllLabelObjects/Documentation.rst - ApplyMorphologicalClosingOnSpecificLabelObject/Documentation.rst - ConvertImageToLabelMap/Documentation.rst - ConvertImageWithLabelsToShapeLabelMap/Documentation.rst - ConvertLabelMapToImage/Documentation.rst - ExtractGivenLabelObject/Documentation.rst - InvertImageUsingBinaryNot/Documentation.rst - KeepBinaryRegionsThatMeetSpecific/Documentation.rst - KeepRegionsAboveLevel/Documentation.rst - KeepRegionsThatMeetSpecific/Documentation.rst - LabelBinaryRegionsAndGetProperties/Documentation.rst - LabelBinaryRegionsInImage/Documentation.rst - MaskOneImageGivenLabelMap/Documentation.rst - MergeLabelMaps/Documentation.rst - RemoveHolesNotConnectedToImageBoundaries/Documentation.rst - RemoveLabelsFromLabelMap/Documentation.rst - ShapeAttributesForBinaryImage/Documentation.rst - - -Note about this module: ------------------------ - -This module contains the infrastructure to store the label images in an efficient and convenient way, including label images with overlapping objects. -All the objects contained in the LabelMap can be associated to values called attributes. -Some filters are available to compute the usual attributes values related to the shape of the objects or the pixels values in the objects and to manipulate the objects based on these values. - - -Implementations were taken from the `Insight Journal paper`_. - -.. _Insight Journal paper: https://www.insight-journal.org/browse/publication/176 - RemoveLabelsFromLabelMap/Documentation.rst - KeepRegionsThatMeetSpecific/Documentation.rst - KeepRegionsAboveLevel/Documentation.rst - KeepBinaryRegionsThatMeetSpecific/Documentation.rst - LabelBinaryRegionsInImage/Documentation.rst - LabelBinaryRegionsAndGetProperties/Documentation.rst - ConvertLabelMapToImage/Documentation.rst - MergeLabelMaps/Documentation.rst - ConvertImageWithLabelsToShapeLabelMap/Documentation.rst - ShapeAttributesForBinaryImage/Documentation.rst - InvertImageUsingBinaryNot/Documentation.rst - ConvertImageToLabelMap/Documentation.rst diff --git a/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.md b/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.md new file mode 100644 index 000000000..4920607ea --- /dev/null +++ b/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.md @@ -0,0 +1,28 @@ +--- +name: CreateABinaryBallStructuringElement +--- + +# Create a Binary Ball Structuring Element + +```{index} single: BinaryBallStructuringElement +``` + +## Synopsis + +Create an elliptical structuring element + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryBallStructuringElement +``` diff --git a/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.rst b/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.rst deleted file mode 100644 index 0c7191fdf..000000000 --- a/src/Filtering/MathematicalMorphology/CreateABinaryBallStructuringElement/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: CreateABinaryBallStructuringElement - -Create a Binary Ball Structuring Element -======================================== - -.. index:: - single: BinaryBallStructuringElement - -Synopsis --------- - - -Create an elliptical structuring element - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryBallStructuringElement diff --git a/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.md b/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.md new file mode 100644 index 000000000..18dd90e25 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.md @@ -0,0 +1,53 @@ +--- +name: DilateAGrayscaleImage +--- + +# Dilate a grayscale image + +```{index} single: FlatStructuringElement single: GrayscaleDilateImageFilter pair: mathematical morphology; dilation +``` + +:::{seealso} +dilation; erosion +::: + +## Synopsis + +Dilate regions by using a specified kernel, also known as a structuring element. In this example, the white regions are enlarged. + +## Results + +:::{figure} cthead1.png +:alt: Input ct head image. +:scale: 50% + +Input grayscale image. +::: + +:::{figure} OutputBaseline.png +:alt: Dilated output. +:scale: 50% + +Dilated output. +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GrayscaleDilateImageFilter itk::FlatStructuringElement +``` diff --git a/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.rst b/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.rst deleted file mode 100644 index ae8758535..000000000 --- a/src/Filtering/MathematicalMorphology/DilateAGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: DilateAGrayscaleImage - -Dilate a grayscale image -======================== - -.. index:: - single: FlatStructuringElement - single: GrayscaleDilateImageFilter - pair: mathematical morphology; dilation - -.. seealso:: dilation; erosion - - -Synopsis --------- - -Dilate regions by using a specified kernel, also known as a structuring element. In this example, the white regions are enlarged. - - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input ct head image. - - Input grayscale image. - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Dilated output. - - Dilated output. - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GrayscaleDilateImageFilter itk::FlatStructuringElement diff --git a/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.md b/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.md new file mode 100644 index 000000000..06aa810d9 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.md @@ -0,0 +1,53 @@ +--- +name: ErodeAGrayscaleImage +--- + +# Erode a Grayscale Image + +```{index} single: FlatStructuringElement single: GrayscaleErodeImageFilter pair: mathematical morphology; erosion +``` + +:::{seealso} +erosion; dilation +::: + +## Synopsis + +Erode regions by using a specified kernel, also known as a structuring element. In this example, the white regions shrink. + +## Results + +:::{figure} cthead1.png +:alt: Input ct head image. +:scale: 50% + +Input grayscale image. +::: + +:::{figure} OutputBaseline.png +:alt: Eroded output. +:scale: 50% + +Eroded output. +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GrayscaleErodeImageFilter itk::FlatStructuringElement +``` diff --git a/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.rst b/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.rst deleted file mode 100644 index d9db6c09e..000000000 --- a/src/Filtering/MathematicalMorphology/ErodeAGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: ErodeAGrayscaleImage - -Erode a Grayscale Image -======================= - -.. index:: - single: FlatStructuringElement - single: GrayscaleErodeImageFilter - pair: mathematical morphology; erosion - -.. seealso:: erosion; dilation - - -Synopsis --------- -Erode regions by using a specified kernel, also known as a structuring element. In this example, the white regions shrink. - - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input ct head image. - - Input grayscale image. - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Eroded output. - - Eroded output. - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GrayscaleErodeImageFilter itk::FlatStructuringElement diff --git a/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.md b/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.md new file mode 100644 index 000000000..60f3d615a --- /dev/null +++ b/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ErodeBinaryImageUsingFlatStruct +--- + +# Erode Binary Image Using Flat Structure Element + +```{index} single: FlatStructuringElement pair: binary; image +``` + +## Synopsis + +Erode a binary image using a flat (box) structuring element. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} ErodeBinaryImageUsingFlatStruct.png +:scale: 70% + +Yinyang.png And Output.png When Radius = 7 +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FlatStructuringElement +``` diff --git a/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.rst b/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.rst deleted file mode 100644 index 9e9b42a46..000000000 --- a/src/Filtering/MathematicalMorphology/ErodeBinaryImageUsingFlatStruct/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: ErodeBinaryImageUsingFlatStruct - -Erode Binary Image Using Flat Structure Element -=============================================== - -.. index:: - single: FlatStructuringElement - pair: binary; image - -Synopsis --------- - -Erode a binary image using a flat (box) structuring element. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: ErodeBinaryImageUsingFlatStruct.png - :scale: 70% - - Yinyang.png And Output.png When Radius = 7 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::FlatStructuringElement diff --git a/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.md b/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.md new file mode 100644 index 000000000..836d98d15 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.md @@ -0,0 +1,136 @@ +--- +name: GenerateStructureElementsWithAccurateArea +--- + +# Generate Structuring Elements With Accurate Area + +```{index} single: FlatStructuringElement pair: structuring; elements +``` + +## Synopsis + +Generate structuring elements with accurate area. + +## Results + +Output: + +``` +2D ball of radius 5 with radiusIsParametric mode off: +0 0 0 1 1 1 1 1 0 0 0 +0 0 1 1 1 1 1 1 1 0 0 +0 1 1 1 1 1 1 1 1 1 0 +1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 +0 1 1 1 1 1 1 1 1 1 0 +0 0 1 1 1 1 1 1 1 0 0 +0 0 0 1 1 1 1 1 0 0 0 +Expected foreground area: 78.5398 +Computed foreground area: 97 +Foreground area error: 23.5042% + +2D ball of radius 5 with radiusIsParametric mode on: +0 0 0 0 0 1 0 0 0 0 0 +0 0 1 1 1 1 1 1 1 0 0 +0 1 1 1 1 1 1 1 1 1 0 +0 1 1 1 1 1 1 1 1 1 0 +0 1 1 1 1 1 1 1 1 1 0 +1 1 1 1 1 1 1 1 1 1 1 +0 1 1 1 1 1 1 1 1 1 0 +0 1 1 1 1 1 1 1 1 1 0 +0 1 1 1 1 1 1 1 1 1 0 +0 0 1 1 1 1 1 1 1 0 0 +0 0 0 0 0 1 0 0 0 0 0 +Expected foreground area: 78.5398 +Computed foreground area: 81 +Foreground area error: 3.1324% + +2D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: +0 0 0 1 1 1 1 1 0 0 0 +0 0 1 1 1 1 1 1 1 0 0 +0 1 1 1 0 0 0 1 1 1 0 +1 1 1 0 0 0 0 0 1 1 1 +1 1 0 0 0 0 0 0 0 1 1 +1 1 0 0 0 0 0 0 0 1 1 +1 1 0 0 0 0 0 0 0 1 1 +1 1 1 0 0 0 0 0 1 1 1 +0 1 1 1 0 0 0 1 1 1 0 +0 0 1 1 1 1 1 1 1 0 0 +0 0 0 1 1 1 1 1 0 0 0 +Expected foreground area: 50.2655 +Computed foreground area: 60 +Foreground area error: 19.3662% + +2D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: +0 0 0 0 0 1 0 0 0 0 0 +0 0 1 1 1 1 1 1 1 0 0 +0 1 1 1 1 0 1 1 1 1 0 +0 1 1 0 0 0 0 0 1 1 0 +0 1 1 0 0 0 0 0 1 1 0 +1 1 0 0 0 0 0 0 0 1 1 +0 1 1 0 0 0 0 0 1 1 0 +0 1 1 0 0 0 0 0 1 1 0 +0 1 1 1 1 0 1 1 1 1 0 +0 0 1 1 1 1 1 1 1 0 0 +0 0 0 0 0 1 0 0 0 0 0 +Expected foreground area: 50.2655 +Computed foreground area: 52 +Foreground area error: 3.45071% + +3D ball of radius 5 with radiusIsParametric mode off: +Expected foreground area: 523.599 +Computed foreground area: 739 +Foreground area error: 41.1386% + +3D ball of radius 5 with radiusIsParametric mode on: +Expected foreground area: 523.599 +Computed foreground area: 515 +Foreground area error: 1.64224% + +3D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: +Expected foreground area: 410.501 +Computed foreground area: 560 +Foreground area error: 36.4185% + +3D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: +Expected foreground area: 410.501 +Computed foreground area: 392 +Foreground area error: 4.50703% + +4D ball of radius 5 with radiusIsParametric mode off: +Expected foreground area: 3084.25 +Computed foreground area: 4785 +Foreground area error: 55.143% + +4D ball of radius 5 with radiusIsParametric mode on: +Expected foreground area: 3084.25 +Computed foreground area: 2929 +Foreground area error: 5.03368% + +4D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: +Expected foreground area: 2684.53 +Computed foreground area: 4024 +Foreground area error: 49.8957% + +4D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: +Expected foreground area: 2684.53 +Computed foreground area: 2504 +Foreground area error: 6.72491% +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::FlatStructuringElement +``` diff --git a/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.rst b/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.rst deleted file mode 100644 index 82f4c5abc..000000000 --- a/src/Filtering/MathematicalMorphology/GenerateStructureElementsWithAccurateArea/Documentation.rst +++ /dev/null @@ -1,138 +0,0 @@ -:name: GenerateStructureElementsWithAccurateArea - -Generate Structuring Elements With Accurate Area -================================================ - -.. index:: - single: FlatStructuringElement - pair: structuring; elements - -Synopsis --------- - -Generate structuring elements with accurate area. - - -Results -------- -Output:: - - 2D ball of radius 5 with radiusIsParametric mode off: - 0 0 0 1 1 1 1 1 0 0 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 1 1 1 1 1 1 1 1 1 0 - 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 - 0 1 1 1 1 1 1 1 1 1 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 0 0 1 1 1 1 1 0 0 0 - Expected foreground area: 78.5398 - Computed foreground area: 97 - Foreground area error: 23.5042% - - 2D ball of radius 5 with radiusIsParametric mode on: - 0 0 0 0 0 1 0 0 0 0 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 1 1 1 1 1 1 1 1 1 0 - 0 1 1 1 1 1 1 1 1 1 0 - 0 1 1 1 1 1 1 1 1 1 0 - 1 1 1 1 1 1 1 1 1 1 1 - 0 1 1 1 1 1 1 1 1 1 0 - 0 1 1 1 1 1 1 1 1 1 0 - 0 1 1 1 1 1 1 1 1 1 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 0 0 0 0 1 0 0 0 0 0 - Expected foreground area: 78.5398 - Computed foreground area: 81 - Foreground area error: 3.1324% - - 2D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: - 0 0 0 1 1 1 1 1 0 0 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 1 1 1 0 0 0 1 1 1 0 - 1 1 1 0 0 0 0 0 1 1 1 - 1 1 0 0 0 0 0 0 0 1 1 - 1 1 0 0 0 0 0 0 0 1 1 - 1 1 0 0 0 0 0 0 0 1 1 - 1 1 1 0 0 0 0 0 1 1 1 - 0 1 1 1 0 0 0 1 1 1 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 0 0 1 1 1 1 1 0 0 0 - Expected foreground area: 50.2655 - Computed foreground area: 60 - Foreground area error: 19.3662% - - 2D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: - 0 0 0 0 0 1 0 0 0 0 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 1 1 1 1 0 1 1 1 1 0 - 0 1 1 0 0 0 0 0 1 1 0 - 0 1 1 0 0 0 0 0 1 1 0 - 1 1 0 0 0 0 0 0 0 1 1 - 0 1 1 0 0 0 0 0 1 1 0 - 0 1 1 0 0 0 0 0 1 1 0 - 0 1 1 1 1 0 1 1 1 1 0 - 0 0 1 1 1 1 1 1 1 0 0 - 0 0 0 0 0 1 0 0 0 0 0 - Expected foreground area: 50.2655 - Computed foreground area: 52 - Foreground area error: 3.45071% - - 3D ball of radius 5 with radiusIsParametric mode off: - Expected foreground area: 523.599 - Computed foreground area: 739 - Foreground area error: 41.1386% - - 3D ball of radius 5 with radiusIsParametric mode on: - Expected foreground area: 523.599 - Computed foreground area: 515 - Foreground area error: 1.64224% - - 3D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: - Expected foreground area: 410.501 - Computed foreground area: 560 - Foreground area error: 36.4185% - - 3D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: - Expected foreground area: 410.501 - Computed foreground area: 392 - Foreground area error: 4.50703% - - 4D ball of radius 5 with radiusIsParametric mode off: - Expected foreground area: 3084.25 - Computed foreground area: 4785 - Foreground area error: 55.143% - - 4D ball of radius 5 with radiusIsParametric mode on: - Expected foreground area: 3084.25 - Computed foreground area: 2929 - Foreground area error: 5.03368% - - 4D annulus of radius 5 and thickness 2 with radiusIsParametric mode off: - Expected foreground area: 2684.53 - Computed foreground area: 4024 - Foreground area error: 49.8957% - - 4D annulus of radius 5 and thickness 2 with radiusIsParametric mode on: - Expected foreground area: 2684.53 - Computed foreground area: 2504 - Foreground area error: 6.72491% - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::FlatStructuringElement diff --git a/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.md b/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.md new file mode 100644 index 000000000..665e51328 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.md @@ -0,0 +1,42 @@ +--- +name: RegionalMaximal +--- + +# Regional Maximal + +```{index} single: RegionalMaximaImageFilter pair: region; maximal +``` + +## Synopsis + +Regional maximal image filter. + +## Results + +:::{figure} intensityblobs.png +:alt: intensityblobs.png +:scale: 70% + +intensityblobs.png +::: + +:::{figure} maximal.png +:alt: maximal.png +:scale: 70% + +maximal.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RegionalMaximaImageFilter +``` diff --git a/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.rst b/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.rst deleted file mode 100644 index 40c4c2d74..000000000 --- a/src/Filtering/MathematicalMorphology/RegionalMaximal/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: RegionalMaximal - -Regional Maximal -================ - -.. index:: - single: RegionalMaximaImageFilter - pair: region; maximal - -Synopsis --------- - -Regional maximal image filter. - - -Results -------- -.. figure:: intensityblobs.png - :scale: 70% - :alt: intensityblobs.png - - intensityblobs.png - -.. figure:: maximal.png - :scale: 70% - :alt: maximal.png - - maximal.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RegionalMaximaImageFilter diff --git a/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.md b/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.md new file mode 100644 index 000000000..6854d0dc8 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.md @@ -0,0 +1,42 @@ +--- +name: RegionalMinimal +--- + +# Regional Minimal + +```{index} single: RegionalMinimaImageFilter pair: region; minimal +``` + +## Synopsis + +Regional minimal image filter. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RegionalMinimaImageFilter +``` diff --git a/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.rst b/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.rst deleted file mode 100644 index 6173d916c..000000000 --- a/src/Filtering/MathematicalMorphology/RegionalMinimal/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: RegionalMinimal - -Regional Minimal -================ - -.. index:: - single: RegionalMinimaImageFilter - pair: region; minimal - -Synopsis --------- - -Regional minimal image filter. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RegionalMinimaImageFilter diff --git a/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.md b/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.md new file mode 100644 index 000000000..dfc89b9da --- /dev/null +++ b/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ValuedRegionalMaximaImage +--- + +# Valued Regional Maxima Image + +```{index} single: ValuedRegionalMaximaImageFilter +``` + +## Synopsis + +Valued regional maximal of an image. + +## Results + +:::{figure} intensityblobs.png +:alt: intensityblobs.png +:scale: 70% + +intensityblobs.png +::: + +:::{figure} maximal.png +:alt: maximal.png +:scale: 70% + +maximal.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ValuedRegionalMaximaImageFilter +``` diff --git a/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.rst b/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.rst deleted file mode 100644 index 949c9f657..000000000 --- a/src/Filtering/MathematicalMorphology/ValuedRegionalMaximaImage/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: ValuedRegionalMaximaImage - -Valued Regional Maxima Image -============================ - -.. index:: - single: ValuedRegionalMaximaImageFilter - -Synopsis --------- -Valued regional maximal of an image. - -Results -------- -.. figure:: intensityblobs.png - :scale: 70% - :alt: intensityblobs.png - - intensityblobs.png - -.. figure:: maximal.png - :scale: 70% - :alt: maximal.png - - maximal.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ValuedRegionalMaximaImageFilter diff --git a/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.md b/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.md new file mode 100644 index 000000000..db2d5050e --- /dev/null +++ b/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: ValuedRegionalMinimalImage +--- + +# Valued Regional Minimal Image + +```{index} single: ValuedRegionalMinimaImageFilter single: minimal +``` + +## Synopsis + +Valued regional minimal of an image. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ValuedRegionalMinimaImageFilter +``` diff --git a/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.rst b/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.rst deleted file mode 100644 index 661d0ebb8..000000000 --- a/src/Filtering/MathematicalMorphology/ValuedRegionalMinimalImage/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ValuedRegionalMinimalImage - -Valued Regional Minimal Image -============================= - -.. index:: - single: ValuedRegionalMinimaImageFilter - single: minimal - -Synopsis --------- - -Valued regional minimal of an image. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ValuedRegionalMinimaImageFilter diff --git a/src/Filtering/MathematicalMorphology/index.md b/src/Filtering/MathematicalMorphology/index.md new file mode 100644 index 000000000..c4ff22bd6 --- /dev/null +++ b/src/Filtering/MathematicalMorphology/index.md @@ -0,0 +1,15 @@ +# MathematicalMorphology + +```{toctree} +:maxdepth: 1 + +CreateABinaryBallStructuringElement/Documentation.rst +DilateAGrayscaleImage/Documentation.rst +ErodeAGrayscaleImage/Documentation.rst +ErodeBinaryImageUsingFlatStruct/Documentation.rst +GenerateStructureElementsWithAccurateArea/Documentation.rst +RegionalMaximal/Documentation.rst +RegionalMinimal/Documentation.rst +ValuedRegionalMaximaImage/Documentation.rst +ValuedRegionalMinimalImage/Documentation.rst +``` diff --git a/src/Filtering/MathematicalMorphology/index.rst b/src/Filtering/MathematicalMorphology/index.rst deleted file mode 100644 index 3c0eb0b6d..000000000 --- a/src/Filtering/MathematicalMorphology/index.rst +++ /dev/null @@ -1,15 +0,0 @@ -MathematicalMorphology -====================== - -.. toctree:: - :maxdepth: 1 - - CreateABinaryBallStructuringElement/Documentation.rst - DilateAGrayscaleImage/Documentation.rst - ErodeAGrayscaleImage/Documentation.rst - ErodeBinaryImageUsingFlatStruct/Documentation.rst - GenerateStructureElementsWithAccurateArea/Documentation.rst - RegionalMaximal/Documentation.rst - RegionalMinimal/Documentation.rst - ValuedRegionalMaximaImage/Documentation.rst - ValuedRegionalMinimalImage/Documentation.rst diff --git a/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.md b/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.md new file mode 100644 index 000000000..d9ba5b55c --- /dev/null +++ b/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.md @@ -0,0 +1,53 @@ +--- +name: DataStructureForPieceWiseLinearCurve +--- + +# Data Structure for Piece-Wise Linear Curve + +```{index} single: PolyLineParametricPath pair: data; structure pair: piece-wise; curve +``` + +## Synopsis + +A data structure for a piece-wise linear curve. + +## Results + +Output: + +``` +[0, 0] +[0, 1] +[0, 2] +[0, 3] +[0, 4] +[0, 5] +[0, 6] +[0, 7] +[0, 8] +[0, 9] +[0, 10] +[0, 11] +[0, 12] +[0, 13] +[0, 14] +[0, 15] +[0, 16] +[0, 17] +[0, 18] +[0, 19] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::PolyLineParametricPath +``` diff --git a/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.rst b/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.rst deleted file mode 100644 index a5079316e..000000000 --- a/src/Filtering/Path/DataStructureForPieceWiseLinearCurve/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: DataStructureForPieceWiseLinearCurve - -Data Structure for Piece-Wise Linear Curve -========================================== - -.. index:: - single: PolyLineParametricPath - pair: data; structure - pair: piece-wise; curve - -Synopsis --------- - -A data structure for a piece-wise linear curve. - - -Results -------- - -Output:: - - [0, 0] - [0, 1] - [0, 2] - [0, 3] - [0, 4] - [0, 5] - [0, 6] - [0, 7] - [0, 8] - [0, 9] - [0, 10] - [0, 11] - [0, 12] - [0, 13] - [0, 14] - [0, 15] - [0, 16] - [0, 17] - [0, 18] - [0, 19] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::PolyLineParametricPath diff --git a/src/Filtering/Path/ExtractContoursFromImage/Documentation.md b/src/Filtering/Path/ExtractContoursFromImage/Documentation.md new file mode 100644 index 000000000..c98468bdf --- /dev/null +++ b/src/Filtering/Path/ExtractContoursFromImage/Documentation.md @@ -0,0 +1,142 @@ +--- +name: ExtractContoursFromImage +--- + +# Extract Contours From Image + +```{index} single: ContourExtractor2DImageFilter single: contour +``` + +## Synopsis + +Extract contours from an image. + +## Results + +Output: + +``` +There are 2 contours + +Contour 0: +[10.5, 19] +[10.4603, 18] +[10.4603, 17] +[10.4603, 16] +[10.4603, 15] +[10.4603, 14] +[10.4603, 13] +[10.4603, 12] +[10.4603, 11] +[10.5, 10] +[10, 9.58579] +[9.5, 10] +[9.5397, 11] +[9.5397, 12] +[9.5397, 13] +[9.5397, 14] +[9.5397, 15] +[9.5397, 16] +[9.5397, 17] +[9.5397, 18] +[9.5, 19] +[10, 19.4142] +[10.5, 19] + +Contour 1: +[59.4142, 59] +[59, 58.5] +[58.5, 58] +[58, 57.5] +[57.5, 57] +[57, 56.5] +[56.5, 56] +[56, 55.5] +[55.5, 55] +[55, 54.5] +[54.5, 54] +[54, 53.5] +[53.5, 53] +[53, 52.5] +[52.5, 52] +[52, 51.5] +[51.5, 51] +[51, 50.5] +[50.5, 50] +[50, 49.5] +[49.5, 49] +[49, 48.5] +[48.5, 48] +[48, 47.5] +[47.5, 47] +[47, 46.5] +[46.5, 46] +[46, 45.5] +[45.5, 45] +[45, 44.5] +[44.5, 44] +[44, 43.5] +[43.5, 43] +[43, 42.5] +[42.5, 42] +[42, 41.5] +[41.5, 41] +[41, 40.5] +[40.5, 40] +[40, 39.5858] +[39.5858, 40] +[40, 40.5] +[40.5, 41] +[41, 41.5] +[41.5, 42] +[42, 42.5] +[42.5, 43] +[43, 43.5] +[43.5, 44] +[44, 44.5] +[44.5, 45] +[45, 45.5] +[45.5, 46] +[46, 46.5] +[46.5, 47] +[47, 47.5] +[47.5, 48] +[48, 48.5] +[48.5, 49] +[49, 49.5] +[49.5, 50] +[50, 50.5] +[50.5, 51] +[51, 51.5] +[51.5, 52] +[52, 52.5] +[52.5, 53] +[53, 53.5] +[53.5, 54] +[54, 54.5] +[54.5, 55] +[55, 55.5] +[55.5, 56] +[56, 56.5] +[56.5, 57] +[57, 57.5] +[57.5, 58] +[58, 58.5] +[58.5, 59] +[59, 59.4142] +[59.4142, 59] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ContourExtractor2DImageFilter +``` diff --git a/src/Filtering/Path/ExtractContoursFromImage/Documentation.rst b/src/Filtering/Path/ExtractContoursFromImage/Documentation.rst deleted file mode 100644 index add996969..000000000 --- a/src/Filtering/Path/ExtractContoursFromImage/Documentation.rst +++ /dev/null @@ -1,142 +0,0 @@ -:name: ExtractContoursFromImage - -Extract Contours From Image -=========================== - -.. index:: - single: ContourExtractor2DImageFilter - single: contour - -Synopsis --------- - -Extract contours from an image. - - -Results -------- -Output:: - - There are 2 contours - - Contour 0: - [10.5, 19] - [10.4603, 18] - [10.4603, 17] - [10.4603, 16] - [10.4603, 15] - [10.4603, 14] - [10.4603, 13] - [10.4603, 12] - [10.4603, 11] - [10.5, 10] - [10, 9.58579] - [9.5, 10] - [9.5397, 11] - [9.5397, 12] - [9.5397, 13] - [9.5397, 14] - [9.5397, 15] - [9.5397, 16] - [9.5397, 17] - [9.5397, 18] - [9.5, 19] - [10, 19.4142] - [10.5, 19] - - Contour 1: - [59.4142, 59] - [59, 58.5] - [58.5, 58] - [58, 57.5] - [57.5, 57] - [57, 56.5] - [56.5, 56] - [56, 55.5] - [55.5, 55] - [55, 54.5] - [54.5, 54] - [54, 53.5] - [53.5, 53] - [53, 52.5] - [52.5, 52] - [52, 51.5] - [51.5, 51] - [51, 50.5] - [50.5, 50] - [50, 49.5] - [49.5, 49] - [49, 48.5] - [48.5, 48] - [48, 47.5] - [47.5, 47] - [47, 46.5] - [46.5, 46] - [46, 45.5] - [45.5, 45] - [45, 44.5] - [44.5, 44] - [44, 43.5] - [43.5, 43] - [43, 42.5] - [42.5, 42] - [42, 41.5] - [41.5, 41] - [41, 40.5] - [40.5, 40] - [40, 39.5858] - [39.5858, 40] - [40, 40.5] - [40.5, 41] - [41, 41.5] - [41.5, 42] - [42, 42.5] - [42.5, 43] - [43, 43.5] - [43.5, 44] - [44, 44.5] - [44.5, 45] - [45, 45.5] - [45.5, 46] - [46, 46.5] - [46.5, 47] - [47, 47.5] - [47.5, 48] - [48, 48.5] - [48.5, 49] - [49, 49.5] - [49.5, 50] - [50, 50.5] - [50.5, 51] - [51, 51.5] - [51.5, 52] - [52, 52.5] - [52.5, 53] - [53, 53.5] - [53.5, 54] - [54, 54.5] - [54.5, 55] - [55, 55.5] - [55.5, 56] - [56, 56.5] - [56.5, 57] - [57, 57.5] - [57.5, 58] - [58, 58.5] - [58.5, 59] - [59, 59.4142] - [59.4142, 59] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ContourExtractor2DImageFilter diff --git a/src/Filtering/Path/index.md b/src/Filtering/Path/index.md new file mode 100644 index 000000000..072e96e0b --- /dev/null +++ b/src/Filtering/Path/index.md @@ -0,0 +1,8 @@ +# Path + +```{toctree} +:maxdepth: 1 + +DataStructureForPieceWiseLinearCurve/Documentation.rst +ExtractContoursFromImage/Documentation.rst +``` diff --git a/src/Filtering/Path/index.rst b/src/Filtering/Path/index.rst deleted file mode 100644 index c1ccf0afd..000000000 --- a/src/Filtering/Path/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Path -==== - -.. toctree:: - :maxdepth: 1 - - DataStructureForPieceWiseLinearCurve/Documentation.rst - ExtractContoursFromImage/Documentation.rst diff --git a/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.md b/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.md new file mode 100644 index 000000000..40c5c0eaf --- /dev/null +++ b/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.md @@ -0,0 +1,33 @@ +--- +name: CleanQuadEdgeMesh +--- + +# Clean Quad Edge Mesh + +```{index} single: CleanQuadEdgeMeshFilter +``` + +## Synopsis + +Clean quad edge mesh + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::CleanQuadEdgeMeshFilter +``` diff --git a/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.rst b/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.rst deleted file mode 100644 index aad8593f7..000000000 --- a/src/Filtering/QuadEdgeMeshFiltering/CleanQuadEdgeMesh/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: CleanQuadEdgeMesh - -Clean Quad Edge Mesh -==================== - -.. index:: - single: CleanQuadEdgeMeshFilter - -Synopsis --------- - - -Clean quad edge mesh - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::CleanQuadEdgeMeshFilter diff --git a/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.md b/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.md new file mode 100644 index 000000000..560b706da --- /dev/null +++ b/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.md @@ -0,0 +1,84 @@ +--- +name: ComputeNormalsOfAMesh +--- + +# Compute Normals of a Mesh + +```{index} single: NormalQuadEdgeMeshFilter single: QuadEdgeMesh single: MeshFileReader pair: NormalQuadEdgeMeshFilter; SetWeight +``` + +## Synopsis + +Compute normals of a mesh + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+``` + +Output: + +``` +Index * Point * Normal +0 * [0.461602, -0.018446, -0.115989] * [0.964656, 0.0898966, -0.247704] +1 * [0.202784, 0.359481, -0.217858] * [0.398458, 0.53089, -0.747922] +2 * [-0.481417, -0.046787, 0.167623] * [-0.987132, 0.0342443, 0.1562] +3 * [-0.028388, -0.193602, -0.329748] * [-0.73488, -0.637902, -0.230287] +4 * [-0.087584, 0.116513, -0.399884] * [-0.396325, 0.718368, -0.571729] +5 * [0.310978, -0.239208, -0.176146] * [-0.256754, 0.55162, -0.793595] +6 * [-0.303314, 0.043035, -0.515252] * [-0.26465, 0.684736, -0.679041] +7 * [-0.256717, -0.39897, 0.177429] * [0.0907732, -0.987892, 0.125819] +8 * [0.393919, -0.388691, -0.207638] * [0.290631, -0.955747, -0.0456223] +9 * [-0.225987, -0.368634, -0.367823] * [0.154093, 0.365541, -0.917952] +10 * [-0.142556, -0.187471, -0.613449] * [0.902758, -0.0825592, -0.422153] +11 * [0.405923, -0.12839, -0.433595] * [0.432278, -0.901416, 0.0241831] +12 * [0.107094, 0.05873, -0.53405] * [0.452665, 0.664453, -0.594639] +13 * [0.179737, -0.358912, 0.264171] * [0.622873, -0.779647, 0.0646554] +14 * [0.270291, 0.167529, -0.267412] * [0.282452, 0.630941, -0.722588] +15 * [0.190508, -0.139941, -0.30917] * [0.642572, -0.758423, 0.109063] +16 * [-0.405901, 0.088723, -0.347001] * [-0.736406, 0.557068, -0.383904] +17 * [0.150462, -0.314033, -0.695425] * [-0.171163, -0.38232, -0.908039] +18 * [-0.134383, -0.384493, 0.060186] * [-0.0256952, -0.994633, 0.100226] +19 * [-0.333505, -0.116041, -0.567548] * [-0.847824, -0.186998, -0.496212] +20 * [-0.133643, -0.267196, -0.238155] * [0.123997, 0.550013, -0.8259] +21 * [-0.274406, 0.185852, -0.366349] * [-0.0630695, 0.682696, -0.727976] +22 * [-0.34352, -0.372556, 0.17102] * [-0.565292, -0.779407, 0.270129] +23 * [-0.468522, 0.005617, -0.307273] * [-0.945988, 0.0866878, -0.312397] +24 * [0.012837, 0.243987, -0.417788] * [-0.288839, 0.714998, -0.636671] +25 * [0.004712, 0.118755, -0.486604] * [-0.451072, 0.542366, -0.708783] + +[...] + +1300 * [0.429046, 0.119465, 0.002968] * [0.838127, 0.413114, -0.356201] +1301 * [-0.346539, -0.163042, 0.316913] * [-0.323662, 0.716134, 0.618381] +1302 * [-0.111388, 0.551166, -0.050984] * [-0.558618, 0.686741, -0.465115] +1303 * [0.376285, 0.211351, 0.347429] * [0.754427, -0.0746173, 0.652129] +1304 * [-0.026005, 0.583073, 0.081228] * [0.60426, 0.298334, 0.738828] +1305 * [-0.196168, -0.079437, 0.372088] * [-0.859283, 0.463078, 0.217237] +1306 * [-0.000569, 0.431162, 0.415514] * [0.683671, 0.70426, 0.191341] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NormalQuadEdgeMeshFilter +``` diff --git a/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.rst b/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.rst deleted file mode 100644 index 16f43edff..000000000 --- a/src/Filtering/QuadEdgeMeshFiltering/ComputeNormalsOfAMesh/Documentation.rst +++ /dev/null @@ -1,88 +0,0 @@ -:name: ComputeNormalsOfAMesh - -Compute Normals of a Mesh -========================= - -.. index:: - single: NormalQuadEdgeMeshFilter - single: QuadEdgeMesh - single: MeshFileReader - pair: NormalQuadEdgeMeshFilter; SetWeight - -Synopsis --------- - -Compute normals of a mesh - - -Results -------- - -.. figure:: InputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- -Output:: - - Index * Point * Normal - 0 * [0.461602, -0.018446, -0.115989] * [0.964656, 0.0898966, -0.247704] - 1 * [0.202784, 0.359481, -0.217858] * [0.398458, 0.53089, -0.747922] - 2 * [-0.481417, -0.046787, 0.167623] * [-0.987132, 0.0342443, 0.1562] - 3 * [-0.028388, -0.193602, -0.329748] * [-0.73488, -0.637902, -0.230287] - 4 * [-0.087584, 0.116513, -0.399884] * [-0.396325, 0.718368, -0.571729] - 5 * [0.310978, -0.239208, -0.176146] * [-0.256754, 0.55162, -0.793595] - 6 * [-0.303314, 0.043035, -0.515252] * [-0.26465, 0.684736, -0.679041] - 7 * [-0.256717, -0.39897, 0.177429] * [0.0907732, -0.987892, 0.125819] - 8 * [0.393919, -0.388691, -0.207638] * [0.290631, -0.955747, -0.0456223] - 9 * [-0.225987, -0.368634, -0.367823] * [0.154093, 0.365541, -0.917952] - 10 * [-0.142556, -0.187471, -0.613449] * [0.902758, -0.0825592, -0.422153] - 11 * [0.405923, -0.12839, -0.433595] * [0.432278, -0.901416, 0.0241831] - 12 * [0.107094, 0.05873, -0.53405] * [0.452665, 0.664453, -0.594639] - 13 * [0.179737, -0.358912, 0.264171] * [0.622873, -0.779647, 0.0646554] - 14 * [0.270291, 0.167529, -0.267412] * [0.282452, 0.630941, -0.722588] - 15 * [0.190508, -0.139941, -0.30917] * [0.642572, -0.758423, 0.109063] - 16 * [-0.405901, 0.088723, -0.347001] * [-0.736406, 0.557068, -0.383904] - 17 * [0.150462, -0.314033, -0.695425] * [-0.171163, -0.38232, -0.908039] - 18 * [-0.134383, -0.384493, 0.060186] * [-0.0256952, -0.994633, 0.100226] - 19 * [-0.333505, -0.116041, -0.567548] * [-0.847824, -0.186998, -0.496212] - 20 * [-0.133643, -0.267196, -0.238155] * [0.123997, 0.550013, -0.8259] - 21 * [-0.274406, 0.185852, -0.366349] * [-0.0630695, 0.682696, -0.727976] - 22 * [-0.34352, -0.372556, 0.17102] * [-0.565292, -0.779407, 0.270129] - 23 * [-0.468522, 0.005617, -0.307273] * [-0.945988, 0.0866878, -0.312397] - 24 * [0.012837, 0.243987, -0.417788] * [-0.288839, 0.714998, -0.636671] - 25 * [0.004712, 0.118755, -0.486604] * [-0.451072, 0.542366, -0.708783] - - [...] - - 1300 * [0.429046, 0.119465, 0.002968] * [0.838127, 0.413114, -0.356201] - 1301 * [-0.346539, -0.163042, 0.316913] * [-0.323662, 0.716134, 0.618381] - 1302 * [-0.111388, 0.551166, -0.050984] * [-0.558618, 0.686741, -0.465115] - 1303 * [0.376285, 0.211351, 0.347429] * [0.754427, -0.0746173, 0.652129] - 1304 * [-0.026005, 0.583073, 0.081228] * [0.60426, 0.298334, 0.738828] - 1305 * [-0.196168, -0.079437, 0.372088] * [-0.859283, 0.463078, 0.217237] - 1306 * [-0.000569, 0.431162, 0.415514] * [0.683671, 0.70426, 0.191341] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::NormalQuadEdgeMeshFilter diff --git a/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.md b/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.md new file mode 100644 index 000000000..cc7444ef7 --- /dev/null +++ b/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.md @@ -0,0 +1,61 @@ +--- +name: ComputePlanarParameterizationOfAMesh +--- + +# Compute Planar Parameterization of a Mesh + +```{index} single: ParameterizationQuadEdgeMeshFilter +``` + +## Synopsis + +Compute planar parameterization of a surface mesh represented by one itk::QuadEdgeMesh. + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 100% + +Input mesh +::: + +:::{figure} OutputMeshes.png +:alt: Output meshes +:scale: 100% + +Output planes with left column) SQUARE, and right column) DISK BorderType, +and row 1) OnesMatrix, 2) InverseEuclideanMatrix 3) ConformalMatrix, 4) +AuthalicMatrix, and 5) HarmonicMatrix CoefficientType. +::: + +```{raw} html +
+ +

Interactive input mesh

+
+ +
+ +

Interactive SQUARE BorderType, OnesMatrix CoefficientType output

+
+ +
+ +

Interactive DISK BorderType, OnesMatrix CoefficientType output

+
+``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ParameterizationQuadEdgeMeshFilter +``` diff --git a/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.rst b/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.rst deleted file mode 100644 index 1e37e8622..000000000 --- a/src/Filtering/QuadEdgeMeshFiltering/ComputePlanarParameterizationOfAMesh/Documentation.rst +++ /dev/null @@ -1,63 +0,0 @@ -:name: ComputePlanarParameterizationOfAMesh - -Compute Planar Parameterization of a Mesh -========================================= - -.. index:: - single: ParameterizationQuadEdgeMeshFilter - -Synopsis --------- - -Compute planar parameterization of a surface mesh represented by one itk::QuadEdgeMesh. - - -Results -------- - -.. figure:: InputMesh.png - :scale: 100% - :alt: Input mesh - - Input mesh - -.. figure:: OutputMeshes.png - :scale: 100% - :alt: Output meshes - - Output planes with left column) SQUARE, and right column) DISK BorderType, - and row 1) OnesMatrix, 2) InverseEuclideanMatrix 3) ConformalMatrix, 4) - AuthalicMatrix, and 5) HarmonicMatrix CoefficientType. - -.. raw:: html - -
- -

Interactive input mesh

-
- -
- -

Interactive SQUARE BorderType, OnesMatrix CoefficientType output

-
- -
- -

Interactive DISK BorderType, OnesMatrix CoefficientType output

-
- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ParameterizationQuadEdgeMeshFilter diff --git a/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.md b/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.md new file mode 100644 index 000000000..24e9357b7 --- /dev/null +++ b/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.md @@ -0,0 +1,49 @@ +--- +name: DelaunayConformEdgeFlipping +--- + +# Delaunay Conform Edge Flipping + +```{index} single: DelaunayConformingQuadEdgeMeshFilter single: MeshFileReader single: MeshFileWriter single: QuadEdgeMesh +``` + +## Synopsis + +Flip the edges of one itk::QuadEdgeMesh to satisfy Delaunay condition. + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +:::{figure} OutputMesh.png +:alt: Output image +:scale: 50% + +Output mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DelaunayConformingQuadEdgeMeshFilter +``` diff --git a/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.rst b/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.rst deleted file mode 100644 index 3ac710213..000000000 --- a/src/Filtering/QuadEdgeMeshFiltering/DelaunayConformEdgeFlipping/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: DelaunayConformEdgeFlipping - -Delaunay Conform Edge Flipping -============================== - -.. index:: - single: DelaunayConformingQuadEdgeMeshFilter - single: MeshFileReader - single: MeshFileWriter - single: QuadEdgeMesh - -Synopsis --------- - - -Flip the edges of one itk::QuadEdgeMesh to satisfy Delaunay condition. - - -Results -------- - -.. figure:: InputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. figure:: OutputMesh.png - :scale: 50% - :alt: Output image - - Output mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::DelaunayConformingQuadEdgeMeshFilter diff --git a/src/Filtering/QuadEdgeMeshFiltering/index.md b/src/Filtering/QuadEdgeMeshFiltering/index.md new file mode 100644 index 000000000..c5033417b --- /dev/null +++ b/src/Filtering/QuadEdgeMeshFiltering/index.md @@ -0,0 +1,10 @@ +# QuadEdgeMeshFiltering + +```{toctree} +:maxdepth: 1 + +CleanQuadEdgeMesh/Documentation.rst +ComputeNormalsOfAMesh/Documentation.rst +ComputePlanarParameterizationOfAMesh/Documentation.rst +DelaunayConformEdgeFlipping/Documentation.rst +``` diff --git a/src/Filtering/QuadEdgeMeshFiltering/index.rst b/src/Filtering/QuadEdgeMeshFiltering/index.rst deleted file mode 100644 index fa8a8c626..000000000 --- a/src/Filtering/QuadEdgeMeshFiltering/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -QuadEdgeMeshFiltering -===================== - -.. toctree:: - :maxdepth: 1 - - CleanQuadEdgeMesh/Documentation.rst - ComputeNormalsOfAMesh/Documentation.rst - ComputePlanarParameterizationOfAMesh/Documentation.rst - DelaunayConformEdgeFlipping/Documentation.rst diff --git a/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.md b/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.md new file mode 100644 index 000000000..d39fd287b --- /dev/null +++ b/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.md @@ -0,0 +1,50 @@ +--- +name: BlurringAnImageUsingABinomialKernel +--- + +# Blurring an Image Using a Binomial Kernel + +```{index} single: BinomialBlurImageFilter +``` + +## Synopsis + +The BinomialBlurImageFilter computes a nearest neighbor average +along each dimension. The process is repeated a number of times, as +specified by the user. In principle, after a large number of iterations +the result will approach the convolution with a Gaussian. + +## Results + +% figure::cthead1.png +% :scale: 50% +% :alt: Input image +% +% Input image + +% figure::OutputBaseline.png +% :scale: 50% +% :alt: Output image +% +% Output image + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinomialBlurImageFilter +``` diff --git a/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.rst b/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.rst deleted file mode 100644 index 97c131d20..000000000 --- a/src/Filtering/Smoothing/BlurringAnImageUsingABinomialKernel/Documentation.rst +++ /dev/null @@ -1,54 +0,0 @@ -:name: BlurringAnImageUsingABinomialKernel - -Blurring an Image Using a Binomial Kernel -========================================= - -.. index:: - single: BinomialBlurImageFilter - -Synopsis --------- - -The BinomialBlurImageFilter computes a nearest neighbor average -along each dimension. The process is repeated a number of times, as -specified by the user. In principle, after a large number of iterations -the result will approach the convolution with a Gaussian. - - -Results -------- - -.. figure::cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure::OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinomialBlurImageFilter diff --git a/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.md b/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.md new file mode 100644 index 000000000..ed32e48aa --- /dev/null +++ b/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.md @@ -0,0 +1,47 @@ +--- +name: ComputesSmoothingWithGaussianKernel +--- + +# Computes Smoothing With Gaussian Kernel + +```{index} single: SmoothingRecursiveGaussianImageFilter single: smooth +``` + +## Synopsis + +Computes the smoothing of an image by convolution with Gaussian kernels. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::SmoothingRecursiveGaussianImageFilter +``` diff --git a/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.rst b/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.rst deleted file mode 100644 index 7a7af976c..000000000 --- a/src/Filtering/Smoothing/ComputesSmoothingWithGaussianKernel/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: ComputesSmoothingWithGaussianKernel - -Computes Smoothing With Gaussian Kernel -======================================= - -.. index:: - single: SmoothingRecursiveGaussianImageFilter - single: smooth - -Synopsis --------- - -Computes the smoothing of an image by convolution with Gaussian kernels. - - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::SmoothingRecursiveGaussianImageFilter diff --git a/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.md b/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.md new file mode 100644 index 000000000..a330d3507 --- /dev/null +++ b/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.md @@ -0,0 +1,42 @@ +--- +name: FindHigherDerivativesOfImage +--- + +# Find Higher Derivatives of Image + +```{index} single: RecursiveGaussianImageFilter pair: higher; derivative +``` + +## Synopsis + +Find higher derivatives of an image. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} FindHigherDerivativesOfImage.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RecursiveGaussianImageFilter +``` diff --git a/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.rst b/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.rst deleted file mode 100644 index 029b697fd..000000000 --- a/src/Filtering/Smoothing/FindHigherDerivativesOfImage/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: FindHigherDerivativesOfImage - -Find Higher Derivatives of Image -================================ - -.. index:: - single: RecursiveGaussianImageFilter - pair: higher; derivative - -Synopsis --------- - -Find higher derivatives of an image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: FindHigherDerivativesOfImage.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RecursiveGaussianImageFilter diff --git a/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.md b/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.md new file mode 100644 index 000000000..92e58ab7a --- /dev/null +++ b/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.md @@ -0,0 +1,47 @@ +--- +name: MeanFilteringOfAnImage +--- + +# Mean Filtering of an Image + +```{index} single: MeanImageFilter single: smooth +``` + +## Synopsis + +Apply mean filtering on an image. + +## Results + +:::{figure} Gourds.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MeanImageFilter +``` diff --git a/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.rst b/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.rst deleted file mode 100644 index f85577e84..000000000 --- a/src/Filtering/Smoothing/MeanFilteringOfAnImage/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: MeanFilteringOfAnImage - -Mean Filtering of an Image -========================== - -.. index:: - single: MeanImageFilter - single: smooth - -Synopsis --------- - -Apply mean filtering on an image. - - -Results -------- - -.. figure:: Gourds.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MeanImageFilter diff --git a/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.md b/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.md new file mode 100644 index 000000000..22cdb8d5e --- /dev/null +++ b/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.md @@ -0,0 +1,47 @@ +--- +name: MedianFilteringOfAnImage +--- + +# Median Filtering of an Image + +```{index} single: MedianImageFilter single: smooth +``` + +## Synopsis + +Apply median filtering on an image. + +## Results + +:::{figure} Gourds.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MedianImageFilter +``` diff --git a/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.rst b/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.rst deleted file mode 100644 index c86abcdab..000000000 --- a/src/Filtering/Smoothing/MedianFilteringOfAnImage/Documentation.rst +++ /dev/null @@ -1,49 +0,0 @@ -:name: MedianFilteringOfAnImage - -Median Filtering of an Image -============================ - -.. index:: - single: MedianImageFilter - single: smooth - -Synopsis --------- - -Apply median filtering on an image. - - -Results -------- - -.. figure:: Gourds.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MedianImageFilter diff --git a/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.md b/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.md new file mode 100644 index 000000000..1ee56174f --- /dev/null +++ b/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: MedianFilteringOfAnRGBImage +--- + +# Median Filtering of an RGB Image + +```{index} single: MedianImageFilter single: smooth +``` + +## Synopsis + +Apply median filtering on a RGB Image. The sorting of pixel is performed on their luminance. + +## Results + +:::{figure} GourdsRGB.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MedianImageFilter +``` diff --git a/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.rst b/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.rst deleted file mode 100644 index 7dee7c248..000000000 --- a/src/Filtering/Smoothing/MedianFilteringOfAnRGBImage/Documentation.rst +++ /dev/null @@ -1,43 +0,0 @@ -:name: MedianFilteringOfAnRGBImage - -Median Filtering of an RGB Image -================================ - -.. index:: - single: MedianImageFilter - single: smooth - -Synopsis --------- - -Apply median filtering on a RGB Image. The sorting of pixel is performed on their luminance. - - -Results -------- - -.. figure:: GourdsRGB.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MedianImageFilter diff --git a/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.md b/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.md new file mode 100644 index 000000000..6753912de --- /dev/null +++ b/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SmoothImageWithDiscreteGaussianFilter +--- + +# Smooth Image With Discrete Gaussian Filter + +```{index} single: DiscreteGaussianImageFilter pair: gaussian; filter +``` + +## Synopsis + +Smooth an image with a discrete Gaussian filter. + +## Results + +:::{figure} Yinyang.png +:scale: 70% + +Input image. +::: + +:::{figure} SmoothImageWithDiscreteGaussianFilter.png +:scale: 70% + +Yinyang.png And Output.png With Variance = 8 +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::DiscreteGaussianImageFilter +``` diff --git a/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.rst b/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.rst deleted file mode 100644 index 8ed28e370..000000000 --- a/src/Filtering/Smoothing/SmoothImageWithDiscreteGaussianFilter/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: SmoothImageWithDiscreteGaussianFilter - -Smooth Image With Discrete Gaussian Filter -========================================== - -.. index:: - single: DiscreteGaussianImageFilter - pair: gaussian; filter - -Synopsis --------- - -Smooth an image with a discrete Gaussian filter. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - - Input image. - -.. figure:: SmoothImageWithDiscreteGaussianFilter.png - :scale: 70% - - Yinyang.png And Output.png With Variance = 8 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::DiscreteGaussianImageFilter diff --git a/src/Filtering/Smoothing/index.md b/src/Filtering/Smoothing/index.md new file mode 100644 index 000000000..9f4a5acde --- /dev/null +++ b/src/Filtering/Smoothing/index.md @@ -0,0 +1,13 @@ +# Smoothing + +```{toctree} +:maxdepth: 1 + +BlurringAnImageUsingABinomialKernel/Documentation.rst +ComputesSmoothingWithGaussianKernel/Documentation.rst +FindHigherDerivativesOfImage/Documentation.rst +MeanFilteringOfAnImage/Documentation.rst +MedianFilteringOfAnImage/Documentation.rst +MedianFilteringOfAnRGBImage/Documentation.rst +SmoothImageWithDiscreteGaussianFilter/Documentation.rst +``` diff --git a/src/Filtering/Smoothing/index.rst b/src/Filtering/Smoothing/index.rst deleted file mode 100644 index 755177561..000000000 --- a/src/Filtering/Smoothing/index.rst +++ /dev/null @@ -1,13 +0,0 @@ -Smoothing -========= - -.. toctree:: - :maxdepth: 1 - - BlurringAnImageUsingABinomialKernel/Documentation.rst - ComputesSmoothingWithGaussianKernel/Documentation.rst - FindHigherDerivativesOfImage/Documentation.rst - MeanFilteringOfAnImage/Documentation.rst - MedianFilteringOfAnImage/Documentation.rst - MedianFilteringOfAnRGBImage/Documentation.rst - SmoothImageWithDiscreteGaussianFilter/Documentation.rst diff --git a/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.md b/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.md new file mode 100644 index 000000000..7c51767bd --- /dev/null +++ b/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.md @@ -0,0 +1,42 @@ +--- +name: DemonstrateThresholdAlgorithms +--- + +# Demonstrate Available Threshold Algorithms + +```{index} single: LiThresholdImageFilter +``` + +## Synopsis + +Demonstrate available threshold algorithms. + +## Results + +:::{figure} Yinyang.png +:alt: Input yin-yang image. +:scale: 50% + +Input Image +::: + +:::{figure} DemonstrateThresholdAlgorithmsQuickview.png +:alt: QuickView output. +:scale: 50% + +Output In QuickView +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LiThresholdImageFilter +``` diff --git a/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.rst b/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.rst deleted file mode 100644 index 514b05442..000000000 --- a/src/Filtering/Thresholding/DemonstrateThresholdAlgorithms/Documentation.rst +++ /dev/null @@ -1,41 +0,0 @@ -:name: DemonstrateThresholdAlgorithms - -Demonstrate Available Threshold Algorithms -========================================== - -.. index:: - single: LiThresholdImageFilter - -Synopsis --------- - -Demonstrate available threshold algorithms. - - -Results -------- -.. figure:: Yinyang.png - :scale: 50% - :alt: Input yin-yang image. - - Input Image - -.. figure:: DemonstrateThresholdAlgorithmsQuickview.png - :scale: 50% - :alt: QuickView output. - - Output In QuickView - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LiThresholdImageFilter diff --git a/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.md b/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.md new file mode 100644 index 000000000..9d7984b6a --- /dev/null +++ b/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SeparateGroundUsingOtsu +--- + +# Separate Foreround and Background Using Otsu Method + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: OtsuThresholdImageFilter +``` + +## Synopsis + +Separate foreground and background using Otsu's method. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::OtsuThresholdImageFilter +``` diff --git a/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.rst b/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.rst deleted file mode 100644 index 696f288f2..000000000 --- a/src/Filtering/Thresholding/SeparateGroundUsingOtsu/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: SeparateGroundUsingOtsu - -Separate Foreround and Background Using Otsu Method -=================================================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: OtsuThresholdImageFilter - -Synopsis --------- - -Separate foreground and background using Otsu's method. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::OtsuThresholdImageFilter diff --git a/src/Filtering/Thresholding/ThresholdAnImage/Documentation.md b/src/Filtering/Thresholding/ThresholdAnImage/Documentation.md new file mode 100644 index 000000000..7fb4153d3 --- /dev/null +++ b/src/Filtering/Thresholding/ThresholdAnImage/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ThresholdAnImage +--- + +# Threshold an Image + +```{index} single: ThresholdImageFilter +``` + +## Synopsis + +Threshold an image using itk::ThresholdImageFilter + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ThresholdImageFilter +``` diff --git a/src/Filtering/Thresholding/ThresholdAnImage/Documentation.rst b/src/Filtering/Thresholding/ThresholdAnImage/Documentation.rst deleted file mode 100644 index 194e45bb0..000000000 --- a/src/Filtering/Thresholding/ThresholdAnImage/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: ThresholdAnImage - -Threshold an Image -================== - -.. index:: - single: ThresholdImageFilter - -Synopsis --------- - -Threshold an image using itk::ThresholdImageFilter - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ThresholdImageFilter diff --git a/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.md b/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.md new file mode 100644 index 000000000..30c50f3b6 --- /dev/null +++ b/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ThresholdAnImageUsingBinary +--- + +# Threshold an Image Using Binary Thresholding + +```{index} single: BinaryThresholdImageFilter +``` + +## Synopsis + +Binarize an input image by thresholding. + +## Results + +:::{figure} cthead1.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BinaryThresholdImageFilter +``` diff --git a/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.rst b/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.rst deleted file mode 100644 index 74eef33ba..000000000 --- a/src/Filtering/Thresholding/ThresholdAnImageUsingBinary/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: ThresholdAnImageUsingBinary - -Threshold an Image Using Binary Thresholding -============================================ - -.. index:: - single: BinaryThresholdImageFilter - -Synopsis --------- - - -Binarize an input image by thresholding. - - -Results -------- - -.. figure:: cthead1.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BinaryThresholdImageFilter diff --git a/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.md b/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.md new file mode 100644 index 000000000..d85455bfd --- /dev/null +++ b/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ThresholdAnImageUsingOtsu +--- + +# Threshold an Image Using Otsu + +```{index} single: OtsuMultipleThresholdsImageFilter +``` + +## Synopsis + +Threshold an Image using Otsu's method. + +## Results + +:::{figure} Gourds.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::OtsuMultipleThresholdsImageFilter +``` diff --git a/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.rst b/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.rst deleted file mode 100644 index 193c9b13f..000000000 --- a/src/Filtering/Thresholding/ThresholdAnImageUsingOtsu/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: ThresholdAnImageUsingOtsu - -Threshold an Image Using Otsu -============================= - -.. index:: - single: OtsuMultipleThresholdsImageFilter - -Synopsis --------- - - -Threshold an Image using Otsu's method. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::OtsuMultipleThresholdsImageFilter diff --git a/src/Filtering/Thresholding/index.md b/src/Filtering/Thresholding/index.md new file mode 100644 index 000000000..eed02e39e --- /dev/null +++ b/src/Filtering/Thresholding/index.md @@ -0,0 +1,11 @@ +# Thresholding + +```{toctree} +:maxdepth: 1 + +DemonstrateThresholdAlgorithms/Documentation.rst +SeparateGroundUsingOtsu/Documentation.rst +ThresholdAnImage/Documentation.rst +ThresholdAnImageUsingBinary/Documentation.rst +ThresholdAnImageUsingOtsu/Documentation.rst +``` diff --git a/src/Filtering/Thresholding/index.rst b/src/Filtering/Thresholding/index.rst deleted file mode 100644 index 4e3a540ea..000000000 --- a/src/Filtering/Thresholding/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -Thresholding -============ - -.. toctree:: - :maxdepth: 1 - - DemonstrateThresholdAlgorithms/Documentation.rst - SeparateGroundUsingOtsu/Documentation.rst - ThresholdAnImage/Documentation.rst - ThresholdAnImageUsingBinary/Documentation.rst - ThresholdAnImageUsingOtsu/Documentation.rst diff --git a/src/Filtering/index.md b/src/Filtering/index.md new file mode 100644 index 000000000..d156f1e60 --- /dev/null +++ b/src/Filtering/index.md @@ -0,0 +1,31 @@ +# Filtering + +```{toctree} +:maxdepth: 2 + +AnisotropicSmoothing/index.rst +AntiAlias/index.rst +BinaryMathematicalMorphology/index.rst +Colormap/index.rst +Convolution/index.rst +CurvatureFlow/index.rst +DistanceMap/index.rst +FastMarching/index.rst +FFT/index.rst +ImageCompare/index.rst +ImageCompose/index.rst +ImageFeature/index.rst +ImageFilterBase/index.rst +ImageFusion/index.rst +ImageGradient/index.rst +ImageGrid/index.rst +ImageIntensity/index.rst +ImageLabel/index.rst +ImageStatistics/index.rst +LabelMap/index.rst +MathematicalMorphology/index.rst +Path/index.rst +QuadEdgeMeshFiltering/index.rst +Smoothing/index.rst +Thresholding/index.rst +``` diff --git a/src/Filtering/index.rst b/src/Filtering/index.rst deleted file mode 100644 index 1dd658a02..000000000 --- a/src/Filtering/index.rst +++ /dev/null @@ -1,31 +0,0 @@ -Filtering -========= - -.. toctree:: - :maxdepth: 2 - - AnisotropicSmoothing/index.rst - AntiAlias/index.rst - BinaryMathematicalMorphology/index.rst - Colormap/index.rst - Convolution/index.rst - CurvatureFlow/index.rst - DistanceMap/index.rst - FastMarching/index.rst - FFT/index.rst - ImageCompare/index.rst - ImageCompose/index.rst - ImageFeature/index.rst - ImageFilterBase/index.rst - ImageFusion/index.rst - ImageGradient/index.rst - ImageGrid/index.rst - ImageIntensity/index.rst - ImageLabel/index.rst - ImageStatistics/index.rst - LabelMap/index.rst - MathematicalMorphology/index.rst - Path/index.rst - QuadEdgeMeshFiltering/index.rst - Smoothing/index.rst - Thresholding/index.rst diff --git a/src/GPU/index.md b/src/GPU/index.md new file mode 100644 index 000000000..8b5daf13f --- /dev/null +++ b/src/GPU/index.md @@ -0,0 +1,5 @@ +# GPU + +```{toctree} +:maxdepth: 2 +``` diff --git a/src/GPU/index.rst b/src/GPU/index.rst deleted file mode 100644 index 7730dfdf2..000000000 --- a/src/GPU/index.rst +++ /dev/null @@ -1,5 +0,0 @@ -GPU -=== - -.. toctree:: - :maxdepth: 2 diff --git a/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.md b/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.md new file mode 100644 index 000000000..9e2b9ad35 --- /dev/null +++ b/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.md @@ -0,0 +1,133 @@ +--- +name: ReadAndPrintDICOMTags +--- + +# Read and Print DICOM Tags + +```{index} single: GDCMImageIO +``` + +## Synopsis + +Example to read, search and print DICOM image metadata tags + +## Results + +```none +0008|0000 = 406 +0008|0005 = ISO_IR 100 +0008|0008 = ORIGINAL\PRIMARY\OTHER +0008|0016 = 1.2.840.10008.5.1.4.1.1.4 +0008|0018 = 1.2.840.113619.2.133.1762890640.1886.1055165016.76 +0008|0020 = 20030625 +0008|0021 = 20030625 +0008|0022 = 20030625 +0008|0023 = 20030625 +0008|0030 = 152734 +0008|0031 = 153128 +0008|0032 = 153128 +0008|0033 = 153128 +0008|0050 = +0008|0060 = MR +0008|0070 = GE MEDICAL SYSTEMS +0008|0080 = crd +0008|0090 = +0008|1010 = sig3ow0 +0008|1030 = Tech_1 +0008|103e = head scan +0008|1070 = RPM +0008|1090 = GENESIS_SIGNA +0010|0000 = 82 +0010|0010 = Wes Turner +0010|0020 = 1111 +0010|0030 = +0010|0040 = O +0010|1010 = 000Y +0010|1030 = 68.039 +0010|21b0 = +0018|0000 = 428 +0018|0020 = GR +0018|0021 = SS\SP +0018|0022 = FC\VB_GEMS\VASCTOF_GEMS\PFF +0018|0023 = 3D +0018|0025 = N +0018|0050 = 1.6 +0018|0080 = 23 +0018|0081 = 10 +0018|0083 = 1 +0018|0084 = 6.38883e+08 +0018|0085 = H1 +0018|0086 = 1 +0018|0087 = 15000 +0018|0088 = 1.6 +0018|0091 = 0 +0018|0093 = 100 +0018|0094 = 75 +0018|0095 = 97.6562 +0018|1000 = 0000018387rdmr3 +0018|1020 = 09 +0018|1050 = 1.14585 +0018|1088 = 0 +0018|1090 = 0 +0018|1094 = 0 +0018|1100 = 220 +0018|1250 = HEAD +0018|1251 = HEAD +0018|1310 = 0\256\192\0 +0018|1312 = ROW +0018|1314 = 25 +0018|1315 = N +0018|1316 = 0.004169 +0018|5100 = HFS +0020|0000 = 340 +0020|000d = 1.2.840.113619.2.133.1762890640.1886.1055165015.961 +0020|000e = 1.2.840.113619.2.133.1762890640.1886.1055165015.999 +0020|0010 = 361 +0020|0011 = 3 +0020|0012 = 0 +0020|0013 = 77 +0020|0032 = -112\-18.8578\ 128.388 +0020|0037 = 1\ 0\ 0\ 0\0.466651\ -0.884442 +0020|0052 = 1.2.840.113619.2.133.1762890640.1910.1055164903.673 +0020|0060 = +0020|0110 = 0 +0020|1040 = +0020|1041 = -32.4746742249 +0028|0000 = 148 +0028|0002 = 1 +0028|0004 = MONOCHROME2 +0028|0010 = 256 +0028|0011 = 256 +0028|0030 = 0.85939\0.859375 +0028|0100 = 16 +0028|0101 = 16 +0028|0102 = 15 +0028|0103 = 1 +0028|0120 = 0 +0028|1050 = 86 +0028|1051 = 173 +7fe0|0000 = 131084 +Patient's Name (0010|0010) is: Wes Turner +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1,16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GDCMImageIO +``` diff --git a/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.rst b/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.rst deleted file mode 100644 index 121e90ccd..000000000 --- a/src/IO/GDCM/ReadAndPrintDICOMTags/Documentation.rst +++ /dev/null @@ -1,137 +0,0 @@ -:name: ReadAndPrintDICOMTags - -Read and Print DICOM Tags -========================= - -.. index:: - single: GDCMImageIO - -Synopsis --------- - - -Example to read, search and print DICOM image metadata tags - - -Results -------- - -.. code-block:: none - - 0008|0000 = 406 - 0008|0005 = ISO_IR 100 - 0008|0008 = ORIGINAL\PRIMARY\OTHER - 0008|0016 = 1.2.840.10008.5.1.4.1.1.4 - 0008|0018 = 1.2.840.113619.2.133.1762890640.1886.1055165016.76 - 0008|0020 = 20030625 - 0008|0021 = 20030625 - 0008|0022 = 20030625 - 0008|0023 = 20030625 - 0008|0030 = 152734 - 0008|0031 = 153128 - 0008|0032 = 153128 - 0008|0033 = 153128 - 0008|0050 = - 0008|0060 = MR - 0008|0070 = GE MEDICAL SYSTEMS - 0008|0080 = crd - 0008|0090 = - 0008|1010 = sig3ow0 - 0008|1030 = Tech_1 - 0008|103e = head scan - 0008|1070 = RPM - 0008|1090 = GENESIS_SIGNA - 0010|0000 = 82 - 0010|0010 = Wes Turner - 0010|0020 = 1111 - 0010|0030 = - 0010|0040 = O - 0010|1010 = 000Y - 0010|1030 = 68.039 - 0010|21b0 = - 0018|0000 = 428 - 0018|0020 = GR - 0018|0021 = SS\SP - 0018|0022 = FC\VB_GEMS\VASCTOF_GEMS\PFF - 0018|0023 = 3D - 0018|0025 = N - 0018|0050 = 1.6 - 0018|0080 = 23 - 0018|0081 = 10 - 0018|0083 = 1 - 0018|0084 = 6.38883e+08 - 0018|0085 = H1 - 0018|0086 = 1 - 0018|0087 = 15000 - 0018|0088 = 1.6 - 0018|0091 = 0 - 0018|0093 = 100 - 0018|0094 = 75 - 0018|0095 = 97.6562 - 0018|1000 = 0000018387rdmr3 - 0018|1020 = 09 - 0018|1050 = 1.14585 - 0018|1088 = 0 - 0018|1090 = 0 - 0018|1094 = 0 - 0018|1100 = 220 - 0018|1250 = HEAD - 0018|1251 = HEAD - 0018|1310 = 0\256\192\0 - 0018|1312 = ROW - 0018|1314 = 25 - 0018|1315 = N - 0018|1316 = 0.004169 - 0018|5100 = HFS - 0020|0000 = 340 - 0020|000d = 1.2.840.113619.2.133.1762890640.1886.1055165015.961 - 0020|000e = 1.2.840.113619.2.133.1762890640.1886.1055165015.999 - 0020|0010 = 361 - 0020|0011 = 3 - 0020|0012 = 0 - 0020|0013 = 77 - 0020|0032 = -112\-18.8578\ 128.388 - 0020|0037 = 1\ 0\ 0\ 0\0.466651\ -0.884442 - 0020|0052 = 1.2.840.113619.2.133.1762890640.1910.1055164903.673 - 0020|0060 = - 0020|0110 = 0 - 0020|1040 = - 0020|1041 = -32.4746742249 - 0028|0000 = 148 - 0028|0002 = 1 - 0028|0004 = MONOCHROME2 - 0028|0010 = 256 - 0028|0011 = 256 - 0028|0030 = 0.85939\0.859375 - 0028|0100 = 16 - 0028|0101 = 16 - 0028|0102 = 15 - 0028|0103 = 1 - 0028|0120 = 0 - 0028|1050 = 86 - 0028|1051 = 173 - 7fe0|0000 = 131084 - Patient's Name (0010|0010) is: Wes Turner - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1,16- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GDCMImageIO diff --git a/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.md b/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.md new file mode 100644 index 000000000..36698654c --- /dev/null +++ b/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.md @@ -0,0 +1,51 @@ +--- +name: ReadDICOMSeriesAndWrite3DImage +--- + +# Read DICOM Series and Write 3D Image + +```{index} pair: GDCMSeriesFileNames; GDCMImageIO +``` + +## Synopsis + +This example reads all the DICOM series in a given folder argv\[1\] +and writes them in the same folder with following file pattern: +seriesIdentifier.nrrd + +if output file name argv\[2\] and series name argv\[3\] are given, +then it behaves like DicomSeriesReadImageWrite2.cxx +(writing just the requested series with the specified name). + +Based on DicomSeriesReadImageWrite2.cxx + +Author: Dženan Zukić \<> + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GDCMSeriesFileNames +``` + +```{eval-rst} +.. breathelink:: itk::GDCMImageIO +``` + +```{eval-rst} +.. breathelink:: itk::ImageSeriesReader +``` diff --git a/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.rst b/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.rst deleted file mode 100644 index 10495d4e9..000000000 --- a/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: ReadDICOMSeriesAndWrite3DImage - -Read DICOM Series and Write 3D Image -==================================== - -.. index:: - pair: GDCMSeriesFileNames; GDCMImageIO - -Synopsis --------- - -This example reads all the DICOM series in a given folder argv[1] -and writes them in the same folder with following file pattern: -seriesIdentifier.nrrd - -if output file name argv[2] and series name argv[3] are given, -then it behaves like DicomSeriesReadImageWrite2.cxx -(writing just the requested series with the specified name). - -Based on DicomSeriesReadImageWrite2.cxx - -Author: Dženan Zukić - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::GDCMSeriesFileNames -.. breathelink:: itk::GDCMImageIO -.. breathelink:: itk::ImageSeriesReader diff --git a/src/IO/GDCM/ResampleDICOMSeries/Documentation.md b/src/IO/GDCM/ResampleDICOMSeries/Documentation.md new file mode 100644 index 000000000..d866882a5 --- /dev/null +++ b/src/IO/GDCM/ResampleDICOMSeries/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ResampleDICOMSeries +--- + +# Resample DICOM Series + +```{index} single: GDCMImageIO single: DICOM pair: resample; DICOM +``` + +## Synopsis + +Resample a DICOM series. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GDCMImageIO +``` diff --git a/src/IO/GDCM/ResampleDICOMSeries/Documentation.rst b/src/IO/GDCM/ResampleDICOMSeries/Documentation.rst deleted file mode 100644 index 735b1eb39..000000000 --- a/src/IO/GDCM/ResampleDICOMSeries/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ResampleDICOMSeries - -Resample DICOM Series -===================== - -.. index:: - single: GDCMImageIO - single: DICOM - pair: resample; DICOM - -Synopsis --------- - -Resample a DICOM series. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GDCMImageIO diff --git a/src/IO/GDCM/index.md b/src/IO/GDCM/index.md new file mode 100644 index 000000000..7d06662dd --- /dev/null +++ b/src/IO/GDCM/index.md @@ -0,0 +1,9 @@ +# GDCM + +```{toctree} +:maxdepth: 1 + +ReadAndPrintDICOMTags/Documentation.rst +ReadDICOMSeriesAndWrite3DImage/Documentation.rst +ResampleDICOMSeries/Documentation.rst +``` diff --git a/src/IO/GDCM/index.rst b/src/IO/GDCM/index.rst deleted file mode 100644 index c448e2426..000000000 --- a/src/IO/GDCM/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -GDCM -==== - -.. toctree:: - :maxdepth: 1 - - ReadAndPrintDICOMTags/Documentation.rst - ReadDICOMSeriesAndWrite3DImage/Documentation.rst - ResampleDICOMSeries/Documentation.rst diff --git a/src/IO/ImageBase/ConvertFileFormats/Documentation.md b/src/IO/ImageBase/ConvertFileFormats/Documentation.md new file mode 100644 index 000000000..8e378de31 --- /dev/null +++ b/src/IO/ImageBase/ConvertFileFormats/Documentation.md @@ -0,0 +1,45 @@ +--- +name: ConvertFileFormats +--- + +# Convert File Formats + +```{index} single: ImageFileReader, ImageFileWriter +``` + +## Synopsis + +Convert from one image file format to another. ITK will automatically detect +the file type of the input and output files by their extension, and an +`itk::ImageFileReader` and `itk::ImageFileWriter` will use the appropriate +`ImageIO` class. + +## Results + +:::{figure} Gourds.png +:alt: Gourds.png +:scale: 50% + +Gourds.png +::: + +:::{figure} OutputBaseline.jpg +:alt: Gourds.jpg +:scale: 50% + +Gourds.jpg +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageFileReader itk::ImageFileWriter +``` diff --git a/src/IO/ImageBase/ConvertFileFormats/Documentation.rst b/src/IO/ImageBase/ConvertFileFormats/Documentation.rst deleted file mode 100644 index 71afa882b..000000000 --- a/src/IO/ImageBase/ConvertFileFormats/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: ConvertFileFormats - -Convert File Formats -==================== - -.. index:: - single: ImageFileReader, ImageFileWriter - -Synopsis --------- - -Convert from one image file format to another. ITK will automatically detect -the file type of the input and output files by their extension, and an -`itk::ImageFileReader` and `itk::ImageFileWriter` will use the appropriate -`ImageIO` class. - - -Results -------- - -.. figure:: Gourds.png - :scale: 50% - :alt: Gourds.png - - Gourds.png - -.. figure:: OutputBaseline.jpg - :scale: 50% - :alt: Gourds.jpg - - Gourds.jpg - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageFileReader itk::ImageFileWriter diff --git a/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.md b/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.md new file mode 100644 index 000000000..81e189cc3 --- /dev/null +++ b/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.md @@ -0,0 +1,28 @@ +--- +name: ConvertImageToAnotherType +--- + +# Convert Image to Another Type + +```{index} single: ConvertPixelBuffer single: Image pair: convert; type +``` + +## Synopsis + +Converts an image to another type of image. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConvertPixelBuffer +``` diff --git a/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.rst b/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.rst deleted file mode 100644 index 0ab2cc745..000000000 --- a/src/IO/ImageBase/ConvertImageToAnotherType/Documentation.rst +++ /dev/null @@ -1,32 +0,0 @@ -:name: ConvertImageToAnotherType - -Convert Image to Another Type -============================= - -.. index:: - single: ConvertPixelBuffer - single: Image - pair: convert; type - -Synopsis --------- - -Converts an image to another type of image. - - -Results -------- - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConvertPixelBuffer diff --git a/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.md b/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.md new file mode 100644 index 000000000..a0754c1bc --- /dev/null +++ b/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.md @@ -0,0 +1,35 @@ +--- +name: Create3DFromSeriesOf2D +--- + +# Create 3D Volume From Series of 2D Images + +```{index} single: ImageSeriesReader +``` + +## Synopsis + +Create a 3D volume from a series of 2D images. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageSeriesReader +``` diff --git a/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.rst b/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.rst deleted file mode 100644 index 6b2a67321..000000000 --- a/src/IO/ImageBase/Create3DFromSeriesOf2D/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: Create3DFromSeriesOf2D - -Create 3D Volume From Series of 2D Images -========================================= - -.. index:: - single: ImageSeriesReader - -Synopsis --------- - -Create a 3D volume from a series of 2D images. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageSeriesReader diff --git a/src/IO/ImageBase/CreateAListOfFileNames/Documentation.md b/src/IO/ImageBase/CreateAListOfFileNames/Documentation.md new file mode 100644 index 000000000..3eb995701 --- /dev/null +++ b/src/IO/ImageBase/CreateAListOfFileNames/Documentation.md @@ -0,0 +1,75 @@ +--- +name: CreateAListOfFileNames +--- + +# Create a List of File Names + +```{index} single: NumericSeriesFileNames +``` + +## Synopsis + +Create a list of numbered file names. + +## Results + +Output: + +``` +output_0.png +output_10.png +output_20.png +output_30.png +output_40.png +output_50.png +output_60.png +output_70.png +output_80.png +output_90.png +output_100.png +output_110.png +output_120.png +output_130.png +output_140.png +output_150.png + +*************** + +output_0000.png +output_0010.png +output_0020.png +output_0030.png +output_0040.png +output_0050.png +output_0060.png +output_0070.png +output_0080.png +output_0090.png +output_0100.png +output_0110.png +output_0120.png +output_0130.png +output_0140.png +output_0150.png +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NumericSeriesFileNames +``` diff --git a/src/IO/ImageBase/CreateAListOfFileNames/Documentation.rst b/src/IO/ImageBase/CreateAListOfFileNames/Documentation.rst deleted file mode 100644 index 6d0f43a75..000000000 --- a/src/IO/ImageBase/CreateAListOfFileNames/Documentation.rst +++ /dev/null @@ -1,77 +0,0 @@ -:name: CreateAListOfFileNames - -Create a List of File Names -=========================== - -.. index:: - single: NumericSeriesFileNames - -Synopsis --------- - -Create a list of numbered file names. - - -Results -------- - -Output:: - - output_0.png - output_10.png - output_20.png - output_30.png - output_40.png - output_50.png - output_60.png - output_70.png - output_80.png - output_90.png - output_100.png - output_110.png - output_120.png - output_130.png - output_140.png - output_150.png - - *************** - - output_0000.png - output_0010.png - output_0020.png - output_0030.png - output_0040.png - output_0050.png - output_0060.png - output_0070.png - output_0080.png - output_0090.png - output_0100.png - output_0110.png - output_0120.png - output_0130.png - output_0140.png - output_0150.png - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::NumericSeriesFileNames diff --git a/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.md b/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.md new file mode 100644 index 000000000..984de94fb --- /dev/null +++ b/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.md @@ -0,0 +1,58 @@ +--- +name: GenerateSlicesFromVolume +--- + +# Generate Slices From Volume + +```{index} single: ImageSeriesWriter single: NumericSeriesFileNames +``` + +## Synopsis + +Create series of 2D images from a given volume. + +## Results + +:::{figure} Input.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} Output-20Baseline.png +:alt: Output image, slice 20 +:scale: 200% + +Output image, slice 20 +::: + +:::{figure} Output-30Baseline.png +:alt: Output image, slice 30 +:scale: 200% + +Output image, slice 30 +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +```{literalinclude} Code.py +:language: python +:lines: 1, 17- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::NumericSeriesFileNames +``` + +```{eval-rst} +.. breathelink:: itk::ImageSeriesWriter +``` diff --git a/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.rst b/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.rst deleted file mode 100644 index a123e5839..000000000 --- a/src/IO/ImageBase/GenerateSlicesFromVolume/Documentation.rst +++ /dev/null @@ -1,56 +0,0 @@ -:name: GenerateSlicesFromVolume - -Generate Slices From Volume -=========================== - -.. index:: - single: ImageSeriesWriter - single: NumericSeriesFileNames - -Synopsis --------- - -Create series of 2D images from a given volume. - - -Results -------- - -.. figure:: Input.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: Output-20Baseline.png - :scale: 200% - :alt: Output image, slice 20 - - Output image, slice 20 - -.. figure:: Output-30Baseline.png - :scale: 200% - :alt: Output image, slice 30 - - Output image, slice 30 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -.. literalinclude:: Code.py - :language: python - :lines: 1, 17- - -Classes demonstrated --------------------- - -.. breathelink:: itk::NumericSeriesFileNames - -.. breathelink:: itk::ImageSeriesWriter diff --git a/src/IO/ImageBase/ProcessImageChunks/Documentation.md b/src/IO/ImageBase/ProcessImageChunks/Documentation.md new file mode 100644 index 000000000..fb0bb9c2d --- /dev/null +++ b/src/IO/ImageBase/ProcessImageChunks/Documentation.md @@ -0,0 +1,49 @@ +--- +name: ProcessImageChunks +--- + +# Process Image Chunks + +```{index} single: ImageFileWriter +``` + +## Synopsis + +Process an image in small chunks. + +## Results + +:::{figure} Gourds.png +:alt: Input image + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MedianImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::ImageFileWriter +``` diff --git a/src/IO/ImageBase/ProcessImageChunks/Documentation.rst b/src/IO/ImageBase/ProcessImageChunks/Documentation.rst deleted file mode 100644 index eaf49d351..000000000 --- a/src/IO/ImageBase/ProcessImageChunks/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: ProcessImageChunks - -Process Image Chunks -==================== - -.. index:: - single: ImageFileWriter - -Synopsis --------- - -Process an image in small chunks. - - -Results -------- - -.. figure:: Gourds.png - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MedianImageFilter - -.. breathelink:: itk::ImageFileWriter diff --git a/src/IO/ImageBase/ReadAnImage/Documentation.md b/src/IO/ImageBase/ReadAnImage/Documentation.md new file mode 100644 index 000000000..d30e2b41a --- /dev/null +++ b/src/IO/ImageBase/ReadAnImage/Documentation.md @@ -0,0 +1,38 @@ +--- +name: ReadAnImage +--- + +# Read an Image + +```{index} single: ImageFileReader +``` + +## Synopsis + +This examples demonstrates how to read an image file into an itk::Image. +The file type is determined by the extension of the specified filename. + +## Results + +NA + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageFileReader +``` diff --git a/src/IO/ImageBase/ReadAnImage/Documentation.rst b/src/IO/ImageBase/ReadAnImage/Documentation.rst deleted file mode 100644 index a574ab741..000000000 --- a/src/IO/ImageBase/ReadAnImage/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: ReadAnImage - -Read an Image -============= - -.. index:: - single: ImageFileReader - -Synopsis --------- - -This examples demonstrates how to read an image file into an itk::Image. -The file type is determined by the extension of the specified filename. - - -Results -------- - -NA - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageFileReader diff --git a/src/IO/ImageBase/ReadUnknownImageType/Documentation.md b/src/IO/ImageBase/ReadUnknownImageType/Documentation.md new file mode 100644 index 000000000..0cd170189 --- /dev/null +++ b/src/IO/ImageBase/ReadUnknownImageType/Documentation.md @@ -0,0 +1,26 @@ +--- +name: ReadUnknownImageType +--- + +# Read Unknown Image Type + +```{index} single: ImageIOBase +``` + +## Synopsis + +Read one unknown image + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageIOBase +``` diff --git a/src/IO/ImageBase/ReadUnknownImageType/Documentation.rst b/src/IO/ImageBase/ReadUnknownImageType/Documentation.rst deleted file mode 100644 index 9220c34ef..000000000 --- a/src/IO/ImageBase/ReadUnknownImageType/Documentation.rst +++ /dev/null @@ -1,28 +0,0 @@ -:name: ReadUnknownImageType - -Read Unknown Image Type -======================= - -.. index:: - single: ImageIOBase - -Synopsis --------- - -Read one unknown image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageIOBase diff --git a/src/IO/ImageBase/RegisterIOFactories/Documentation.md b/src/IO/ImageBase/RegisterIOFactories/Documentation.md new file mode 100644 index 000000000..b5963ef9b --- /dev/null +++ b/src/IO/ImageBase/RegisterIOFactories/Documentation.md @@ -0,0 +1,61 @@ +--- +name: RegisterIOFactories +--- + +# Register IO Factories + +```{index} single: ImageFileReader single: ObjectFactoryBase single: MetaImageIOFactory single: PNGImageIOFactory +``` + +## Synopsis + +When CMake is not used to build an executable or library against ITK, the +Image and Transform IO format objects are not automatically registered to +ITK's object factory system, so they must be manually registered. There is not +a static list of IO classes because the classes available depend on which +modules are enabled when ITK is configured. This examples shows how to +register the ImageIOBase objects so the ImageFileReader can read the +formats corresponding to the registered objects. + +## Results + +``` +When CMake is not used to register the IO classes, there are +0 IO objects available to the ImageFileReader. + +When we try to read a MetaImage, we will fail. + +After registering the MetaImageIO object, there are +1 IO objects available to the ImageFileReader. + +Now, when we try to read a MetaImage, we will succeed. + +Every format desired to be supported by the reader +must be registered. +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageFileReader +``` + +```{eval-rst} +.. breathelink:: itk::ObjectFactoryBase +``` + +```{eval-rst} +.. breathelink:: itk::MetaImageIOFactory +``` + +```{eval-rst} +.. breathelink:: itk::PNGImageIOFactory +``` diff --git a/src/IO/ImageBase/RegisterIOFactories/Documentation.rst b/src/IO/ImageBase/RegisterIOFactories/Documentation.rst deleted file mode 100644 index 59ab29b3c..000000000 --- a/src/IO/ImageBase/RegisterIOFactories/Documentation.rst +++ /dev/null @@ -1,62 +0,0 @@ -:name: RegisterIOFactories - -Register IO Factories -===================== - -.. index:: - single: ImageFileReader - single: ObjectFactoryBase - single: MetaImageIOFactory - single: PNGImageIOFactory - -Synopsis --------- - -When CMake is not used to build an executable or library against ITK, the -Image and Transform IO format objects are not automatically registered to -ITK's object factory system, so they must be manually registered. There is not -a static list of IO classes because the classes available depend on which -modules are enabled when ITK is configured. This examples shows how to -register the ImageIOBase objects so the ImageFileReader can read the -formats corresponding to the registered objects. - - -Results -------- - -:: - - When CMake is not used to register the IO classes, there are - 0 IO objects available to the ImageFileReader. - - When we try to read a MetaImage, we will fail. - - After registering the MetaImageIO object, there are - 1 IO objects available to the ImageFileReader. - - Now, when we try to read a MetaImage, we will succeed. - - Every format desired to be supported by the reader - must be registered. - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageFileReader - -.. breathelink:: itk::ObjectFactoryBase - -.. breathelink:: itk::MetaImageIOFactory - -.. breathelink:: itk::PNGImageIOFactory diff --git a/src/IO/ImageBase/WriteAnImage/Documentation.md b/src/IO/ImageBase/WriteAnImage/Documentation.md new file mode 100644 index 000000000..aeb746e42 --- /dev/null +++ b/src/IO/ImageBase/WriteAnImage/Documentation.md @@ -0,0 +1,43 @@ +--- +name: WriteAnImage +--- + +# Write an Image + +```{index} single: ImageFileWriter +``` + +## Synopsis + +This example demonstrates how to write an itk::Image to a file. The file +type is determined by the extension of the specified filename. + +## Results + +:::{figure} WriteAnImage.png +:alt: test.png +:scale: 70% + +test.png +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageFileWriter +``` diff --git a/src/IO/ImageBase/WriteAnImage/Documentation.rst b/src/IO/ImageBase/WriteAnImage/Documentation.rst deleted file mode 100644 index 7f65beb8e..000000000 --- a/src/IO/ImageBase/WriteAnImage/Documentation.rst +++ /dev/null @@ -1,46 +0,0 @@ -:name: WriteAnImage - -Write an Image -============== - -.. index:: - single: ImageFileWriter - -Synopsis --------- - - -This example demonstrates how to write an itk::Image to a file. The file -type is determined by the extension of the specified filename. - - -Results -------- -.. figure:: WriteAnImage.png - :scale: 70% - :alt: test.png - - test.png - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageFileWriter diff --git a/src/IO/ImageBase/index.md b/src/IO/ImageBase/index.md new file mode 100644 index 000000000..36b1e416a --- /dev/null +++ b/src/IO/ImageBase/index.md @@ -0,0 +1,16 @@ +# ImageBase + +```{toctree} +:maxdepth: 1 + +ConvertFileFormats/Documentation.rst +ConvertImageToAnotherType/Documentation.rst +Create3DFromSeriesOf2D/Documentation.rst +CreateAListOfFileNames/Documentation.rst +GenerateSlicesFromVolume/Documentation.rst +ProcessImageChunks/Documentation.rst +ReadAnImage/Documentation.rst +ReadUnknownImageType/Documentation.rst +RegisterIOFactories/Documentation.rst +WriteAnImage/Documentation.rst +``` diff --git a/src/IO/ImageBase/index.rst b/src/IO/ImageBase/index.rst deleted file mode 100644 index 7c8077776..000000000 --- a/src/IO/ImageBase/index.rst +++ /dev/null @@ -1,16 +0,0 @@ -ImageBase -========= - -.. toctree:: - :maxdepth: 1 - - ConvertFileFormats/Documentation.rst - ConvertImageToAnotherType/Documentation.rst - Create3DFromSeriesOf2D/Documentation.rst - CreateAListOfFileNames/Documentation.rst - GenerateSlicesFromVolume/Documentation.rst - ProcessImageChunks/Documentation.rst - ReadAnImage/Documentation.rst - ReadUnknownImageType/Documentation.rst - RegisterIOFactories/Documentation.rst - WriteAnImage/Documentation.rst diff --git a/src/IO/Mesh/ReadMesh/Documentation.md b/src/IO/Mesh/ReadMesh/Documentation.md new file mode 100644 index 000000000..15665e9f0 --- /dev/null +++ b/src/IO/Mesh/ReadMesh/Documentation.md @@ -0,0 +1,48 @@ +--- +name: ReadMesh +--- + +# Read Mesh + +```{index} single: MeshFileReader single: Mesh pair: Mesh; GetPoint pair: Point; EuclideanDistanceTo +``` + +## Synopsis + +Read a mesh and display the Euclidean distance in between 2 given vertices + +## Results + +:::{figure} InputMesh.png +:alt: Input mesh +:scale: 50% + +Input mesh +::: + +```{raw} html +
+ +

Interactive input mesh

+
+``` + +Distance: + +``` +0.604093 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MeshFileReader +``` diff --git a/src/IO/Mesh/ReadMesh/Documentation.rst b/src/IO/Mesh/ReadMesh/Documentation.rst deleted file mode 100644 index 7993f83a1..000000000 --- a/src/IO/Mesh/ReadMesh/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: ReadMesh - -Read Mesh -========= - -.. index:: - single: MeshFileReader - single: Mesh - pair: Mesh; GetPoint - pair: Point; EuclideanDistanceTo - -Synopsis --------- - -Read a mesh and display the Euclidean distance in between 2 given vertices - - -Results -------- - -.. figure:: InputMesh.png - :scale: 50% - :alt: Input mesh - - Input mesh - -.. raw:: html - -
- -

Interactive input mesh

-
- -Distance:: - - 0.604093 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MeshFileReader diff --git a/src/IO/Mesh/index.md b/src/IO/Mesh/index.md new file mode 100644 index 000000000..f5e76100f --- /dev/null +++ b/src/IO/Mesh/index.md @@ -0,0 +1,7 @@ +# Mesh + +```{toctree} +:maxdepth: 1 + +ReadMesh/Documentation.rst +``` diff --git a/src/IO/Mesh/index.rst b/src/IO/Mesh/index.rst deleted file mode 100644 index e4f1da946..000000000 --- a/src/IO/Mesh/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -Mesh -==== - -.. toctree:: - :maxdepth: 1 - - ReadMesh/Documentation.rst diff --git a/src/IO/TIFF/WriteATIFFImage/Documentation.md b/src/IO/TIFF/WriteATIFFImage/Documentation.md new file mode 100644 index 000000000..4a79926fc --- /dev/null +++ b/src/IO/TIFF/WriteATIFFImage/Documentation.md @@ -0,0 +1,26 @@ +--- +name: WriteATIFFImage +--- + +# Write a TIFF Image + +```{index} single: TIFFImageIO +``` + +## Synopsis + +This example demonstrates how to explicitly specify the type of the image to write, regardless of the extension of the specified filename. + +## Results + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +. breathelink: itk::TIFFImageIO diff --git a/src/IO/TIFF/WriteATIFFImage/Documentation.rst b/src/IO/TIFF/WriteATIFFImage/Documentation.rst deleted file mode 100644 index adf1bf4e9..000000000 --- a/src/IO/TIFF/WriteATIFFImage/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: WriteATIFFImage - -Write a TIFF Image -================== - -.. index:: - single: TIFFImageIO - -Synopsis --------- - - -This example demonstrates how to explicitly specify the type of the image to write, regardless of the extension of the specified filename. - - -Results -------- - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -. breathelink: itk::TIFFImageIO diff --git a/src/IO/TIFF/index.md b/src/IO/TIFF/index.md new file mode 100644 index 000000000..42ee313fd --- /dev/null +++ b/src/IO/TIFF/index.md @@ -0,0 +1,7 @@ +# TIFF + +```{toctree} +:maxdepth: 1 + +WriteATIFFImage/Documentation.rst +``` diff --git a/src/IO/TIFF/index.rst b/src/IO/TIFF/index.rst deleted file mode 100644 index 01461ea27..000000000 --- a/src/IO/TIFF/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -TIFF -==== - -.. toctree:: - :maxdepth: 1 - - WriteATIFFImage/Documentation.rst diff --git a/src/IO/TransformBase/ReadTransformFromFile/Documentation.md b/src/IO/TransformBase/ReadTransformFromFile/Documentation.md new file mode 100644 index 000000000..d62baf052 --- /dev/null +++ b/src/IO/TransformBase/ReadTransformFromFile/Documentation.md @@ -0,0 +1,35 @@ +--- +name: ReadTransformFromFile +--- + +# Read Transform From File + +```{index} single: TransformFileReader pair: read; transform pair: file; transform +``` + +## Synopsis + +Read a transform from a file. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TransformFileReaderTemplate +``` diff --git a/src/IO/TransformBase/ReadTransformFromFile/Documentation.rst b/src/IO/TransformBase/ReadTransformFromFile/Documentation.rst deleted file mode 100644 index 50a160628..000000000 --- a/src/IO/TransformBase/ReadTransformFromFile/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ReadTransformFromFile - -Read Transform From File -======================== - -.. index:: - single: TransformFileReader - pair: read; transform - pair: file; transform - -Synopsis --------- - -Read a transform from a file. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::TransformFileReaderTemplate diff --git a/src/IO/TransformBase/WriteTransformToFile/Documentation.md b/src/IO/TransformBase/WriteTransformToFile/Documentation.md new file mode 100644 index 000000000..8eeb47806 --- /dev/null +++ b/src/IO/TransformBase/WriteTransformToFile/Documentation.md @@ -0,0 +1,35 @@ +--- +name: WriteTransformToFile +--- + +# Write Transform From File + +```{index} single: TransformFileReader +``` + +## Synopsis + +Write a transform from a file. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TransformFileReaderTemplate +``` diff --git a/src/IO/TransformBase/WriteTransformToFile/Documentation.rst b/src/IO/TransformBase/WriteTransformToFile/Documentation.rst deleted file mode 100644 index 0d27206e7..000000000 --- a/src/IO/TransformBase/WriteTransformToFile/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: WriteTransformToFile - -Write Transform From File -========================= - -.. index:: - single: TransformFileReader - -Synopsis --------- - -Write a transform from a file. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::TransformFileReaderTemplate diff --git a/src/IO/TransformBase/index.md b/src/IO/TransformBase/index.md new file mode 100644 index 000000000..f1f9048e5 --- /dev/null +++ b/src/IO/TransformBase/index.md @@ -0,0 +1,8 @@ +# TransformBase + +```{toctree} +:maxdepth: 1 + +ReadTransformFromFile/Documentation.rst +WriteTransformToFile/Documentation.rst +``` diff --git a/src/IO/TransformBase/index.rst b/src/IO/TransformBase/index.rst deleted file mode 100644 index 4c4d38d77..000000000 --- a/src/IO/TransformBase/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -TransformBase -============= - -.. toctree:: - :maxdepth: 1 - - ReadTransformFromFile/Documentation.rst - WriteTransformToFile/Documentation.rst diff --git a/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.md b/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.md new file mode 100644 index 000000000..7553dc7f6 --- /dev/null +++ b/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.md @@ -0,0 +1,33 @@ +--- +name: RegisterTransformWithTransformFactory +--- + +# Register Transform With Transform Factory + +```{index} single: TransformFactory pair: factory; transform pair: register; transform +``` + +## Synopsis + +Register a non-default transform with the transform factory. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::TransformFactory +``` diff --git a/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.rst b/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.rst deleted file mode 100644 index c6e11f798..000000000 --- a/src/IO/TransformFactory/RegisterTransformWithTransformFactory/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: RegisterTransformWithTransformFactory - -Register Transform With Transform Factory -========================================= - -.. index:: - single: TransformFactory - pair: factory; transform - pair: register; transform - -Synopsis --------- - -Register a non-default transform with the transform factory. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::TransformFactory diff --git a/src/IO/TransformFactory/index.md b/src/IO/TransformFactory/index.md new file mode 100644 index 000000000..79967c21a --- /dev/null +++ b/src/IO/TransformFactory/index.md @@ -0,0 +1,7 @@ +# TransformFactory + +```{toctree} +:maxdepth: 1 + +RegisterTransformWithTransformFactory/Documentation.rst +``` diff --git a/src/IO/TransformFactory/index.rst b/src/IO/TransformFactory/index.rst deleted file mode 100644 index 332fc45e6..000000000 --- a/src/IO/TransformFactory/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -TransformFactory -================ - -.. toctree:: - :maxdepth: 1 - - RegisterTransformWithTransformFactory/Documentation.rst diff --git a/src/IO/index.md b/src/IO/index.md new file mode 100644 index 000000000..f3dbda97f --- /dev/null +++ b/src/IO/index.md @@ -0,0 +1,12 @@ +# IO + +```{toctree} +:maxdepth: 2 + +GDCM/index.rst +ImageBase/index.rst +Mesh/index.rst +TIFF/index.rst +TransformBase/index.rst +TransformFactory/index.rst +``` diff --git a/src/IO/index.rst b/src/IO/index.rst deleted file mode 100644 index 2fe930eb7..000000000 --- a/src/IO/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -IO -== - -.. toctree:: - :maxdepth: 2 - - GDCM/index.rst - ImageBase/index.rst - Mesh/index.rst - TIFF/index.rst - TransformBase/index.rst - TransformFactory/index.rst diff --git a/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.md b/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.md new file mode 100644 index 000000000..84e689410 --- /dev/null +++ b/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.md @@ -0,0 +1,153 @@ +--- +name: GeometricPropertiesOfRegion +--- + +# Geometric Properties of Labeled Region + +```{index} single: LabelGeometryImageFilter pair: geometric; property pair: geometric; region +``` + +## Synopsis + +Get geometric properties of labeled regions in an image. + +## Results + +:::{figure} GeometricPropertiesOfRegionQuickview.png +:alt: QuickView output. +:scale: 50% + +Output In QuickView +::: + +Output: + +``` +Image (0x7fd274c5f3c0) +RTTI typeinfo: itk::Image +Reference Count: 1 +Modified Time: 46 +Debug: Off +Object Name: +Observers: + none +Source: (none) +Source output name: (none) +Release Data: Off +Data Released: False +Global Release Data: Off +PipelineMTime: 0 +UpdateMTime: 0 +RealTimeStamp: 0 seconds +LargestPossibleRegion: + Dimension: 2 + Index: [0, 0] + Size: [20, 20] +BufferedRegion: + Dimension: 2 + Index: [0, 0] + Size: [20, 20] +RequestedRegion: + Dimension: 2 + Index: [0, 0] + Size: [20, 20] +Spacing: [1, 1] +Origin: [0, 0] +Direction: +1 0 +0 1 + +IndexToPointMatrix: +1 0 +0 1 + +PointToIndexMatrix: +1 0 +0 1 + +Inverse Direction: +1 0 +0 1 + +PixelContainer: + ImportImageContainer (0x7fd274c5f5b0) + RTTI typeinfo: itk::ImportImageContainer + Reference Count: 1 + Modified Time: 47 + Debug: Off + Object Name: + Observers: + none + Pointer: 0x7fd27502d800 + Container manages memory: true + Size: 400 + Capacity: 400 +Number of labels: 4 + +Label: 0 +Volume: 344 +Integrated Intensity: 44128 +Centroid: [9.06977, 9.54942] +Weighted Centroid: [9.44273, 9.96021] +Axes Length: [23.6173, 23.9599] +MajorAxisLength: 23.9599 +MinorAxisLength: 23.6173 +Eccentricity: 0.168492 +Elongation: 1.0145 +Orientation: 2.74768 +Bounding box: [0, 19, 0, 19] + + +Label: 85 +Volume: 16 +Integrated Intensity: 2544 +Centroid: [7.5, 7.5] +Weighted Centroid: [7.44811, 7.47602] +Axes Length: [4.6188, 4.6188] +MajorAxisLength: 4.6188 +MinorAxisLength: 4.6188 +Eccentricity: 0 +Elongation: 1 +Orientation: 1.5708 +Bounding box: [6, 9, 6, 9] + +Label: 127 +Volume: 25 +Integrated Intensity: 3263 +Centroid: [14, 14] +Weighted Centroid: [13.6883, 14.1192] +Axes Length: [5.7735, 5.7735] +MajorAxisLength: 5.7735 +MinorAxisLength: 5.7735 +Eccentricity: 0 +Elongation: 1 +Orientation: 1.5708 +Bounding box: [12, 16, 12, 16] + +Label: 191 +Volume: 15 +Integrated Intensity: 1840 +Centroid: [14, 3] +Weighted Centroid: [13.8647, 3.10978] +Axes Length: [3.4641, 5.7735] +MajorAxisLength: 5.7735 +MinorAxisLength: 3.4641 +Eccentricity: 0.8 +Elongation: 1.66667 +Orientation: 0 +Bounding box: [12, 16, 2, 4] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LabelGeometryImageFilter +``` diff --git a/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.rst b/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.rst deleted file mode 100644 index a29ac360b..000000000 --- a/src/Nonunit/Review/GeometricPropertiesOfRegion/Documentation.rst +++ /dev/null @@ -1,153 +0,0 @@ -:name: GeometricPropertiesOfRegion - -Geometric Properties of Labeled Region -====================================== - -.. index:: - single: LabelGeometryImageFilter - pair: geometric; property - pair: geometric; region - -Synopsis --------- - -Get geometric properties of labeled regions in an image. - - -Results -------- -.. figure:: GeometricPropertiesOfRegionQuickview.png - :scale: 50% - :alt: QuickView output. - - Output In QuickView - -Output:: - - Image (0x7fd274c5f3c0) - RTTI typeinfo: itk::Image - Reference Count: 1 - Modified Time: 46 - Debug: Off - Object Name: - Observers: - none - Source: (none) - Source output name: (none) - Release Data: Off - Data Released: False - Global Release Data: Off - PipelineMTime: 0 - UpdateMTime: 0 - RealTimeStamp: 0 seconds - LargestPossibleRegion: - Dimension: 2 - Index: [0, 0] - Size: [20, 20] - BufferedRegion: - Dimension: 2 - Index: [0, 0] - Size: [20, 20] - RequestedRegion: - Dimension: 2 - Index: [0, 0] - Size: [20, 20] - Spacing: [1, 1] - Origin: [0, 0] - Direction: - 1 0 - 0 1 - - IndexToPointMatrix: - 1 0 - 0 1 - - PointToIndexMatrix: - 1 0 - 0 1 - - Inverse Direction: - 1 0 - 0 1 - - PixelContainer: - ImportImageContainer (0x7fd274c5f5b0) - RTTI typeinfo: itk::ImportImageContainer - Reference Count: 1 - Modified Time: 47 - Debug: Off - Object Name: - Observers: - none - Pointer: 0x7fd27502d800 - Container manages memory: true - Size: 400 - Capacity: 400 - Number of labels: 4 - - Label: 0 - Volume: 344 - Integrated Intensity: 44128 - Centroid: [9.06977, 9.54942] - Weighted Centroid: [9.44273, 9.96021] - Axes Length: [23.6173, 23.9599] - MajorAxisLength: 23.9599 - MinorAxisLength: 23.6173 - Eccentricity: 0.168492 - Elongation: 1.0145 - Orientation: 2.74768 - Bounding box: [0, 19, 0, 19] - - - Label: 85 - Volume: 16 - Integrated Intensity: 2544 - Centroid: [7.5, 7.5] - Weighted Centroid: [7.44811, 7.47602] - Axes Length: [4.6188, 4.6188] - MajorAxisLength: 4.6188 - MinorAxisLength: 4.6188 - Eccentricity: 0 - Elongation: 1 - Orientation: 1.5708 - Bounding box: [6, 9, 6, 9] - - Label: 127 - Volume: 25 - Integrated Intensity: 3263 - Centroid: [14, 14] - Weighted Centroid: [13.6883, 14.1192] - Axes Length: [5.7735, 5.7735] - MajorAxisLength: 5.7735 - MinorAxisLength: 5.7735 - Eccentricity: 0 - Elongation: 1 - Orientation: 1.5708 - Bounding box: [12, 16, 12, 16] - - Label: 191 - Volume: 15 - Integrated Intensity: 1840 - Centroid: [14, 3] - Weighted Centroid: [13.8647, 3.10978] - Axes Length: [3.4641, 5.7735] - MajorAxisLength: 5.7735 - MinorAxisLength: 3.4641 - Eccentricity: 0.8 - Elongation: 1.66667 - Orientation: 0 - Bounding box: [12, 16, 2, 4] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LabelGeometryImageFilter diff --git a/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md b/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md new file mode 100644 index 000000000..dd132769e --- /dev/null +++ b/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md @@ -0,0 +1,44 @@ +--- +name: MultiphaseChanAndVeseSparseFieldLevelSetSegmentation +--- + +# Multiphase Chan and Vese Sparse Field Level Set Segmentation + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ScalarChanAndVeseSparseLevelSetImageFilter single: ScalarChanAndVeseLevelSetFunction +``` + +## Synopsis + +Multiphase Chan And Vese Sparse Field Level Set Segmentation. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarChanAndVeseSparseLevelSetImageFilter +``` + +```{eval-rst} +.. breathelink:: itk::ScalarChanAndVeseLevelSetFunction +``` diff --git a/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst b/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst deleted file mode 100644 index 98301672f..000000000 --- a/src/Nonunit/Review/MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst +++ /dev/null @@ -1,39 +0,0 @@ -:name: MultiphaseChanAndVeseSparseFieldLevelSetSegmentation - -Multiphase Chan and Vese Sparse Field Level Set Segmentation -============================================================ -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ScalarChanAndVeseSparseLevelSetImageFilter - single: ScalarChanAndVeseLevelSetFunction - -Synopsis --------- - -Multiphase Chan And Vese Sparse Field Level Set Segmentation. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarChanAndVeseSparseLevelSetImageFilter -.. breathelink:: itk::ScalarChanAndVeseLevelSetFunction diff --git a/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.md b/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.md new file mode 100644 index 000000000..5e0cab7fe --- /dev/null +++ b/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.md @@ -0,0 +1,49 @@ +--- +name: SegmentBloodVesselsWithMultiScaleHessianBasedMeasure +--- + +# Segment Blood Vessels With Multi-Scale Hessian-Based Measure + +```{index} single: MultiScaleHessianBasedMeasureImageFilter pair: segment; vessel pair: segment; tube +``` + +## Synopsis + +Segment blood vessels with multi-scale Hessian-based measure. + +## Results + +:::{figure} Sidestream_dark_field_image.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MultiScaleHessianBasedMeasureImageFilter +``` diff --git a/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.rst b/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.rst deleted file mode 100644 index 24ca699ce..000000000 --- a/src/Nonunit/Review/SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.rst +++ /dev/null @@ -1,52 +0,0 @@ -:name: SegmentBloodVesselsWithMultiScaleHessianBasedMeasure - -Segment Blood Vessels With Multi-Scale Hessian-Based Measure -============================================================ - -.. index:: - single: MultiScaleHessianBasedMeasureImageFilter - pair: segment; vessel - pair: segment; tube - -Synopsis --------- - -Segment blood vessels with multi-scale Hessian-based measure. - - -Results -------- - -.. figure:: Sidestream_dark_field_image.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MultiScaleHessianBasedMeasureImageFilter diff --git a/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.md b/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.md new file mode 100644 index 000000000..050b8b013 --- /dev/null +++ b/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SinglephaseChanAndVeseDenseFieldLevelSetSegmentation +--- + +# Singlephase Chan and Vese Dense Field Level Set Segmentation + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ScalarChanAndVeseDenseLevelSetImageFilter single: ScalarChanAndVeseLevelSetFunction +``` + +## Synopsis + +Single-phase Chan And Vese Dense Field Level Set Segmentation + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarChanAndVeseDenseLevelSetImageFilter +``` diff --git a/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.rst b/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.rst deleted file mode 100644 index fe4d6749a..000000000 --- a/src/Nonunit/Review/SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: SinglephaseChanAndVeseDenseFieldLevelSetSegmentation - -Singlephase Chan and Vese Dense Field Level Set Segmentation -============================================================ -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ScalarChanAndVeseDenseLevelSetImageFilter - single: ScalarChanAndVeseLevelSetFunction - -Synopsis --------- - -Single-phase Chan And Vese Dense Field Level Set Segmentation - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarChanAndVeseDenseLevelSetImageFilter diff --git a/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md b/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md new file mode 100644 index 000000000..2ad2b5c10 --- /dev/null +++ b/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.md @@ -0,0 +1,40 @@ +--- +name: SinglephaseChanAndVeseSparseFieldLevelSetSegmentation +--- + +# Singlephase Chan and Vese Sparse Field Level Set Segmentation + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ScalarChanAndVeseSparseLevelSetImageFilter single: ScalarChanAndVeseLevelSetFunction +``` + +## Synopsis + +Single-phase Chan And Vese Sparse Field Level Set Segmentation. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarChanAndVeseSparseLevelSetImageFilter +``` diff --git a/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst b/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst deleted file mode 100644 index 7c6790ef7..000000000 --- a/src/Nonunit/Review/SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: SinglephaseChanAndVeseSparseFieldLevelSetSegmentation - -Singlephase Chan and Vese Sparse Field Level Set Segmentation -============================================================= -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ScalarChanAndVeseSparseLevelSetImageFilter - single: ScalarChanAndVeseLevelSetFunction - -Synopsis --------- - -Single-phase Chan And Vese Sparse Field Level Set Segmentation. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarChanAndVeseSparseLevelSetImageFilter diff --git a/src/Nonunit/Review/index.md b/src/Nonunit/Review/index.md new file mode 100644 index 000000000..d0d37f532 --- /dev/null +++ b/src/Nonunit/Review/index.md @@ -0,0 +1,11 @@ +# Review + +```{toctree} +:maxdepth: 1 + +GeometricPropertiesOfRegion/Documentation.rst +MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst +SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.rst +SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.rst +SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst +``` diff --git a/src/Nonunit/Review/index.rst b/src/Nonunit/Review/index.rst deleted file mode 100644 index e528479f4..000000000 --- a/src/Nonunit/Review/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -Review -====== - -.. toctree:: - :maxdepth: 1 - - GeometricPropertiesOfRegion/Documentation.rst - MultiphaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst - SegmentBloodVesselsWithMultiScaleHessianBasedMeasure/Documentation.rst - SinglephaseChanAndVeseDenseFieldLevelSetSegmentation/Documentation.rst - SinglephaseChanAndVeseSparseFieldLevelSetSegmentation/Documentation.rst diff --git a/src/Nonunit/index.md b/src/Nonunit/index.md new file mode 100644 index 000000000..7e684f620 --- /dev/null +++ b/src/Nonunit/index.md @@ -0,0 +1,7 @@ +# Nonunit + +```{toctree} +:maxdepth: 2 + +Review/index.rst +``` diff --git a/src/Nonunit/index.rst b/src/Nonunit/index.rst deleted file mode 100644 index e8027e26d..000000000 --- a/src/Nonunit/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -Nonunit -======= - -.. toctree:: - :maxdepth: 2 - - Review/index.rst diff --git a/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.md b/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.md new file mode 100644 index 000000000..6fb3d2b93 --- /dev/null +++ b/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.md @@ -0,0 +1,35 @@ +--- +name: AmoebaOptimizer +--- + +# Amoeba Optimizer + +```{index} single: AmoebaOptimizer +``` + +## Synopsis + +This will optimize a function using the AmoebaOptimizer class. This example demonstrates optimizing a simple paraboloid function. + +## Results + +Output: + +``` +Position: [-5.003825599641884, 6.998563761340231] +Value: 5.00002 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::AmoebaOptimizer +``` diff --git a/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.rst b/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.rst deleted file mode 100644 index 4bd1d6db8..000000000 --- a/src/Numerics/Optimizers/AmoebaOptimizer/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: AmoebaOptimizer - -Amoeba Optimizer -================ - -.. index:: - single: AmoebaOptimizer - -Synopsis --------- - -This will optimize a function using the AmoebaOptimizer class. This example demonstrates optimizing a simple paraboloid function. - - -Results -------- -Output:: - - Position: [-5.003825599641884, 6.998563761340231] - Value: 5.00002 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::AmoebaOptimizer diff --git a/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.md b/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.md new file mode 100644 index 000000000..438ec3baf --- /dev/null +++ b/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.md @@ -0,0 +1,54 @@ +--- +name: ExhaustiveOptimizer +--- + +# Exhaustive Optimizer + +```{index} single: ExhaustiveOptimizer +``` + +```{toctree} +:maxdepth: 1 + +PlotExhaustiveOptimizer.ipynb +``` + +## Synopsis + +An optimizer that fully samples a grid on the parametric space. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Jupyter Notebook + +```{image} https://mybinder.org/badge_logo.svg +:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FNumerics%2FOptimizers%2FExhaustiveOptimizer%2FPlotExhaustiveOptimizer.ipynb +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ExhaustiveOptimizer +``` diff --git a/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.rst b/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.rst deleted file mode 100644 index 403f6de2a..000000000 --- a/src/Numerics/Optimizers/ExhaustiveOptimizer/Documentation.rst +++ /dev/null @@ -1,54 +0,0 @@ -:name: ExhaustiveOptimizer - -Exhaustive Optimizer -==================== - -.. index:: - single: ExhaustiveOptimizer - -.. toctree:: - :maxdepth: 1 - - PlotExhaustiveOptimizer.ipynb - -Synopsis --------- - -An optimizer that fully samples a grid on the parametric space. - - -Results -------- - -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Jupyter Notebook ------------------ - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FNumerics%2FOptimizers%2FExhaustiveOptimizer%2FPlotExhaustiveOptimizer.ipynb - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 20- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ExhaustiveOptimizer diff --git a/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.md b/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.md new file mode 100644 index 000000000..6820bca93 --- /dev/null +++ b/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.md @@ -0,0 +1,35 @@ +--- +name: LevenbergMarquardtOptimization +--- + +# Levenberg-Marquardt Optimization + +```{index} single: LevenbergMarquardtOptimizer +``` + +## Synopsis + +Optimize a function using the LevenbergMarquardtOptimization class. + +## Results + +Output: + +``` +Position: [5.762595813691092, 0.4800781816497411] +Value: [0.18761225810035853, 0.22149805874930717, 0.19626506063745364, 0.008440292123000681, -0.2246669049722252, -0.06499867890559052, -0.03009462205999469, 0.037078071678616986, 0.1179535364891624, -0.20197691757229475, 0.23114283424137572, -0.09633797060122617, -0.1181447420933539, -0.016296554008191855, 0.15351231349591643, 0.04282427169413161, -0.011028322317460315, -0.014874778904555797, 0.026054762464067238, 0.08282156821610176, -0.18170363558960823, 0.014342598340990165, -0.05669067326929067, -0.19960985461710923, 0.07906076620078828, 0.053467861432614505, -0.04393281305375307, -0.21198352299156475, 0.13281781677553717, 0.19836431320892967, -0.05863022207617963, 0.04153068096802581, 0.027536776558543252, -0.2217222950679556, -0.052451620797857146, 0.0037302084610484343, 0.10780178216799818, 0.03909757445646189, -0.19500845421763202, 0.13552303389775222, 0.12067588331830059, -0.1646559748487526, -0.17905579039027675, -0.2047507980917569, 0.13126702388154232, 0.2038583258729716, 0.2315159987359916, 0.03741545669200619, 0.0640979627527889, -0.2180880841666788, 0.09985426440562328, 0.05599101173689913, 0.018079402649374465, -0.11392806561205493, 0.12335904899417738, -0.1946137987174792, -0.11640787926864604, 0.02577531924348353, -0.20075160702307215, -0.06148859349321256, 0.13543279691396393, -0.017197866393147798, -0.034013725658296856, -0.057410320040360396, 0.03428199478561922, 0.12079221893803638, -0.16693885394333918, 0.21030957837668662, -0.11858742760250163, -0.05222840443865451, -0.20187684802252903, 0.13116194362153877, -0.04916327491714512, 0.1116844217460855, -0.05268803531855326, 0.18635323207406884, -0.2359521189116638, -0.03685975982932632, -0.1408713799105108, 0.04996752375214619, -0.1635648070609097, 0.2208479366940992, 0.000060936209241191364, 0.12473423700590125, -0.061608327743822855, -0.20618061051637326, -0.012960406675505354, 0.1520753363006424, -0.006297055122873374, 0.1324731913025463, 0.2377413446210319, -0.13626735303743231, -0.005897280453501352, -0.09485834355640499, 0.19074286440427457, -0.19759247327942475, 0.159875584380206, 0.18354609840799085, 0.13071872295595632, -0.24643784133671076] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LevenbergMarquardtOptimizer +``` diff --git a/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.rst b/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.rst deleted file mode 100644 index 1e8428f35..000000000 --- a/src/Numerics/Optimizers/LevenbergMarquardtOptimization/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: LevenbergMarquardtOptimization - -Levenberg-Marquardt Optimization -================================ - -.. index:: - single: LevenbergMarquardtOptimizer - -Synopsis --------- - -Optimize a function using the LevenbergMarquardtOptimization class. - - -Results -------- -Output:: - - Position: [5.762595813691092, 0.4800781816497411] - Value: [0.18761225810035853, 0.22149805874930717, 0.19626506063745364, 0.008440292123000681, -0.2246669049722252, -0.06499867890559052, -0.03009462205999469, 0.037078071678616986, 0.1179535364891624, -0.20197691757229475, 0.23114283424137572, -0.09633797060122617, -0.1181447420933539, -0.016296554008191855, 0.15351231349591643, 0.04282427169413161, -0.011028322317460315, -0.014874778904555797, 0.026054762464067238, 0.08282156821610176, -0.18170363558960823, 0.014342598340990165, -0.05669067326929067, -0.19960985461710923, 0.07906076620078828, 0.053467861432614505, -0.04393281305375307, -0.21198352299156475, 0.13281781677553717, 0.19836431320892967, -0.05863022207617963, 0.04153068096802581, 0.027536776558543252, -0.2217222950679556, -0.052451620797857146, 0.0037302084610484343, 0.10780178216799818, 0.03909757445646189, -0.19500845421763202, 0.13552303389775222, 0.12067588331830059, -0.1646559748487526, -0.17905579039027675, -0.2047507980917569, 0.13126702388154232, 0.2038583258729716, 0.2315159987359916, 0.03741545669200619, 0.0640979627527889, -0.2180880841666788, 0.09985426440562328, 0.05599101173689913, 0.018079402649374465, -0.11392806561205493, 0.12335904899417738, -0.1946137987174792, -0.11640787926864604, 0.02577531924348353, -0.20075160702307215, -0.06148859349321256, 0.13543279691396393, -0.017197866393147798, -0.034013725658296856, -0.057410320040360396, 0.03428199478561922, 0.12079221893803638, -0.16693885394333918, 0.21030957837668662, -0.11858742760250163, -0.05222840443865451, -0.20187684802252903, 0.13116194362153877, -0.04916327491714512, 0.1116844217460855, -0.05268803531855326, 0.18635323207406884, -0.2359521189116638, -0.03685975982932632, -0.1408713799105108, 0.04996752375214619, -0.1635648070609097, 0.2208479366940992, 0.000060936209241191364, 0.12473423700590125, -0.061608327743822855, -0.20618061051637326, -0.012960406675505354, 0.1520753363006424, -0.006297055122873374, 0.1324731913025463, 0.2377413446210319, -0.13626735303743231, -0.005897280453501352, -0.09485834355640499, 0.19074286440427457, -0.19759247327942475, 0.159875584380206, 0.18354609840799085, 0.13071872295595632, -0.24643784133671076] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LevenbergMarquardtOptimizer diff --git a/src/Numerics/Optimizers/index.md b/src/Numerics/Optimizers/index.md new file mode 100644 index 000000000..edc832ea3 --- /dev/null +++ b/src/Numerics/Optimizers/index.md @@ -0,0 +1,9 @@ +# Optimizers + +```{toctree} +:maxdepth: 1 + +AmoebaOptimizer/Documentation.rst +ExhaustiveOptimizer/Documentation.rst +LevenbergMarquardtOptimization/Documentation.rst +``` diff --git a/src/Numerics/Optimizers/index.rst b/src/Numerics/Optimizers/index.rst deleted file mode 100644 index af6d375b7..000000000 --- a/src/Numerics/Optimizers/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -Optimizers -========== - -.. toctree:: - :maxdepth: 1 - - AmoebaOptimizer/Documentation.rst - ExhaustiveOptimizer/Documentation.rst - LevenbergMarquardtOptimization/Documentation.rst diff --git a/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.md b/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.md new file mode 100644 index 000000000..fd6fdcbc1 --- /dev/null +++ b/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.md @@ -0,0 +1,41 @@ +--- +name: 2DGaussianMixtureModelExpectMax +--- + +# 2D Gaussian Mixture Model Expectation Maximum + +```{index} single: ExpectationMaximizationMixtureModelEstimator single: max pair: 2D; gaussian +``` + +## Synopsis + +2D Gaussian Mixture Model Expectation Maximization. + +## Results + +Output: + +``` +Cluster[0] + Parameters: + [101.40933830302448, 99.43004497807948, 1098.5993639665169, -107.16526601343287, -107.16526601343287, 913.9641556669595] + Proportion: 0.495716 +Cluster[1] + Parameters: + [196.3354813961237, 195.29542020949035, 991.7367739288584, 84.51759523418217, 84.51759523418217, 845.9604643808337] + Proportion: 0.504284 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator +``` diff --git a/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.rst b/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.rst deleted file mode 100644 index d6bb0ec98..000000000 --- a/src/Numerics/Statistics/2DGaussianMixtureModelExpectMax/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: 2DGaussianMixtureModelExpectMax - -2D Gaussian Mixture Model Expectation Maximum -============================================= - -.. index:: - single: ExpectationMaximizationMixtureModelEstimator - single: max - pair: 2D; gaussian - -Synopsis --------- - -2D Gaussian Mixture Model Expectation Maximization. - - -Results -------- -Output:: - - Cluster[0] - Parameters: - [101.40933830302448, 99.43004497807948, 1098.5993639665169, -107.16526601343287, -107.16526601343287, 913.9641556669595] - Proportion: 0.495716 - Cluster[1] - Parameters: - [196.3354813961237, 195.29542020949035, 991.7367739288584, 84.51759523418217, 84.51759523418217, 845.9604643808337] - Proportion: 0.504284 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator diff --git a/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.md b/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.md new file mode 100644 index 000000000..e4ef9d982 --- /dev/null +++ b/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.md @@ -0,0 +1,56 @@ +--- +name: ComputeHistogramFromGrayscaleImage +--- + +# Compute Histogram From Grayscale Image + +```{index} single: ImageToHistogramFilter +``` + +## Synopsis + +Compute a histogram from a grayscale image + +## Results + +:::{figure} sf4.png +:alt: Input grayscale image. +:scale: 100% + +Input grayscale image. +::: + +Output: + +``` +Frequency = [ 0, +8593, +17734, +11515, +5974, +2225, +2400, +3422, +3531, +3283, +2125, +2628, +1954, +152, +0, +0 ] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ImageToHistogramFilter +``` diff --git a/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.rst b/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.rst deleted file mode 100644 index 7021f5b99..000000000 --- a/src/Numerics/Statistics/ComputeHistogramFromGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,58 +0,0 @@ -:name: ComputeHistogramFromGrayscaleImage - -Compute Histogram From Grayscale Image -====================================== - -.. index:: - single: ImageToHistogramFilter - - -Synopsis --------- - -Compute a histogram from a grayscale image - - -Results -------- - -.. figure:: sf4.png - :scale: 100% - :alt: Input grayscale image. - - Input grayscale image. - -Output:: - - Frequency = [ 0, - 8593, - 17734, - 11515, - 5974, - 2225, - 2400, - 3422, - 3531, - 3283, - 2125, - 2628, - 1954, - 152, - 0, - 0 ] - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ImageToHistogramFilter diff --git a/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.md b/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.md new file mode 100644 index 000000000..26677081c --- /dev/null +++ b/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ComputeHistogramOfMaskedRegion +--- + +# Compute Histogram of Masked Region in Image + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: MaskedImageToHistogramFilter pair: masked; region +``` + +## Synopsis + +Compute the histogram of a masked region of an image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::MaskedImageToHistogramFilter +``` diff --git a/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.rst b/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.rst deleted file mode 100644 index 1abf1c70f..000000000 --- a/src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: ComputeHistogramOfMaskedRegion - -Compute Histogram of Masked Region in Image -=========================================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: MaskedImageToHistogramFilter - pair: masked; region - -Synopsis --------- - -Compute the histogram of a masked region of an image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::MaskedImageToHistogramFilter diff --git a/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.md b/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.md new file mode 100644 index 000000000..58b119218 --- /dev/null +++ b/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ComputeTextureFeatures +--- + +# Compute Texture Features + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ScalarImageToTextureFeaturesFilter +``` + +## Synopsis + +Compute texture features. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ScalarImageToTextureFeaturesFilter +``` diff --git a/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.rst b/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.rst deleted file mode 100644 index 9a53a011d..000000000 --- a/src/Numerics/Statistics/ComputeTextureFeatures/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ComputeTextureFeatures - -Compute Texture Features -======================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ScalarImageToTextureFeaturesFilter - -Synopsis --------- - -Compute texture features. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ScalarImageToTextureFeaturesFilter diff --git a/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.md b/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.md new file mode 100644 index 000000000..33cee5e9c --- /dev/null +++ b/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.md @@ -0,0 +1,34 @@ +--- +name: CreateGaussianDistribution +--- + +# Create Gaussian Distribution + +```{index} single: GaussianDistribution +``` + +## Synopsis + +Create a Gaussian distribution. + +## Results + +Output: + +``` +0.396953 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::GaussianDistribution +``` diff --git a/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.rst b/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.rst deleted file mode 100644 index 3766e556e..000000000 --- a/src/Numerics/Statistics/CreateGaussianDistribution/Documentation.rst +++ /dev/null @@ -1,33 +0,0 @@ -:name: CreateGaussianDistribution - -Create Gaussian Distribution -============================ - -.. index:: - single: GaussianDistribution - -Synopsis --------- - -Create a Gaussian distribution. - - -Results -------- -Output:: - - 0.396953 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::GaussianDistribution diff --git a/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.md b/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.md new file mode 100644 index 000000000..7d189ba0b --- /dev/null +++ b/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.md @@ -0,0 +1,45 @@ +--- +name: CreateHistogramFromListOfMeasurements +--- + +# Create Histogram From List of Measurements + +```{index} single: SampleToHistogramFilter single: Histogram +``` + +## Synopsis + +Create a histogram from a list of sample measurements. + +## Results + +Output: + +``` +Histogram vector size: 1 +Frequency of 0 : (1 to 1.1001) = 2 +Frequency of 1 : (1.1001 to 1.2002) = 0 +Frequency of 2 : (1.2002 to 1.3003) = 0 +Frequency of 3 : (1.3003 to 1.4004) = 0 +Frequency of 4 : (1.4004 to 1.5005) = 0 +Frequency of 5 : (1.5005 to 1.6006) = 0 +Frequency of 6 : (1.6006 to 1.7007) = 0 +Frequency of 7 : (1.7007 to 1.8008) = 0 +Frequency of 8 : (1.8008 to 1.9009) = 0 +Frequency of 9 : (1.9009 to 2.001) = 1 +Total count 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::SampleToHistogramFilter +``` diff --git a/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.rst b/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.rst deleted file mode 100644 index a513d6bb2..000000000 --- a/src/Numerics/Statistics/CreateHistogramFromListOfMeasurements/Documentation.rst +++ /dev/null @@ -1,45 +0,0 @@ -:name: CreateHistogramFromListOfMeasurements - -Create Histogram From List of Measurements -========================================== - -.. index:: - single: SampleToHistogramFilter - single: Histogram - -Synopsis --------- - -Create a histogram from a list of sample measurements. - - -Results -------- -Output:: - - Histogram vector size: 1 - Frequency of 0 : (1 to 1.1001) = 2 - Frequency of 1 : (1.1001 to 1.2002) = 0 - Frequency of 2 : (1.2002 to 1.3003) = 0 - Frequency of 3 : (1.3003 to 1.4004) = 0 - Frequency of 4 : (1.4004 to 1.5005) = 0 - Frequency of 5 : (1.5005 to 1.6006) = 0 - Frequency of 6 : (1.6006 to 1.7007) = 0 - Frequency of 7 : (1.7007 to 1.8008) = 0 - Frequency of 8 : (1.8008 to 1.9009) = 0 - Frequency of 9 : (1.9009 to 2.001) = 1 - Total count 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::SampleToHistogramFilter diff --git a/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.md b/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.md new file mode 100644 index 000000000..5456b5623 --- /dev/null +++ b/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.md @@ -0,0 +1,41 @@ +--- +name: CreateListOfSampleMeasurements +--- + +# Create List of Sample Measurements + +```{index} single: ListSample +``` + +## Synopsis + +Create a lsit of sample measurements. + +## Results + +Output: + +``` +id = 0 measurement vector = [1, 2, 4] frequency = 1 +id = 1 measurement vector = [2, 4, 5] frequency = 1 +id = 2 measurement vector = [3, 8, 6] frequency = 1 +id = 0 measurement vector = [1, 2, 4] frequency = 1 +id = 1 measurement vector = [2, 4, 5] frequency = 1 +id = 2 measurement vector = [3, 8, 6] frequency = 1 +Size = 3 +Total frequency = 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ListSample +``` diff --git a/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.rst b/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.rst deleted file mode 100644 index b134e1000..000000000 --- a/src/Numerics/Statistics/CreateListOfSampleMeasurements/Documentation.rst +++ /dev/null @@ -1,40 +0,0 @@ -:name: CreateListOfSampleMeasurements - -Create List of Sample Measurements -================================== - -.. index:: - single: ListSample - -Synopsis --------- - -Create a lsit of sample measurements. - - -Results -------- -Output:: - - id = 0 measurement vector = [1, 2, 4] frequency = 1 - id = 1 measurement vector = [2, 4, 5] frequency = 1 - id = 2 measurement vector = [3, 8, 6] frequency = 1 - id = 0 measurement vector = [1, 2, 4] frequency = 1 - id = 1 measurement vector = [2, 4, 5] frequency = 1 - id = 2 measurement vector = [3, 8, 6] frequency = 1 - Size = 3 - Total frequency = 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ListSample diff --git a/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.md b/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.md new file mode 100644 index 000000000..e83647908 --- /dev/null +++ b/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.md @@ -0,0 +1,67 @@ +--- +name: CreateListOfSamplesFromImageWithoutDuplication +--- + +# Create List of Samples From Image Without Duplication + +```{index} single: ImageToListSampleAdaptor pair: without; duplication +``` + +## Synopsis + +Create a list of samples from an image without duplicating the data. + +## Results + +Output: + +``` +[96.6165] +[833.994] +[935.002] +[571.885] +[663.087] +[496.426] +[429.681] +[649.809] +[333.22] +[425.118] +[965.227] +[568.819] +[133.191] +[547.472] +[361.405] +[136.599] +[823.276] +[802.849] +[475.275] +[947.74] +[96.6244] +[965.532] +[690.606] +[13.2403] +[529.497] +[258.332] +[780.933] +[135.776] +[985.543] +[23.581] +[325.735] +[623.222] +[485.055] +... +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ImageToListSampleAdaptor +``` diff --git a/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.rst b/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.rst deleted file mode 100644 index d7f80e300..000000000 --- a/src/Numerics/Statistics/CreateListOfSamplesFromImageWithoutDuplication/Documentation.rst +++ /dev/null @@ -1,67 +0,0 @@ -:name: CreateListOfSamplesFromImageWithoutDuplication - -Create List of Samples From Image Without Duplication -===================================================== - -.. index:: - single: ImageToListSampleAdaptor - pair: without; duplication - -Synopsis --------- - -Create a list of samples from an image without duplicating the data. - - -Results -------- -Output:: - - [96.6165] - [833.994] - [935.002] - [571.885] - [663.087] - [496.426] - [429.681] - [649.809] - [333.22] - [425.118] - [965.227] - [568.819] - [133.191] - [547.472] - [361.405] - [136.599] - [823.276] - [802.849] - [475.275] - [947.74] - [96.6244] - [965.532] - [690.606] - [13.2403] - [529.497] - [258.332] - [780.933] - [135.776] - [985.543] - [23.581] - [325.735] - [623.222] - [485.055] - ... - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ImageToListSampleAdaptor diff --git a/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.md b/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.md new file mode 100644 index 000000000..74f0a0a6c --- /dev/null +++ b/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.md @@ -0,0 +1,38 @@ +--- +name: CreateListOfSamplesWithIDs +--- + +# Create List of Samples With Associated ID's + +```{index} single: MembershipSample +``` + +## Synopsis + +Create a list of samples with associated class IDs. + +## Results + +Output: + +``` +instance identifier = 0 measurement vector = [1, 2, 4] frequency = 1 class label = 0 +instance identifier = 1 measurement vector = [2, 4, 5] frequency = 1 class label = 0 +instance identifier = 2 measurement vector = [3, 8, 6] frequency = 1 class label = 1 +instance identifier = 0 measurement vector = [1, 2, 4] frequency = 1 +instance identifier = 1 measurement vector = [2, 4, 5] frequency = 1 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::MembershipSample +``` diff --git a/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.rst b/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.rst deleted file mode 100644 index 66854a8de..000000000 --- a/src/Numerics/Statistics/CreateListOfSamplesWithIDs/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: CreateListOfSamplesWithIDs - -Create List of Samples With Associated ID's -=========================================== - -.. index:: - single: MembershipSample - -Synopsis --------- - -Create a list of samples with associated class IDs. - - -Results -------- -Output:: - - instance identifier = 0 measurement vector = [1, 2, 4] frequency = 1 class label = 0 - instance identifier = 1 measurement vector = [2, 4, 5] frequency = 1 class label = 0 - instance identifier = 2 measurement vector = [3, 8, 6] frequency = 1 class label = 1 - instance identifier = 0 measurement vector = [1, 2, 4] frequency = 1 - instance identifier = 1 measurement vector = [2, 4, 5] frequency = 1 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::MembershipSample diff --git a/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.md b/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.md new file mode 100644 index 000000000..41b567829 --- /dev/null +++ b/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.md @@ -0,0 +1,40 @@ +--- +name: DistributeSamplingUsingGMM +--- + +# Distribute Sampling Using GMM EM + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ExpectationMaximizationMixtureModelEstimator +``` + +## Synopsis + +Compute distributions of samples using GMM EM. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator +``` diff --git a/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.rst b/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.rst deleted file mode 100644 index 2b6b52cdc..000000000 --- a/src/Numerics/Statistics/DistributeSamplingUsingGMM/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: DistributeSamplingUsingGMM - -Distribute Sampling Using GMM EM -================================ -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ExpectationMaximizationMixtureModelEstimator - -Synopsis --------- - -Compute distributions of samples using GMM EM. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator diff --git a/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.md b/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.md new file mode 100644 index 000000000..8da1cf44a --- /dev/null +++ b/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.md @@ -0,0 +1,40 @@ +--- +name: DistributionOfPixelsUsingGMM +--- + +# Distribution of Pixels Using GMM EM + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ExpectationMaximizationMixtureModelEstimator +``` + +## Synopsis + +Compute distributions of image pixels using GMM EM. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator +``` diff --git a/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.rst b/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.rst deleted file mode 100644 index c0bec881e..000000000 --- a/src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: DistributionOfPixelsUsingGMM - -Distribution of Pixels Using GMM EM -=================================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ExpectationMaximizationMixtureModelEstimator - -Synopsis --------- - -Compute distributions of image pixels using GMM EM. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::ExpectationMaximizationMixtureModelEstimator diff --git a/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.md b/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.md new file mode 100644 index 000000000..65c1e1289 --- /dev/null +++ b/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.md @@ -0,0 +1,59 @@ +--- +name: HistogramCreationAndBinAccess +--- + +# Histogram Creation and Bin Access + +```{index} single: Histogram +``` + +## Synopsis + +This example shows how to create a `Histogram` object and use it. + +We call an instance in a `Histogram` object a *bin*. +The Histogram differs from the {itkdox}`itk::Statistics::ListSample`, +{itkdox}`itk::Statistics::ImageToListSampleAdaptor`, or +{itkdox}`itk::Statistics::PointSetToListSampleAdaptor` in significant +ways. Histograms can have a variable number of values (`unsigned +long` type) for each measurement vector, while the three other +classes have a fixed value (one) for all measurement vectors. Also +those array-type containers can have multiple instances (data +elements) with identical measurement vector values. However, in a +Histogram object, there is one unique instance for any given +measurement vector. + +Here we create a histogram with dense frequency containers. In this +example we will not have any zero-frequency measurements, so the dense +frequency container is the appropriate choice. If the histogram is +expected to have many empty (zero) bins, a sparse frequency container +would be the better option. Note that this is not configurable in +Python. Here we also set the size of the measurement vectors to be 2 +components. + +Output from the code below: + +```none +Frequency of the bin at index [0, 2] is 5 and the bin's instance identifier is 6 +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::Histogram +``` diff --git a/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.rst b/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.rst deleted file mode 100644 index fabcee5cc..000000000 --- a/src/Numerics/Statistics/HistogramCreationAndBinAccess/Documentation.rst +++ /dev/null @@ -1,61 +0,0 @@ -:name: HistogramCreationAndBinAccess - -Histogram Creation and Bin Access -================================= - -.. index:: - single: Histogram - -Synopsis --------- - -This example shows how to create a ``Histogram`` object and use it. - -We call an instance in a ``Histogram`` object a *bin*. -The Histogram differs from the :itkdox:`itk::Statistics::ListSample`, -:itkdox:`itk::Statistics::ImageToListSampleAdaptor`, or -:itkdox:`itk::Statistics::PointSetToListSampleAdaptor` in significant -ways. Histograms can have a variable number of values (``unsigned -long`` type) for each measurement vector, while the three other -classes have a fixed value (one) for all measurement vectors. Also -those array-type containers can have multiple instances (data -elements) with identical measurement vector values. However, in a -Histogram object, there is one unique instance for any given -measurement vector. - -Here we create a histogram with dense frequency containers. In this -example we will not have any zero-frequency measurements, so the dense -frequency container is the appropriate choice. If the histogram is -expected to have many empty (zero) bins, a sparse frequency container -would be the better option. Note that this is not configurable in -Python. Here we also set the size of the measurement vectors to be 2 -components. - -Output from the code below: - -.. code-block:: none - - Frequency of the bin at index [0, 2] is 5 and the bin's instance identifier is 6 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::Histogram diff --git a/src/Numerics/Statistics/SpatialSearch/Documentation.md b/src/Numerics/Statistics/SpatialSearch/Documentation.md new file mode 100644 index 000000000..f8efe115d --- /dev/null +++ b/src/Numerics/Statistics/SpatialSearch/Documentation.md @@ -0,0 +1,43 @@ +--- +name: SpatialSearch +--- + +# Spatial Search + +```{index} single: KdTreeGenerator +``` + +## Synopsis + +Spatial search. + +## Results + +Output: + +``` +K-Neighbor search: +[9, 9] +[7, 7] +[8, 8] +Radius search: +There are 4 neighbors. +[7, 7] +[8, 8] +[9, 9] +[10, 10] +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::Statistics::KdTreeGenerator +``` diff --git a/src/Numerics/Statistics/SpatialSearch/Documentation.rst b/src/Numerics/Statistics/SpatialSearch/Documentation.rst deleted file mode 100644 index 2f7f19ba5..000000000 --- a/src/Numerics/Statistics/SpatialSearch/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -:name: SpatialSearch - -Spatial Search -============== - -.. index:: - single: KdTreeGenerator - -Synopsis --------- - -Spatial search. - - -Results -------- -Output:: - - K-Neighbor search: - [9, 9] - [7, 7] - [8, 8] - Radius search: - There are 4 neighbors. - [7, 7] - [8, 8] - [9, 9] - [10, 10] - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::Statistics::KdTreeGenerator diff --git a/src/Numerics/Statistics/index.md b/src/Numerics/Statistics/index.md new file mode 100644 index 000000000..9468056f9 --- /dev/null +++ b/src/Numerics/Statistics/index.md @@ -0,0 +1,19 @@ +# Statistics + +```{toctree} +:maxdepth: 1 + +2DGaussianMixtureModelExpectMax/Documentation.rst +ComputeHistogramFromGrayscaleImage/Documentation.rst +ComputeHistogramOfMaskedRegion/Documentation.rst +ComputeTextureFeatures/Documentation.rst +CreateGaussianDistribution/Documentation.rst +CreateHistogramFromListOfMeasurements/Documentation.rst +CreateListOfSampleMeasurements/Documentation.rst +CreateListOfSamplesFromImageWithoutDuplication/Documentation.rst +CreateListOfSamplesWithIDs/Documentation.rst +DistributeSamplingUsingGMM/Documentation.rst +DistributionOfPixelsUsingGMM/Documentation.rst +HistogramCreationAndBinAccess/Documentation.rst +SpatialSearch/Documentation.rst +``` diff --git a/src/Numerics/Statistics/index.rst b/src/Numerics/Statistics/index.rst deleted file mode 100644 index d09eedc8f..000000000 --- a/src/Numerics/Statistics/index.rst +++ /dev/null @@ -1,19 +0,0 @@ -Statistics -========== - -.. toctree:: - :maxdepth: 1 - - 2DGaussianMixtureModelExpectMax/Documentation.rst - ComputeHistogramFromGrayscaleImage/Documentation.rst - ComputeHistogramOfMaskedRegion/Documentation.rst - ComputeTextureFeatures/Documentation.rst - CreateGaussianDistribution/Documentation.rst - CreateHistogramFromListOfMeasurements/Documentation.rst - CreateListOfSampleMeasurements/Documentation.rst - CreateListOfSamplesFromImageWithoutDuplication/Documentation.rst - CreateListOfSamplesWithIDs/Documentation.rst - DistributeSamplingUsingGMM/Documentation.rst - DistributionOfPixelsUsingGMM/Documentation.rst - HistogramCreationAndBinAccess/Documentation.rst - SpatialSearch/Documentation.rst diff --git a/src/Numerics/index.md b/src/Numerics/index.md new file mode 100644 index 000000000..e85057c2b --- /dev/null +++ b/src/Numerics/index.md @@ -0,0 +1,8 @@ +# Numerics + +```{toctree} +:maxdepth: 2 + +Optimizers/index.rst +Statistics/index.rst +``` diff --git a/src/Numerics/index.rst b/src/Numerics/index.rst deleted file mode 100644 index 6736f173b..000000000 --- a/src/Numerics/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Numerics -======== - -.. toctree:: - :maxdepth: 2 - - Optimizers/index.rst - Statistics/index.rst diff --git a/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.md b/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.md new file mode 100644 index 000000000..bd87541f4 --- /dev/null +++ b/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.md @@ -0,0 +1,80 @@ +--- +name: ComputeMeanSquareBetweenTwoImages +--- + +# Compute Mean Squares Metric Between Two Images + +```{index} single: MeanSquaresImageToImageMetric single: mean +``` + +## Synopsis + +Compute the mean squares metric between two images. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image 1. +::: + +:::{figure} Gourds.png +:alt: input image +:scale: 70% + +Input image 2. +::: + +Data from 2 images passed through +Output: + +``` +[-10, -10]: 23101.7 +[-10, -5]: 23205.7 +[-10, 0]: 23260.4 +[-10, 5]: 23064.5 +[-10, 10]: 22914.5 +[-5, -10]: 23271.1 +[-5, -5]: 23351.3 +[-5, 0]: 23401 +[-5, 5]: 23185.1 +[-5, 10]: 23026.5 +[0, -10]: 23486.5 +[0, -5]: 23538.2 +[0, 0]: 23566.2 +[0, 5]: 23352.1 +[0, 10]: 23175.2 +[5, -10]: 23590.7 +[5, -5]: 23625.7 +[5, 0]: 23633.4 +[5, 5]: 23401.1 +[5, 10]: 23196.7 +[10, -10]: 23723.5 +[10, -5]: 23762.9 +[10, 0]: 23767.1 +[10, 5]: 23504.9 +[10, 10]: 23298.3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +Python +... + +```{literalinclude} Code.py +:lines: 21- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MeanSquaresImageToImageMetric +``` diff --git a/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.rst b/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.rst deleted file mode 100644 index d880a5e71..000000000 --- a/src/Registration/Common/ComputeMeanSquareBetweenTwoImages/Documentation.rst +++ /dev/null @@ -1,78 +0,0 @@ -:name: ComputeMeanSquareBetweenTwoImages - -Compute Mean Squares Metric Between Two Images -============================================== - -.. index:: - single: MeanSquaresImageToImageMetric - single: mean - -Synopsis --------- - -Compute the mean squares metric between two images. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image 1. - -.. figure:: Gourds.png - :scale: 70% - :alt: input image - - Input image 2. - -Data from 2 images passed through -Output:: - - [-10, -10]: 23101.7 - [-10, -5]: 23205.7 - [-10, 0]: 23260.4 - [-10, 5]: 23064.5 - [-10, 10]: 22914.5 - [-5, -10]: 23271.1 - [-5, -5]: 23351.3 - [-5, 0]: 23401 - [-5, 5]: 23185.1 - [-5, 10]: 23026.5 - [0, -10]: 23486.5 - [0, -5]: 23538.2 - [0, 0]: 23566.2 - [0, 5]: 23352.1 - [0, 10]: 23175.2 - [5, -10]: 23590.7 - [5, -5]: 23625.7 - [5, 0]: 23633.4 - [5, 5]: 23401.1 - [5, 10]: 23196.7 - [10, -10]: 23723.5 - [10, -5]: 23762.9 - [10, 0]: 23767.1 - [10, 5]: 23504.9 - [10, 10]: 23298.3 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Python -... - -.. literalinclude:: Code.py - :lines: 21- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MeanSquaresImageToImageMetric diff --git a/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.md b/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.md new file mode 100644 index 000000000..60f6af0e5 --- /dev/null +++ b/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.md @@ -0,0 +1,63 @@ +--- +name: GlobalRegistrationOfTwoImages +--- + +# Global Registration of Two Images + +```{index} single: ImageRegistrationMethod single: TranslationTransform +``` + +## Synopsis + +A basic global registration of two images. + +## Results + +:::{figure} fixed.png +:alt: fixing.png +:scale: 70% + +fixing.png +::: + +:::{figure} moving.png +:alt: moving.png +:scale: 70% + +moving.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +Output: + +``` +Result = +Translation X = 15.0103 +Translation Y = -1.12679 +Iterations = 15 +Metric value = 2374.3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegistrationMethod +``` + +```{eval-rst} +.. breathelink:: itk::TranslationTransform +``` diff --git a/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.rst b/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.rst deleted file mode 100644 index 10fc8764f..000000000 --- a/src/Registration/Common/GlobalRegistrationOfTwoImages/Documentation.rst +++ /dev/null @@ -1,58 +0,0 @@ -:name: GlobalRegistrationOfTwoImages - -Global Registration of Two Images -================================= - -.. index:: - single: ImageRegistrationMethod - single: TranslationTransform - -Synopsis --------- - -A basic global registration of two images. - - -Results -------- -.. figure:: fixed.png - :scale: 70% - :alt: fixing.png - - fixing.png - -.. figure:: moving.png - :scale: 70% - :alt: moving.png - - moving.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Output:: - - Result = - Translation X = 15.0103 - Translation Y = -1.12679 - Iterations = 15 - Metric value = 2374.3 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegistrationMethod -.. breathelink:: itk::TranslationTransform diff --git a/src/Registration/Common/MatchFeaturePoints/Documentation.md b/src/Registration/Common/MatchFeaturePoints/Documentation.md new file mode 100644 index 000000000..ab25278b6 --- /dev/null +++ b/src/Registration/Common/MatchFeaturePoints/Documentation.md @@ -0,0 +1,40 @@ +--- +name: MatchFeaturePoints +--- + +# Match Feature Points + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: BlockMatchingImageFilter +``` + +## Synopsis + +Match feature points. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::BlockMatchingImageFilter +``` diff --git a/src/Registration/Common/MatchFeaturePoints/Documentation.rst b/src/Registration/Common/MatchFeaturePoints/Documentation.rst deleted file mode 100644 index b8855c438..000000000 --- a/src/Registration/Common/MatchFeaturePoints/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: MatchFeaturePoints - -Match Feature Points -==================== -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. - -.. index:: - single: BlockMatchingImageFilter - -Synopsis --------- - -Match feature points. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::BlockMatchingImageFilter diff --git a/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.md b/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.md new file mode 100644 index 000000000..7f25f477e --- /dev/null +++ b/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.md @@ -0,0 +1,65 @@ +--- +name: MultiresolutionPyramidFromImage +--- + +# Multiresolution Pyramid From Image + +```{index} single: RecursiveMultiResolutionPyramidImageFilter +``` + +## Synopsis + +Construct a multiresolution pyramid from an image. + +## Results + +Output: + +``` +Writing output_0.png +Writing output_1.png +Writing output_2.png +Writing output_3.png +``` + +:::{figure} output_0.png +:alt: output_0.png +:scale: 70% + +output_0.png +::: + +:::{figure} output_1.png +:alt: output_1.png +:scale: 70% + +output_1.png +::: + +:::{figure} output_2.png +:alt: output_2.png +:scale: 70% + +output_2.png +::: + +:::{figure} output_3.png +:alt: output_3.png +:scale: 70% + +output_3.png +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RecursiveMultiResolutionPyramidImageFilter +``` diff --git a/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.rst b/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.rst deleted file mode 100644 index 97a07a58f..000000000 --- a/src/Registration/Common/MultiresolutionPyramidFromImage/Documentation.rst +++ /dev/null @@ -1,61 +0,0 @@ -:name: MultiresolutionPyramidFromImage - -Multiresolution Pyramid From Image -================================== - -.. index:: - single: RecursiveMultiResolutionPyramidImageFilter - -Synopsis --------- - -Construct a multiresolution pyramid from an image. - - -Results -------- -Output:: - - Writing output_0.png - Writing output_1.png - Writing output_2.png - Writing output_3.png - -.. figure:: output_0.png - :scale: 70% - :alt: output_0.png - - output_0.png - -.. figure:: output_1.png - :scale: 70% - :alt: output_1.png - - output_1.png - -.. figure:: output_2.png - :scale: 70% - :alt: output_2.png - - output_2.png - -.. figure:: output_3.png - :scale: 70% - :alt: output_3.png - - output_3.png - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RecursiveMultiResolutionPyramidImageFilter diff --git a/src/Registration/Common/MutualInformation/Documentation.md b/src/Registration/Common/MutualInformation/Documentation.md new file mode 100644 index 000000000..d2cf65118 --- /dev/null +++ b/src/Registration/Common/MutualInformation/Documentation.md @@ -0,0 +1,78 @@ +--- +name: MutualInformation +--- + +# Mutual Information + +```{index} single: MutualInformationImageToImageMetric single: TranslationTransform +``` + +```{toctree} +:maxdepth: 1 + +MutualInformation.ipynb +``` + +## Synopsis + +Global registration by maximizing the mutual information and using a translation only transform. + +## Results + +:::{figure} fixed.png +:alt: fixed.png +:scale: 70% + +fixed.png +::: + +:::{figure} moving.png +:alt: moving.png +:scale: 70% + +moving.png +::: + +:::{figure} OutputBaseline.png +:alt: OutputBaseline.png +:scale: 70% + +OutputBaseline.png +::: + +Output: + +``` +Optimizer stop condition: GradientDescentOptimizer: Maximum number of iterations (200) exceeded. + + Result = + Translation X = 12.9484 + Translation Y = 17.0856 + Iterations = 200 + Metric value = 0.594482 + Numb. Samples = 567 +``` + +## Jupyter Notebook + +```{image} https://mybinder.org/badge_logo.svg +:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FRegistration%2FCommon%2FMutualInformation%2FMutualInformation.ipynb +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MutualInformationImageToImageMetric +``` + +```{eval-rst} +.. breathelink:: itk::TranslationTransform +``` diff --git a/src/Registration/Common/MutualInformation/Documentation.rst b/src/Registration/Common/MutualInformation/Documentation.rst deleted file mode 100644 index e7cab01d4..000000000 --- a/src/Registration/Common/MutualInformation/Documentation.rst +++ /dev/null @@ -1,72 +0,0 @@ -:name: MutualInformation - -Mutual Information -================== - -.. index:: - single: MutualInformationImageToImageMetric - single: TranslationTransform - -.. toctree:: - :maxdepth: 1 - - MutualInformation.ipynb - -Synopsis --------- - -Global registration by maximizing the mutual information and using a translation only transform. - - -Results -------- -.. figure:: fixed.png - :scale: 70% - :alt: fixed.png - - fixed.png - -.. figure:: moving.png - :scale: 70% - :alt: moving.png - - moving.png - -.. figure:: OutputBaseline.png - :scale: 70% - :alt: OutputBaseline.png - - OutputBaseline.png - -Output:: - - Optimizer stop condition: GradientDescentOptimizer: Maximum number of iterations (200) exceeded. - - Result = - Translation X = 12.9484 - Translation Y = 17.0856 - Iterations = 200 - Metric value = 0.594482 - Numb. Samples = 567 - -Jupyter Notebook ----------------- - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FRegistration%2FCommon%2FMutualInformation%2FMutualInformation.ipynb - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MutualInformationImageToImageMetric -.. breathelink:: itk::TranslationTransform diff --git a/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.md b/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.md new file mode 100644 index 000000000..ed7de071d --- /dev/null +++ b/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.md @@ -0,0 +1,87 @@ +--- +name: Perform2DTranslationRegistrationWithMeanSquares +substitutions: + diff1: |- + ```{image} ImageRegistration1DifferenceBefore.png + :alt: Image difference before registration. + ``` + diff2: |- + ```{image} ImageRegistration1DifferenceAfter.png + :alt: Image difference after registration. + ``` + input1: |- + ```{image} BrainProtonDensitySliceBorder20.png + :alt: Input images + ``` + input2: |- + ```{image} BrainProtonDensitySliceShifted13x17y.png + :alt: Input images + ``` +--- + +# Perform 2D Translation Registration With Mean Squares + +```{index} single: ImageRegistrationMethodv4, TranslationTransform single: ImageRegistrationMethodv4, MeanSquaresImageToImageMetricv4 single: ImageRegistrationMethodv4, RegularStepGradientDescentOptimizerv4 +``` + +## Synopsis + +This example illustrates the use of the image registration framework in +Insight. It should be read as a `Hello World` for ITK registration. +Instead of means to an end, this example should be read as a basic +introduction to the elements typically involved when solving a problem +of image registration. + +A registration method requires the following set of components: two input +images, a transform, a metric and an optimizer. Some of these components +are parameterized by the image type for which the registration is intended. +The following header files provide declarations of common types used for +these components. + +This example corresponds to the ImageRegistration1.cxx example from +the ITK software guide. + +## Results + +```{eval-rst} ++----------+----------+ +| |input1| | |input2| | ++----------+----------+ +``` + +> Input images (fixed image left/ moving image right). + +:::{figure} OutputBaseline.png +:alt: Output image + +Output registered image. +::: + +```{eval-rst} ++---------+---------+ +| |diff1| | |diff2| | ++---------+---------+ +``` + +> Image difference between moving and fixed image (left before registration, right after registration). + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageRegistrationMethodv4 +``` diff --git a/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.rst b/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.rst deleted file mode 100644 index 60d110ab7..000000000 --- a/src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Documentation.rst +++ /dev/null @@ -1,81 +0,0 @@ -:name: Perform2DTranslationRegistrationWithMeanSquares - -Perform 2D Translation Registration With Mean Squares -===================================================== - -.. index:: - single: ImageRegistrationMethodv4, TranslationTransform - single: ImageRegistrationMethodv4, MeanSquaresImageToImageMetricv4 - single: ImageRegistrationMethodv4, RegularStepGradientDescentOptimizerv4 - -Synopsis --------- - -This example illustrates the use of the image registration framework in -Insight. It should be read as a ``Hello World`` for ITK registration. -Instead of means to an end, this example should be read as a basic -introduction to the elements typically involved when solving a problem -of image registration. - -A registration method requires the following set of components: two input -images, a transform, a metric and an optimizer. Some of these components -are parameterized by the image type for which the registration is intended. -The following header files provide declarations of common types used for -these components. - -This example corresponds to the ImageRegistration1.cxx example from -the ITK software guide. - -Results -------- - -.. |input1| image:: BrainProtonDensitySliceBorder20.png - :alt: Input images - -.. |input2| image:: BrainProtonDensitySliceShifted13x17y.png - :alt: Input images - -+----------+----------+ -| |input1| | |input2| | -+----------+----------+ - - Input images (fixed image left/ moving image right). - -.. figure:: OutputBaseline.png - :alt: Output image - - Output registered image. - -.. |diff1| image:: ImageRegistration1DifferenceBefore.png - :alt: Image difference before registration. - -.. |diff2| image:: ImageRegistration1DifferenceAfter.png - :alt: Image difference after registration. - -+---------+---------+ -| |diff1| | |diff2| | -+---------+---------+ - - Image difference between moving and fixed image (left before registration, right after registration). - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageRegistrationMethodv4 diff --git a/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.md b/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.md new file mode 100644 index 000000000..5c0265afb --- /dev/null +++ b/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.md @@ -0,0 +1,46 @@ +--- +name: PerformMultiModalityRegistrationWithMutualInformation +--- + +# Perform Multi Modality Registration With Viola Wells Mutual Information + +```{index} single: MutualInformationImageToImageMetric, GradientDescentOptimizer single: RegularStepGradientDescentOptimizer, NormalizeImageFilter single: DiscreteGaussianImageFilter, Command pair: registration; multi-modality pair: MutualInformationImageToImageMetric; SetNumberOfSpatialSamples +``` + +## Synopsis + +Rigid registration between two modalities with a Viola-Wells like mutual information metric. + +## Results + +:::{figure} PerformMultiModalityRegistrationWithMutualInformationInputImagesFigure.png +:alt: Input images + +Input fixed image (left) and moving image (right); +::: + +:::{figure} OutputBaseline.png +:alt: Output image + +Output registered image. +::: + +:::{figure} PerformMultiModalityRegistrationWithMutualInformationCheckerboardsFigure.png +:alt: Checkerboards before and after. + +Fixed/moving image checkerboard before (left) and after (right). +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MutualInformationImageToImageMetric +``` diff --git a/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.rst b/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.rst deleted file mode 100644 index 17d872fb4..000000000 --- a/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Documentation.rst +++ /dev/null @@ -1,50 +0,0 @@ -:name: PerformMultiModalityRegistrationWithMutualInformation - -Perform Multi Modality Registration With Viola Wells Mutual Information -======================================================================= - -.. index:: - single: MutualInformationImageToImageMetric, GradientDescentOptimizer - single: RegularStepGradientDescentOptimizer, NormalizeImageFilter - single: DiscreteGaussianImageFilter, Command - pair: registration; multi-modality - pair: MutualInformationImageToImageMetric; SetNumberOfSpatialSamples - -Synopsis --------- - -Rigid registration between two modalities with a Viola-Wells like mutual information metric. - - -Results -------- - -.. figure:: PerformMultiModalityRegistrationWithMutualInformationInputImagesFigure.png - :alt: Input images - - Input fixed image (left) and moving image (right); - -.. figure:: OutputBaseline.png - :alt: Output image - - Output registered image. - -.. figure:: PerformMultiModalityRegistrationWithMutualInformationCheckerboardsFigure.png - :alt: Checkerboards before and after. - - Fixed/moving image checkerboard before (left) and after (right). - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::MutualInformationImageToImageMetric diff --git a/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.md b/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.md new file mode 100644 index 000000000..54c31d8ad --- /dev/null +++ b/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.md @@ -0,0 +1,56 @@ +--- +name: RegisterImageToAnotherUsingLandmarks +--- + +# Register Image to Another Using Landmarks + +```{index} single: LandmarkBasedTransformInitializer single: landmark +``` + +## Synopsis + +Rigidly register one image to another using manually specified landmarks. + +## Results + +:::{figure} fixed.png +:alt: fixed.png +:scale: 70% + +fixed.png +::: + +:::{figure} moving.png +:alt: moving.png +:scale: 70% + +moving.png +::: + +:::{figure} output.png +:alt: output.png +:scale: 70% + +output.png +::: + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 20- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::LandmarkBasedTransformInitializer +``` diff --git a/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.rst b/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.rst deleted file mode 100644 index b6365d74c..000000000 --- a/src/Registration/Common/RegisterImageToAnotherUsingLandmarks/Documentation.rst +++ /dev/null @@ -1,55 +0,0 @@ -:name: RegisterImageToAnotherUsingLandmarks - -Register Image to Another Using Landmarks -========================================= - -.. index:: - single: LandmarkBasedTransformInitializer - single: landmark - -Synopsis --------- - -Rigidly register one image to another using manually specified landmarks. - - -Results -------- -.. figure:: fixed.png - :scale: 70% - :alt: fixed.png - - fixed.png - -.. figure:: moving.png - :scale: 70% - :alt: moving.png - - moving.png - -.. figure:: output.png - :scale: 70% - :alt: output.png - - output.png - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 20- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::LandmarkBasedTransformInitializer diff --git a/src/Registration/Common/WatchRegistration/Documentation.md b/src/Registration/Common/WatchRegistration/Documentation.md new file mode 100644 index 000000000..7a44391a5 --- /dev/null +++ b/src/Registration/Common/WatchRegistration/Documentation.md @@ -0,0 +1,80 @@ +--- +name: WatchRegistration +--- + +# Watch Registration + +```{index} single: MattesMutualInformationImageToImageMetric +``` + +## Synopsis + +Watch the iterations of a registration using VTK. + +## Results + +:::{figure} fixed.png +:alt: fixed.png +:scale: 70% + +fixed.png +::: + +:::{figure} moving.png +:alt: moving.png +:scale: 70% + +moving.png +::: + +:::{figure} WatchRegistration.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Optimizer stop condition: RegularStepGradientDescentOptimizer: Maximum number of iterations (1000) exceeded. +Final Transform: AffineTransform (0x7f9129d00120) +RTTI typeinfo: itk::AffineTransform +Reference Count: 4 +Modified Time: 215110 +Debug: Off +Object Name: +Observers: + none +Matrix: + 0.789218 0.062097 + 0.139299 0.37936 +Offset: [7.3411, 26.2747] +Center: [49.5, 49.5] +Translation: [-0.0188083, 2.44832] +Inverse: + 1.30477 -0.213577 + -0.479108 2.71444 +Singular: 0 + +Final Parameters: [0.7892180100803599, 0.06209699937125816, 0.13929938284463836, 0.37935986885403217, -0.018808339095318795, 2.448323274873905] + +Result = +Iterations = 1000 +Metric value = -0.00195192 +Numb. Samples = 500 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MattesMutualInformationImageToImageMetric +``` diff --git a/src/Registration/Common/WatchRegistration/Documentation.rst b/src/Registration/Common/WatchRegistration/Documentation.rst deleted file mode 100644 index dca85cc55..000000000 --- a/src/Registration/Common/WatchRegistration/Documentation.rst +++ /dev/null @@ -1,77 +0,0 @@ -:name: WatchRegistration - -Watch Registration -================== - -.. index:: - single: MattesMutualInformationImageToImageMetric - -Synopsis --------- - -Watch the iterations of a registration using VTK. - - -Results -------- -.. figure:: fixed.png - :scale: 70% - :alt: fixed.png - - fixed.png - -.. figure:: moving.png - :scale: 70% - :alt: moving.png - - moving.png - -.. figure:: WatchRegistration.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Output:: - - Optimizer stop condition: RegularStepGradientDescentOptimizer: Maximum number of iterations (1000) exceeded. - Final Transform: AffineTransform (0x7f9129d00120) - RTTI typeinfo: itk::AffineTransform - Reference Count: 4 - Modified Time: 215110 - Debug: Off - Object Name: - Observers: - none - Matrix: - 0.789218 0.062097 - 0.139299 0.37936 - Offset: [7.3411, 26.2747] - Center: [49.5, 49.5] - Translation: [-0.0188083, 2.44832] - Inverse: - 1.30477 -0.213577 - -0.479108 2.71444 - Singular: 0 - - Final Parameters: [0.7892180100803599, 0.06209699937125816, 0.13929938284463836, 0.37935986885403217, -0.018808339095318795, 2.448323274873905] - - Result = - Iterations = 1000 - Metric value = -0.00195192 - Numb. Samples = 500 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MattesMutualInformationImageToImageMetric diff --git a/src/Registration/Common/index.md b/src/Registration/Common/index.md new file mode 100644 index 000000000..473465d20 --- /dev/null +++ b/src/Registration/Common/index.md @@ -0,0 +1,15 @@ +# Common + +```{toctree} +:maxdepth: 1 + +ComputeMeanSquareBetweenTwoImages/Documentation.rst +GlobalRegistrationOfTwoImages/Documentation.rst +MatchFeaturePoints/Documentation.rst +MultiresolutionPyramidFromImage/Documentation.rst +MutualInformation/Documentation.rst +Perform2DTranslationRegistrationWithMeanSquares/Documentation.rst +PerformMultiModalityRegistrationWithMutualInformation/Documentation.rst +RegisterImageToAnotherUsingLandmarks/Documentation.rst +WatchRegistration/Documentation.rst +``` diff --git a/src/Registration/Common/index.rst b/src/Registration/Common/index.rst deleted file mode 100644 index 5754489d7..000000000 --- a/src/Registration/Common/index.rst +++ /dev/null @@ -1,15 +0,0 @@ -Common -====== - -.. toctree:: - :maxdepth: 1 - - ComputeMeanSquareBetweenTwoImages/Documentation.rst - GlobalRegistrationOfTwoImages/Documentation.rst - MatchFeaturePoints/Documentation.rst - MultiresolutionPyramidFromImage/Documentation.rst - MutualInformation/Documentation.rst - Perform2DTranslationRegistrationWithMeanSquares/Documentation.rst - PerformMultiModalityRegistrationWithMutualInformation/Documentation.rst - RegisterImageToAnotherUsingLandmarks/Documentation.rst - WatchRegistration/Documentation.rst diff --git a/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.md b/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.md new file mode 100644 index 000000000..36c001198 --- /dev/null +++ b/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.md @@ -0,0 +1,56 @@ +--- +name: PerformRegistrationOnVectorImages +substitutions: + fixedImage: |- + ```{image} orange.jpg + :alt: Fixed image. + :scale: 50% + ``` + fixedImageCaption: Fixed image. + movingImage: |- + ```{image} apple.jpg + :alt: Moving image. + :scale: 50% + ``` + movingImageCaption: Moving image. + resampledMovingImage: |- + ```{image} OutputBaseline.jpg + :alt: Resampled moving image. + :scale: 50% + ``` + resampledMovingImageCaption: Resampled, registered moving image. +--- + +# Perform Registration on Vector Images + +```{index} single: VectorImageToImageMetricTraitsv4 +``` + +## Synopsis + +Register images that have multi-component pixels like an itk::VectorImage or +an itk::Image\< itk::Vector, Dimension >. + +## Results + +```{eval-rst} ++---------------------+----------------------+-------------------------------+ +| |fixedImage| | |movingImage| | |resampledMovingImage| | ++ + + + +| |fixedImageCaption| | |movingImageCaption| | |resampledMovingImageCaption| | ++---------------------+----------------------+-------------------------------+ +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VectorImageToImageMetricTraitsv4 +``` diff --git a/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.rst b/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.rst deleted file mode 100644 index 14e10005d..000000000 --- a/src/Registration/Metricsv4/PerformRegistrationOnVectorImages/Documentation.rst +++ /dev/null @@ -1,57 +0,0 @@ -:name: PerformRegistrationOnVectorImages - -Perform Registration on Vector Images -===================================== - -.. index:: - single: VectorImageToImageMetricTraitsv4 - -Synopsis --------- - -Register images that have multi-component pixels like an itk::VectorImage or -an itk::Image< itk::Vector, Dimension >. - - -Results -------- - -.. |fixedImage| image:: orange.jpg - :scale: 50% - :alt: Fixed image. - -.. |movingImage| image:: apple.jpg - :scale: 50% - :alt: Moving image. - -.. |resampledMovingImage| image:: OutputBaseline.jpg - :scale: 50% - :alt: Resampled moving image. - -.. |fixedImageCaption| replace:: Fixed image. - -.. |movingImageCaption| replace:: Moving image. - -.. |resampledMovingImageCaption| replace:: Resampled, registered moving image. - -+---------------------+----------------------+-------------------------------+ -| |fixedImage| | |movingImage| | |resampledMovingImage| | -+ + + + -| |fixedImageCaption| | |movingImageCaption| | |resampledMovingImageCaption| | -+---------------------+----------------------+-------------------------------+ - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - - -Classes demonstrated --------------------- - -.. breathelink:: itk::VectorImageToImageMetricTraitsv4 diff --git a/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.md b/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.md new file mode 100644 index 000000000..0e103ff26 --- /dev/null +++ b/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.md @@ -0,0 +1,80 @@ +--- +name: RegisterTwoPointSets +--- + +# Register Two Point Sets + +## Index + +```{index} single: JensenHavrdaCharvatTsallisPointSetToPointSetMetricv4 single: GradientDescentOptimizerv4 single: RegistrationParameterScalesFromPhysicalShift single: AffineTransform single: PointSet +``` + +:::{seealso} +registration; transformation; pointset +::: + +```{toctree} +:maxdepth: 1 + +RegisterTwoPointSets.ipynb +``` + +## Synopsis + +Register two point sets with the Jensen-Havrda-Charvat-Tsallis point set +metric. + +## Results + +``` +It: 0 metric value: -0.0641355 +It: 1 metric value: -0.0955508 +It: 2 metric value: -0.0956365 +It: 3 metric value: -0.0956648 +It: 4 metric value: -0.0956742 +It: 5 metric value: -0.0956774 +It: 6 metric value: -0.0956784 +It: 7 metric value: -0.0956788 +It: 8 metric value: -0.0956789 +It: 9 metric value: -0.0956789 +numberOfIterations: 10 +Moving-source final value: -0.0956789 +Moving-source final position: [0.9999999481711049, 3.6956646020565954e-9, + -3.9958144654776e-8, 1.0000000021678688, + 1.9991709056354183, 1.999169080146488] +Optimizer scales: [10000, 9998.46502472856, + 10000, 9998.46502472848, + 1.0000000000010232, 1.0000000000010232] +Optimizer learning rate: 164.938 +``` + +## Jupyter Notebook + +```{image} https://mybinder.org/badge_logo.svg +:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FRegistration%2FMetricsv4%2FRegisterTwoPointSets%2FRegisterTwoPointSets.ipynb +``` + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 23- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 20- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::JensenHavrdaCharvatTsallisPointSetToPointSetMetricv4 +``` + +```{eval-rst} +.. breathelink:: itk::GradientDescentOptimizerv4Template +``` diff --git a/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.rst b/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.rst deleted file mode 100644 index 6205f0c83..000000000 --- a/src/Registration/Metricsv4/RegisterTwoPointSets/Documentation.rst +++ /dev/null @@ -1,79 +0,0 @@ -:name: RegisterTwoPointSets - -Register Two Point Sets -======================= - -Index --------- -.. index:: - single: JensenHavrdaCharvatTsallisPointSetToPointSetMetricv4 - single: GradientDescentOptimizerv4 - single: RegistrationParameterScalesFromPhysicalShift - single: AffineTransform - single: PointSet - -.. seealso:: registration; transformation; pointset - -.. toctree:: - :maxdepth: 1 - - RegisterTwoPointSets.ipynb - -Synopsis --------- - -Register two point sets with the Jensen-Havrda-Charvat-Tsallis point set -metric. - -Results --------- - -:: - - It: 0 metric value: -0.0641355 - It: 1 metric value: -0.0955508 - It: 2 metric value: -0.0956365 - It: 3 metric value: -0.0956648 - It: 4 metric value: -0.0956742 - It: 5 metric value: -0.0956774 - It: 6 metric value: -0.0956784 - It: 7 metric value: -0.0956788 - It: 8 metric value: -0.0956789 - It: 9 metric value: -0.0956789 - numberOfIterations: 10 - Moving-source final value: -0.0956789 - Moving-source final position: [0.9999999481711049, 3.6956646020565954e-9, - -3.9958144654776e-8, 1.0000000021678688, - 1.9991709056354183, 1.999169080146488] - Optimizer scales: [10000, 9998.46502472856, - 10000, 9998.46502472848, - 1.0000000000010232, 1.0000000000010232] - Optimizer learning rate: 164.938 - -Jupyter Notebook ----------------- - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKSphinxExamples/master?filepath=src%2FRegistration%2FMetricsv4%2FRegisterTwoPointSets%2FRegisterTwoPointSets.ipynb - -Code --------- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 23- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 20- - -Classes demonstrated --------------------- - -.. breathelink:: itk::JensenHavrdaCharvatTsallisPointSetToPointSetMetricv4 -.. breathelink:: itk::GradientDescentOptimizerv4Template diff --git a/src/Registration/Metricsv4/index.md b/src/Registration/Metricsv4/index.md new file mode 100644 index 000000000..9f2d27a3d --- /dev/null +++ b/src/Registration/Metricsv4/index.md @@ -0,0 +1,8 @@ +# Metricsv4 + +```{toctree} +:maxdepth: 1 + +PerformRegistrationOnVectorImages/Documentation.rst +RegisterTwoPointSets/Documentation.rst +``` diff --git a/src/Registration/Metricsv4/index.rst b/src/Registration/Metricsv4/index.rst deleted file mode 100644 index 344538dc4..000000000 --- a/src/Registration/Metricsv4/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Metricsv4 -========= - -.. toctree:: - :maxdepth: 1 - - PerformRegistrationOnVectorImages/Documentation.rst - RegisterTwoPointSets/Documentation.rst diff --git a/src/Registration/index.md b/src/Registration/index.md new file mode 100644 index 000000000..915cb89d7 --- /dev/null +++ b/src/Registration/index.md @@ -0,0 +1,8 @@ +# Registration + +```{toctree} +:maxdepth: 2 + +Common/index.rst +Metricsv4/index.rst +``` diff --git a/src/Registration/index.rst b/src/Registration/index.rst deleted file mode 100644 index de421e326..000000000 --- a/src/Registration/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Registration -============ - -.. toctree:: - :maxdepth: 2 - - Common/index.rst - Metricsv4/index.rst diff --git a/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.md b/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.md new file mode 100644 index 000000000..8297803b7 --- /dev/null +++ b/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.md @@ -0,0 +1,40 @@ +--- +name: CustomUserMatrixToAlignImageWithDICOM +--- + +# Custom User Matrix to Align Image With DICOM + +:::{note} +**Wish List** +Still needs additional work to finish proper creation of example. +::: + +```{index} single: ImageToVTKImageFilter +``` + +## Synopsis + +Uses a custom user matrix to align the image with DICOM physical space. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToVTKImageFilter +``` diff --git a/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.rst b/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.rst deleted file mode 100644 index f5537eed5..000000000 --- a/src/Remote/WikiExamples/CustomUserMatrixToAlignImageWithDICOM/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: CustomUserMatrixToAlignImageWithDICOM - -Custom User Matrix to Align Image With DICOM -============================================ -.. note:: - **Wish List** - Still needs additional work to finish proper creation of example. -.. index:: - single: ImageToVTKImageFilter - -Synopsis --------- - -Uses a custom user matrix to align the image with DICOM physical space. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToVTKImageFilter diff --git a/src/Remote/WikiExamples/DisplayITKImage/Documentation.md b/src/Remote/WikiExamples/DisplayITKImage/Documentation.md new file mode 100644 index 000000000..e90aa7eab --- /dev/null +++ b/src/Remote/WikiExamples/DisplayITKImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: DisplayITKImage +--- + +# Display ITK Image + +```{index} single: ImageToVTKImageFilter +``` + +## Synopsis + +Display an ITK iamge. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageToVTKImageFilter +``` diff --git a/src/Remote/WikiExamples/DisplayITKImage/Documentation.rst b/src/Remote/WikiExamples/DisplayITKImage/Documentation.rst deleted file mode 100644 index 0665a3fd7..000000000 --- a/src/Remote/WikiExamples/DisplayITKImage/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: DisplayITKImage - -Display ITK Image -================= - -.. index:: - single: ImageToVTKImageFilter - -Synopsis --------- - -Display an ITK iamge. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageToVTKImageFilter diff --git a/src/Remote/WikiExamples/index.md b/src/Remote/WikiExamples/index.md new file mode 100644 index 000000000..e4fc635e4 --- /dev/null +++ b/src/Remote/WikiExamples/index.md @@ -0,0 +1,8 @@ +# WikiExamples + +```{toctree} +:maxdepth: 1 + +CustomUserMatrixToAlignImageWithDICOM/Documentation.rst +DisplayITKImage/Documentation.rst +``` diff --git a/src/Remote/WikiExamples/index.rst b/src/Remote/WikiExamples/index.rst deleted file mode 100644 index b326a638a..000000000 --- a/src/Remote/WikiExamples/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -WikiExamples -============ - -.. toctree:: - :maxdepth: 1 - - CustomUserMatrixToAlignImageWithDICOM/Documentation.rst - DisplayITKImage/Documentation.rst diff --git a/src/Remote/index.md b/src/Remote/index.md new file mode 100644 index 000000000..51cd4ed72 --- /dev/null +++ b/src/Remote/index.md @@ -0,0 +1,11 @@ +--- +orphan: true +--- + +# Remote + +```{toctree} +:maxdepth: 2 + +WikiExamples/index.rst +``` diff --git a/src/Remote/index.rst b/src/Remote/index.rst deleted file mode 100644 index f5c41744c..000000000 --- a/src/Remote/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -:orphan: - -Remote -====== - -.. toctree:: - :maxdepth: 2 - - WikiExamples/index.rst \ No newline at end of file diff --git a/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.md b/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.md new file mode 100644 index 000000000..6eada4428 --- /dev/null +++ b/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.md @@ -0,0 +1,44 @@ +--- +name: ClusterPixelsInGrayscaleImage +--- + +# Cluster Pixels in Grayscale Image + +```{index} single: ScalarImageKmeansImageFilter pair: grayscale; image +``` + +## Synopsis + +Cluster the pixels in a greyscale image. + +## Results + +:::{figure} ClusterPixelsInGrayscaleImage.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +cluster[0] estimated mean : 10 +cluster[1] estimated mean : 100 +cluster[2] estimated mean : 200 +Number of pixels per class +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarImageKmeansImageFilter +``` diff --git a/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.rst b/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.rst deleted file mode 100644 index 73c45f387..000000000 --- a/src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: ClusterPixelsInGrayscaleImage - -Cluster Pixels in Grayscale Image -================================= - -.. index:: - single: ScalarImageKmeansImageFilter - pair: grayscale; image - -Synopsis --------- - -Cluster the pixels in a greyscale image. - - -Results -------- -.. figure:: ClusterPixelsInGrayscaleImage.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Output:: - - cluster[0] estimated mean : 10 - cluster[1] estimated mean : 100 - cluster[2] estimated mean : 200 - Number of pixels per class - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarImageKmeansImageFilter diff --git a/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.md b/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.md new file mode 100644 index 000000000..df1703420 --- /dev/null +++ b/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: KMeansClusterOfPixelsInImage +--- + +# K Means Cluster of Pixels in Image + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ImageKmeansModelEstimator +``` + +## Synopsis + +Compute kmeans clusters of pixels in an image + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ImageKmeansModelEstimator +``` diff --git a/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.rst b/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.rst deleted file mode 100644 index 5960accd4..000000000 --- a/src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Documentation.rst +++ /dev/null @@ -1,38 +0,0 @@ -:name: KMeansClusterOfPixelsInImage - -K Means Cluster of Pixels in Image -================================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ImageKmeansModelEstimator - -Synopsis --------- - -Compute kmeans clusters of pixels in an image - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ImageKmeansModelEstimator diff --git a/src/Segmentation/Classifiers/KMeansClustering/Documentation.md b/src/Segmentation/Classifiers/KMeansClustering/Documentation.md new file mode 100644 index 000000000..b8f48ad12 --- /dev/null +++ b/src/Segmentation/Classifiers/KMeansClustering/Documentation.md @@ -0,0 +1,40 @@ +--- +name: KMeansClustering +--- + +# K-Means Clustering + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ScalarImageKmeansImageFilter +``` + +## Synopsis + +KMeans clustering. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarImageKmeansImageFilter +``` diff --git a/src/Segmentation/Classifiers/KMeansClustering/Documentation.rst b/src/Segmentation/Classifiers/KMeansClustering/Documentation.rst deleted file mode 100644 index 66e1118b6..000000000 --- a/src/Segmentation/Classifiers/KMeansClustering/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: KMeansClustering - -K-Means Clustering -================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ScalarImageKmeansImageFilter - -Synopsis --------- - -KMeans clustering. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarImageKmeansImageFilter diff --git a/src/Segmentation/Classifiers/index.md b/src/Segmentation/Classifiers/index.md new file mode 100644 index 000000000..96a415a16 --- /dev/null +++ b/src/Segmentation/Classifiers/index.md @@ -0,0 +1,9 @@ +# Classifiers + +```{toctree} +:maxdepth: 1 + +ClusterPixelsInGrayscaleImage/Documentation.rst +KMeansClustering/Documentation.rst +KMeansClusterOfPixelsInImage/Documentation.rst +``` diff --git a/src/Segmentation/Classifiers/index.rst b/src/Segmentation/Classifiers/index.rst deleted file mode 100644 index 9a2da266e..000000000 --- a/src/Segmentation/Classifiers/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -Classifiers -=========== - -.. toctree:: - :maxdepth: 1 - - ClusterPixelsInGrayscaleImage/Documentation.rst - KMeansClustering/Documentation.rst - KMeansClusterOfPixelsInImage/Documentation.rst diff --git a/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.md b/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.md new file mode 100644 index 000000000..004485fbb --- /dev/null +++ b/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.md @@ -0,0 +1,35 @@ +--- +name: AssignContiguousLabelsToConnectedRegions +--- + +# Assign Contiguous Labels to Connected Regions in an Image + +```{index} single: RelabelComponentImageFilter pair: connect; regions +``` + +## Synopsis + +Assign contiguous labels to connected regions of an image. + +## Results + +:::{figure} AssignContiguousLabelsToConnectedRegions.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RelabelComponentImageFilter +``` diff --git a/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.rst b/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.rst deleted file mode 100644 index 8b76347b7..000000000 --- a/src/Segmentation/ConnectedComponents/AssignContiguousLabelsToConnectedRegions/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: AssignContiguousLabelsToConnectedRegions - -Assign Contiguous Labels to Connected Regions in an Image -========================================================= - -.. index:: - single: RelabelComponentImageFilter - pair: connect; regions - -Synopsis --------- - -Assign contiguous labels to connected regions of an image. - - -Results -------- -.. figure:: AssignContiguousLabelsToConnectedRegions.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RelabelComponentImageFilter diff --git a/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.md b/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.md new file mode 100644 index 000000000..1c6a034fd --- /dev/null +++ b/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.md @@ -0,0 +1,48 @@ +--- +name: ExtraLargestConnectComponentFromBinaryImage +--- + +# Extra Largest Connect Component From Binary Image + +```{index} single: ConnectedComponentImageFilter pair: binary; image +``` + +## Synopsis + +Extract the largest connected component from a Binary Image. + +## Results + +:::{figure} Yinyang.png +:alt: input image +:scale: 70% + +Input image. +::: + +:::{figure} ExtraLargestConnectComponentFromBinaryImage.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +Output: + +``` +Number of objects: 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConnectedComponentImageFilter +``` diff --git a/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.rst b/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.rst deleted file mode 100644 index 4191156b1..000000000 --- a/src/Segmentation/ConnectedComponents/ExtraLargestConnectComponentFromBinaryImage/Documentation.rst +++ /dev/null @@ -1,47 +0,0 @@ -:name: ExtraLargestConnectComponentFromBinaryImage - -Extra Largest Connect Component From Binary Image -================================================= - -.. index:: - single: ConnectedComponentImageFilter - pair: binary; image - -Synopsis --------- - -Extract the largest connected component from a Binary Image. - - -Results -------- -.. figure:: Yinyang.png - :scale: 70% - :alt: input image - - Input image. - -.. figure:: ExtraLargestConnectComponentFromBinaryImage.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Output:: - - Number of objects: 3 - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConnectedComponentImageFilter diff --git a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.md b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.md new file mode 100644 index 000000000..26f273d31 --- /dev/null +++ b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.md @@ -0,0 +1,33 @@ +--- +name: LabelConnectComponentsInBinaryImage +--- + +# Label Connect Components in Binary Image + +```{index} single: ConnectedComponentImageFilter pair: binary; image +``` + +## Synopsis + +Label connected components in a binary image. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConnectedComponentImageFilter +``` diff --git a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.rst b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.rst deleted file mode 100644 index c3fec1217..000000000 --- a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Documentation.rst +++ /dev/null @@ -1,34 +0,0 @@ -:name: LabelConnectComponentsInBinaryImage - -Label Connect Components in Binary Image -======================================== - -.. index:: - single: ConnectedComponentImageFilter - pair: binary; image - -Synopsis --------- - -Label connected components in a binary image. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConnectedComponentImageFilter diff --git a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.md b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.md new file mode 100644 index 000000000..956690353 --- /dev/null +++ b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.md @@ -0,0 +1,35 @@ +--- +name: LabelConnectComponentsInGrayscaleImage +--- + +# Label Connect Components in Grayscale Image + +```{index} single: ScalarConnectedComponentImageFilter pair: grayscale; image +``` + +## Synopsis + +Label connected components in a grayscale image. + +## Results + +:::{figure} LabelConnectComponentsInGrayscaleImage.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ScalarConnectedComponentImageFilter +``` diff --git a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.rst b/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.rst deleted file mode 100644 index e6ebbda26..000000000 --- a/src/Segmentation/ConnectedComponents/LabelConnectComponentsInGrayscaleImage/Documentation.rst +++ /dev/null @@ -1,36 +0,0 @@ -:name: LabelConnectComponentsInGrayscaleImage - -Label Connect Components in Grayscale Image -=========================================== - -.. index:: - single: ScalarConnectedComponentImageFilter - pair: grayscale; image - -Synopsis --------- - -Label connected components in a grayscale image. - - -Results -------- -.. figure:: LabelConnectComponentsInGrayscaleImage.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ScalarConnectedComponentImageFilter diff --git a/src/Segmentation/ConnectedComponents/index.md b/src/Segmentation/ConnectedComponents/index.md new file mode 100644 index 000000000..3f45efea4 --- /dev/null +++ b/src/Segmentation/ConnectedComponents/index.md @@ -0,0 +1,10 @@ +# ConnectedComponents + +```{toctree} +:maxdepth: 1 + +AssignContiguousLabelsToConnectedRegions/Documentation.rst +ExtraLargestConnectComponentFromBinaryImage/Documentation.rst +LabelConnectComponentsInBinaryImage/Documentation.rst +LabelConnectComponentsInGrayscaleImage/Documentation.rst +``` diff --git a/src/Segmentation/ConnectedComponents/index.rst b/src/Segmentation/ConnectedComponents/index.rst deleted file mode 100644 index a00be8c82..000000000 --- a/src/Segmentation/ConnectedComponents/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -ConnectedComponents -=================== - -.. toctree:: - :maxdepth: 1 - - AssignContiguousLabelsToConnectedRegions/Documentation.rst - ExtraLargestConnectComponentFromBinaryImage/Documentation.rst - LabelConnectComponentsInBinaryImage/Documentation.rst - LabelConnectComponentsInGrayscaleImage/Documentation.rst diff --git a/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.md b/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.md new file mode 100644 index 000000000..14c8fde5a --- /dev/null +++ b/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.md @@ -0,0 +1,40 @@ +--- +name: BasicRegionGrowing +--- + +# Basic Region Growing + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: RegionGrowImageFilter +``` + +## Synopsis + +Basic region growing. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::RegionGrowImageFilter +``` diff --git a/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.rst b/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.rst deleted file mode 100644 index b8ae610d2..000000000 --- a/src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: BasicRegionGrowing - -Basic Region Growing -==================== -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: RegionGrowImageFilter - -Synopsis --------- - -Basic region growing. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::RegionGrowImageFilter diff --git a/src/Segmentation/KLMRegionGrowing/index.md b/src/Segmentation/KLMRegionGrowing/index.md new file mode 100644 index 000000000..5e2f46b24 --- /dev/null +++ b/src/Segmentation/KLMRegionGrowing/index.md @@ -0,0 +1,7 @@ +# KLMRegionGrowing + +```{toctree} +:maxdepth: 1 + +BasicRegionGrowing/Documentation.rst +``` diff --git a/src/Segmentation/KLMRegionGrowing/index.rst b/src/Segmentation/KLMRegionGrowing/index.rst deleted file mode 100644 index 9e5755cfa..000000000 --- a/src/Segmentation/KLMRegionGrowing/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -KLMRegionGrowing -================ - -.. toctree:: - :maxdepth: 1 - - BasicRegionGrowing/Documentation.rst diff --git a/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.md b/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.md new file mode 100644 index 000000000..41242d7cb --- /dev/null +++ b/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.md @@ -0,0 +1,42 @@ +--- +name: IterativeHoleFilling +--- + +# Iterative Hole Filling + +```{index} single: VotingBinaryIterativeHoleFillingImageFilter +``` + +## Synopsis + +Fill hole or cavity in one itk::Image + +## Results + +:::{figure} BinaryThresholdImageFilter.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 50% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VotingBinaryIterativeHoleFillingImageFilter +``` diff --git a/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.rst b/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.rst deleted file mode 100644 index a1b120d9e..000000000 --- a/src/Segmentation/LabelVoting/IterativeHoleFilling/Documentation.rst +++ /dev/null @@ -1,44 +0,0 @@ -:name: IterativeHoleFilling - -Iterative Hole Filling -====================== - -.. index:: - single: VotingBinaryIterativeHoleFillingImageFilter - -Synopsis --------- - -Fill hole or cavity in one itk::Image - - -Results -------- - -.. figure:: BinaryThresholdImageFilter.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 50% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::VotingBinaryIterativeHoleFillingImageFilter diff --git a/src/Segmentation/LabelVoting/index.md b/src/Segmentation/LabelVoting/index.md new file mode 100644 index 000000000..2a86c91bd --- /dev/null +++ b/src/Segmentation/LabelVoting/index.md @@ -0,0 +1,7 @@ +# LabelVoting + +```{toctree} +:maxdepth: 1 + +IterativeHoleFilling/Documentation.rst +``` diff --git a/src/Segmentation/LabelVoting/index.rst b/src/Segmentation/LabelVoting/index.rst deleted file mode 100644 index 9031c6e61..000000000 --- a/src/Segmentation/LabelVoting/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -LabelVoting -=========== - -.. toctree:: - :maxdepth: 1 - - IterativeHoleFilling/Documentation.rst diff --git a/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.md b/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.md new file mode 100644 index 000000000..3c1947041 --- /dev/null +++ b/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.md @@ -0,0 +1,60 @@ +--- +name: SegmentWithGeodesicActiveContourLevelSet +--- + +# Segment With Geodesic Active Contour Level Set + +```{index} single: GeodesicActiveContourLevelSetImageFilter single: CurvatureAnisotropicDiffusionImageFilter single: GradientMagnitudeRecursiveGaussianImageFilter single: SigmoidImageFilter single: FastMarchingImageFilter single: RescaleIntensityImageFilter single: BinaryThresholdImageFilter +``` + +## Synopsis + +Segments structures in images based on a user supplied edge potential map. + +This example is the same as the one in the ITK software guide. It was re-organized and +does not contain any comments about the executed filters. Please refer to the guide +for more details. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{only} html +```{image} Evolution.gif +:alt: Evolution of the segmentation depending on the number of iterations (10 to 500). +:scale: 50% +``` +::: + +Used parameters: + +- Left ventricle: 81 114 5.0 1.0 -0.5 3.0 2.0 +- Right ventricle: 99 114 5.0 1.0 -0.5 3.0 2.0 +- White matter: 56 92 5.0 1.0 -0.3 2.0 10.0 +- Gray matter: 40 90 5.0 .5 -0.3 2.0 10.0 + +## Code + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::GeodesicActiveContourLevelSetImageFilter +``` diff --git a/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.rst b/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.rst deleted file mode 100644 index 3abd90d39..000000000 --- a/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.rst +++ /dev/null @@ -1,66 +0,0 @@ -:name: SegmentWithGeodesicActiveContourLevelSet - -Segment With Geodesic Active Contour Level Set -============================================== - -.. index:: - single: GeodesicActiveContourLevelSetImageFilter - single: CurvatureAnisotropicDiffusionImageFilter - single: GradientMagnitudeRecursiveGaussianImageFilter - single: SigmoidImageFilter - single: FastMarchingImageFilter - single: RescaleIntensityImageFilter - single: BinaryThresholdImageFilter - -Synopsis --------- - -Segments structures in images based on a user supplied edge potential map. - -This example is the same as the one in the ITK software guide. It was re-organized and -does not contain any comments about the executed filters. Please refer to the guide -for more details. - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. only:: html - - .. image:: Evolution.gif - :scale: 50% - :alt: Evolution of the segmentation depending on the number of iterations (10 to 500). - -Used parameters: - -* Left ventricle: 81 114 5.0 1.0 -0.5 3.0 2.0 -* Right ventricle: 99 114 5.0 1.0 -0.5 3.0 2.0 -* White matter: 56 92 5.0 1.0 -0.3 2.0 10.0 -* Gray matter: 40 90 5.0 .5 -0.3 2.0 10.0 - - -Code ----- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::GeodesicActiveContourLevelSetImageFilter diff --git a/src/Segmentation/LevelSets/index.md b/src/Segmentation/LevelSets/index.md new file mode 100644 index 000000000..56c3a6b7f --- /dev/null +++ b/src/Segmentation/LevelSets/index.md @@ -0,0 +1,7 @@ +# LevelSets + +```{toctree} +:maxdepth: 1 + +SegmentWithGeodesicActiveContourLevelSet/Documentation.rst +``` diff --git a/src/Segmentation/LevelSets/index.rst b/src/Segmentation/LevelSets/index.rst deleted file mode 100644 index e4743476f..000000000 --- a/src/Segmentation/LevelSets/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -LevelSets -========= - -.. toctree:: - :maxdepth: 1 - - SegmentWithGeodesicActiveContourLevelSet/Documentation.rst diff --git a/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.md b/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.md new file mode 100644 index 000000000..03fdfa80c --- /dev/null +++ b/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.md @@ -0,0 +1,40 @@ +--- +name: ConnectedComponentsInImage +--- + +# Connected Components in Image + +:::{warning} +**Fix Problem** +Contains problems not fixed from original wiki. +::: + +```{index} single: ConnectedThresholdImageFilter +``` + +## Synopsis + +Find connected components in an image. + +## Results + +:::{note} +**Help Wanted** +Implementation of Results for sphinx examples containing this message. +Reconfiguration of CMakeList.txt may be necessary. +`Write An Example +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConnectedThresholdImageFilter +``` diff --git a/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.rst b/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.rst deleted file mode 100644 index e4950682c..000000000 --- a/src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Documentation.rst +++ /dev/null @@ -1,37 +0,0 @@ -:name: ConnectedComponentsInImage - -Connected Components in Image -============================= -.. warning:: - **Fix Problem** - Contains problems not fixed from original wiki. -.. index:: - single: ConnectedThresholdImageFilter - -Synopsis --------- - -Find connected components in an image. - - -Results -------- -.. note:: - **Help Wanted** - Implementation of Results for sphinx examples containing this message. - Reconfiguration of CMakeList.txt may be necessary. - `Write An Example - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConnectedThresholdImageFilter diff --git a/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.md b/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.md new file mode 100644 index 000000000..82c27df54 --- /dev/null +++ b/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.md @@ -0,0 +1,35 @@ +--- +name: SegmentPixelsWithSimilarStats +--- + +# Segment Pixels With Similar Statistics + +```{index} single: ConfidenceConnectedImageFilter +``` + +## Synopsis + +Segment pixels with similar statistics using connectivity. + +## Results + +:::{figure} SegmentPixelsWithSimilarStats.png +:alt: VTK Window +:scale: 70% + +Output In VTK Window +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::ConfidenceConnectedImageFilter +``` diff --git a/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.rst b/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.rst deleted file mode 100644 index 39555e71a..000000000 --- a/src/Segmentation/RegionGrowing/SegmentPixelsWithSimilarStats/Documentation.rst +++ /dev/null @@ -1,35 +0,0 @@ -:name: SegmentPixelsWithSimilarStats - -Segment Pixels With Similar Statistics -====================================== - -.. index:: - single: ConfidenceConnectedImageFilter - -Synopsis --------- - -Segment pixels with similar statistics using connectivity. - - -Results -------- -.. figure:: SegmentPixelsWithSimilarStats.png - :scale: 70% - :alt: VTK Window - - Output In VTK Window - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::ConfidenceConnectedImageFilter diff --git a/src/Segmentation/RegionGrowing/index.md b/src/Segmentation/RegionGrowing/index.md new file mode 100644 index 000000000..2df7f7ca5 --- /dev/null +++ b/src/Segmentation/RegionGrowing/index.md @@ -0,0 +1,8 @@ +# RegionGrowing + +```{toctree} +:maxdepth: 1 + +ConnectedComponentsInImage/Documentation.rst +SegmentPixelsWithSimilarStats/Documentation.rst +``` diff --git a/src/Segmentation/RegionGrowing/index.rst b/src/Segmentation/RegionGrowing/index.rst deleted file mode 100644 index ce7374152..000000000 --- a/src/Segmentation/RegionGrowing/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -RegionGrowing -============= - -.. toctree:: - :maxdepth: 1 - - ConnectedComponentsInImage/Documentation.rst - SegmentPixelsWithSimilarStats/Documentation.rst diff --git a/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.md b/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.md new file mode 100644 index 000000000..05291fc98 --- /dev/null +++ b/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.md @@ -0,0 +1,109 @@ +--- +name: VoronoiDiagram +--- + +# Voronoi Diagram + +```{index} single: VoronoiDiagram2D single: VoronoiDiagram2DGenerator +``` + +## Synopsis + +Voronoi diagram. + +## Results + +:::{warning} +**Fix Errors** +Example contains errors needed to be fixed for proper output. +::: + +Output: + +``` +Seed No.0: At (25,25) +Boundary Vertices List (in order):4,8,7,0,1, +Neighbors (Seed No.):2,3,1, + +Seed No.1: At (75,25) +Boundary Vertices List (in order):6,11,7,0,2, +Neighbors (Seed No.):2,4,0, + +Seed No.2: At (50,50) +Boundary Vertices List (in order):2,0,1,3, +Neighbors (Seed No.):0,1,3,4, + +Seed No.3: At (25,75) +Boundary Vertices List (in order):5,9,4,1,3, +Neighbors (Seed No.):2,0,4, + +Seed No.4: At (75,75) +Boundary Vertices List (in order):5,10,6,2,3, +Neighbors (Seed No.):2,3,1, + +Vertices Informations: +Vertices No.0: At (50,25) +Vertices No.1: At (25,50) +Vertices No.2: At (75,50) +Vertices No.3: At (50,75) +Vertices No.4: At (0,50) +Vertices No.5: At (50,100) +Vertices No.6: At (100,50) +Vertices No.7: At (50,0) +Vertices No.8: At (0,0) +Vertices No.9: At (0,100) +Vertices No.10: At (100,100) +Vertices No.11: At (100,0) +IIBI-SYNAPSE006:bin mseng$ ./VoronoiDiagram +Seed No.0: At (25,25) +Boundary Vertices List (in order):4,8,7,0,1, +Neighbors (Seed No.):2,3,1, + +Seed No.1: At (75,25) +Boundary Vertices List (in order):6,11,7,0,2, +Neighbors (Seed No.):2,4,0, + +Seed No.2: At (50,50) +Boundary Vertices List (in order):2,0,1,3, +Neighbors (Seed No.):0,1,3,4, + +Seed No.3: At (25,75) +Boundary Vertices List (in order):5,9,4,1,3, +Neighbors (Seed No.):2,0,4, + +Seed No.4: At (75,75) +Boundary Vertices List (in order):5,10,6,2,3, +Neighbors (Seed No.):2,3,1, + +Vertices Informations: +Vertices No.0: At (50,25) +Vertices No.1: At (25,50) +Vertices No.2: At (75,50) +Vertices No.3: At (50,75) +Vertices No.4: At (0,50) +Vertices No.5: At (50,100) +Vertices No.6: At (100,50) +Vertices No.7: At (50,0) +Vertices No.8: At (0,0) +Vertices No.9: At (0,100) +Vertices No.10: At (100,100) +Vertices No.11: At (100,0) +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::VoronoiDiagram2D +``` + +```{eval-rst} +.. breathelink:: itk::VoronoiDiagram2DGenerator +``` diff --git a/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.rst b/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.rst deleted file mode 100644 index 5ce5ae700..000000000 --- a/src/Segmentation/Voronoi/VoronoiDiagram/Documentation.rst +++ /dev/null @@ -1,105 +0,0 @@ -:name: VoronoiDiagram - -Voronoi Diagram -=============== - -.. index:: - single: VoronoiDiagram2D - single: VoronoiDiagram2DGenerator - -Synopsis --------- - -Voronoi diagram. - - -Results -------- -.. warning:: - **Fix Errors** - Example contains errors needed to be fixed for proper output. - -Output:: - - Seed No.0: At (25,25) - Boundary Vertices List (in order):4,8,7,0,1, - Neighbors (Seed No.):2,3,1, - - Seed No.1: At (75,25) - Boundary Vertices List (in order):6,11,7,0,2, - Neighbors (Seed No.):2,4,0, - - Seed No.2: At (50,50) - Boundary Vertices List (in order):2,0,1,3, - Neighbors (Seed No.):0,1,3,4, - - Seed No.3: At (25,75) - Boundary Vertices List (in order):5,9,4,1,3, - Neighbors (Seed No.):2,0,4, - - Seed No.4: At (75,75) - Boundary Vertices List (in order):5,10,6,2,3, - Neighbors (Seed No.):2,3,1, - - Vertices Informations: - Vertices No.0: At (50,25) - Vertices No.1: At (25,50) - Vertices No.2: At (75,50) - Vertices No.3: At (50,75) - Vertices No.4: At (0,50) - Vertices No.5: At (50,100) - Vertices No.6: At (100,50) - Vertices No.7: At (50,0) - Vertices No.8: At (0,0) - Vertices No.9: At (0,100) - Vertices No.10: At (100,100) - Vertices No.11: At (100,0) - IIBI-SYNAPSE006:bin mseng$ ./VoronoiDiagram - Seed No.0: At (25,25) - Boundary Vertices List (in order):4,8,7,0,1, - Neighbors (Seed No.):2,3,1, - - Seed No.1: At (75,25) - Boundary Vertices List (in order):6,11,7,0,2, - Neighbors (Seed No.):2,4,0, - - Seed No.2: At (50,50) - Boundary Vertices List (in order):2,0,1,3, - Neighbors (Seed No.):0,1,3,4, - - Seed No.3: At (25,75) - Boundary Vertices List (in order):5,9,4,1,3, - Neighbors (Seed No.):2,0,4, - - Seed No.4: At (75,75) - Boundary Vertices List (in order):5,10,6,2,3, - Neighbors (Seed No.):2,3,1, - - Vertices Informations: - Vertices No.0: At (50,25) - Vertices No.1: At (25,50) - Vertices No.2: At (75,50) - Vertices No.3: At (50,75) - Vertices No.4: At (0,50) - Vertices No.5: At (50,100) - Vertices No.6: At (100,50) - Vertices No.7: At (50,0) - Vertices No.8: At (0,0) - Vertices No.9: At (0,100) - Vertices No.10: At (100,100) - Vertices No.11: At (100,0) - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::VoronoiDiagram2D -.. breathelink:: itk::VoronoiDiagram2DGenerator diff --git a/src/Segmentation/Voronoi/index.md b/src/Segmentation/Voronoi/index.md new file mode 100644 index 000000000..ce9406d6a --- /dev/null +++ b/src/Segmentation/Voronoi/index.md @@ -0,0 +1,7 @@ +# Voronoi + +```{toctree} +:maxdepth: 1 + +VoronoiDiagram/Documentation.rst +``` diff --git a/src/Segmentation/Voronoi/index.rst b/src/Segmentation/Voronoi/index.rst deleted file mode 100644 index da0b2a2a5..000000000 --- a/src/Segmentation/Voronoi/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -Voronoi -======= - -.. toctree:: - :maxdepth: 1 - - VoronoiDiagram/Documentation.rst diff --git a/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.md b/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.md new file mode 100644 index 000000000..ac5dc5f90 --- /dev/null +++ b/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.md @@ -0,0 +1,50 @@ +--- +name: MorphologicalWatershedSegmentation +--- + +# Morphological Watershed Segmentation + +```{index} single: MorphologicalWatershedImageFilter single: watershed +``` + +## Synopsis + +Morphological watershed segmentation. + +## Results + +:::{figure} input.png +:alt: input.png +:scale: 70% + +input.png +::: + +:::{figure} output_20_3.png +:alt: output_20_3.png +:scale: 70% + +output_20_3.png +::: + +Output: + +``` +Running with: +Threshold: 20 +Level: 3 +``` + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::MorphologicalWatershedImageFilter +``` diff --git a/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.rst b/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.rst deleted file mode 100644 index b531cb11f..000000000 --- a/src/Segmentation/Watersheds/MorphologicalWatershedSegmentation/Documentation.rst +++ /dev/null @@ -1,48 +0,0 @@ -:name: MorphologicalWatershedSegmentation - -Morphological Watershed Segmentation -==================================== - -.. index:: - single: MorphologicalWatershedImageFilter - single: watershed - -Synopsis --------- - -Morphological watershed segmentation. - - -Results -------- -.. figure:: input.png - :scale: 70% - :alt: input.png - - input.png - -.. figure:: output_20_3.png - :scale: 70% - :alt: output_20_3.png - - output_20_3.png - -Output:: - - Running with: - Threshold: 20 - Level: 3 - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - -Classes demonstrated --------------------- - -.. breathelink:: itk::MorphologicalWatershedImageFilter diff --git a/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.md b/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.md new file mode 100644 index 000000000..c4b0a7146 --- /dev/null +++ b/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.md @@ -0,0 +1,50 @@ +--- +name: SegmentWithWatershedImageFilter +--- + +# Watershed Image Filter + +```{index} single: WatershedImageFilter +``` + +## Synopsis + +This example illustrates how to segment an image using the watershed method. + +## Results + +:::{figure} BrainProtonDensitySlice.png +:alt: Input image +:scale: 50% + +Input image +::: + +:::{figure} SegmentWithWatershedImageFilterTest02Baseline.png +:alt: Segmented image +:scale: 50% + +Segmented image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:language: c++ +:lines: 18- +``` + +### Python + +```{literalinclude} Code.py +:language: python +:lines: 1, 16- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::WatershedImageFilter +``` diff --git a/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.rst b/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.rst deleted file mode 100644 index 0f44d0e9d..000000000 --- a/src/Segmentation/Watersheds/SegmentWithWatershedImageFilter/Documentation.rst +++ /dev/null @@ -1,51 +0,0 @@ -:name: SegmentWithWatershedImageFilter - -Watershed Image Filter -====================== - -.. index:: - single: WatershedImageFilter - -Synopsis --------- - -This example illustrates how to segment an image using the watershed method. - -Results -------- - -.. figure:: BrainProtonDensitySlice.png - :scale: 50% - :alt: Input image - - Input image - -.. figure:: SegmentWithWatershedImageFilterTest02Baseline.png - :scale: 50% - :alt: Segmented image - - Segmented image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :language: c++ - :lines: 18- - -Python -...... - -.. literalinclude:: Code.py - :language: python - :lines: 1, 16- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::WatershedImageFilter diff --git a/src/Segmentation/Watersheds/index.md b/src/Segmentation/Watersheds/index.md new file mode 100644 index 000000000..f2b4b3126 --- /dev/null +++ b/src/Segmentation/Watersheds/index.md @@ -0,0 +1,8 @@ +# Watersheds + +```{toctree} +:maxdepth: 1 + +MorphologicalWatershedSegmentation/Documentation.rst +SegmentWithWatershedImageFilter/Documentation.rst +``` diff --git a/src/Segmentation/Watersheds/index.rst b/src/Segmentation/Watersheds/index.rst deleted file mode 100644 index 33105cfc3..000000000 --- a/src/Segmentation/Watersheds/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -Watersheds -========== - -.. toctree:: - :maxdepth: 1 - - MorphologicalWatershedSegmentation/Documentation.rst - SegmentWithWatershedImageFilter/Documentation.rst diff --git a/src/Segmentation/index.md b/src/Segmentation/index.md new file mode 100644 index 000000000..255820f19 --- /dev/null +++ b/src/Segmentation/index.md @@ -0,0 +1,14 @@ +# Segmentation + +```{toctree} +:maxdepth: 2 + +Classifiers/index.rst +ConnectedComponents/index.rst +KLMRegionGrowing/index.rst +LabelVoting/index.rst +LevelSets/index.rst +RegionGrowing/index.rst +Voronoi/index.rst +Watersheds/index.rst +``` diff --git a/src/Segmentation/index.rst b/src/Segmentation/index.rst deleted file mode 100644 index f85cd6b26..000000000 --- a/src/Segmentation/index.rst +++ /dev/null @@ -1,14 +0,0 @@ -Segmentation -============ - -.. toctree:: - :maxdepth: 2 - - Classifiers/index.rst - ConnectedComponents/index.rst - KLMRegionGrowing/index.rst - LabelVoting/index.rst - LevelSets/index.rst - RegionGrowing/index.rst - Voronoi/index.rst - Watersheds/index.rst diff --git a/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.md b/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.md new file mode 100644 index 000000000..9db62cc36 --- /dev/null +++ b/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.md @@ -0,0 +1,38 @@ +# Convert an ITK Gray Scale Image to CV Mat + +```{index} single: OpenCVImageBridge +``` + +## Synopsis + +Convert an itk::Image (gray scale) to OpenCV cv::Mat. + +## Results + +:::{figure} Yinyang.png +:alt: Input image +:scale: 100% + +Input image +::: + +:::{figure} OutputBaseline.png +:alt: Output image +:scale: 100% + +Output image +::: + +## Code + +### C++ + +```{literalinclude} Code.cxx +:lines: 18- +``` + +## Classes demonstrated + +```{eval-rst} +.. breathelink:: itk::OpenCVImageBridge +``` diff --git a/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.rst b/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.rst deleted file mode 100644 index 28a2e54fa..000000000 --- a/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.rst +++ /dev/null @@ -1,42 +0,0 @@ -Convert an ITK Gray Scale Image to CV Mat -========================================= - -.. index:: - single: OpenCVImageBridge - -Synopsis --------- - -Convert an itk::Image (gray scale) to OpenCV cv::Mat. - - -Results -------- - -.. figure:: Yinyang.png - :scale: 100% - :alt: Input image - - Input image - -.. figure:: OutputBaseline.png - :scale: 100% - :alt: Output image - - Output image - - -Code ----- - -C++ -... - -.. literalinclude:: Code.cxx - :lines: 18- - - -Classes demonstrated --------------------- - -.. breathelink:: itk::OpenCVImageBridge diff --git a/src/Video/BridgeOpenCV/index.md b/src/Video/BridgeOpenCV/index.md new file mode 100644 index 000000000..74730762b --- /dev/null +++ b/src/Video/BridgeOpenCV/index.md @@ -0,0 +1,7 @@ +# BridgeOpenCV + +```{toctree} +:maxdepth: 1 + +ConvertAnITKGrayScaleImageToCVMat/Documentation.rst +``` diff --git a/src/Video/BridgeOpenCV/index.rst b/src/Video/BridgeOpenCV/index.rst deleted file mode 100644 index 21ea380d7..000000000 --- a/src/Video/BridgeOpenCV/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -BridgeOpenCV -============ - -.. toctree:: - :maxdepth: 1 - - ConvertAnITKGrayScaleImageToCVMat/Documentation.rst diff --git a/src/Video/index.md b/src/Video/index.md new file mode 100644 index 000000000..5cfb5c369 --- /dev/null +++ b/src/Video/index.md @@ -0,0 +1,7 @@ +# Video + +```{toctree} +:maxdepth: 2 + +BridgeOpenCV/index.rst +``` diff --git a/src/Video/index.rst b/src/Video/index.rst deleted file mode 100644 index 8a71284c8..000000000 --- a/src/Video/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -Video -===== - -.. toctree:: - :maxdepth: 2 - - BridgeOpenCV/index.rst diff --git a/src/index.md b/src/index.md new file mode 100644 index 000000000..f9a88e3c0 --- /dev/null +++ b/src/index.md @@ -0,0 +1,17 @@ +# Examples + +```{toctree} +:maxdepth: 2 + +Bridge/index.rst +Core/index.rst +External/index.rst +Filtering/index.rst +GPU/index.rst +IO/index.rst +Numerics/index.rst +Nonunit/index.rst +Registration/index.rst +Segmentation/index.rst +Video/index.rst +``` diff --git a/src/index.rst b/src/index.rst deleted file mode 100644 index e5617c6ae..000000000 --- a/src/index.rst +++ /dev/null @@ -1,18 +0,0 @@ -======== -Examples -======== - -.. toctree:: - :maxdepth: 2 - - Bridge/index.rst - Core/index.rst - External/index.rst - Filtering/index.rst - GPU/index.rst - IO/index.rst - Numerics/index.rst - Nonunit/index.rst - Registration/index.rst - Segmentation/index.rst - Video/index.rst