🆕 Use Annotations as a Filter for Patch Extraction #822

measty · 2024-06-13T18:08:10Z

This PR is something i've been thinking about from a conversation with Daan when he was here from Radboud doing a seminar a while back. His comment was that one thing some of his colleges felt was missing in TIAtoolbox was ability to get patches filtered by class/label.

Its not that hard to set up tiatoolbox patch extractor to allow this, which is what i've added in this PR.

it allows you to provide a path to an annotation store as the mask. By default the mask will then be built out of all the annotations, but you can also provide any filter that works in the annotation store, and have only those annotations make the mask. So for example, if you have some pathologist annotations with some regions, and you only want to extract patches which have some overlap with regions labelled 'tumor' or whatever, you would just have to provide the appropriate string ("props['label'] == 'tumor'" for example).

codecov · 2024-06-13T18:30:14Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.86%. Comparing base (52792bc) to head (62f3566).
Report is 2 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #822   +/-   ##
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  Coverage    99.86%   99.86%           
========================================
  Files           69       69           
  Lines         8656     8664    +8     
  Branches      1653     1654    +1     
========================================
+ Hits          8644     8652    +8     
  Misses           4        4           
  Partials         8        8

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review-notebook-app · 2024-08-09T11:48:49Z

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tiatoolbox/tools/patchextraction.py

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

…ch-extractor-filter

shaneahmed

Thanks @measty

shaneahmed · 2024-08-21T10:30:54Z

Thanks @measty

@mostafajahanifar Please can you review this PR so we can merge this.

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

shaneahmed · 2024-08-23T12:51:07Z

@mostafajahanifar I have updated the file.

review-notebook-app · 2024-08-30T18:02:04Z

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mostafajahanifar commented on 2024-08-30T18:02:03Z
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Link of documentaiotn is better to be to the main repo instead of the develop

review-notebook-app · 2024-08-30T18:02:04Z

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mostafajahanifar commented on 2024-08-30T18:02:04Z
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Line #3.    pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@patch-extractor-filter | tail -n 1

Just make sure you change this installation back to the main repo before merging.

review-notebook-app · 2024-08-30T18:02:05Z

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mostafajahanifar commented on 2024-08-30T18:02:05Z
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if you want, you can also add a reference to tissue masking example notebook here in the paranthesis in the first sentence.

... wsi through a simple otsu threshold approach (for more information on tissue masking, please see tiatoolbox/examples/03-tissue-masking.ipynb at master · TissueImageAnalytics/tiatoolbox (github.com))

mostafajahanifar

Well done, Mark! Great PR 💯

I only made some minor comments on the Notebook, feel free to make them or to ignore them.

…toolbox into patch-extractor-filter

@GeorgeBatch

## TIAToolbox v1.6.0 (2024-12-12) ### Major Updates and Feature Improvements - **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch) - Introduced `TimmBackbone` for running additional PyTorch Image Models. - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`. - Added an example notebook demonstrating feature extraction with foundation models. - `timm` added as a dependency. - **Performance Enhancements with `torch.compile`** (#716) - Improved performance on newer GPUs using `torch.compile`. - **Multichannel Input Support in `WSIReader`** (#742) - **AnnotationStore Filtering for Patch Extraction** (#822) - **Python 3.12 Support** - **Deprecation of Python 3.8 Support** - **CLI Response Time Improvements** (#795) ### API Changes - **Device Specification Update** (#882) - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality. - **Windows Compatibility Enhancement** (#769) - Replaced `POWER` with explicit multiplication. ### Bug Fixes and Other Changes - **TIFFWSIReader Bound Reading Adjustment** (#777) - Fixed `read_bound` to use adjusted bounds. - Reduced code complexity in `WSIReader` (#814). - **Annotation Rendering Fixes** (#813) - Corrected rendering of annotations with holes. - **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch) - **HoVer-Net Documentation Update** (#751) - Corrected class output information. - **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander) - **Bokeh Compatibility Updates** - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`. - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796). - **JSON Extraction Fixes** (#772) - Restructured SQL expression construction for JSON properties with dots in keys. - **VahadaneExtractor Warning** (#871) - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382). - **PatchExtractor Error Message Refinement** (#883) - **Immutable Output Fix in `WSIReader`** (#850) ### Development-Related Changes - **Mypy Checks Added** - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`. - **ReadTheDocs PDF Build Deprecation** - **Formatter Update** - Replaced `black` with `ruff-format`. - **Dependency Removal** - Removed `jinja2`. - **Test Environment Update** - Updated to `Ubuntu 24.04`. - **Conda Environment Workflow Update** - Implemented `micromamba` setup. - **Codecov Reporting Fix** (#811) **Full Changelog:** v1.5.1...v1.6.0 --------- Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan> Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com> Co-authored-by: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com> Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com> Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com> Co-authored-by: Alon Alexander <alon008@gmail.com>

@GeorgeBatch

## TIAToolbox v1.6.0 (2024-12-12) ### Major Updates and Feature Improvements - **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch) - Introduced `TimmBackbone` for running additional PyTorch Image Models. - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`. - Added an example notebook demonstrating feature extraction with foundation models. - `timm` added as a dependency. - **Performance Enhancements with `torch.compile`** (#716) - Improved performance on newer GPUs using `torch.compile`. - **Multichannel Input Support in `WSIReader`** (#742) - **AnnotationStore Filtering for Patch Extraction** (#822) - **Python 3.12 Support** - **Deprecation of Python 3.8 Support** - **CLI Response Time Improvements** (#795) ### API Changes - **Device Specification Update** (#882) - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality. - **Windows Compatibility Enhancement** (#769) - Replaced `POWER` with explicit multiplication. ### Bug Fixes and Other Changes - **TIFFWSIReader Bound Reading Adjustment** (#777) - Fixed `read_bound` to use adjusted bounds. - Reduced code complexity in `WSIReader` (#814). - **Annotation Rendering Fixes** (#813) - Corrected rendering of annotations with holes. - **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch) - **HoVer-Net Documentation Update** (#751) - Corrected class output information. - **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander) - **Bokeh Compatibility Updates** - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`. - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796). - **JSON Extraction Fixes** (#772) - Restructured SQL expression construction for JSON properties with dots in keys. - **VahadaneExtractor Warning** (#871) - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382). - **PatchExtractor Error Message Refinement** (#883) - **Immutable Output Fix in `WSIReader`** (#850) ### Development-Related Changes - **Mypy Checks Added** - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`. - **ReadTheDocs PDF Build Deprecation** - **Formatter Update** - Replaced `black` with `ruff-format`. - **Dependency Removal** - Removed `jinja2`. - **Test Environment Update** - Updated to `Ubuntu 24.04`. - **Conda Environment Workflow Update** - Implemented `micromamba` setup. - **Codecov Reporting Fix** (#811) **Full Changelog:** v1.5.1...v1.6.0

measty added 4 commits June 13, 2024 18:27

add patch extraction from annotations

8c30e27

add test

4cec9a8

update docstring

9bdbe72

fix deepsource and mypy

87a74ca

deepsource..

413feee

shaneahmed assigned measty Jun 14, 2024

shaneahmed added the enhancement New feature or request label Jun 14, 2024

shaneahmed added this to the Release v1.6.0 milestone Jun 14, 2024

shaneahmed changed the title ~~ENH: Use annotations as a filter for patch extraction~~ 🆕 Use Annotations as a Filter for Patch Extraction Jun 19, 2024

shaneahmed and others added 6 commits June 21, 2024 12:09

Merge branch 'develop' into patch-extractor-filter

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Merge branch 'develop' into patch-extractor-filter

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Merge branch 'develop' of https://github.com/TissueImageAnalytics/tia…

c665ac2

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update notebook 4

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add masking and filtering example to notebook 4

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update notebook 4

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shaneahmed and others added 2 commits August 9, 2024 15:22

Merge branch 'develop' into patch-extractor-filter

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shaneahmed requested review from shaneahmed and mostafajahanifar August 9, 2024 14:23

Merge branch 'develop' into patch-extractor-filter

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shaneahmed reviewed Aug 16, 2024

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shaneahmed and others added 4 commits August 16, 2024 10:53

🧑‍💻 Ignore PLR0913 for SlidingWindowPatchExtractor

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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

📝 Update examples/04-patch-extraction.ipynb

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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Merge remote-tracking branch 'origin/patch-extractor-filter' into pat…

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…ch-extractor-filter

update input mask types

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shaneahmed approved these changes Aug 16, 2024

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Merge branch 'develop' into patch-extractor-filter

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📝 Update 04-patch-extraction.ipynb with outputs.

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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

mostafajahanifar approved these changes Aug 30, 2024

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shaneahmed and others added 4 commits September 20, 2024 12:26

Merge branch 'develop' into patch-extractor-filter

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Merge branch 'develop' of https://github.com/TissueImageAnalytics/tia…

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address review

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Merge branch 'develop' into patch-extractor-filter

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shaneahmed merged commit 76f02f8 into develop Oct 18, 2024
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shaneahmed deleted the patch-extractor-filter branch October 18, 2024 13:53

shaneahmed mentioned this pull request Dec 12, 2024

🔖 Release 1.6.0 #895

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shaneahmed mentioned this pull request Dec 12, 2024

🔖 Release 1.6.0 #898

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🆕 Use Annotations as a Filter for Patch Extraction #822

🆕 Use Annotations as a Filter for Patch Extraction #822

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🆕 Use Annotations as a Filter for Patch Extraction #822

🆕 Use Annotations as a Filter for Patch Extraction #822

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