update to 0.4.1 for new readme (#35)

* simplified loader/writer specification in IO ops

* updated imports in pipeline

* improved ops repr

* minor fixes in IO and segmentation

* matching roi names in StructureSet.to_segmentation is now case-insensitive

* fixed segmentation method call in some functional ops

* fixed typo in pipeline warning message

* StructureSet now correctly handles ROIs with no contour data

* fixed error when trying to detect CSV delimiter in MetadataWriter

* MetadataWriter can now remove existing files from previous runs

* MetadataWriter can now remove existing files from previous runs

* Segmentation object now correctly handles indexing

* fixed segmentation mask handling in image statistics computation

* removed old structure set code

* removed old structure set code

* fixed label handling in image statistics computation

* fixed label handling in image statistics computation

* [In Progress] Adding documentation to ops.py

* added support for dynamic path specification in writers

* image CSV loader now accepts pandas DataFrames

* fixed indentation error

* fixed index column handling in ImageCSVLoader

* Revert "fixed index column handling in ImageCSVLoader"

This reverts commit ac9b8d1.

* fixed index column handling in ImageCSVLoader

* fixed index column handling in ImageCSVLoader

* ImageCSVLoader now returns correct keys

* ImageCSVLoader now correctly handles globbing in paths

* more informative exception handling in pipeline

* pipeline can now warn on error instead of raising exception

* [Docs] Cleaned up extra whitespace in ops.py

* Added convenience method to get all ops in a pipeline

* Fix empty array check in structure set conversion

* Fix segmentation to label image conversion

* Update README.md

* Fix spurious mixin in ops

* Fix type error when passing Numpy array to rotate

* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT

* Fix crop size issue in crop_to_bounding_box

* Make imports easier

* Improved handling of regular expressions in structure set

* Fix slice matching issue when generating binary mask from RTStruct

* Fix binary mask generation from RTStruct when missing labels are present

* little updates

* added seg.nrrd compatibility

* supports RTSTRUCT processing without roi_names

* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.

* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.

* fixed structureset.py:148

* RT dose pipeline completed and tested. Error in segmentation not resolved

* PET readability added

* PET readability added

* Head-Neck-PET-CT pipeline + `read_dicom_auto`

* final pipeline working for doses and PET

* corrected the view

* reading in sitk format from beginning

* Completed PET overlay

* Modified RT dose, pipeline working for PET_CT quebec dataset

* Added DataGraph, now fetching subset of dataset is supported using graph query

* added crawl.py

* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes

* Rectified some bugs, added reference to rtplan in the crawler

* Now missing RTDOSE references are completed by RTPLAN

* small change

* Fixed dataset.csv writing issues

* major refactoring

* more refactoring

* Update radcure_simple.py

* Update loaders.py

* Update pet.py

* Delete .DS_Store

* Delete .DS_Store

* Delete .DS_Store

* Delete .DS_Store

* Delete .DS_Store

* Delete .DS_Store

* Delete .DS_Store

* ignore .DS_Store

* Update README.md

* quick README under ops

* tcia_sample

* example bash script with path parsing, fixed reference_frame

* housekeeping

* fixed dataset.csv

* sanity changes before purging dev-20200414

* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* self.existing, dataset.csv fixed (#10)

* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* Create build-ci.yml

* Update build-ci.yml

* Update requirements.txt

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* Create manual-test.yml

* Update build-ci.yml

* Update manual-test.yml

* PR tests - macos/ubuntu failing (#13)

* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* fixed pipeline tests

* clean tests

* added workflow

* yml

* yml

* matplotlib

* trying other patient to avoid memoryerror

* set roi_names to avoid memoryerror

* cave

* indents

* Update manual-test.yml

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Ready for

* Create main.yml (#15)

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

* merging new features (#16)

* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* fix path backslash issues

* fix path backslashes (#17)

* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

* fix path backslash issues

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* Update main.yml

* Update main.yml

* Update README.md

* Update main.yml (#18)

* Update main.yml

* Update requirements.txt

* Update main.yml

* Update main.yml

* build binary/dist

* removed linter

* Update setup.py

* Update README.md

* Update README.md (#19)

* Update README.md

* added tests for Dataset class

* added tests for Dataset class

* Create LICENSE (#20)

* Create LICENSE

* Update setup.py

* Seg.nrrd quick fix

* Minor bug fixes

* test fix

* Added demo

* Update setup.py (#23)

* updated README

* Update README.md (#24)

* preliminary MRI functionality (MR-RTSTRUCT pairs)

* Skim2257 quick fix (#26)

* Updated crawler to force String on all meta fields

* Update setup.py

* first commit

* removed test files, changed gitignore

* changed file directory structure for imageautooutput

* split mask up into each contour

* change kwargs in put for basesubjectwriter

* still kinda failing...

* brought back basesubjectwriter

* .imgtools directory

* changed absolute paths to relative paths

* changed os.path.join to pathlib.Path.as_posix()

* removed unused cv2 import

* removed cv2 import

* appened is deprecated, changed to concat

* debug print

* removed debug print

* added sparse mask class and generating function

* testing out sparse mask

* funky NaN problem

* commented sparse mask

* overwrite all subjects

* space

* overwrite false

* metadata stuffs

* metadata in dataset.csv

* added modalities, num rtstruct and pixel size to metadata

* metadata bugfix

* a

* fixed wrong variable names for metadata stuff

* fixed pathlib float error

* relative paths and output folder paths for dataset.csv

* put metadata stuff into a util file

* deal with empty metadata

* messing around with sparse mask

* tried to save sparse mask, did some stuff with nnunet output format

* compliant with nnunet directory structure

* CLI Interface, argparse moved to utils

* fixed formatting problems with folder names

* train test split

* train size and random state optional

* merge conflicts

* changed warnings to not interrupt

* changed to warnings.warn for generate_sparse_mask

* merge

* resolving conflicts?

* args

* changes for roi names as a dict

* added regex dictionary option for non nnunet runs

* sparse mask global labelling for contour name: index

* got rid of file_name_convention stuff

* conflicts resolved

* yaml thing

* added list capabilities for the roi names dictionary

* dataset.json for nnunet

* CLI "autonew"

* changed all mutable defaults to None

* moved autotest changes to autopipeline and addede a few CLI args

* getting ready for merge to live

* test_components, test_modalities works with new AutoPipeline

* overwrite changes and error fix for nan paths again

* fixed if statement

* joblib parallel

* warnings for missing patients

* summary messages

* updated, passing tests. Updated version to 0.4

* update test

* yaml path cli

* yaml error check

* pandas error

* Fixed read_dicom_auto

* skips series check if seris is None

* updated readme to reflect v0.4 changes

* updated readme

* minor change

* remove .idea

* remote .idea

* git ignore

* refactor nnunetutils to nnunet

* updated versions

Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com>
Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com>
Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca>
Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster>
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca>
Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local>
Co-authored-by: fishingguy456 <qukevin99@gmail.com>
Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster>
Former-commit-id: 4fc74ad7a233bf80dd95219eea058e86d8170e90
Former-commit-id: be0f5c8
Former-commit-id: 1f70cb08fcf0988d42babbed92c6aa53a49de7c2

README.md

@@ -4,7 +4,7 @@
 ![GitHub stars](https://img.shields.io/github/stars/bhklab/med-imagetools?style=social)
 ![GitHub forks](https://img.shields.io/github/forks/bhklab/med-imagetools?style=social)
 
-### Latest Updates (v0.4) - June 24th, 2022
+### Latest Updates (v0.4.1) - June 24th, 2022
 New features include:
 * AutoPipeline CLI
 * nnU-Net compatibility mode (--nnunet)

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="med-imagetools",
-    version="0.4",
+    version="0.4.1",
     author="Michal Kazmierski, Sejin Kim, Kevin Qu, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",