✨ NEW: DFBR for Registering Images #510

ruqayya · 2022-11-22T01:07:46Z

This PR contains code for the DFBR method for registering pair of images.

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

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- Fix indents

- init files is added - cv2 imresize is replaced with the tiatoolbox resize ftn

…istration.py, due to an error 'fixture not found'.

- Merge develop into dev-feature_extraction_DFBR.

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- Move fixtures to conftest.py

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

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…o dev-feature_extraction_DFBR

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

John-P

Can I just check why the notebook was deleted in this PR? Is this because it is now being done in #494?

tiatoolbox/tools/registration/wsi_registration.py

shaneahmed · 2022-11-25T13:58:43Z

Can I just check why the notebook was deleted in this PR? Is this because it is now being done in #494?

Yes the notebook is being separate from this PR to help David with review.

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- Update documentation for get_tissue_regions

- Restore files from develop as these will be updated in #494

shaneahmed

Thanks @ruqayya

- Fix indent for documentation

- Fix tests for transformation

# 1.3.1 (2022-12-20) ### Major Updates and Feature Improvements - Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 ### Changes to API - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 ### Bug Fixes and Other Changes - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility ### Development related changes - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>

- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>

# 1.3.1 (2022-12-20) ### Major Updates and Feature Improvements - Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 ### Changes to API - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 ### Bug Fixes and Other Changes - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility ### Development related changes - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Kesi Xu<98600542+kesixu@users.noreply.github.com>

ruqayya and others added 30 commits July 30, 2022 17:31

Feature extraction for DFBR.

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Feature extraction for DFBR.

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Update tiatoolbox/tools/registration/wsi_registration.py

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

Update tiatoolbox/tools/registration/wsi_registration.py

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Update tiatoolbox/tools/registration/wsi_registration.py

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Feature extraction for DFBR.

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assert statement is added to check if the output is as expected

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DOC: Fix indents

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- Fix indents

- urls are added to remote_samples.yaml

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- init files is added - cv2 imresize is replaced with the tiatoolbox resize ftn

- tests added to conftest and removed from test_wsi_registration.py

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- removed fixture tests from conftest and placed them to test_wsi_reg…

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…istration.py, due to an error 'fixture not found'.

MERGE: Merge develop into dev-feature_extraction_DFBR

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DEV: Move fixtures to conftest.py

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DEV: Move fixtures to conftest.py

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- Move fixtures to conftest.py

Update tiatoolbox/tools/registration/wsi_registration.py

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DEV: Replaced png images with jpeg images for test.

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DEV: Feature matching functions added.

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DEV: Assert statement removed.

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DEV: Convert functions to static function.

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Merge branch 'develop' into dev-feature_matching_DFBR

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DEV: Compute transformation matrix.

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DOC: Add return values.

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ruqayya and others added 3 commits November 22, 2022 14:27

Update tiatoolbox/tools/registration/wsi_registration.py

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

Update tiatoolbox/tools/registration/wsi_registration.py

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Update tiatoolbox/tools/registration/wsi_registration.py

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John-P changed the title ~~DEV: DFBR for registering images~~ DEV: DFBR for Registering Images Nov 23, 2022

John-P reviewed Nov 23, 2022

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shaneahmed added 2 commits November 25, 2022 09:49

Merge branch 'develop' into dev-DFBR

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ruqayya and others added 6 commits November 27, 2022 10:22

Rename wsi_reader as reader.

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DOC: Update documentation for get_tissue_regions

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REV: Restore files from develop

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- Restore files from develop as these will be updated in #494

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shaneahmed added 3 commits November 30, 2022 13:29

DOC: Fix indent for documentation

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DOC: Fix indent for documentation

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Merge branch 'develop' into dev-DFBR

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John-P changed the title ~~DEV: DFBR for Registering Images~~ ✨ DEV: DFBR for Registering Images Dec 7, 2022

shaneahmed changed the title ~~✨ DEV: DFBR for Registering Images~~ ✨ NEW: DFBR for Registering Images Dec 7, 2022

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📝 [skip ci] DOC: DFBR Jupyter Notebook revised #494

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🐛 DEV: Fix tests for transformation

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- Fix tests for transformation

shaneahmed merged commit 3a31586 into develop Dec 9, 2022

shaneahmed deleted the dev-DFBR branch December 9, 2022 13:11

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🔖 REL: Release 1.3.1 #523

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🔖 REL: REL: Release 1.3.1 #524

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✨ NEW: DFBR for Registering Images #510

✨ NEW: DFBR for Registering Images #510

ruqayya commented Nov 22, 2022

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✨ NEW: DFBR for Registering Images #510

✨ NEW: DFBR for Registering Images #510

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