Unknown
* Subseries (61)
* subseries implementation step 1
* Fixes for issues 57, 53.
* update README.
* fixed pytest error ([`f8f3606`](https://github.com/bhklab/med-imagetools/commit/f8f3606f4340e57e224bbc1ea0b33398db39b61b))
* update github actions ([`4adf148`](https://github.com/bhklab/med-imagetools/commit/4adf148f30fbd0772b514c0a2ae90b2b088037ea))
* Update build-pkg.yml ([`ec167b7`](https://github.com/bhklab/med-imagetools/commit/ec167b731df27b245be615105b474d79bd83389f))
* Update build-pkg.yml ([`4154d26`](https://github.com/bhklab/med-imagetools/commit/4154d267ef4675a185f5cba520756f7728b65e1d))
* Update build-pkg.yml ([`b2ab181`](https://github.com/bhklab/med-imagetools/commit/b2ab18129e24d248c358b9d7127502d176da4ca7))
* Update build-pkg.yml ([`be566e8`](https://github.com/bhklab/med-imagetools/commit/be566e8cb568c39ca007844c068b220341f9810f))
* Update build-pkg.yml ([`8265aff`](https://github.com/bhklab/med-imagetools/commit/8265aff2ea33f2a94393df5eee5ce60afdc33acd))
* Merge pull request 60 from bhklab/sw-fix
Sw fix ([`91330f0`](https://github.com/bhklab/med-imagetools/commit/91330f063467731bc42c310d58306d5de2a16e65))
* Merge branch &39;master&39; of github.com:bhklab/med-imagetools into sw-fix ([`c743a98`](https://github.com/bhklab/med-imagetools/commit/c743a9804382a45ec283d12e34342a48959a7a9b))
* Update build-pkg.yml ([`072d597`](https://github.com/bhklab/med-imagetools/commit/072d597dddde90a899a43f0144fc97474478752b))
* Skim2257 patch 1 (59)
* Update README.md
* Update setup.py
* Update build-pkg.yml ([`ce5ee0c`](https://github.com/bhklab/med-imagetools/commit/ce5ee0c0fcf0735407cf8bedbf42aa9e95c4e8e9))
* updated dose ([`645aae7`](https://github.com/bhklab/med-imagetools/commit/645aae7fd039bb60798ef48777b407a6e1b2fa78))
* Merge branch &39;master&39; of github.com:bhklab/med-imagetools into sw-fix ([`c6f8376`](https://github.com/bhklab/med-imagetools/commit/c6f8376c216a4828c8746eb74e86a8ad8d39e480))
* temporary dose fix loading error with Sejin ([`abb452f`](https://github.com/bhklab/med-imagetools/commit/abb452f1a1b3fd4c2ad4f7538116ca39d6adf64f))
* Update README.md (58) ([`edb8612`](https://github.com/bhklab/med-imagetools/commit/edb86123a4eae8394bf08ecee51d0ce68ca95273))
* Update build-pkg.yml ([`954b224`](https://github.com/bhklab/med-imagetools/commit/954b22468682f779b89d2ea5ed851eb30b076de9))
* multi-modality fix
* adding test param for better QC
checking patient_ID error for issue 53
* Relative robust fix for issue 53
* Update setup.py
* Update README.md ([`bc43f29`](https://github.com/bhklab/med-imagetools/commit/bc43f29d96b0c4f6de11bc8fb9a57364ca764e55))
* Update setup.py ([`56faf21`](https://github.com/bhklab/med-imagetools/commit/56faf21378841d993756194e48857af5edae166b))
* Create LICENSE ([`a01891f`](https://github.com/bhklab/med-imagetools/commit/a01891fe9ba76ab3256ef73683126a83e246c6da))
* 1.0.0 (52)
* Update README.md
* Update setup.py ([`3ceaf19`](https://github.com/bhklab/med-imagetools/commit/3ceaf19dea6c622fddacee98670114ddcb34d37b))
* 0.4.4 (49)
* Update setup.py
* Update README.md
* readme changes
* Update README.md
* Delete autopipeline.png
Co-authored-by: Kevin <qukevin99gmail.com> ([`2d2079c`](https://github.com/bhklab/med-imagetools/commit/2d2079c8346869588ed3531af86e5ead07ac45d4))
* Delete autopipeline.png ([`6a5b7d0`](https://github.com/bhklab/med-imagetools/commit/6a5b7d0fe506abcd2bfb82fdea93e2bca84a8767))
* Markdown Report and new CLI options (48)
* markdown report generator
* update version to push to pypi
* working on changes for nnunet inference
* update version to push to pypi
* nnunet inference formatting
* dry run and continue flags
* fixed up dry run and continute processing
* fixing error that scout CT causes
* dill in requirements
* isabs for rel path args
* Update main-ci.yml
* fixed failing tests
* another pytest fix
* error check
* error check 2
* Update test_components.py
* test if values are working
* missing values?
* more ci tests
* more ci tests 2
* ci tests 3
* ci tests 4
* ci tests 5
* ci tests 5
* ci tests 6
* ci tests 7
* ci tests 7
* removed debugging prints
Co-authored-by: Sejin Kim <40668167+skim2257users.noreply.github.com> ([`37f89b9`](https://github.com/bhklab/med-imagetools/commit/37f89b9f111b18111674e962f9c3f86733c7833e))
* Update main-ci.yml ([`c6851d9`](https://github.com/bhklab/med-imagetools/commit/c6851d97aa4aaeda1d920799519b96998113ed65))
* Add files via upload ([`52364da`](https://github.com/bhklab/med-imagetools/commit/52364da5bfb0301f45fdc76270d037210253c2a5))
* Add files via upload ([`677221b`](https://github.com/bhklab/med-imagetools/commit/677221b19240f685731f6968082c676e2b441571))
* Add files via upload ([`99c90d2`](https://github.com/bhklab/med-imagetools/commit/99c90d252f976a97b454fbc81030e3c94be6edd5))
* Delete methodology.png ([`c960771`](https://github.com/bhklab/med-imagetools/commit/c960771c517e85f59f80e38ce337183170b91fa6))
* Delete autopipeline.png ([`51944f8`](https://github.com/bhklab/med-imagetools/commit/51944f8818b1eb0e83bbce7fd82943993c990b33))
* Add files via upload ([`d5599f1`](https://github.com/bhklab/med-imagetools/commit/d5599f19ea11c76c4a1888efccb065050923b1ec))
* Update readme (43)
* Update README.md
* redesigned autopipeline diagram
* Delete build-ci.yml
* Delete main.yml
* Delete manual-test.yml ([`d54d704`](https://github.com/bhklab/med-imagetools/commit/d54d7042e568363c9f664aba5120e0718aa2e3d1))
* Markdown report (42)
* markdown report generator
* update version to push to pypi
Co-authored-by: Kevin <qukevin99gmail.com> ([`3a2f742`](https://github.com/bhklab/med-imagetools/commit/3a2f7428992e6987cd5c34f99cecc1792d56be85))
* Nnunet demo (41)
* uncommented one line pytest
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* uncommented one line pytest
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* 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 <vishweshramanathangmail.com>
Former-commit-id: f2480c3bd2fba4498c609ef1efc031e1d4f7e2cd
* 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 <vishweshramanathangmail.com>
* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
* Create build-ci.yml
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* Create build-ci.yml
* Update build-ci.yml
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* Update build-ci.yml
* Update requirements.txt
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* Update requirements.txt
* bug fixes_1.0
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* bug fixes_1.0
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* bug fixes_1.0
* test and autopipe fixed
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* test and autopipe fixed
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* test and autopipe fixed
* bug fixes 2
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* bug fixes 2
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* bug fixes 2
* bug fixes 2
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* bug fixes 2
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* bug fixes 2
* added visualizations and some more bug fixes
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* added visualizations and some more bug fixes
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* added visualizations and some more bug fixes
* Create manual-test.yml
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* Create manual-test.yml
* Update build-ci.yml
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* Update build-ci.yml
* Update manual-test.yml
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5
* 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 <vishweshramanathangmail.com>
* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
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* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
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* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
* small bug fix
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* small bug fix
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* small bug fix
* added demo.py
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* added demo.py
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* Ready for
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* Ready for
* Create main.yml (15)
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* Create main.yml (15)
* Changed dataset class returns
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* fix conflicts
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* fixed test autopipe
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c
* 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 <vishweshramanathangmail.com>
* fix path backslash issues
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* fix path backslash issues
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 5c6f7b00b440c06a730ff7ee289e0dd0f146a4dd
* 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 <vishweshramanathangmail.com>
* Update main.yml
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* Update main.yml
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* Update main.yml
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* 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
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* 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
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* Update README.md
* Update README.md (19)
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* Update README.md (19)
* Update README.md
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* added tests for Dataset class
* Create LICENSE (20)
* Create LICENSE
* Update setup.py
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* Create LICENSE (20)
* Create LICENSE
* Update setup.py
* Seg.nrrd quick fix
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* Seg.nrrd quick fix
* Minor bug fixes
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* test fix
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* Added demo
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* Added demo
* Update setup.py (23)
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* updated README
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* updated README
* Update README.md (24)
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* Update README.md (24)
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* Update README.md (24)
* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
* quick fixes
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* quick fixes
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* 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 &34;autonew&34;
* 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 <vishweshramanathangmail.com>
Co-authored-by: Sejin Kim <40668167+skim2257users.noreply.github.com>
Co-authored-by: Sejin Kim <hellosejin.kim>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster> ([`f3e5307`](https://github.com/bhklab/med-imagetools/commit/f3e5307f9687d070ec848d028bd949996a0d9da0))
* Nnunet demo (40)
* uncommented one line pytest
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* 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 <vishweshramanathangmail.com>
Former-commit-id: f2480c3bd2fba4498c609ef1efc031e1d4f7e2cd
* 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 <vishweshramanathangmail.com>
* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
* Create build-ci.yml
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* Create build-ci.yml
* Update build-ci.yml
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* Update build-ci.yml
* Update requirements.txt
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* Update requirements.txt
* bug fixes_1.0
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* bug fixes_1.0
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* test and autopipe fixed
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* test and autopipe fixed
* bug fixes 2
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* bug fixes 2
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* bug fixes 2
* bug fixes 2
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* bug fixes 2
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* bug fixes 2
* added visualizations and some more bug fixes
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* added visualizations and some more bug fixes
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* Create manual-test.yml
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* Create manual-test.yml
* Update build-ci.yml
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* Update build-ci.yml
* Update manual-test.yml
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5
* 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 <vishweshramanathangmail.com>
* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
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* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
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* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
* small bug fix
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* small bug fix
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* small bug fix
* added demo.py
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* added demo.py
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* added demo.py
* Ready for
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* Ready for
* Create main.yml (15)
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* Create main.yml (15)
* Changed dataset class returns
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* Changed dataset class returns
* fix conflicts
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* fix conflicts
* fixed test autopipe
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* fixed test autopipe
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c
* 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 <vishweshramanathangmail.com>
* fix path backslash issues
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* fix path backslash issues
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* 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 <vishweshramanathangmail.com>
Former-commit-id: 5c6f7b00b440c06a730ff7ee289e0dd0f146a4dd
* 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 <vishweshramanathangmail.com>
* Update main.yml
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* Update main.yml
* Update main.yml
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* Update main.yml
* Update README.md
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* 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
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* 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
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* Update README.md
* Update README.md (19)
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* Update README.md (19)
* Update README.md
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* Update README.md
* added tests for Dataset class
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* added tests for Dataset class
* Create LICENSE (20)
* Create LICENSE
* Update setup.py
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* Create LICENSE (20)
* Create LICENSE
* Update setup.py
* Seg.nrrd quick fix
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* Seg.nrrd quick fix
* Minor bug fixes
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* Minor bug fixes
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* Minor bug fixes
* test fix
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* test fix
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* test fix
* Added demo
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* Added demo
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* Added demo
* Update setup.py (23)
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* Update setup.py (23)
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* Update setup.py (23)
* updated README
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* updated README
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* updated README
* Update README.md (24)
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* Update README.md (24)
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* Update README.md (24)
* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
* quick fixes
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* quick fixes
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* 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 &34;autonew&34;
* 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 <vishweshramanathangmail.com>
Co-authored-by: Sejin Kim <40668167+skim2257users.noreply.github.com>
Co-authored-by: Sejin Kim <hellosejin.kim>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster> ([`31cecbe`](https://github.com/bhklab/med-imagetools/commit/31cecbeb04078bdf97beccc03682cecd0b72d918))
* Update README.md ([`c39ffe6`](https://github.com/bhklab/med-imagetools/commit/c39ffe6f4775e4bdd8218ff8b983ad21bc03cee1))
* Ci update (39)
* new ci/cd actions
* updated pathing too
* updated ci/cd actions
* update
* update ([`df61201`](https://github.com/bhklab/med-imagetools/commit/df61201ff26765f1f37a3a6c670f57a057eaa764))
* Update build-pkg.yml ([`5a314e5`](https://github.com/bhklab/med-imagetools/commit/5a314e5a873f3ec308ef8cb10bc1cceada1bdc2c))
* Update build-pkg.yml ([`630c184`](https://github.com/bhklab/med-imagetools/commit/630c1844d0781ba5c6e14065ccdcb6b65a83a5dd))
* Update build-pkg.yml ([`1ff1b2b`](https://github.com/bhklab/med-imagetools/commit/1ff1b2ba533640c76b3c12c5e913fc3fc3241a95))
* Create build-pkg.yml ([`c9d1f42`](https://github.com/bhklab/med-imagetools/commit/c9d1f4214fa4664c89bccd326cf8195ad00671e9))
* post-rebase (38)
* 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 &34;fixed index column handling in ImageCSVLoader&34;
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
* 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: 03f99572453723e4a3e895acac0996997f090168
* PT/RTDOSE metadata to csv
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* fixed some bugs in autopipeline.py
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* now the pipeline saves on exit
Former-commit-id: 9cd421dd778df1afc6eb3e8a30a032f676f9b3b3
* deleted data
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* now checks for existing subject id
Former-commit-id: bf4de755d0618dd037c32b5365a05d939878067f
* uncommented one line pytest
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* uncommented one line pytest
Former-commit-id: 2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe
* 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 <vishweshramanathangmail.com>
* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
Former-commit-id: 1cd89845970f294417d95d0792bdcb817b0324d7
* Create build-ci.yml
* Update build-ci.yml
* Update requirements.txt
* bug fixes_1.0
Former-commit-id: d2556741284260f74609ead96c2e64621af8511a
* test and autopipe fixed
Former-commit-id: 9cc88b1b402108310dbbc8e09a8b13730aa72102
* bug fixes 2
Former-commit-id: e7f4b424ecf5519ded2352b3d6266a7da07a5b07
* bug fixes 2
Former-commit-id: 90732d81ff1873e24cd501283e4cdd2326febd28
* added visualizations and some more bug fixes
Former-commit-id: 735b26c9de88e0a48b468f8fca490bcc68d4cf6c
* 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 <vishweshramanathangmail.com>
* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
Former-commit-id: 1528efc88ca4952ce570721832a339ff8274b4fa
* small bug fix
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* added demo.py
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* Ready for
* Create main.yml (15)
* Changed dataset class returns
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* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
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* bug fixes 2
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* added demo.py
* Changed dataset class returns
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Co-authored-by: Vishwesh <vishweshramanathangmail.com>
* fix path backslash issues
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* 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 <vishweshramanathangmail.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
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* removed linter
* Update setup.py
* Update README.md
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* Update README.md
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* Create LICENSE
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* Updated crawler to force String on all meta fields
* Update setup.py
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* metadata bugfix
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* CLI Interface, argparse moved to utils
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* changed to warnings.warn for generate_sparse_mask
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* args
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* changes for roi names as a dict
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* added regex dictionary option for non nnunet runs
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* sparse mask global labelling for contour name: index
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* got rid of file_name_convention stuff
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* conflicts resolved
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* yaml thing
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* added list capabilities for the roi names dictionary
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* dataset.json for nnunet
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* CLI &34;autonew&34;
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* changed all mutable defaults to None
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* moved autotest changes to autopipeline and addede a few CLI args
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* getting ready for merge to live
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* overwrite changes and error fix for nan paths again
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* fixed if statement
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* joblib parallel
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* summary messages
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* updated, passing tests. Updated version to 0.4
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* update test
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* yaml path cli
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* yaml error check
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* pandas error
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* Fixed read_dicom_auto
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* skips series check if seris is None
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* updated readme to reflect v0.4 changes
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* updated readme
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* minor change
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* remove .idea
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* remote .idea
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* git ignore
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* refactor nnunetutils to nnunet
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* updated versions
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* new experimental segmentation class
* minor fixes in segmentation module
* matching roi names in StructureSet.to_segmentation is now case-insensitive
* StructureSet now correctly handles ROIs with no contour data
* Segmentation object now correctly handles indexing
* Fix empty array check in structure set conversion
* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT
* Fix slice matching issue when generating binary mask from RTStruct
* CLI &34;autonew&34;
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* changed all mutable defaults to None
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* remote .idea
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* git ignore
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Co-authored-by: mkazmier <mkazmierski.poznangmail.com>
Co-authored-by: Minoru Nakano <minoru.nakanogmail.com>
Co-authored-by: Sejin Kim <sejinkimuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode88.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode40.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode97.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimh4huhnlogin2.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-Air.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode38.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode49.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode53.uhnh4h.cluster>
Co-authored-by: Vishwesh <vishweshramanathangmail.com>
Co-authored-by: Benjamin Haibe-Kains <bhaibekabhaibek1.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode89.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: fishingguy456 <qukevin99gmail.com>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster> ([`7dcea06`](https://github.com/bhklab/med-imagetools/commit/7dcea0612043d0d03b68ac335a3e4ea9e2641b4c))
* Update README.md ([`49aa813`](https://github.com/bhklab/med-imagetools/commit/49aa813278f1b295cfc7d539fa7bbdf30af12679))
* Update setup.py (37)
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* Kevin branch (36)
* 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 &34;fixed index column handling in ImageCSVLoader&34;
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
* 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
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* PT/RTDOSE metadata to csv
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* fixed some bugs in autopipeline.py
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* now the pipeline saves on exit
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* deleted data
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* now checks for existing subject id
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* uncommented one line pytest
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* uncommented one line pytest
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* 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 <vishweshramanathangmail.com>
* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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* Create build-ci.yml
* Update build-ci.yml
* Update requirements.txt
* bug fixes_1.0
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* test and autopipe fixed
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* bug fixes 2
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* bug fixes 2
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* added visualizations and some more bug fixes
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* 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 <vishweshramanathangmail.com>
* fixed bugs regarding multiple connections, saving of metadata and loading of metadata
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* small bug fix
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* added demo.py
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* Ready for
* Create main.yml (15)
* Changed dataset class returns
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* fix conflicts
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* fixed test autopipe
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* 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 <vishweshramanathangmail.com>
* fix path backslash issues
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* 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 <vishweshramanathangmail.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
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* added tests for Dataset class
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* Create LICENSE (20)
* Create LICENSE
* Update setup.py
* Seg.nrrd quick fix
* Minor bug fixes
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* test fix
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* Added demo
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* Update setup.py (23)
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* updated README
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* Update README.md (24)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* first commit
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* removed test files, changed gitignore
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* changed file directory structure for imageautooutput
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* split mask up into each contour
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* change kwargs in put for basesubjectwriter
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* still kinda failing...
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* brought back basesubjectwriter
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* .imgtools directory
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* changed absolute paths to relative paths
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* changed os.path.join to pathlib.Path.as_posix()
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* removed unused cv2 import
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* removed cv2 import
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* appened is deprecated, changed to concat
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* debug print
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* removed debug print
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* added sparse mask class and generating function
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* testing out sparse mask
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* funky NaN problem
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* commented sparse mask
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* overwrite all subjects
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* space
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* overwrite false
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* metadata stuffs
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* metadata in dataset.csv
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* added modalities, num rtstruct and pixel size to metadata
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* metadata bugfix
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* a
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* fixed wrong variable names for metadata stuff
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* fixed pathlib float error
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* relative paths and output folder paths for dataset.csv
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* put metadata stuff into a util file
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* deal with empty metadata
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* messing around with sparse mask
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* tried to save sparse mask, did some stuff with nnunet output format
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* compliant with nnunet directory structure
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* CLI Interface, argparse moved to utils
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* fixed formatting problems with folder names
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* train test split
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* train size and random state optional
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* merge conflicts
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* changed warnings to not interrupt
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* changed to warnings.warn for generate_sparse_mask
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* merge
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* resolving conflicts?
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* args
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* changes for roi names as a dict
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* added regex dictionary option for non nnunet runs
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* sparse mask global labelling for contour name: index
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* got rid of file_name_convention stuff
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* conflicts resolved
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* yaml thing
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* added list capabilities for the roi names dictionary
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* dataset.json for nnunet
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* CLI &34;autonew&34;
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* changed all mutable defaults to None
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* moved autotest changes to autopipeline and addede a few CLI args
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* getting ready for merge to live
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* test_components, test_modalities works with new AutoPipeline
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* overwrite changes and error fix for nan paths again
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* fixed if statement
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* joblib parallel
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* warnings for missing patients
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* summary messages
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* updated, passing tests. Updated version to 0.4
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* update test
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* yaml path cli
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* yaml error check
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* pandas error
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* Fixed read_dicom_auto
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* skips series check if seris is None
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* updated readme to reflect v0.4 changes
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* updated readme
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* minor change
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* remove .idea
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* remote .idea
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* git ignore
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* refactor nnunetutils to nnunet
Former-commit-id: 6d89ab1ce84d16a9a759f45530fc87eab46962d5 [formerly 8ae957266df825e1687e1d49a6114b6e657240e8] [formerly d996869c596f2c5353254d0cdc73d9f19e97fe69]
* updated versions
Former-commit-id: 980b5ea62602c4194a6a3014ce04d34e348bce8f [formerly 66542e225383a7edc3d21e06b728a17ccdf4761a] [formerly 41c8c88d93bb7a625eb9c31e400be8902500f13f]
Co-authored-by: przebieglykaziu <mkazmierski.poznangmail.com>
Co-authored-by: Minoru Nakano <minoru.nakanogmail.com>
Co-authored-by: Sejin Kim <sejinkimuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode88.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode40.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode97.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimh4huhnlogin2.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-Air.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode38.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode49.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode53.uhnh4h.cluster>
Co-authored-by: Vishwesh <vishweshramanathangmail.com>
Co-authored-by: Benjamin Haibe-Kains <bhaibekabhaibek1.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode89.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: fishingguy456 <qukevin99gmail.com>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster>
Former-commit-id: a17183df96a623e372011e66cc7a8eef287ef497
Former-commit-id: 9535d8f43d2c6437176fe22c7c249481b23c777c ([`4fba9bc`](https://github.com/bhklab/med-imagetools/commit/4fba9bcf83984e249c8d6eeebc3f5c8b715b32f8))
* update to 0.4.1 for new readme (35)
* 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 &34;fixed index column handling in ImageCSVLoader&34;
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
* 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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 &34;autonew&34;
* 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.poznangmail.com>
Co-authored-by: Minoru Nakano <minoru.nakanogmail.com>
Co-authored-by: Sejin Kim <sejinkimuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode88.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode40.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode97.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimh4huhnlogin2.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-Air.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode38.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode49.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode53.uhnh4h.cluster>
Co-authored-by: Vishwesh <vishweshramanathangmail.com>
Co-authored-by: Benjamin Haibe-Kains <bhaibekabhaibek1.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode89.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: fishingguy456 <qukevin99gmail.com>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster>
Former-commit-id: 4fc74ad7a233bf80dd95219eea058e86d8170e90
Former-commit-id: be0f5c830268c987ce5b3b921a1a1e0476e1f0ea
Former-commit-id: 1f70cb08fcf0988d42babbed92c6aa53a49de7c2 ([`f0c10b6`](https://github.com/bhklab/med-imagetools/commit/f0c10b660300ab271968ec91815eba63e346263f))
* Kevin branch (34)
* 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 &34;fixed index column handling in ImageCSVLoader&34;
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
* 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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 <vishweshramanathangmail.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 &34;autonew&34;
* 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.poznangmail.com>
Co-authored-by: Minoru Nakano <minoru.nakanogmail.com>
Co-authored-by: Sejin Kim <sejinkimuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode88.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode40.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimnode97.uhnh4h.cluster>
Co-authored-by: Sejin Kim <sejinkimh4huhnlogin2.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-Air.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode38.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode49.uhnh4h.cluster>
Co-authored-by: Vishwesh Ramanathan <ramanavnode53.uhnh4h.cluster>
Co-authored-by: Vishwesh <vishweshramanathangmail.com>
Co-authored-by: Benjamin Haibe-Kains <bhaibekabhaibek1.uhn.ca>
Co-authored-by: Sejin Kim <sejinkimnode89.uhnh4h.cluster>
Co-authored-by: Sejin Kim <hellosejin.kim>
Co-authored-by: Sejin Kim <40668167+skim2257users.noreply.github.com>
Co-authored-by: Vishwesh Ramanathan <vishweshVishweshs-MacBook-Air.local>
Co-authored-by: Kevin Qu <kquuhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqunode90.uhnh4h.cluster>
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* Merge branch &39;master&39; of github.com:bhklab/med-imagetools
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* quick fixes
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* quick fixes
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Skim2257 quick fix (26)
* Updated crawler to force String on all meta fields
* Update setup.py
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* Merge branch &39;master&39; of github.com:bhklab/imgtools
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* Merge branch &39;master&39; of github.com:bhklab/imgtools
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* preliminary MRI functionality (MR-RTSTRUCT pairs)
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* Update README.md (24)
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* Update README.md (24)
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* Update README.md (19)
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* Update README.md
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* Update main.yml (18)
* Update main.yml
* Update requirements.txt
* Update main.yml
* Update main.yml
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* Update setup.py
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* Update README.md
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* Update main.yml
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* Update main.yml
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* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
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* fixed some bugs in autopipeline.py
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* bug fixes 2
* added visualizations and some more bug fixes
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* small bug fix
* added demo.py
* Changed dataset class returns
* fix conflicts
* fixed test autopipe
* fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathangmail.com>
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* fixed some bugs in autopipeline.py
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* deleted data
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* test and autopipe fixed
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* 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 <vishweshramanathangmail.com>
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* fix conflicts
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* Create main.yml (15)
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* Ready for
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* added demo.py
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* 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 <vishweshramanathangmail.com>
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* Update manual-test.yml
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* Update build-ci.yml
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* Create manual-test.yml
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* bug fixes 2
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* bug fixes_1.0
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* Update build-ci.yml
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* Create build-ci.yml
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* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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* 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 <vishweshramanathangmail.com>
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* uncommented one line pytest
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* uncommented one line pytest
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* Merge branch &39;add_capabilities&39; of https://github.com/bhklab/imgtools into add_capabilities
merging sejin&39;s addition
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* Merge branch &39;add_capabilities&39; of https://github.com/bhklab/imgtools into add_capabilities
merging sejin&39;s addition
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* deleted data
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* now the pipeline saves on exit
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* now the pipeline saves on exit
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* fixed some bugs in autopipeline.py
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* fixed some bugs in autopipeline.py
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* PT/RTDOSE metadata to csv
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* PT/RTDOSE metadata to csv
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* uptodate with master, merged
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* uptodate with master, merged
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* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
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* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
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* sanity changes before purging dev-20200414
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* fixed dataset.csv
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* housekeeping
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* example bash script with path parsing, fixed reference_frame
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* Merge pull request 8 from bhklab/tcia_sample
attached tcia_sample repo + sample autopipeline scripts
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* tcia_sample
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* quick README under ops
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* Update README.md
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* ignore .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Delete .DS_Store
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* Update pet.py
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* Update loaders.py
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* Merge pull request 7 from bhklab/label_save
merge added features
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* Update radcure_simple.py
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* Merge pull request 6 from bhklab/complete_pipe
merge into label_save
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* Merge branch &39;label_save&39; of github.com:bhklab/imgtools into complete_pipe
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* more refactoring
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* Merge branch &39;complete_pipe&39; of github.com:bhklab/imgtools into complete_pipe
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* major refactoring
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* Fixed dataset.csv writing issues
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* small change
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* Now missing RTDOSE references are completed by RTPLAN
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* Rectified some bugs, added reference to rtplan in the crawler
Former-commit-id: 39b298376295d79beaa0fc003ed3c2c5bd79132c ([`15f958e`](https://github.com/bhklab/med-imagetools/commit/15f958e8cd70e5731d08270f62655899e6a59532))
* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes
Former-commit-id: bb446096a2315e8c52b2c0d74facebe8b967f7ee ([`8bd3804`](https://github.com/bhklab/med-imagetools/commit/8bd3804d67fc31b6b3fb50f35f443cdd32b1f100))
* added crawl.py
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* Added DataGraph, now fetching subset of dataset is supported using graph query
Former-commit-id: 032e45294efaa8d9d0a39fd97d4eaa50e2a0bb0b ([`dc66a4a`](https://github.com/bhklab/med-imagetools/commit/dc66a4ac31e1750a0ced8ca1c9b34f68e8f9aa41))
* Modified RT dose, pipeline working for PET_CT quebec dataset
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* Completed PET overlay
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* reading in sitk format from beginning
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* corrected the view
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* final pipeline working for doses and PET
Former-commit-id: c2e2d1ceff9c932e2c210cc305fe2545f239eae8 ([`7991481`](https://github.com/bhklab/med-imagetools/commit/79914814e778c359f2c72af058cfdc69ec071204))
* Merge branch &39;RTdose&39; into complete_pipe
RT dose and PET done. Now focusing on the completion of pipeline
Former-commit-id: 5725a1ca40cf21162204435f9944d84460712c21 ([`71fc6ac`](https://github.com/bhklab/med-imagetools/commit/71fc6acf309656b8c326b7c5a024627f7d8c11af))
* Head-Neck-PET-CT pipeline + `read_dicom_auto`
Former-commit-id: fa6408c11a2b9b6bd80279504ba4c79975ad3582 ([`6e6be59`](https://github.com/bhklab/med-imagetools/commit/6e6be592285e808d11798294396d0f20db562060))
* PET readability added
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* PET readability added
Former-commit-id: d7b309bb898286e9c4a000511ed2c585df931045 ([`b30508d`](https://github.com/bhklab/med-imagetools/commit/b30508dd7234c1452f6aa13598dac3b41ada91a2))
* RT dose pipeline completed and tested. Error in segmentation not resolved
Former-commit-id: 716c9f682863f75a1dbcc2bd1956d3c8160757c6 ([`91a9330`](https://github.com/bhklab/med-imagetools/commit/91a9330edfbcfb42370b7cd6c58ce5ae3b7f16ad))
* fixed structureset.py:148
Former-commit-id: eabd7eb1b07017713184a81bfb418fd4596025e3 ([`65340cd`](https://github.com/bhklab/med-imagetools/commit/65340cd03d9b25bd79d7c7b90e1c7df30053bd75))
* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.
Former-commit-id: 3a0d0d98a583d35609ed11a1fccb65e621751ad1 ([`bc1d3c2`](https://github.com/bhklab/med-imagetools/commit/bc1d3c2edcf10979bf4d274f1595895290fd9cbe))
* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.
Former-commit-id: bf0a595feb28c2b23dac6d9fd7991ed966678a60 ([`6398fe6`](https://github.com/bhklab/med-imagetools/commit/6398fe6c92f1f657202123b73d8b44b53e04d553))
* supports RTSTRUCT processing without roi_names
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* added seg.nrrd compatibility
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* little updates
Former-commit-id: 310406647bdfcbb9bfcc8fef2c2cae320ac2f2ce ([`b5948ab`](https://github.com/bhklab/med-imagetools/commit/b5948ab178f13ce5ef94e5377eb8f65fa428691a))
* Fix binary mask generation from RTStruct when missing labels are present
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* Fix slice matching issue when generating binary mask from RTStruct
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* Improved handling of regular expressions in structure set
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* Make imports easier
Former-commit-id: 184319338f0ba88439f6145726f24903128b75ba ([`ed7918c`](https://github.com/bhklab/med-imagetools/commit/ed7918c171d305072d35808d740da454102d5ed2))
* Fix crop size issue in crop_to_bounding_box
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* Merge branch &39;master&39; of https://github.com/bhklab/imgtools
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* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT
Former-commit-id: 919ea491ae01f0e6c87731bcd7ebe4d89a325042 ([`f662f90`](https://github.com/bhklab/med-imagetools/commit/f662f902df7f5de3c696969a71135bdd9976aaca))
* Fix type error when passing Numpy array to rotate
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* Fix spurious mixin in ops
Former-commit-id: 8e19d063d2d59b883aaa8e69da10050047b8c60c ([`61ce543`](https://github.com/bhklab/med-imagetools/commit/61ce543e55daca7d83adceb1bd6d0f76a9e83d05))
* Update README.md
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* Fix segmentation to label image conversion
Former-commit-id: 404793bb4f835b18529ae24b3fd8e2a2373c59e0 ([`14fe19c`](https://github.com/bhklab/med-imagetools/commit/14fe19c3937b83d9aea986fbfa3140b0f395ea72))
* Fix empty array check in structure set conversion
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* Added convenience method to get all ops in a pipeline
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* [Docs] Cleaned up extra whitespace in ops.py
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* pipeline can now warn on error instead of raising exception
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* more informative exception handling in pipeline
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* ImageCSVLoader now correctly handles globbing in paths
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* ImageCSVLoader now returns correct keys
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* fixed index column handling in ImageCSVLoader
Former-commit-id: 45af80b94a7343d452970cce620cc0310781766e ([`6eb93ba`](https://github.com/bhklab/med-imagetools/commit/6eb93ba49632654160d958ce6f5d643ec387f791))
* fixed index column handling in ImageCSVLoader
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* Revert &34;fixed index column handling in ImageCSVLoader&34;
This reverts commit 5561121c00024f8ebf72b83b9605a6ffe655eb23 [formerly ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33].
Former-commit-id: 678fc6ea41b8f29fed3c4b0af74e03971526816b ([`e6d66a8`](https://github.com/bhklab/med-imagetools/commit/e6d66a8945f540c85b8ef3a5c695416210286b98))
* fixed index column handling in ImageCSVLoader
Former-commit-id: ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33 ([`5561121`](https://github.com/bhklab/med-imagetools/commit/5561121c00024f8ebf72b83b9605a6ffe655eb23))
* fixed indentation error
Former-commit-id: 61cec9cdb9d05bdf9693c33b0a12cac14da31da0 ([`2b5c9f3`](https://github.com/bhklab/med-imagetools/commit/2b5c9f3f7e0e96daa1130944284a23a45ea0a9a6))
* Merge branch &39;master&39; of https://github.com/bhklab/imgtools
Former-commit-id: aee62cb868378e8437033ae82a422c060d4ff854 ([`5e33ff5`](https://github.com/bhklab/med-imagetools/commit/5e33ff50ff3afd5941cee62a83e248de7b4549eb))
* image CSV loader now accepts pandas DataFrames
Former-commit-id: 5f25bfdb51761b8bb4d870e682991492c900852a ([`84c7c77`](https://github.com/bhklab/med-imagetools/commit/84c7c77c30cd5802f41b1ae7d139632b36cc9265))
* added support for dynamic path specification in writers
Former-commit-id: 57b944e8dbd4d74d09f72baac19bd090af220c15 ([`006b352`](https://github.com/bhklab/med-imagetools/commit/006b35282d0360a54ba34b4ab67e0b09eb34fc32))
* Merge branch &39;master&39; of https://github.com/bhklab/imgtools
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* [In Progress] Adding documentation to ops.py
Former-commit-id: 0463acabdfb879de5467f813d90bae6c537e957f ([`3b706fa`](https://github.com/bhklab/med-imagetools/commit/3b706fabfaaabbe86ed9b4c5ca9801abb3267298))
* fixed label handling in image statistics computation
Former-commit-id: 12eecd14267a570f5bd7254a5e481e6dbf6afc6c ([`f56d634`](https://github.com/bhklab/med-imagetools/commit/f56d63422a950865287437cfc06e2734b3f9656f))
* fixed label handling in image statistics computation
Former-commit-id: f9144f000a3c186a2de0c499055ef5915b2657b9 ([`ef0ab45`](https://github.com/bhklab/med-imagetools/commit/ef0ab458fa0ce7d3839697f710a960893831f2d1))
* removed old structure set code
Former-commit-id: 8383fe62e5c2a59229f4919361bbbfe0cd3a259a ([`0477848`](https://github.com/bhklab/med-imagetools/commit/047784844d5acc308547dfbde2101ea5e868b587))
* removed old structure set code
Former-commit-id: c73d187e52d14c78789e0beee5ad4b11f8490895 ([`6f3c5b0`](https://github.com/bhklab/med-imagetools/commit/6f3c5b05dfa0028129a1928c6a360452758064d7))
* fixed segmentation mask handling in image statistics computation
Former-commit-id: e237e89ab03e8ed377023794afc7429e43cd901c ([`bd0e0ca`](https://github.com/bhklab/med-imagetools/commit/bd0e0ca0895d34ee396f5077600bd2a1784af08f))
* Segmentation object now correctly handles indexing
Former-commit-id: 5cee77d4a553bae602cc019876754130055aad81 ([`107c807`](https://github.com/bhklab/med-imagetools/commit/107c8074d0a00150e15eafb05f206304a674373a))
* MetadataWriter can now remove existing files from previous runs
Former-commit-id: 4550b0c040d1b7ee21bf20975cc437a17afe080f ([`26328f7`](https://github.com/bhklab/med-imagetools/commit/26328f7d874484e5e08b4d1a8679e2e901c52bbf))
* MetadataWriter can now remove existing files from previous runs
Former-commit-id: 0b8d94c02e9e49b95db70392574899bbe8f7a50c ([`edc5db2`](https://github.com/bhklab/med-imagetools/commit/edc5db2b795bb89653a2d0fa28958810381e1232))
* fixed error when trying to detect CSV delimiter in MetadataWriter
Former-commit-id: 4dac32399e9918d6fe41c5e34a834e0307fd54a1 ([`3087492`](https://github.com/bhklab/med-imagetools/commit/30874920ecb010d383c41b7c47401a71b70109d5))
* StructureSet now correctly handles ROIs with no contour data
Former-commit-id: 0ffaca0302bf3bf1b8c9722f6e7c64b2967018ec ([`bbf6529`](https://github.com/bhklab/med-imagetools/commit/bbf652914c620ae4c8ca3a92ed7e8a39c3337e75))
* fixed typo in pipeline warning message
Former-commit-id: 9b8d5148a1460f83b5e23c961c752988bed03916 ([`f5cf3c2`](https://github.com/bhklab/med-imagetools/commit/f5cf3c21da5977d9b49ce11c718c019bc22f89c1))
* fixed segmentation method call in some functional ops
Former-commit-id: cf2d9fc2b9e9f0725cf641ae6633e8f1f69d61d6 ([`4f20f12`](https://github.com/bhklab/med-imagetools/commit/4f20f126413d41602ca2f150b11261242e024ab8))
* matching roi names in StructureSet.to_segmentation is now case-insensitive
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* minor fixes in IO and segmentation
Former-commit-id: ef05b1c3be698e100422f6d0fc6dfa7f30703a14 ([`fb7bb7c`](https://github.com/bhklab/med-imagetools/commit/fb7bb7cf5ef14e491ae0bb85421f05f969b1a7a3))
* improved ops repr
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* updated imports in pipeline
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* simplified loader/writer specification in IO ops
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* simplified loader/writer specification in IO ops
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* ops using segmentation masks now accept Segmentation
Former-commit-id: 7ffbc49381db1d4d7127fc6fc1c61b7df6a10317 ([`81ae38d`](https://github.com/bhklab/med-imagetools/commit/81ae38d92ca9f31dcb978137f42a7d21d2d2f79c))
* minor fixes in segmentation module
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* updated examples to use the new Segmentation API
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* updated method names to reflect usage of Segmentation class
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* loaders will now use the new structureset
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* new experimental segmentation class
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* moved lower level reading functions to loaders.py
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* bounding box is now returned in a frendlier format
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* refactored subdirectory handling into BaseWriter
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* fixed typo in ops
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* structure set now supports passing list of regexes for roi names
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* added a writer for metadata
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* ImageFileWriter now correctly handles subdirectories in filename_format
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* added support for compression in ImageFileWriter
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* added example data & updated example pipeline
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* structureset now correctly handles missing ROIs ([`a2fd796`](https://github.com/bhklab/med-imagetools/commit/a2fd7968926d8d042c52747c44c42aa861d6b04c))
* fixed typo in resample ([`cfa1443`](https://github.com/bhklab/med-imagetools/commit/cfa1443d13ba59a0077e7c5c3e544e5333454e27))
* updated gitignore ([`bdb9a3e`](https://github.com/bhklab/med-imagetools/commit/bdb9a3e8fb79edc67dbf3fafbebfe2efbdf39aaf))
* updated arguments in resample op ([`d5e5268`](https://github.com/bhklab/med-imagetools/commit/d5e5268c42d1130d1958b8573b50acaa2ea7533e))
* Merge branch &39;master&39; of https://github.com/bhklab/imgtools ([`ebd0717`](https://github.com/bhklab/med-imagetools/commit/ebd07173f9b8745f6ea750e53a7d15fd57b7badf))
* updated readme with development mode installation instructions ([`2fe5e95`](https://github.com/bhklab/med-imagetools/commit/2fe5e956147556de0d6e4ffb369d211efd30d3c6))
* [quick fix] removed a syntax error, = that was added with __init__ function&39;s output_directory parameter ([`8657727`](https://github.com/bhklab/med-imagetools/commit/865772722d9c1f2ad582fbe021c23866692dfa6d))
* added zoom operation ([`0426d0e`](https://github.com/bhklab/med-imagetools/commit/0426d0edbb6425f6a41f4b557d065539ef11d1c9))
* added more pipeline ops from functional module ([`e33c83f`](https://github.com/bhklab/med-imagetools/commit/e33c83fa5683dacd9da1fcc3e50d1f5b06b359c2))
* refactored image statistics computation ([`265e19a`](https://github.com/bhklab/med-imagetools/commit/265e19a7ce232f15738f870ba870b1196a58ca23))
* minor documentation & type annotation fixes ([`01b5295`](https://github.com/bhklab/med-imagetools/commit/01b5295fb1cd03c8f5cf3957ee8c2786225cfb07))
* fixed standard scaling function ([`f74a78f`](https://github.com/bhklab/med-imagetools/commit/f74a78fbea6df123784898692a27e53e9b10454d))
* fixed standard scaling function ([`36145fc`](https://github.com/bhklab/med-imagetools/commit/36145fc4a536a8061365b45b8161f5b933d62ceb))
* minor style fixes ([`d81f46d`](https://github.com/bhklab/med-imagetools/commit/d81f46df35baec8f8aea73627797f3c21d4c92d6))
* fixed type annotations in resample ([`25007be`](https://github.com/bhklab/med-imagetools/commit/25007bee9a14bdf267d0ce6ee8d5848d5dc223cc))
* implemented better sigma computation when downsampling ([`feee338`](https://github.com/bhklab/med-imagetools/commit/feee3389c3f7be3b52a5ba89b599f45c959c8a42))
* output size can now be specified when resampling ([`f644c26`](https://github.com/bhklab/med-imagetools/commit/f644c263ceb41c19860b7a111eded1b7f0b169b0))
* moved examples outside package code ([`a5fd368`](https://github.com/bhklab/med-imagetools/commit/a5fd368455673f328255b5c43c2a83cd42067ba8))
* Revert &34;minor fixes in RADCURE example&34;
This reverts commit 3ed090c6554e61eee35d4d3161ca5489a56b49ee. ([`b68c6f4`](https://github.com/bhklab/med-imagetools/commit/b68c6f4b89abc74586f11417fb6b2e8ccb424f75))
* Revert &34;moved examples outside package code&34;
This reverts commit 0014e6526bf37062ef6e3bb686f42538d8d075a0. ([`25cf496`](https://github.com/bhklab/med-imagetools/commit/25cf4965c8d9bf293c30c2b7d854b6af46a8a656))
* removed datasets directory ([`483f449`](https://github.com/bhklab/med-imagetools/commit/483f4494ac69b169df660d6ffabafd73bf4d3ffe))
* support for 3D rotations ([`14f7120`](https://github.com/bhklab/med-imagetools/commit/14f712023a215beec5a157598bf99fd0e72cf6ad))
* fixed unbound variable error in ImageFileLoader ([`9100032`](https://github.com/bhklab/med-imagetools/commit/9100032ed8b4d720877a06b2fd0d086b6412c439))
* improved documentation and type annotation in ops.functional ([`6c3b04e`](https://github.com/bhklab/med-imagetools/commit/6c3b04e0dcf15c520e8376f90dd4c8de6342248d))
* added functions for computing bounding box and centroid ([`a87deb2`](https://github.com/bhklab/med-imagetools/commit/a87deb2a595caafbd097570f04332aa2ea6d40c9))
* added intensity statistics functions ([`d9bf8ab`](https://github.com/bhklab/med-imagetools/commit/d9bf8ab38889482361c748e938420f1ed543f36f))
* crop function now correctly handles the crop size ([`fa887eb`](https://github.com/bhklab/med-imagetools/commit/fa887eb94c50f042a0b80267ff7f86f20f1d6e7e))
* moved examples outside package code ([`0014e65`](https://github.com/bhklab/med-imagetools/commit/0014e6526bf37062ef6e3bb686f42538d8d075a0))
* minor fixes in RADCURE example ([`3ed090c`](https://github.com/bhklab/med-imagetools/commit/3ed090c6554e61eee35d4d3161ca5489a56b49ee))
* Merge branch &39;master&39; of https://github.com/bhklab/imgtools ([`f617f7e`](https://github.com/bhklab/med-imagetools/commit/f617f7e0330c06b035ace3e503884bea8e5a7ec3))
* lazy import matplotlib in imageutils ([`eefaef6`](https://github.com/bhklab/med-imagetools/commit/eefaef6c0fa6520cbe0851c667d3746fa19343db))
* fixed BaseOp repr ([`f6a34c4`](https://github.com/bhklab/med-imagetools/commit/f6a34c486097a078681131fd3d68bc6db2650ff2))
* minor fixes in RADCURE example ([`f65f050`](https://github.com/bhklab/med-imagetools/commit/f65f050696be761ab637eaede2515f6c44fd9ee3))
* clean up variable names in writers ([`8f93220`](https://github.com/bhklab/med-imagetools/commit/8f93220ed69cae206ee097695e6b510f05e936fe))
* fixed subject id handling in ImageFileLoader when subdir path is passed ([`0d4d117`](https://github.com/bhklab/med-imagetools/commit/0d4d117fc40ee7667553e28bd0a764319962250b))
* updated conda installation instructions ([`8f34ea3`](https://github.com/bhklab/med-imagetools/commit/8f34ea3baddd62dbf333ae8f51717ebdc4261528))
* Update README.md ([`1dc8d33`](https://github.com/bhklab/med-imagetools/commit/1dc8d33cde8048e57318ff77a11030ba61e11796))
* added README ([`01f04c4`](https://github.com/bhklab/med-imagetools/commit/01f04c49dda61860834111a0cc2d7ed129e27134))
* fixed parameter names in RADCURE example ([`8578ef8`](https://github.com/bhklab/med-imagetools/commit/8578ef81364eb6ca45e90acaa636970de688f26e))
* added setup.py ([`2720532`](https://github.com/bhklab/med-imagetools/commit/2720532b3347c04efb93edcbbd6a04d5c2f65fa0))
* added requirements file ([`ddedcc1`](https://github.com/bhklab/med-imagetools/commit/ddedcc1899aae10b9f13b1408200b3683f338442))
* fixed pipeline repr ([`7b95202`](https://github.com/bhklab/med-imagetools/commit/7b95202629a602e8009b578f4350b28e5acf2c8f))
* added requirements file ([`a4dcd7d`](https://github.com/bhklab/med-imagetools/commit/a4dcd7db0ce5b0514ce554351d8f945a0312fe39))
* pipeline now issues warning for missing data in loaders ([`5530a6a`](https://github.com/bhklab/med-imagetools/commit/5530a6a4d779f22fea34b30867e9fca652c986cf))
* improved variable and class names in loaders ([`ba12cb0`](https://github.com/bhklab/med-imagetools/commit/ba12cb0adcdd26dafa65f196ec08ece3dc2adfbb))
* changed subject ID naming convention in loaders ([`ddc0e39`](https://github.com/bhklab/med-imagetools/commit/ddc0e3900d82be9d3af899424bce15c6f95114d8))
* test pipeline now generates test data on the fly ([`c4022d7`](https://github.com/bhklab/med-imagetools/commit/c4022d758b25401697139b9625c7476f593a616c))
* updated gitignore ([`b09cd8d`](https://github.com/bhklab/med-imagetools/commit/b09cd8d484ff80f0ccc99ec854b8a132bba784fb))
* fixed multiprocessing issue related to sitk object pickling ([`30c42b4`](https://github.com/bhklab/med-imagetools/commit/30c42b477decb6a25ee803e04093811e6d6e5ffc))
* changed RADCURE example to follow current AP ([`fdfb4e6`](https://github.com/bhklab/med-imagetools/commit/fdfb4e6aa7718cefb77fa0c12dda68e28ca795e3))
* cleaned up ops ([`d2c1154`](https://github.com/bhklab/med-imagetools/commit/d2c11543ab88d2139620370c7e41124c433fe81f))
* cleaned up writers ([`7419f21`](https://github.com/bhklab/med-imagetools/commit/7419f21437fbef4db7a8aa5f5676e64700350129))
* cleanup before initial release ([`66183dd`](https://github.com/bhklab/med-imagetools/commit/66183ddc3601a430619467144a6e7b85f472c739))
* cleanup before initial release ([`ead8cbf`](https://github.com/bhklab/med-imagetools/commit/ead8cbf68d219b930546cb992e6f6ff7573e35af))
* updated gitignore ([`e11ca58`](https://github.com/bhklab/med-imagetools/commit/e11ca58a9f70b8ad4c6b000bcdbc80f9bba16ae7))
* demo ([`bd73693`](https://github.com/bhklab/med-imagetools/commit/bd73693a8ee1a59c1491266c389499df391b4c36))
* demo ([`5fb8266`](https://github.com/bhklab/med-imagetools/commit/5fb8266c85e41ab0f9211f55567085fc3fd5035d))
* demo ([`f4ca619`](https://github.com/bhklab/med-imagetools/commit/f4ca61945b2fba4862bcd24e1e4e888953452071))
* demo ([`6e4a93a`](https://github.com/bhklab/med-imagetools/commit/6e4a93ac8ab53eff3c219894266a5edd3f607864))
* initial implementation of Image class ([`4288b5b`](https://github.com/bhklab/med-imagetools/commit/4288b5bd8e2f81b31e0eb7f409598aef35bb7f3b))
* added docstrings to io functions ([`0037a15`](https://github.com/bhklab/med-imagetools/commit/0037a15c610b442e368b02faf4b6621a4b4a5b53))
* implemented cropping and padding transforms ([`2cf5a9c`](https://github.com/bhklab/med-imagetools/commit/2cf5a9cf906bcab5520ca16da30f75430469ef64))
* removed mask argument and renamed the resampling transform ([`40e391d`](https://github.com/bhklab/med-imagetools/commit/40e391db5ac7652aa9265a120e9fbfcfacf8ccbe))
* improved type annotations in transforms.spatial.resample_image ([`d125e12`](https://github.com/bhklab/med-imagetools/commit/d125e12f4702791bde29c2a22490a8d448f20069))
* improved spacing specification for resampling ([`7237ee5`](https://github.com/bhklab/med-imagetools/commit/7237ee5b284b37b745a825dd0c123465aaf86c60))
* minor fixes in transforms.spatial.resample_image ([`02d3ed0`](https://github.com/bhklab/med-imagetools/commit/02d3ed001849474a02095c967db43c37125a3cbb))
* added documentation and type annotations to transforms.spatial.resample_image ([`d7862f0`](https://github.com/bhklab/med-imagetools/commit/d7862f0f58c8d113a5841cbc7dcc33932b4811eb))
* fixed interpolator choice in resample_image ([`d0c80d7`](https://github.com/bhklab/med-imagetools/commit/d0c80d7c426a2967513745a1a63efff6e98a7595))
* utility function to check mask geometry ([`4316546`](https://github.com/bhklab/med-imagetools/commit/4316546a8ba421993718f53310c7a141996f88e6))
* first implementation of image resampling ([`180f759`](https://github.com/bhklab/med-imagetools/commit/180f759653617dca7054c11fa81db41809420994))
* added basic IO functions ([`dfb11dd`](https://github.com/bhklab/med-imagetools/commit/dfb11dd20374659a826cf84657f9df79e3a76f6b))
* initial commit ([`2afb431`](https://github.com/bhklab/med-imagetools/commit/2afb43157eaacde0a88d8336ffa59c68ce25a9bf))