Make affine and space metadata consistent as well as updating support of latest holoscan SDK CUDA 12 version #565
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Pull Request Overview
Copilot reviewed 6 out of 7 changed files in this pull request and generated 2 comments.
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…transforms Signed-off-by: M Q <[email protected]>
Signed-off-by: M Q <[email protected]>
Signed-off-by: M Q <[email protected]>
Co-authored-by: Copilot <[email protected]> Signed-off-by: Ming M Qin <[email protected]>
Signed-off-by: M Q <[email protected]>
Signed-off-by: M Q <[email protected]>
Signed-off-by: M Q <[email protected]>
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Signed-off-by: M Q <[email protected]>
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… of latest holoscan SDK CUDA 12 version (#565) * Make affine and space consistent as space is properly parse by MONAI transforms Signed-off-by: M Q <[email protected]> * Typing improvements Signed-off-by: M Q <[email protected]> * Make image metadata Affine and Space consistent, either LPS or RAS Signed-off-by: M Q <[email protected]> * Update monai/deploy/operators/monai_seg_inference_operator.py Co-authored-by: Copilot <[email protected]> Signed-off-by: Ming M Qin <[email protected]> * Correct CoPilot suggested code which failed liniting Signed-off-by: M Q <[email protected]> * Fix complaint from new version of mypy Signed-off-by: M Q <[email protected]> * Support the latest holoscan SDK CUDA 12 version, holoscan-cu12 Signed-off-by: M Q <[email protected]> * Docs gen works with Python 3.10+ Signed-off-by: M Q <[email protected]> * Fix complaints on single quote vs dhouble quote for string Signed-off-by: M Q <[email protected]> * Making docs gen require python >= 3.10 Signed-off-by: M Q <[email protected]> * Fix docs build error on readthedocs, although local builds had no issues Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Ming M Qin <[email protected]> Co-authored-by: Copilot <[email protected]>
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) * Initial code for making a RESTful miscroservice with MONAI App SDK Signed-off-by: M Q <[email protected]> * Removed operator local fix and use newly released MONAI App SDK v3.5.1 release Signed-off-by: M Q <[email protected]> * Removed local copy of operator that had a temp fix Signed-off-by: M Q <[email protected]> * Add proper callback message Signed-off-by: M Q <[email protected]> * Proper json string and security fix Signed-off-by: M Q <[email protected]> * Fix complaints Signed-off-by: M Q <[email protected]> * Updated readme Signed-off-by: M Q <[email protected]> * Update per review comments Signed-off-by: M Q <[email protected]> * More update Signed-off-by: M Q <[email protected]> * Set header Signed-off-by: M Q <[email protected]> * Added packaging and running MAP of the REST service Signed-off-by: M Q <[email protected]> * Add app.yaml that has missed the checkin Signed-off-by: M Q <[email protected]> * pin monai<=1.5.0 for now as 1.5.1 has breaking changes Signed-off-by: M Q <[email protected]> * Add CCHMC nnUNet fifteen checkpoint application example Signed-off-by: Elan Somasundaram <[email protected]> Signed-off-by: chezhia <[email protected]> * Update README documentation Signed-off-by: Elan Somasundaram <[email protected]> Signed-off-by: chezhia <[email protected]> * flake8 fixed Signed-off-by: chezhia <[email protected]> * all tests pass Signed-off-by: chezhia <[email protected]> * Make affine and space metadata consistent as well as updating support of latest holoscan SDK CUDA 12 version (#565) * Make affine and space consistent as space is properly parse by MONAI transforms Signed-off-by: M Q <[email protected]> * Typing improvements Signed-off-by: M Q <[email protected]> * Make image metadata Affine and Space consistent, either LPS or RAS Signed-off-by: M Q <[email protected]> * Update monai/deploy/operators/monai_seg_inference_operator.py Co-authored-by: Copilot <[email protected]> Signed-off-by: Ming M Qin <[email protected]> * Correct CoPilot suggested code which failed liniting Signed-off-by: M Q <[email protected]> * Fix complaint from new version of mypy Signed-off-by: M Q <[email protected]> * Support the latest holoscan SDK CUDA 12 version, holoscan-cu12 Signed-off-by: M Q <[email protected]> * Docs gen works with Python 3.10+ Signed-off-by: M Q <[email protected]> * Fix complaints on single quote vs dhouble quote for string Signed-off-by: M Q <[email protected]> * Making docs gen require python >= 3.10 Signed-off-by: M Q <[email protected]> * Fix docs build error on readthedocs, although local builds had no issues Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Ming M Qin <[email protected]> Co-authored-by: Copilot <[email protected]> * Mq/release 3.3 (#567) * Update release notes for v3.3.0 Signed-off-by: M Q <[email protected]> * Update the index file Signed-off-by: M Q <[email protected]> * Bump version: 3.2.0 → 3.3.0 Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> * Use string enum for status Signed-off-by: M Q <[email protected]> * Fix the lovely formatting complaint Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Elan Somasundaram <[email protected]> Signed-off-by: chezhia <[email protected]> Signed-off-by: Ming M Qin <[email protected]> Co-authored-by: Elan Somasundaram <[email protected]> Co-authored-by: Copilot <[email protected]>
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This Pull Request is to ensure the volume image have consistent affine and space metadata after it is converted from DICOM instances.
As described in [BUG] Examples using older MONAI Bundles not compatible with MONAI v1.5.1 (which reveals errors in older MONAI bundles) #557 , the affine derived from the DICOM metadata had been switched to be in
RAS+space to be more aligned with the norm of MONAI models/bundles, while the original orientation from the DICOMImage Orientation Patientmetadata is inLPS+.The resulting
spacemetadata for the converted image was then supposedly to be switched toRASfromLPS, but was inadvertently missed due partly to the fact that this metadata was ignored in the MONAI Orientation transform in v1.5.0 and below. Now with MONAI v1.5.1 parsing and using this data, this inconsistency causes image flipping issues.So
affineandspaceconsistentTest result:
Changes were tested by running the example apps and Jupyter notebook.