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Nnunet demo (#41)
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* uncommented one line pytest


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* uncommented one line pytest


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* uncommented one line pytest

* 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 <vishweshramanathan@gmail.com>
Former-commit-id: f2480c3

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

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

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

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


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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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* 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 <vishweshramanathan@gmail.com>
Former-commit-id: 47f3122

* PR tests - macos/ubuntu failing (#13)

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

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

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

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* fixed pipeline tests

* clean tests

* added workflow

* yml

* yml

* matplotlib

* trying other patient to avoid memoryerror

* set roi_names to avoid memoryerror

* cave

* indents

* Update manual-test.yml

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

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


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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


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* Changed dataset class returns

* fix conflicts


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* 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 <vishweshramanathan@gmail.com>
Former-commit-id: 539777c

* merging new features (#16)

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

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

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

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

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

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* fix path backslash issues


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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 <vishweshramanathan@gmail.com>
Former-commit-id: 5c6f7b0

* fix path backslashes (#17)

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

* PT/RTDOSE metadata to csv

* fixed some bugs in autopipeline.py

* now the pipeline saves on exit

* deleted data

* now checks for existing subject id

* uncommented one line pytest

* uncommented one line pytest

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

* bug fixes_1.0

* test and autopipe fixed

* bug fixes 2

* bug fixes 2

* added visualizations and some more bug fixes

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

* small bug fix

* added demo.py

* Changed dataset class returns

* fix conflicts

* fixed test autopipe

* fix path backslash issues

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>

* Update main.yml

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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


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* added tests for Dataset class

* added tests for Dataset class


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* 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 "autonew"

* changed all mutable defaults to None

* moved autotest changes to autopipeline and addede a few CLI args

* getting ready for merge to live

* test_components, test_modalities works with new AutoPipeline

* overwrite changes and error fix for nan paths again

* fixed if statement

* joblib parallel

* warnings for missing patients

* summary messages

* updated, passing tests. Updated version to 0.4

* update test

* yaml path cli

* yaml error check

* pandas error

* Fixed read_dicom_auto

* skips series check if seris is None

* updated readme to reflect v0.4 changes

* updated readme

* minor change

* remove .idea

* remote .idea

* git ignore

* transpose for nnunet

* skip if no mask for nnunet and nnunet folder names

* bugs in nnunet folder stuff

* rename nnunetutil (again)

* sorting the output streams

* shell script

* shell script in autopipeline

* bug

* forgot CopyInformation for nnunet

* ignore deprecation warning

* moved sh file down one dir

* set -e for stopping execution if there is an error

* broken checker for missing labels

* train test fix for 1 patient

* fix for broken self.existing_roi_names caused by joblib

* added autotest to gitignore

* sorted list for train test split

* custom train test split

* custom train test split

Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com>
Co-authored-by: Sejin Kim <hello@sejin.kim>
Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local>
Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster>
Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster>
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