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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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