Skim2257 quick fix #26
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skim2257
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May 17, 2022
* Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381
skim2257
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Jun 25, 2022
* ops using segmentation masks now accept Segmentation * simplified loader/writer specification in IO ops * 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 fab58d2. * 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 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: Sejin Kim <hello@sejin.kim> Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster>
skim2257
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Jun 25, 2022
* 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 fab58d2. * 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
skim2257
added a commit
that referenced
this pull request
Jun 25, 2022
* Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381
skim2257
added a commit
that referenced
this pull request
Jun 25, 2022
* 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 fab58d2. * 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 Former-commit-id: 03f9957 * PT/RTDOSE metadata to csv Former-commit-id: 08616a5 * fixed some bugs in autopipeline.py Former-commit-id: e05ea38 * now the pipeline saves on exit Former-commit-id: 9cd421d * deleted data Former-commit-id: d3e6b6a * now checks for existing subject id Former-commit-id: bf4de75 * uncommented one line pytest Former-commit-id: 3dc8cd3 * uncommented one line pytest Former-commit-id: 2b9d6d4 * 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 Former-commit-id: 1cd8984 * Create build-ci.yml * Update build-ci.yml * Update requirements.txt * bug fixes_1.0 Former-commit-id: d255674 * test and autopipe fixed Former-commit-id: 9cc88b1 * bug fixes 2 Former-commit-id: e7f4b42 * bug fixes 2 Former-commit-id: 90732d8 * added visualizations and some more bug fixes Former-commit-id: 735b26c * 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 Former-commit-id: 1528efc * small bug fix Former-commit-id: 7a27ee3 * added demo.py Former-commit-id: b644919 * Ready for * Create main.yml (#15) * Changed dataset class returns Former-commit-id: 3c6d7f5 * fix conflicts Former-commit-id: caad95a * fixed test autopipe Former-commit-id: 63b9543 * 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 Former-commit-id: d81a74d * 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 Former-commit-id: 8d345fb * added tests for Dataset class Former-commit-id: 7747a81 * Create LICENSE (#20) * Create LICENSE * Update setup.py * Seg.nrrd quick fix * Minor bug fixes Former-commit-id: f18aa1b * test fix Former-commit-id: 2fad37e * Added demo Former-commit-id: 48ea411 * Update setup.py (#23) Former-commit-id: 9e24716 * updated README Former-commit-id: 0f04145 * Update README.md (#24) Former-commit-id: 9aaf51b * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3c01806 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381 * first commit Former-commit-id: 971e8d6 * removed test files, changed gitignore Former-commit-id: ff42f8a * changed file directory structure for imageautooutput Former-commit-id: c2d8c68 * split mask up into each contour Former-commit-id: 7a8285c * change kwargs in put for basesubjectwriter Former-commit-id: a9f093c * still kinda failing... Former-commit-id: 358df05 * brought back basesubjectwriter Former-commit-id: 9a8ff65 * .imgtools directory Former-commit-id: 455c027 * changed absolute paths to relative paths Former-commit-id: e1e5d0d * changed os.path.join to pathlib.Path.as_posix() Former-commit-id: 042aa1f * removed unused cv2 import Former-commit-id: 9d5bc56 * removed cv2 import Former-commit-id: 36aab93 * appened is deprecated, changed to concat Former-commit-id: f6d997b * debug print Former-commit-id: 5a6caa5 * removed debug print Former-commit-id: 49c575a * added sparse mask class and generating function Former-commit-id: 8dab6bc * testing out sparse mask Former-commit-id: 19b0ad5 * funky NaN problem Former-commit-id: 7e96504 * commented sparse mask Former-commit-id: 915d769 * overwrite all subjects Former-commit-id: f0ebe6a * space Former-commit-id: eb30814 * overwrite false Former-commit-id: ff3a115 * metadata stuffs Former-commit-id: c236408 * metadata in dataset.csv Former-commit-id: ae09827 * added modalities, num rtstruct and pixel size to metadata Former-commit-id: 51634e6 * metadata bugfix Former-commit-id: 0042f14 * a Former-commit-id: f43b45e * fixed wrong variable names for metadata stuff Former-commit-id: 67449ca * fixed pathlib float error Former-commit-id: aa36b2d * relative paths and output folder paths for dataset.csv Former-commit-id: 2ce5ade * put metadata stuff into a util file Former-commit-id: 69f4ee7 * deal with empty metadata Former-commit-id: 31d0411 * messing around with sparse mask Former-commit-id: a66925c * tried to save sparse mask, did some stuff with nnunet output format Former-commit-id: 6b54305 * compliant with nnunet directory structure Former-commit-id: 1407e1d * CLI Interface, argparse moved to utils Former-commit-id: 6bf5f4f * fixed formatting problems with folder names Former-commit-id: 437db52 * train test split Former-commit-id: 15bab7b * train size and random state optional Former-commit-id: 3ac4016 * merge conflicts Former-commit-id: f96833d * changed warnings to not interrupt Former-commit-id: 154819e * changed to warnings.warn for generate_sparse_mask Former-commit-id: 1aec56d * merge Former-commit-id: 29bc242 * resolving conflicts? Former-commit-id: 0d16b02 * args Former-commit-id: f4f6d2d * changes for roi names as a dict Former-commit-id: 0479cb8 * added regex dictionary option for non nnunet runs Former-commit-id: eeae5b7 * sparse mask global labelling for contour name: index Former-commit-id: d65c6d8 * got rid of file_name_convention stuff Former-commit-id: effac09 * conflicts resolved Former-commit-id: ab1e87b * yaml thing Former-commit-id: 23b76e4 * added list capabilities for the roi names dictionary Former-commit-id: 2293242 * dataset.json for nnunet Former-commit-id: 156553f * CLI "autonew" Former-commit-id: c8351e4 * changed all mutable defaults to None Former-commit-id: 41630cd * moved autotest changes to autopipeline and addede a few CLI args Former-commit-id: d8ff8d7 * getting ready for merge to live Former-commit-id: a786724 * test_components, test_modalities works with new AutoPipeline Former-commit-id: e51fe82 * overwrite changes and error fix for nan paths again Former-commit-id: b138fe2 * fixed if statement Former-commit-id: c6a5f4d * joblib parallel Former-commit-id: 7a47740 * warnings for missing patients Former-commit-id: abc0428 * summary messages Former-commit-id: 6729aa5 * updated, passing tests. Updated version to 0.4 Former-commit-id: 81d6795 * update test Former-commit-id: 7bc3588 * yaml path cli Former-commit-id: 67ef10d * yaml error check Former-commit-id: fdeabd1 * pandas error Former-commit-id: 4745da2 * Fixed read_dicom_auto Former-commit-id: a9a297e * skips series check if seris is None Former-commit-id: eb8fb65 * updated readme to reflect v0.4 changes Former-commit-id: d355cf5 * updated readme Former-commit-id: 84d607f * minor change Former-commit-id: 6a02036 * remove .idea Former-commit-id: 8bd0a0f * remote .idea Former-commit-id: cf18c39 * git ignore Former-commit-id: 7d5b46a * refactor nnunetutils to nnunet Former-commit-id: d996869 * updated versions Former-commit-id: 41c8c88 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>
skim2257
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* Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381 Former-commit-id: d83fb0135155c4c94846c23614e75805db63cf37
skim2257
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Jun 25, 2022
* 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
skim2257
added a commit
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Jun 25, 2022
* 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 Former-commit-id: 941669e [formerly 03f9957] * PT/RTDOSE metadata to csv Former-commit-id: 34b9b7f [formerly 08616a5] * fixed some bugs in autopipeline.py Former-commit-id: f7a4031 [formerly e05ea38] * now the pipeline saves on exit Former-commit-id: 099d6ca [formerly 9cd421d] * deleted data Former-commit-id: 8c55bc4 [formerly d3e6b6a] * now checks for existing subject id Former-commit-id: d65b305 [formerly bf4de75] * uncommented one line pytest Former-commit-id: 797c47c [formerly 3dc8cd3] * uncommented one line pytest Former-commit-id: f3ba678 [formerly 2b9d6d4] * 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 Former-commit-id: 21a8546 [formerly 1cd8984] * Create build-ci.yml * Update build-ci.yml * Update requirements.txt * bug fixes_1.0 Former-commit-id: 384794a [formerly d255674] * test and autopipe fixed Former-commit-id: 2ef1bb6 [formerly 9cc88b1] * bug fixes 2 Former-commit-id: d523d79 [formerly e7f4b42] * bug fixes 2 Former-commit-id: c0aa46e [formerly 90732d8] * added visualizations and some more bug fixes Former-commit-id: bfc7839 [formerly 735b26c] * 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 Former-commit-id: bf97b7f [formerly 1528efc] * small bug fix Former-commit-id: c5de9fa [formerly 7a27ee3] * added demo.py Former-commit-id: fcd6610 [formerly b644919] * Ready for * Create main.yml (#15) * Changed dataset class returns Former-commit-id: 40c53e6 [formerly 3c6d7f5] * fix conflicts Former-commit-id: f2304e1 [formerly caad95a] * fixed test autopipe Former-commit-id: 12f9098 [formerly 63b9543] * 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 Former-commit-id: e620739 [formerly d81a74d] * 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 Former-commit-id: c44cfcd [formerly 8d345fb] * added tests for Dataset class Former-commit-id: 608b9c7 [formerly 7747a81] * Create LICENSE (#20) * Create LICENSE * Update setup.py * Seg.nrrd quick fix * Minor bug fixes Former-commit-id: 52cf95f [formerly f18aa1b] * test fix Former-commit-id: 424dc17 [formerly 2fad37e] * Added demo Former-commit-id: e8eb00b [formerly 48ea411] * Update setup.py (#23) Former-commit-id: a00e8f2 [formerly 9e24716] * updated README Former-commit-id: 4757ba8 [formerly c406bfc9526357e2091e1348d837c68cd5633801] [formerly 0f04145] * Update README.md (#24) Former-commit-id: 213a9a7 [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] [formerly 9aaf51b] * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: bfaaae9 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] [formerly 3c01806] * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: e942f7e [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly 5e93381] * first commit Former-commit-id: 7aa40dd [formerly d8ab6611d1233f9d30cc2b3fcfcd1e5e3ecb6b07] [formerly 971e8d6] * removed test files, changed gitignore Former-commit-id: fe47ed2 [formerly 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[formerly c6c303b9edbca9cac83b6d417e28cca11d763e2f] [formerly 7e96504] * commented sparse mask Former-commit-id: 59a894685fffb3cf9a7637c1b05e45c65e88fc24 [formerly 4857e6d3cbba5ca6e0b7225840a0215c6417abe4] [formerly 915d769] * overwrite all subjects Former-commit-id: 9a363bc044b845e0eefe4848fe7e1f1b935e0fbd [formerly 0c9dbf7794429d9ae1b07b233b7cc7afab53ff82] [formerly f0ebe6a] * space Former-commit-id: 2c29c5240901280de454bdd9bba068cdae4cdb64 [formerly 76e32213006c7e539134d9ff58317e351eb7f9f4] [formerly eb30814] * overwrite false Former-commit-id: a543516b1aaa5c95be63d0742a260621bb3f9565 [formerly ba00389611de0fb57a8600ee91ae2abddda94196] [formerly ff3a115] * metadata stuffs Former-commit-id: 1cc883fde3c03e5032b5fff818c0a7477eaa9bf8 [formerly cafb7dd92b568dad012c7a5aff300977545cf806] [formerly c236408] * metadata in dataset.csv Former-commit-id: 495be0c7138afc8736d619575cadfa2ad04e3608 [formerly ebe757ba380553f0146ae9863278e6a2d4e90cdb] [formerly ae09827] * added modalities, num rtstruct and pixel size to metadata Former-commit-id: 824dff5edad36be6564032c1d3e8f0c99d7648ff [formerly 8a922f22af15bc03873eb9506f5d6e4251ce87f8] [formerly 51634e6] * metadata bugfix Former-commit-id: 5b785f868771e591ab99db4453dc433a5f452247 [formerly 2784a5a0e188fd1db91773e911f7f8140a233314] [formerly 0042f14] * a Former-commit-id: 74d08455dfdce9eedfbe0aa3f994ac1b31dd4826 [formerly a86c79965207aaa572f32d394ac69d322217a8a2] [formerly f43b45e] * fixed wrong variable names for metadata stuff Former-commit-id: 6af5032314885c9fa27ff5d560dafe2b2e682ffe [formerly 716e4631a647d2f9ed74f497ce0de0c4d2d1a8cf] [formerly 67449ca] * fixed pathlib float error Former-commit-id: d88e5bdb7353c64e85d303ff09e0305c5ffac02c [formerly b90a56572ed01863a3b7bf82bf738f2408f6153d] [formerly aa36b2d] * relative paths and output folder paths for dataset.csv Former-commit-id: b263aa4d894fe21adeea7911dc139d601747ed0a [formerly 6d7a0a9cb299b11fac3679c99e1e650919ca7809] [formerly 2ce5ade] * put metadata stuff into a util file Former-commit-id: 732a68434e6f37d72c65e7cc701b3c5dca6833a1 [formerly cf894ec5e2c312b97b2c3f29abc758b78ac05bd0] [formerly 69f4ee7] * deal with empty metadata Former-commit-id: 3c02cba89c72bb66025c0479fb6a6a57ff597316 [formerly 47ac4fc0e2b571d4a618a75475011d0ce8c339e1] [formerly 31d0411] * messing around with sparse mask Former-commit-id: 03e625794f8b717e9ec87145c278e99460d247fb [formerly be555b7876505f07a34bf058bcee177653ca20cc] [formerly a66925c] * tried to save sparse mask, did some stuff with nnunet output format Former-commit-id: 72d1a9549f7dfb36efedd35461b437630b9a29f3 [formerly dbde3a7840296a376f8fed58a828d1f261441459] [formerly 6b54305] * compliant with nnunet directory structure Former-commit-id: 9150f3de85f07dfefb14283b5582a91d06037943 [formerly 3b2c07ac39e311f7f906671f8644a8b477e383ab] [formerly 1407e1d] * CLI Interface, argparse moved to utils Former-commit-id: 1b107a2669ac370dd90760faf2952898d88fe4b8 [formerly c13cd8b357c2edae1635254ee4d6159954e6e80e] [formerly 6bf5f4f] * fixed formatting problems with folder names Former-commit-id: a9eb4b030058a069335a8704e4925f0de2bb0473 [formerly 300ee2d95bc3fcc6545675f24661fb1f416f7895] [formerly 437db52] * train test split Former-commit-id: db3882971f1f961cec443e449111c71ac665f6e6 [formerly 305005399fb502199817eb435622b4ba4a81de7a] [formerly 15bab7b] * train size and random state optional Former-commit-id: cc03dba021510c01edf76a31d8b70751558876c6 [formerly 3308255c03f05615ccadd0fd931f0d902b2e5b4a] [formerly 3ac4016] * merge conflicts Former-commit-id: 8ff52b0fd72b316f8be7ac268da9b0a2ea0a61dd [formerly a656be7176df1771f21681d7df59f783e2c2dda5] [formerly f96833d] * changed warnings to not interrupt Former-commit-id: 1ca7741c16c5b04f851c7921bdc4bf0cfb0a57b4 [formerly f88061e09b4a6d271f778bd5889adbf3536b5e2d] [formerly 154819e] * changed to warnings.warn for generate_sparse_mask Former-commit-id: 1feda712797971e5a36320fd63126ca719a57d77 [formerly 597312fc926e2b97a4e805027e008d45fdf99716] [formerly 1aec56d] * merge Former-commit-id: ff8ce2b070216cb186f03f482785cfba9afffd22 [formerly 2cef89dbc46edc56252cd2f19aef3140d984a680] [formerly 29bc242] * resolving conflicts? Former-commit-id: 01a1f3fde11fef8535ea0b28e21857c976dbfe05 [formerly 92f19d8a14fe1c239968da5ebd714d3d46c68146] [formerly 0d16b02] * args Former-commit-id: c2219aa34ce847e7ef45c5313312468866a12d39 [formerly fb2cfa05a8a4d7d38d00ed577c89f18a1e34d75b] [formerly f4f6d2d] * changes for roi names as a dict Former-commit-id: 61ca8205f587076868c1f5292df10c7d70223a23 [formerly 63c94a0e2d99a982b4aaab2c4f93b7df46ae6b06] [formerly 0479cb8] * added regex dictionary option for non nnunet runs Former-commit-id: bd6ecddd1a789d551745d183029e1085f3f40ac9 [formerly 96571ba87279a56a70daab3a67598141f5e94c07] [formerly eeae5b7] * sparse mask global labelling for contour name: index Former-commit-id: a7e74efa4b971e6938a32781890717d68dedfcdb [formerly a6e60ffcfb64418abf48ea2f197ac8756e0ba2f8] [formerly d65c6d8] * got rid of file_name_convention stuff Former-commit-id: a26041eb99e93a1187897144354de34184a31cb8 [formerly fe7181c01ec460afff78c9d53e42c09b116593f5] [formerly effac09] * conflicts resolved Former-commit-id: 009d0a220a5c68e86dbb9620310737f6362c9844 [formerly eef9ba3d593416abcbe1fbd4b4cc67c0abdd79ea] [formerly ab1e87b] * yaml thing Former-commit-id: b6c34510abcf88db660c87b3eb6febc065c12557 [formerly 75e9d5502e30a417146c5dc593f405baf1bb1091] [formerly 23b76e4] * added list capabilities for the roi names dictionary Former-commit-id: 3673c52328420b58bf5633f52592e6df48dc95af [formerly 905ebfeb9724ffdd5e895f145fdb042bef7b9f60] [formerly 2293242] * dataset.json for nnunet Former-commit-id: b1144425cc6c499370d981eafdf24f7707595a23 [formerly 19f19ab7f235d9848f54f99ce3afed0040ff6560] [formerly 156553f] * CLI "autonew" Former-commit-id: 8e33cf5a2ee0d285f2f243b72fa1d10ee1a3a77e [formerly 71e5b751d9c83e0be441a52bc314b6def1c8c53a] [formerly c8351e4] * changed all mutable defaults to None Former-commit-id: e72e1e50633d56cd20ddd6b8e19c56bd650dd20c [formerly f1f225e4551b6d8a728d71b362a0cb0619df07ac] [formerly 41630cd] * moved autotest changes to autopipeline and addede a few CLI args Former-commit-id: 3698af5f0f0ab2e83e79d65749415915f1e531dd [formerly 55c91a8afcf22b1c1280103256ebc1c519ad701f] [formerly d8ff8d7] * getting ready for merge to live Former-commit-id: decd0fe54d13f23a0f0dd190cf812c5a507a182f [formerly 30b981fa409c4e5c7ada6d58418f298b351478d4] [formerly a786724] * test_components, test_modalities works with new AutoPipeline Former-commit-id: fcb3184ce3ff37b02fc030c7fad7b66ab7ececcc [formerly 7c7ab366d00183daa077681d74a16e09c7897e5c] [formerly e51fe82] * overwrite changes and error fix for nan paths again Former-commit-id: 423cd0e71c01feb457ad920904fe2e887c70695e [formerly ecc51505211d6173e6b614232f4980c7b2a3aa76] [formerly b138fe2] * fixed if statement Former-commit-id: ed57bd69287eab17b7ad3238df652e341729bd0f [formerly c0a10ed840cbf71c902edd9b12fe83eb0f03e633] [formerly c6a5f4d] * joblib parallel Former-commit-id: 6dc7d86b38520600a7afcf1d1df5f7af08e3834c [formerly 6dd94b9cdb121a1aac22a25084fd893a5e3bfab4] [formerly 7a47740] * warnings for missing patients Former-commit-id: 9a322f23144bde1e9718d2b3eaa882aa26e8838d [formerly df376a9a782322c15b56df52e5c93b5fa7cd16ea] [formerly abc0428] * summary messages Former-commit-id: f762b74fdbd7dcc4ccf8d77115ecd1cb0ce77345 [formerly 4bd68fff72c376be8b4cb149d9a0a9c3c1e77c87] [formerly 6729aa5] * updated, passing tests. Updated version to 0.4 Former-commit-id: 4749c41ca0d3ea0acc1552436accc03b8fbc2b46 [formerly 7ff2fc9eab44411dd6083418e1a47da687818d84] [formerly 81d6795] * update test Former-commit-id: 7a2c4fe052aa1cd927c4b1b4ea86b3eddfb44577 [formerly 756c3f15fa10a3d81c721c58a881fe73a89fe6d8] [formerly 7bc3588] * yaml path cli Former-commit-id: eb9b162b497d297909998189840d6599e3dd6a5f [formerly a949496578406d7424559c557b7111ab2a47c4bf] [formerly 67ef10d] * yaml error check Former-commit-id: 2d4df3538d8fc9ff9ae2fbc088481e69ace3c603 [formerly c8d6d77b19dcf488aacc647bbf6f5eaa21e444d3] [formerly fdeabd1] * pandas error Former-commit-id: 9622190857e20fa17ebae5cb701c278182014a2e [formerly 9dce7c9809282dc6a85d748171a8ff1c412d8c63] [formerly 4745da2] * Fixed read_dicom_auto Former-commit-id: fcaf7edeb3b45d840c2348a9390a76af0289f892 [formerly 347f1e1d22d5a27427f25fdf4f4a27b2f028a513] [formerly a9a297e] * skips series check if seris is None Former-commit-id: 480d450a1b53de81c0d95ae952cc408c2f132d93 [formerly 34d6e52e16297d89b1fe14a64e18b608d0bbbbbe] [formerly eb8fb65] * updated readme to reflect v0.4 changes Former-commit-id: efb59b2544d0ec8c061eb97387e8862cfd8aa5c4 [formerly 4b5d39c072a9d43c535c6b3770c2cd4095f3e685] [formerly d355cf5] * updated readme Former-commit-id: 3acbd335dc773c09d5fea9837306082ed60c9c1c [formerly 29ec4759bcb7fec2c930b9e40dd00ed2ed77e8bc] [formerly 84d607f] * minor change Former-commit-id: 7a14eb65f36888ed3aad61d12d0e00acdbcd8993 [formerly 92f7b812c855b1026f32ee2697e23e70b974c504] [formerly 6a02036] * remove .idea Former-commit-id: 05d7a38d8cfb15806bf732822d0ec928ba77e108 [formerly 94d2ecbf167651819e828eca69445a69ef627fd4] [formerly 8bd0a0f] * remote .idea Former-commit-id: 844a85d794b13a74179515b9450cebc6c5a40e9a [formerly aa9eafea5fa992c46cf1bda5ca3f00b5b1ec1f02] [formerly cf18c39] * git ignore Former-commit-id: f0590a6162204eb487716ea9aac9f398dee837fa [formerly e3a31a1dc0121f146f455773fafa8e791675c49c] [formerly 7d5b46a] * refactor nnunetutils to nnunet Former-commit-id: 6d89ab1ce84d16a9a759f45530fc87eab46962d5 [formerly 8ae957266df825e1687e1d49a6114b6e657240e8] [formerly d996869] * updated versions Former-commit-id: 980b5ea62602c4194a6a3014ce04d34e348bce8f [formerly 66542e225383a7edc3d21e06b728a17ccdf4761a] [formerly 41c8c88] 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: a17183d Former-commit-id: 9535d8f43d2c6437176fe22c7c249481b23c777c
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this pull request
Jun 27, 2022
* 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 Former-commit-id: 03f9957 * PT/RTDOSE metadata to csv Former-commit-id: 08616a5 * fixed some bugs in autopipeline.py Former-commit-id: e05ea38 * now the pipeline saves on exit Former-commit-id: 9cd421d * deleted data Former-commit-id: d3e6b6a * now checks for existing subject id Former-commit-id: bf4de75 * uncommented one line pytest Former-commit-id: 3dc8cd3 * uncommented one line pytest Former-commit-id: 2b9d6d4 * 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 Former-commit-id: 1cd8984 * Create build-ci.yml * Update build-ci.yml * Update requirements.txt * bug fixes_1.0 Former-commit-id: d255674 * test and autopipe fixed Former-commit-id: 9cc88b1 * bug fixes 2 Former-commit-id: e7f4b42 * bug fixes 2 Former-commit-id: 90732d8 * added visualizations and some more bug fixes Former-commit-id: 735b26c * 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 Former-commit-id: 1528efc * small bug fix Former-commit-id: 7a27ee3 * added demo.py Former-commit-id: b644919 * Ready for * Create main.yml (#15) * Changed dataset class returns Former-commit-id: 3c6d7f5 * fix conflicts Former-commit-id: caad95a * fixed test autopipe Former-commit-id: 63b9543 * 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 Former-commit-id: d81a74d * 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 Former-commit-id: 8d345fb * added tests for Dataset class Former-commit-id: 7747a81 * Create LICENSE (#20) * Create LICENSE * Update setup.py * Seg.nrrd quick fix * Minor bug fixes Former-commit-id: f18aa1b * test fix Former-commit-id: 2fad37e * Added demo Former-commit-id: 48ea411 * Update setup.py (#23) Former-commit-id: 9e24716 * updated README Former-commit-id: 0f04145 Former-commit-id: c406bfc9526357e2091e1348d837c68cd5633801 * Update README.md (#24) Former-commit-id: 9aaf51b Former-commit-id: 4e7335ef07059daa9dd3743e0727d63610e9da62 * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3c01806 Former-commit-id: 12b031d46c1c3ddbd1917b4037d9164ca3402ff2 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381 Former-commit-id: d83fb0135155c4c94846c23614e75805db63cf37 * first commit Former-commit-id: 971e8d6 Former-commit-id: d8ab6611d1233f9d30cc2b3fcfcd1e5e3ecb6b07 * removed test files, changed gitignore Former-commit-id: ff42f8a Former-commit-id: 7eaef9c15385ac64d755c8f95cfdc31c8d1c92e3 * changed file directory structure for imageautooutput Former-commit-id: c2d8c68 Former-commit-id: 77425123598eecd2c3911ca150142b7d3703fd01 * split mask up into each contour Former-commit-id: 7a8285c Former-commit-id: 3607e0b8a2b74b8ba859b5aeceab6019cf28a620 * change kwargs in put for basesubjectwriter Former-commit-id: a9f093c Former-commit-id: e7747e4a255aa0b53f5788d92db01b1ac4df2b32 * still kinda failing... 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a mask from RTSTRUCT * Fix slice matching issue when generating binary mask from RTStruct * CLI "autonew" Former-commit-id: 8e33cf5a2ee0d285f2f243b72fa1d10ee1a3a77e [formerly 71e5b751d9c83e0be441a52bc314b6def1c8c53a] [formerly c8351e4] Former-commit-id: c818a4c Former-commit-id: 160208aa5919b57bfb6ea552d8a583919a19feee * changed all mutable defaults to None Former-commit-id: e72e1e50633d56cd20ddd6b8e19c56bd650dd20c [formerly f1f225e4551b6d8a728d71b362a0cb0619df07ac] [formerly 41630cd] Former-commit-id: f626aaa Former-commit-id: a31c31bcfa4e66e9ba60710c7826bd16046af3a7 * remote .idea Former-commit-id: 844a85d794b13a74179515b9450cebc6c5a40e9a [formerly aa9eafea5fa992c46cf1bda5ca3f00b5b1ec1f02] [formerly cf18c39] Former-commit-id: abab7e9 Former-commit-id: d18186a612ac3f4c77f2fa6fc5e104b341bc1ab7 * git ignore Former-commit-id: f0590a6162204eb487716ea9aac9f398dee837fa [formerly e3a31a1dc0121f146f455773fafa8e791675c49c] [formerly 7d5b46a] Former-commit-id: 04668ec Former-commit-id: 705ae3b7631140cbaf362e853c9c4ceb62233ec8 Co-authored-by: mkazmier <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>
skim2257
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Jul 6, 2022
* uncommented one line pytest Former-commit-id: 3dc8cd3 * uncommented one line pytest Former-commit-id: 01fb59285920aaa2fd8c3f355feab86619938568 [formerly 6da65dd] [formerly 6da65dd [formerly 3dc8cd3]] Former-commit-id: fa09db6 Former-commit-id: 652bd34dc69873469e060381ef0d8995d93335b5 * uncommented one line pytest * uncommented one line pytest Former-commit-id: 2b9d6d4 * uncommented one line pytest Former-commit-id: 7aa572b0b68fa17a57d73a7b5f677af269e19154 [formerly 3f87849] [formerly 3f87849 [formerly 2b9d6d4]] Former-commit-id: 11196a3 Former-commit-id: 2046fb64b2d129db338c3d3f2a70e3640eea80ab * 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> Former-commit-id: f2480c3 * 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 Former-commit-id: 1cd8984 * Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset Former-commit-id: 29118a6 [formerly 29118a6 [formerly 1cd8984]] Former-commit-id: ea70778 Former-commit-id: aa2d95a7888dd213554c627c0d76b4237a1967bf * Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset * Create build-ci.yml Former-commit-id: 5a0e945 * Create build-ci.yml * Update build-ci.yml Former-commit-id: 33a1d60 * Update build-ci.yml * Update requirements.txt Former-commit-id: fcd6cb4 * Update requirements.txt * bug fixes_1.0 Former-commit-id: d255674 * bug fixes_1.0 Former-commit-id: 3344042ddfb1ef709ec4fa02628c0c97a6ebd477 [formerly a27dc3c] [formerly a27dc3c [formerly d255674]] Former-commit-id: 63604ae Former-commit-id: b7161a48f3fffb445336ea2a3d827cdb5686deab * bug fixes_1.0 * test and autopipe fixed Former-commit-id: 9cc88b1 * test and autopipe fixed Former-commit-id: bbd1dc9a718bf69247befc0e1e99d1c75519eeef [formerly 2aca001] [formerly 2aca001 [formerly 9cc88b1]] Former-commit-id: 0784880 Former-commit-id: a402b01f18507176c1de523fb5e978552ea8f01c * test and autopipe fixed * bug fixes 2 Former-commit-id: e7f4b42 * bug fixes 2 Former-commit-id: a513f1a9102c236845fa273100bb39112b092bf7 [formerly 374041f] [formerly 374041f [formerly e7f4b42]] Former-commit-id: 15bc931 Former-commit-id: 4dd4c4a0b4238a97d93d3df36268108de9c7fb2a * bug fixes 2 * bug fixes 2 Former-commit-id: 90732d8 * bug fixes 2 Former-commit-id: 5ed5f32cea580aab518d28154a9e47c5b344c3c6 [formerly ad812ba] [formerly ad812ba [formerly 90732d8]] Former-commit-id: 843025f Former-commit-id: ab086810cefee5270450561b6db2cfb999416c27 * bug fixes 2 * added visualizations and some more bug fixes Former-commit-id: 735b26c * added visualizations and some more bug fixes Former-commit-id: 68280704e6bdc7afb814166dc4d9ea1c69cc0111 [formerly 2daaf02] [formerly 2daaf02 [formerly 735b26c]] Former-commit-id: 9bdf715 Former-commit-id: 856e72bf73fef22350f1d53fcad601fe3d76798e * added visualizations and some more bug fixes * Create manual-test.yml Former-commit-id: d0b495c * Create manual-test.yml * Update build-ci.yml Former-commit-id: f77c367 * Update build-ci.yml * Update manual-test.yml Former-commit-id: c17f6b5 * 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> Former-commit-id: 47f3122 * 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 Former-commit-id: 1528efc * fixed bugs regarding multiple connections, saving of metadata and loading of metadata Former-commit-id: ab236e5 [formerly ab236e5 [formerly 1528efc]] Former-commit-id: 3e374bf Former-commit-id: 82e0e186b9d508c398f798469326c643cd6527c2 * fixed bugs regarding multiple connections, saving of metadata and loading of metadata * small bug fix Former-commit-id: 7a27ee3 * small bug fix Former-commit-id: 43e3c6b [formerly 43e3c6b [formerly 7a27ee3]] Former-commit-id: 9c20b59 Former-commit-id: 137b961a46c61f43f19f56f0c2564d14992a3d56 * small bug fix * added demo.py Former-commit-id: b644919 * added demo.py Former-commit-id: 64a7701 [formerly 64a7701 [formerly b644919]] Former-commit-id: 3b3ca59 Former-commit-id: 52754c4f09646cc9386b8f2699a2718edb77eaf8 * added demo.py * Ready for Former-commit-id: 9e5d03a * Ready for * Create main.yml (#15) Former-commit-id: 700fbe6 * Create main.yml (#15) * Changed dataset class returns Former-commit-id: 3c6d7f5 * Changed dataset class returns Former-commit-id: caa9c4d839ff599f63c9ad68c9bc4e844d96092d [formerly 180fe18] [formerly 180fe18 [formerly 3c6d7f5]] Former-commit-id: 8a66def Former-commit-id: 51ff2b743a26bfc2ec123e67a1cf8e77245aa75a * Changed dataset class returns * fix conflicts Former-commit-id: caad95a * fix conflicts Former-commit-id: 3e769f713eead224f382b5abe98f9f90c69fcc65 [formerly c70d9c8] [formerly c70d9c8 [formerly caad95a]] Former-commit-id: c207bb5 Former-commit-id: 0cf3b71107adb75b3ebf4c2babf2ba344e7b91cd * fix conflicts * fixed test autopipe Former-commit-id: 63b9543 * fixed test autopipe Former-commit-id: eb71a6ece7d1b92ce1575fbf38354fde98ccc697 [formerly 3817bbb] [formerly 3817bbb [formerly 63b9543]] Former-commit-id: dc5e065 Former-commit-id: 0de4a6d07c1b07618fa0e6ddd0bf5ce4553aa8ca * 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> Former-commit-id: 539777c * 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 Former-commit-id: d81a74d * fix path backslash issues Former-commit-id: c9fcbbe [formerly c9fcbbe [formerly d81a74d]] Former-commit-id: 0dd174d Former-commit-id: 26d44c87a36a8ed5cd64b5553ac8bf5a1c5e7af3 * 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> Former-commit-id: 5c6f7b0 * 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 Former-commit-id: c0bf276 * Update main.yml * Update main.yml Former-commit-id: f539726 * Update main.yml * Update README.md Former-commit-id: acf8cfb * 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 Former-commit-id: 9011025 * 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 Former-commit-id: 2a36b04 * Update README.md * Update README.md (#19) Former-commit-id: bde03e1 * Update README.md (#19) * Update README.md Former-commit-id: edb278f * Update README.md * added tests for Dataset class Former-commit-id: 8d345fb * added tests for Dataset class Former-commit-id: d75ee6e437692650f4a7d62833946161acb12d79 [formerly abfd4db] [formerly abfd4db [formerly 8d345fb]] Former-commit-id: d8a5980 Former-commit-id: 3b16fbef699e13a000b61cfcc6a031c455b5abac * added tests for Dataset class * added tests for Dataset class Former-commit-id: 7747a81 * added tests for Dataset class Former-commit-id: 71334289e578249681a435d7781c8955b6cabe1d [formerly 1f9c17c] [formerly 1f9c17c [formerly 7747a81]] Former-commit-id: bcff97c Former-commit-id: 21f753f606167a4258d70f8ac6f8fc23d3a8d175 * added tests for Dataset class * Create LICENSE (#20) * Create LICENSE * Update setup.py Former-commit-id: 7ec143e * Create LICENSE (#20) * Create LICENSE * Update setup.py * Seg.nrrd quick fix Former-commit-id: 7f3b5c6 * Seg.nrrd quick fix * Minor bug fixes Former-commit-id: f18aa1b * Minor bug fixes Former-commit-id: 7162d45 [formerly 7162d45 [formerly f18aa1b]] Former-commit-id: 96c6e3e Former-commit-id: 0858b138f03a568de16d582d42509ba40dc40903 * Minor bug fixes * test fix Former-commit-id: 2fad37e * test fix Former-commit-id: d55216a [formerly d55216a [formerly 2fad37e]] Former-commit-id: 5e3f932 Former-commit-id: 37aa5e3e74d6e25b4f8766938462a60601c29ab3 * test fix * Added demo Former-commit-id: 48ea411 * Added demo Former-commit-id: 1ec6966 [formerly 1ec6966 [formerly 48ea411]] Former-commit-id: fe9d3f4 Former-commit-id: a054f7d9cba105a4d40f2605ad6ea5e954b4a1a1 * Added demo * Update setup.py (#23) Former-commit-id: 9e24716 * Update setup.py (#23) Former-commit-id: ce8e287 [formerly ce8e287 [formerly 9e24716]] Former-commit-id: b9fe363 Former-commit-id: 0cb0b099ffa6d3d67738f40e211e566049a109ca * Update setup.py (#23) * updated README Former-commit-id: 0f04145 * updated README Former-commit-id: e35f91d [formerly e35f91d [formerly 0f04145]] Former-commit-id: bc9c6a2 Former-commit-id: d353efbbdace157b77f9bedf74654b5b96cda5f9 * updated README * Update README.md (#24) Former-commit-id: 9aaf51b * Update README.md (#24) Former-commit-id: 27494c0 [formerly 27494c0 [formerly 9aaf51b]] Former-commit-id: 84c0753 Former-commit-id: 63106282d3b55f6d008ae03c60c4a32babcb7d1b * Update README.md (#24) * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3c01806 * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3cdc5eb2ad84488f20323b1933c4285eac78d60d [formerly 11971c8] [formerly 11971c8 [formerly 3c01806]] Former-commit-id: b4abcac Former-commit-id: 2a0158397a55d783d6b627181a8af123952df3dc * preliminary MRI functionality (MR-RTSTRUCT pairs) * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5116186cc44acffc828b7983e84ec2db49b628cb [formerly 65d66d2] [formerly 65d66d2 [formerly 5e93381]] Former-commit-id: 5b66da4 Former-commit-id: 9bbf4aebbf1978a63dd49de045cc91e4893a5237 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py * quick fixes Former-commit-id: 5e118add39a6796a6d03d9c6729146981da7f44f * quick fixes Former-commit-id: d444cb8e2b63900c7747d9a405125066fb67d88e [formerly 8ac1dfd] [formerly 8ac1dfd [formerly 5e118add39a6796a6d03d9c6729146981da7f44f]] Former-commit-id: b1c528e7b1f32acf42a18cd78f37b462bfa05171 Former-commit-id: 79e19c892e15d254c60b16b4ee67e9c16ca59f91 * 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 * transpose for nnunet * skip if no mask for nnunet and nnunet folder names * bugs in nnunet folder stuff * rename nnunetutil (again) * sorting the output streams * shell script * shell script in autopipeline * bug * forgot CopyInformation for nnunet * ignore deprecation warning * moved sh file down one dir * set -e for stopping execution if there is an error * broken checker for missing labels * train test fix for 1 patient * fix for broken self.existing_roi_names caused by joblib * added autotest to gitignore * sorted list for train test split Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> Co-authored-by: Sejin Kim <hello@sejin.kim> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster>
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* uncommented one line pytest Former-commit-id: 3dc8cd3 * uncommented one line pytest Former-commit-id: 01fb59285920aaa2fd8c3f355feab86619938568 [formerly 6da65dd] [formerly 6da65dd [formerly 3dc8cd3]] Former-commit-id: fa09db6 Former-commit-id: 652bd34dc69873469e060381ef0d8995d93335b5 * uncommented one line pytest * uncommented one line pytest Former-commit-id: 2b9d6d4 * uncommented one line pytest Former-commit-id: 7aa572b0b68fa17a57d73a7b5f677af269e19154 [formerly 3f87849] [formerly 3f87849 [formerly 2b9d6d4]] Former-commit-id: 11196a3 Former-commit-id: 2046fb64b2d129db338c3d3f2a70e3640eea80ab * 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> Former-commit-id: f2480c3 * 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 Former-commit-id: 1cd8984 * Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset Former-commit-id: 29118a6 [formerly 29118a6 [formerly 1cd8984]] Former-commit-id: ea70778 Former-commit-id: aa2d95a7888dd213554c627c0d76b4237a1967bf * Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset * Create build-ci.yml Former-commit-id: 5a0e945 * Create build-ci.yml * Update build-ci.yml Former-commit-id: 33a1d60 * Update build-ci.yml * Update requirements.txt Former-commit-id: fcd6cb4 * Update requirements.txt * bug fixes_1.0 Former-commit-id: d255674 * bug fixes_1.0 Former-commit-id: 3344042ddfb1ef709ec4fa02628c0c97a6ebd477 [formerly a27dc3c] [formerly a27dc3c [formerly d255674]] Former-commit-id: 63604ae Former-commit-id: b7161a48f3fffb445336ea2a3d827cdb5686deab * bug fixes_1.0 * test and autopipe fixed Former-commit-id: 9cc88b1 * test and autopipe fixed Former-commit-id: bbd1dc9a718bf69247befc0e1e99d1c75519eeef [formerly 2aca001] [formerly 2aca001 [formerly 9cc88b1]] Former-commit-id: 0784880 Former-commit-id: a402b01f18507176c1de523fb5e978552ea8f01c * test and autopipe fixed * bug fixes 2 Former-commit-id: e7f4b42 * bug fixes 2 Former-commit-id: a513f1a9102c236845fa273100bb39112b092bf7 [formerly 374041f] [formerly 374041f [formerly e7f4b42]] Former-commit-id: 15bc931 Former-commit-id: 4dd4c4a0b4238a97d93d3df36268108de9c7fb2a * bug fixes 2 * bug fixes 2 Former-commit-id: 90732d8 * bug fixes 2 Former-commit-id: 5ed5f32cea580aab518d28154a9e47c5b344c3c6 [formerly ad812ba] [formerly ad812ba [formerly 90732d8]] Former-commit-id: 843025f Former-commit-id: ab086810cefee5270450561b6db2cfb999416c27 * bug fixes 2 * added visualizations and some more bug fixes Former-commit-id: 735b26c * added visualizations and some more bug fixes Former-commit-id: 68280704e6bdc7afb814166dc4d9ea1c69cc0111 [formerly 2daaf02] [formerly 2daaf02 [formerly 735b26c]] Former-commit-id: 9bdf715 Former-commit-id: 856e72bf73fef22350f1d53fcad601fe3d76798e * added visualizations and some more bug fixes * Create manual-test.yml Former-commit-id: d0b495c * Create manual-test.yml * Update build-ci.yml Former-commit-id: f77c367 * Update build-ci.yml * Update manual-test.yml Former-commit-id: c17f6b5 * 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> Former-commit-id: 47f3122 * 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 Former-commit-id: 1528efc * fixed bugs regarding multiple connections, saving of metadata and loading of metadata Former-commit-id: ab236e5 [formerly ab236e5 [formerly 1528efc]] Former-commit-id: 3e374bf Former-commit-id: 82e0e186b9d508c398f798469326c643cd6527c2 * fixed bugs regarding multiple connections, saving of metadata and loading of metadata * small bug fix Former-commit-id: 7a27ee3 * small bug fix Former-commit-id: 43e3c6b [formerly 43e3c6b [formerly 7a27ee3]] Former-commit-id: 9c20b59 Former-commit-id: 137b961a46c61f43f19f56f0c2564d14992a3d56 * small bug fix * added demo.py Former-commit-id: b644919 * added demo.py Former-commit-id: 64a7701 [formerly 64a7701 [formerly b644919]] Former-commit-id: 3b3ca59 Former-commit-id: 52754c4f09646cc9386b8f2699a2718edb77eaf8 * added demo.py * Ready for Former-commit-id: 9e5d03a * Ready for * Create main.yml (#15) Former-commit-id: 700fbe6 * Create main.yml (#15) * Changed dataset class returns Former-commit-id: 3c6d7f5 * Changed dataset class returns Former-commit-id: caa9c4d839ff599f63c9ad68c9bc4e844d96092d [formerly 180fe18] [formerly 180fe18 [formerly 3c6d7f5]] Former-commit-id: 8a66def Former-commit-id: 51ff2b743a26bfc2ec123e67a1cf8e77245aa75a * Changed dataset class returns * fix conflicts Former-commit-id: caad95a * fix conflicts Former-commit-id: 3e769f713eead224f382b5abe98f9f90c69fcc65 [formerly c70d9c8] [formerly c70d9c8 [formerly caad95a]] Former-commit-id: c207bb5 Former-commit-id: 0cf3b71107adb75b3ebf4c2babf2ba344e7b91cd * fix conflicts * fixed test autopipe Former-commit-id: 63b9543 * fixed test autopipe Former-commit-id: eb71a6ece7d1b92ce1575fbf38354fde98ccc697 [formerly 3817bbb] [formerly 3817bbb [formerly 63b9543]] Former-commit-id: dc5e065 Former-commit-id: 0de4a6d07c1b07618fa0e6ddd0bf5ce4553aa8ca * 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> Former-commit-id: 539777c * 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 Former-commit-id: d81a74d * fix path backslash issues Former-commit-id: c9fcbbe [formerly c9fcbbe [formerly d81a74d]] Former-commit-id: 0dd174d Former-commit-id: 26d44c87a36a8ed5cd64b5553ac8bf5a1c5e7af3 * 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> Former-commit-id: 5c6f7b0 * 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 Former-commit-id: c0bf276 * Update main.yml * Update main.yml Former-commit-id: f539726 * Update main.yml * Update README.md Former-commit-id: acf8cfb * 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 Former-commit-id: 9011025 * 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 Former-commit-id: 2a36b04 * Update README.md * Update README.md (#19) Former-commit-id: bde03e1 * Update README.md (#19) * Update README.md Former-commit-id: edb278f * Update README.md * added tests for Dataset class Former-commit-id: 8d345fb * added tests for Dataset class Former-commit-id: d75ee6e437692650f4a7d62833946161acb12d79 [formerly abfd4db] [formerly abfd4db [formerly 8d345fb]] Former-commit-id: d8a5980 Former-commit-id: 3b16fbef699e13a000b61cfcc6a031c455b5abac * added tests for Dataset class * added tests for Dataset class Former-commit-id: 7747a81 * added tests for Dataset class Former-commit-id: 71334289e578249681a435d7781c8955b6cabe1d [formerly 1f9c17c] [formerly 1f9c17c [formerly 7747a81]] Former-commit-id: bcff97c Former-commit-id: 21f753f606167a4258d70f8ac6f8fc23d3a8d175 * added tests for Dataset class * Create LICENSE (#20) * Create LICENSE * Update setup.py Former-commit-id: 7ec143e * Create LICENSE (#20) * Create LICENSE * Update setup.py * Seg.nrrd quick fix Former-commit-id: 7f3b5c6 * Seg.nrrd quick fix * Minor bug fixes Former-commit-id: f18aa1b * Minor bug fixes Former-commit-id: 7162d45 [formerly 7162d45 [formerly f18aa1b]] Former-commit-id: 96c6e3e Former-commit-id: 0858b138f03a568de16d582d42509ba40dc40903 * Minor bug fixes * test fix Former-commit-id: 2fad37e * test fix Former-commit-id: d55216a [formerly d55216a [formerly 2fad37e]] Former-commit-id: 5e3f932 Former-commit-id: 37aa5e3e74d6e25b4f8766938462a60601c29ab3 * test fix * Added demo Former-commit-id: 48ea411 * Added demo Former-commit-id: 1ec6966 [formerly 1ec6966 [formerly 48ea411]] Former-commit-id: fe9d3f4 Former-commit-id: a054f7d9cba105a4d40f2605ad6ea5e954b4a1a1 * Added demo * Update setup.py (#23) Former-commit-id: 9e24716 * Update setup.py (#23) Former-commit-id: ce8e287 [formerly ce8e287 [formerly 9e24716]] Former-commit-id: b9fe363 Former-commit-id: 0cb0b099ffa6d3d67738f40e211e566049a109ca * Update setup.py (#23) * updated README Former-commit-id: 0f04145 * updated README Former-commit-id: e35f91d [formerly e35f91d [formerly 0f04145]] Former-commit-id: bc9c6a2 Former-commit-id: d353efbbdace157b77f9bedf74654b5b96cda5f9 * updated README * Update README.md (#24) Former-commit-id: 9aaf51b * Update README.md (#24) Former-commit-id: 27494c0 [formerly 27494c0 [formerly 9aaf51b]] Former-commit-id: 84c0753 Former-commit-id: 63106282d3b55f6d008ae03c60c4a32babcb7d1b * Update README.md (#24) * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3c01806 * preliminary MRI functionality (MR-RTSTRUCT pairs) Former-commit-id: 3cdc5eb2ad84488f20323b1933c4285eac78d60d [formerly 11971c8] [formerly 11971c8 [formerly 3c01806]] Former-commit-id: b4abcac Former-commit-id: 2a0158397a55d783d6b627181a8af123952df3dc * preliminary MRI functionality (MR-RTSTRUCT pairs) * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5e93381 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py Former-commit-id: 5116186cc44acffc828b7983e84ec2db49b628cb [formerly 65d66d2] [formerly 65d66d2 [formerly 5e93381]] Former-commit-id: 5b66da4 Former-commit-id: 9bbf4aebbf1978a63dd49de045cc91e4893a5237 * Skim2257 quick fix (#26) * Updated crawler to force String on all meta fields * Update setup.py * quick fixes Former-commit-id: 5e118add39a6796a6d03d9c6729146981da7f44f * quick fixes Former-commit-id: d444cb8e2b63900c7747d9a405125066fb67d88e [formerly 8ac1dfd] [formerly 8ac1dfd [formerly 5e118add39a6796a6d03d9c6729146981da7f44f]] Former-commit-id: b1c528e7b1f32acf42a18cd78f37b462bfa05171 Former-commit-id: 79e19c892e15d254c60b16b4ee67e9c16ca59f91 * 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 * transpose for nnunet * skip if no mask for nnunet and nnunet folder names * bugs in nnunet folder stuff * rename nnunetutil (again) * sorting the output streams * shell script * shell script in autopipeline * bug * forgot CopyInformation for nnunet * ignore deprecation warning * moved sh file down one dir * set -e for stopping execution if there is an error * broken checker for missing labels * train test fix for 1 patient * fix for broken self.existing_roi_names caused by joblib * added autotest to gitignore * sorted list for train test split * custom train test split * custom train test split Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> Co-authored-by: Sejin Kim <hello@sejin.kim> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster>
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