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Nnunet demo #40

Merged
merged 489 commits into from
Jul 6, 2022
Merged

Nnunet demo #40

merged 489 commits into from
Jul 6, 2022
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Commits on Dec 8, 2021

  1. Merge branch 'add_capabilities' of https://github.com/bhklab/imgtools … 

    …into add_capabilities

merging sejin's addition


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  2. Merge branch 'add_capabilities' of https://github.com/bhklab/imgtools … 

    …into add_capabilities

merging sejin's addition


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  3. Merge branch 'add_capabilities' of https://github.com/bhklab/imgtools … 

    …into add_capabilities

merging sejin's addition
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  4. uncommented one line pytest 

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  5. uncommented one line pytest 

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  6. uncommented one line pytest

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  7. uncommented one line pytest 

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  8. uncommented one line pytest 

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  9. uncommented one line pytest

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  10. self.existing, dataset.csv fixed (#10) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  11. self.existing, dataset.csv fixed (#10) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
    @skim2257 @Vishwesh4
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Commits on Dec 9, 2021

  1. Added dataset class which can load from nrrds or directly from the da… 

    …taset and convert to pytorch dataset

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  2. Added dataset class which can load from nrrds or directly from the da… 

    …taset and convert to pytorch dataset

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  3. Added dataset class which can load from nrrds or directly from the da… 

    …taset and convert to pytorch dataset
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  4. Create build-ci.yml 

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  5. Create build-ci.yml

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  6. Update build-ci.yml 

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  7. Update build-ci.yml

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  8. Update requirements.txt 

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  9. Update requirements.txt

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  10. bug fixes_1.0 

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  11. bug fixes_1.0 

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  12. bug fixes_1.0

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  13. test and autopipe fixed 

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  14. test and autopipe fixed 

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  15. test and autopipe fixed

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  16. bug fixes 2 

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  17. bug fixes 2 

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  18. bug fixes 2

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  19. bug fixes 2 

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  20. bug fixes 2 

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  21. bug fixes 2

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Commits on Dec 10, 2021

  1. added visualizations and some more bug fixes 

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  2. added visualizations and some more bug fixes 

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  3. added visualizations and some more bug fixes

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  4. Create manual-test.yml 

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  5. Create manual-test.yml

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  6. Update build-ci.yml 

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  7. Update build-ci.yml

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  8. Update manual-test.yml 

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  9. Update manual-test.yml

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  10. PR tests - macos/ubuntu failing (#13) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* fixed pipeline tests

* clean tests

* added workflow

* yml

* yml

* matplotlib

* trying other patient to avoid memoryerror

* set roi_names to avoid memoryerror

* cave

* indents

* Update manual-test.yml

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  11. PR tests - macos/ubuntu failing (#13) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* fixed pipeline tests

* clean tests

* added workflow

* yml

* yml

* matplotlib

* trying other patient to avoid memoryerror

* set roi_names to avoid memoryerror

* cave

* indents

* Update manual-test.yml

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
    @skim2257 @Vishwesh4
    skim2257 and Vishwesh4 authored Dec 10, 2021
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  12. fixed bugs regarding multiple connections, saving of metadata and loa… 

    …ding of metadata

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  13. fixed bugs regarding multiple connections, saving of metadata and loa… 

    …ding of metadata

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  14. fixed bugs regarding multiple connections, saving of metadata and loa… 

    …ding of metadata
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Commits on Dec 11, 2021

  1. small bug fix 

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  2. small bug fix 

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  3. small bug fix

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  4. added demo.py 

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  5. added demo.py 

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  6. added demo.py

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Commits on Dec 13, 2021

  1. Ready for 

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  2. Ready for

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  3. Create main.yml (#15) 

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  4. Create main.yml (#15)

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  5. Changed dataset class returns 

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  6. Changed dataset class returns 

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  7. Changed dataset class returns

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  8. Merge branch 'master' of github.com:bhklab/imgtools 

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  9. Merge branch 'master' of github.com:bhklab/imgtools 

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  10. Merge branch 'master' of github.com:bhklab/imgtools

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  11. fix conflicts 

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  12. fix conflicts 

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  13. fix conflicts

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  14. fixed test autopipe 

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  15. fixed test autopipe 

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  16. fixed test autopipe

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  17. merging new features (#16) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  18. merging new features (#16) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  19. fix path backslash issues 

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  20. fix path backslash issues 

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  21. fix path backslash issues

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  22. fix 

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  23. fix 

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  24. fix

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  25. fix path backslashes (#17) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

* fix path backslash issues

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  26. fix path backslashes (#17) 

    * Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

* fixed bugs regarding multiple connections, saving of metadata and loading of metadata

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

* fix path backslash issues

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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  27. Update main.yml 

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  28. Update main.yml

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  29. Update main.yml 

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  30. Update main.yml

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  31. Update README.md 

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  32. Update README.md

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  33. 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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  34. 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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  35. Update README.md 

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  36. Update README.md

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Commits on Dec 14, 2021

  1. Update README.md (#19) 

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  2. Update README.md (#19)

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  3. Update README.md 

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  4. Update README.md

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Commits on Dec 15, 2021

  1. added tests for Dataset class 

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  2. added tests for Dataset class 

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  3. added tests for Dataset class

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  4. added tests for Dataset class 

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  5. added tests for Dataset class 

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  6. added tests for Dataset class

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  7. Create LICENSE (#20) 

    * Create LICENSE

* Update setup.py

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  8. Create LICENSE (#20) 

    * Create LICENSE

* Update setup.py
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  9. Seg.nrrd quick fix 

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  10. Seg.nrrd quick fix

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  11. Minor bug fixes 

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  12. Minor bug fixes 

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  13. Minor bug fixes

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  14. Merge branch 'add_capabilities' 

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  15. Merge branch 'add_capabilities' 

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  16. Merge branch 'add_capabilities' 

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  17. test fix 

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  18. test fix 

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  19. test fix

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Commits on Dec 16, 2021

  1. Added demo 

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  2. Added demo 

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  3. Added demo

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Commits on Dec 17, 2021

  1. Update setup.py (#23) 

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  2. Update setup.py (#23) 

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  3. Update setup.py (#23)

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Commits on Dec 21, 2021

  1. updated README 

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  2. updated README 

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  3. updated README

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Commits on Jan 18, 2022

  1. Update README.md (#24) 

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  3. Update README.md (#24)

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  4. preliminary MRI functionality (MR-RTSTRUCT pairs) 

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  5. preliminary MRI functionality (MR-RTSTRUCT pairs) 

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  6. preliminary MRI functionality (MR-RTSTRUCT pairs)

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  7. Merge branch 'master' of github.com:bhklab/imgtools 

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  8. Merge branch 'master' of github.com:bhklab/imgtools 

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  9. Merge branch 'master' of github.com:bhklab/imgtools

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Commits on Apr 26, 2022

  1. Skim2257 quick fix (#26) 

    * Updated crawler to force String on all meta fields

* Update setup.py

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  2. Skim2257 quick fix (#26) 

    * Updated crawler to force String on all meta fields

* Update setup.py

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  3. Skim2257 quick fix (#26) 

    * Updated crawler to force String on all meta fields

* Update setup.py
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Commits on May 11, 2022

  1. quick fixes 

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  2. quick fixes 

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Commits on May 13, 2022

  1. first commit

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  2. removed test files, changed gitignore

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Commits on May 17, 2022

  1. changed file directory structure for imageautooutput

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  2. Merge branch 'master' of github.com:bhklab/med-imagetools 

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Commits on May 18, 2022

  1. split mask up into each contour

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Commits on May 19, 2022

  1. change kwargs in put for basesubjectwriter

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  2. Co-authored-by: Sejin Kim <skim2257@users.noreply.github.com>

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  3. still kinda failing...

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  4. brought back basesubjectwriter

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Commits on May 24, 2022

  1. .imgtools directory

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Commits on May 25, 2022

  1. changed absolute paths to relative paths

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  2. changed os.path.join to pathlib.Path.as_posix()

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Commits on May 26, 2022

  1. starter pipeline, pathlib for tests

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Commits on May 27, 2022

  1. removed unused cv2 import

    Kevin Qu committed May 27, 2022
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  2. Merge branch 'kevin-branch' of github.com:bhklab/med-imagetools into … 

    …kevin-branch

merge conflict for one line
    Kevin Qu committed May 27, 2022
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  3. removed cv2 import

    @fishingguy456
    fishingguy456 committed May 27, 2022
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  4. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed May 27, 2022
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  5. appened is deprecated, changed to concat

    @fishingguy456
    fishingguy456 committed May 27, 2022
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  6. debug print

    Kevin Qu committed May 27, 2022
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  7. removed debug print

    @fishingguy456
    fishingguy456 committed May 27, 2022
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  8. added sparse mask class and generating function

    @fishingguy456
    fishingguy456 committed May 27, 2022
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Commits on May 30, 2022

  1. testing out sparse mask

    @fishingguy456
    fishingguy456 committed May 30, 2022
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Commits on May 31, 2022

  1. funky NaN problem

    @fishingguy456
    fishingguy456 committed May 31, 2022
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  2. commented sparse mask

    Kevin Qu committed May 31, 2022
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  3. Merge branch 'kevin-branch' of github.com:bhklab/med-imagetools into … 

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asdf
    Kevin Qu committed May 31, 2022
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  4. overwrite all subjects

    @fishingguy456
    fishingguy456 committed May 31, 2022
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Commits on Jun 1, 2022

  1. space

    Kevin Qu committed Jun 1, 2022
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  2. Merge branch 'kevin-branch' of github.com:bhklab/med-imagetools into … 

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space
    Kevin Qu committed Jun 1, 2022
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  3. overwrite false

    @fishingguy456
    fishingguy456 committed Jun 1, 2022
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  4. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 1, 2022
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Commits on Jun 2, 2022

  1. metadata stuffs

    @fishingguy456
    fishingguy456 committed Jun 2, 2022
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Commits on Jun 3, 2022

  1. metadata in dataset.csv

    @fishingguy456
    fishingguy456 committed Jun 3, 2022
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  2. added modalities, num rtstruct and pixel size to metadata

    @fishingguy456
    fishingguy456 committed Jun 3, 2022
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Commits on Jun 6, 2022

  1. metadata bugfix

    @fishingguy456
    fishingguy456 committed Jun 6, 2022
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  2. a

    Kevin Qu committed Jun 6, 2022
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  3. Merge branch 'kevin-branch' of github.com:bhklab/med-imagetools into … 

    …kevin-branch

merging small changes
    Kevin Qu committed Jun 6, 2022
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  4. fixed wrong variable names for metadata stuff

    @fishingguy456
    fishingguy456 committed Jun 6, 2022
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Commits on Jun 7, 2022

  1. fixed pathlib float error

    Kevin Qu committed Jun 7, 2022
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  2. relative paths and output folder paths for dataset.csv

    @fishingguy456
    fishingguy456 committed Jun 7, 2022
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Commits on Jun 8, 2022

  1. put metadata stuff into a util file

    @fishingguy456
    fishingguy456 committed Jun 8, 2022
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  2. deal with empty metadata

    @fishingguy456
    fishingguy456 committed Jun 8, 2022
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Commits on Jun 9, 2022

  1. messing around with sparse mask

    @fishingguy456
    fishingguy456 committed Jun 9, 2022
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  2. tried to save sparse mask, did some stuff with nnunet output format

    @fishingguy456
    fishingguy456 committed Jun 9, 2022
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Commits on Jun 10, 2022

  1. compliant with nnunet directory structure

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    fishingguy456 committed Jun 10, 2022
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  2. CLI Interface, argparse moved to utils

    @skim2257
    skim2257 committed Jun 10, 2022
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  3. fixed formatting problems with folder names

    @fishingguy456
    fishingguy456 committed Jun 10, 2022
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  4. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 10, 2022
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Commits on Jun 13, 2022

  1. train test split

    @fishingguy456
    fishingguy456 committed Jun 13, 2022
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  2. train size and random state optional

    @fishingguy456
    fishingguy456 committed Jun 13, 2022
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  3. merge conflicts

    @skim2257
    skim2257 committed Jun 13, 2022
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  4. Merge branch 'kevin-branch' of github.com:bhklab/imgtools into kevin-… 

    …branch
    @skim2257
    skim2257 committed Jun 13, 2022
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  5. changed warnings to not interrupt

    @fishingguy456
    fishingguy456 committed Jun 13, 2022
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  6. changed to warnings.warn for generate_sparse_mask

    @fishingguy456
    fishingguy456 committed Jun 13, 2022
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  7. Merge branch 'kevin-branch' of github.com:bhklab/imgtools into kevin-… 

    …branch

Conflicts:
	imgtools/modules/segmentation.py
    @skim2257
    skim2257 committed Jun 13, 2022
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  8. merge

    @skim2257
    skim2257 committed Jun 13, 2022
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  9. resolving conflicts?

    @skim2257
    skim2257 committed Jun 13, 2022
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  10. args

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  11. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 13, 2022
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Commits on Jun 14, 2022

  1. changes for roi names as a dict

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    fishingguy456 committed Jun 14, 2022
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Commits on Jun 15, 2022

  1. added regex dictionary option for non nnunet runs

    @fishingguy456
    fishingguy456 committed Jun 15, 2022
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  2. sparse mask global labelling for contour name: index

    @fishingguy456
    fishingguy456 committed Jun 15, 2022
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  3. got rid of file_name_convention stuff

    @fishingguy456
    fishingguy456 committed Jun 15, 2022
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Commits on Jun 16, 2022

  1. conflicts resolved

    @skim2257
    skim2257 committed Jun 16, 2022
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  2. yaml thing

    @fishingguy456
    fishingguy456 committed Jun 16, 2022
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  3. added list capabilities for the roi names dictionary

    @fishingguy456
    fishingguy456 committed Jun 16, 2022
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  4. dataset.json for nnunet

    @fishingguy456
    fishingguy456 committed Jun 16, 2022
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Commits on Jun 17, 2022

  1. Merge branch 'kevin-branch' of github.com:bhklab/imgtools into kevin-… 

    …branch
    @skim2257
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  2. CLI "autonew"

    @skim2257
    skim2257 committed Jun 17, 2022
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  3. changed all mutable defaults to None

    @fishingguy456
    fishingguy456 committed Jun 17, 2022
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  4. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 17, 2022
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  5. moved autotest changes to autopipeline and addede a few CLI args

    @fishingguy456
    fishingguy456 committed Jun 17, 2022
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Commits on Jun 18, 2022

  1. getting ready for merge to live

    @skim2257
    skim2257 committed Jun 18, 2022
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Commits on Jun 19, 2022

  1. test_components, test_modalities works with new AutoPipeline

    @skim2257
    skim2257 committed Jun 19, 2022
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Commits on Jun 20, 2022

  1. overwrite changes and error fix for nan paths again

    @fishingguy456
    fishingguy456 committed Jun 20, 2022
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  2. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 20, 2022
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Commits on Jun 21, 2022

  1. fixed if statement

    @fishingguy456
    fishingguy456 committed Jun 21, 2022
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  2. joblib parallel

    Kevin Qu committed Jun 21, 2022
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  3. Merge branch 'kevin-branch' of github.com:bhklab/med-imagetools into … 

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joblib
    Kevin Qu committed Jun 21, 2022
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Commits on Jun 22, 2022

  1. warnings for missing patients

    @fishingguy456
    fishingguy456 committed Jun 22, 2022
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  2. summary messages

    @fishingguy456
    fishingguy456 committed Jun 22, 2022
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  3. updated, passing tests. Updated version to 0.4

    @skim2257
    skim2257 committed Jun 22, 2022
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  4. Merge branch 'kevin-branch' of github.com:bhklab/imgtools into kevin-… 

    …branch
    @skim2257
    skim2257 committed Jun 22, 2022
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  5. update test

    @skim2257
    skim2257 committed Jun 22, 2022
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Commits on Jun 23, 2022

  1. yaml path cli

    @fishingguy456
    fishingguy456 committed Jun 23, 2022
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  2. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 23, 2022
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  3. yaml error check

    @fishingguy456
    fishingguy456 committed Jun 23, 2022
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  4. pandas error

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    fishingguy456 committed Jun 23, 2022
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Commits on Jun 24, 2022

  1. Fixed read_dicom_auto

    @skim2257
    skim2257 committed Jun 24, 2022
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  2. skips series check if seris is None

    @skim2257
    skim2257 committed Jun 24, 2022
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  3. updated readme to reflect v0.4 changes

    @skim2257
    skim2257 committed Jun 24, 2022
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  4. updated readme

    @skim2257
    skim2257 committed Jun 24, 2022
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  5. minor change

    @fishingguy456
    fishingguy456 committed Jun 24, 2022
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  6. remove .idea

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  7. remote .idea

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  8. Merge branch 'kevin-branch' of github.com:bhklab/imgtools into kevin-… 

    …branch
    @skim2257
    skim2257 committed Jun 24, 2022
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  9. git ignore

    @fishingguy456
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  10. Merge branch 'kevin-branch' of https://github.com/bhklab/med-imagetools… 

    … into kevin-branch
    @fishingguy456
    fishingguy456 committed Jun 24, 2022
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Commits on Jun 28, 2022

  1. transpose for nnunet

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    fishingguy456 committed Jun 28, 2022
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  2. skip if no mask for nnunet and nnunet folder names

    @fishingguy456
    fishingguy456 committed Jun 28, 2022
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  3. merges

    Kevin Qu committed Jun 28, 2022
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Commits on Jun 29, 2022

  1. bugs in nnunet folder stuff

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  2. Merge branch 'nnunet-demo' of https://github.com/bhklab/med-imagetools … 

    …into nnunet-demo
    @fishingguy456
    fishingguy456 committed Jun 29, 2022
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  3. rename nnunetutil (again)

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  4. sorting the output streams

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    fishingguy456 committed Jun 29, 2022
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  5. shell script

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    fishingguy456 committed Jun 29, 2022
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  6. shell script in autopipeline

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    fishingguy456 committed Jun 29, 2022
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  7. bug

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  8. forgot CopyInformation for nnunet

    @fishingguy456
    fishingguy456 committed Jun 29, 2022
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  9. ignore deprecation warning

    @fishingguy456
    fishingguy456 committed Jun 29, 2022
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  10. moved sh file down one dir

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    fishingguy456 committed Jun 29, 2022
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  11. set -e for stopping execution if there is an error

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Commits on Jun 30, 2022

  1. broken checker for missing labels

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Commits on Jul 4, 2022

  1. train test fix for 1 patient

    @fishingguy456
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  2. fix for broken self.existing_roi_names caused by joblib

    @fishingguy456
    fishingguy456 committed Jul 4, 2022
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Commits on Jul 5, 2022

  1. added autotest to gitignore

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    fishingguy456 committed Jul 5, 2022
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  2. sorted list for train test split

    @fishingguy456
    fishingguy456 committed Jul 5, 2022
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