CHANGELOG

v1.5.4 (2024-06-12)

Fix

fix: License updated to MIT (#119) (6e755dd)

v1.5.3 (2024-06-10)

Chore

chore(sem-ver): 1.5.3 (7effcaf)

Fix

fix: Clarified license in README.md (#118) (a4899ca)

v1.5.2 (2024-05-29)

Chore

chore(sem-ver): 1.5.2 (69a651f)

Fix

fix: upload latest version to pypi (1debad3)

v1.5.1 (2024-05-29)

Chore

chore(sem-ver): 1.5.1 (7890f36)

Fix

fix: format toml (269f55d)

v1.5.0 (2024-05-29)

Chore

chore(sem-ver): 1.5.0 (69626ef)

Feature

feat: update Lock (26590a0)
feat: update readme (7cd808e)

Unknown

patch: pushing to 1.4.1 (#116)
feat: semantic release!
patch: pushing versions (7b4cf22)

v1.4.0 (2024-05-29)

Chore

chore: bump version (58ec67f)

Feature

feat: semantic release (#114)
feat: semantic release
fix: if statement issue (23a2d70)

Fix

fix: add codecov badge (f43d042)
fix: explicit module to track for code coverage (f15d45d)

Unknown

1.1.0

Automatically generated by python-semantic-release (fe25ff2)

Dev (#112)
kill bob the builder
pip publish without semantic release
oops
adding checkout to pip-squeak
fixed main.yml
fixed main.yml
fixed main.yml
skip autopipeline in pip testing
adding code coverage
removed pytest-xdist
xdist removed, -n flag gone
fix: explicit module to track for code coverage
chore: bump version
removed pytest-xdist
xdist removed, -n flag gone
fixing main.yml conflict

Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> (76cea29)

Dev (#111)
kill bob the builder
pip publish without semantic release
oops
adding checkout to pip-squeak
fixed main.yml
fixed main.yml
fixed main.yml
skip autopipeline in pip testing
adding code coverage
removed pytest-xdist
xdist removed, -n flag gone (48fcfd0)
skip autopipeline in pip testing (054d1b4)
fixed main.yml (b5b09e7)
fixed main.yml (560272f)
fixed main.yml (535a1c5)
adding checkout to pip-squeak (da6e006)
oops (8291564)
pip publish without semantic release (5e3cc39)
kill bob the builder (5eacc0f)
Substantial refactoring, linting, CI/CD updates (#107)
Switching to poetry + ruff
fixed main.yml
this will do
maybe this?
update lock
fix: ruff errors
fix: python version error
all lint checks pass
tests should work...
update pytest version
new poetry install
windows ghaction poetry install... work pls
yml fix
poetry version=1.8.2
still fixing main.yml
maybe it's poetry?
oh boy!
kill old unit test ci/cd
update ci/cd badge

Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> (6ddc645)

New tests, improving code coverage. (#105)
new_tests_in_progress
Added majority coverage for imgtools.ops.
updated main-ci.yml with dataset-check.py name change. (c2e8ddb)
Mit lite (#104)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes
no egg please
hm
remove dataset dependency. to be reconciled later
1.2.0.1 hopefully fixed
main-ci removed test_dataset
readding scikit-learn
push to 1.2.0.2 (9137965)
Mit lite (#103)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes
no egg please
hm
remove dataset dependency. to be reconciled later
1.2.0.1 hopefully fixed
main-ci removed test_dataset
readding scikit-learn (4b06915)
MIT lite (#102)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes
no egg please
hm
remove dataset dependency. to be reconciled later
1.2.0.1 hopefully fixed
main-ci removed test_dataset (535bff0)
Mit lite (#101)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes
no egg please
hm (e378eea)
Mit lite (#100)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes
no egg please (3df6f2c)
Mit lite (#99)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work
pypi changes (92da301)
Mit lite (#98)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key
build-pkg pls work (7dfca09)
Mit lite (#97)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio
added missing dep in main-ci
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
updated PyPI push with API key (07dad6c)
Mit lite (#96)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request
added torch and torchio (afea698)
Detached branch (#94) (#95)
Detached branch (#94)
v1.2.0 for lighter install.
update main-ci.yml
fixed test_dataset
added zipfile and request (88857bf)
updated actions to new default branch. 'master' branch is DEPRECATED (d10b5ba)
updated version and default branch to 'main' (8784b5f)
Flake8 linting fixes (#93)
add stop_before_pixels tag and set to True to speed up dcm reads
add ct-seg support
flake8 linting fixes
flake8 linting fixes transforms

Co-authored-by: Umar Yousafzai <umaryousafzai54@gmail.com> (43a72fe)

convert to dicom (#89)

nifti to dicom function (ba50037)

test break during demo (#81)
test break during demo

changed

med-imagetools/imgtools/modules/datagraph.py

Line 61 in d99950f

df_filter = pd.merge(self.df, self.df[["instance_uid","reference_rs"]],

set 2nd half pandasastype(str)

Update setup.py to 1.1.6 (1268cbc)
add stop_before_pixels tag and set to True to speed up dcm reads (#80)

AYE AYE (bb4dad7)

Dicom seg (#78)
DICOM-SEG beta commit
dicom-seg update
some changes
utils for refactoring
add attr to reqs
fixed attr to attrs
update version (d99950f)
Dicom seg (#77)
DICOM-SEG beta commit
dicom-seg update
some changes
utils for refactoring
add attr to reqs
fixed attr to attrs (7634a6c)
DICOM-SEG beta commit (#74) (5c4924d)
Add docstrings to Segmentation init (#73) (223f0b6)
Add raw roi columns (#72)
Change roi_names to roi_indices
Add raw_roi_names
Add raw_roi_names (6327578)
update version (52c3a8d)
Add mr crawls (#71)
added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus
added SEGMENTATION ReferencedSeriesSequence as ref_ct
change pytest version
pytest 6.2.2
whoops
testing nibabel
importlib test
iniconfig test
sitk 2.2.0 test
snumpy21.23test
numpy 1.23 test
changed deprecated numpy np.int to int
deprecated np.warnings
fixed problematic autopipeline:612 (37e5d8e)
updated version to 1.1.0

MR/SEG dicom tags added to crawler
1.1 subversions will add support for mri sorting, segmentation files, and multi-acquisition series (8a95ae7)

added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFiel… (#70)
added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus
added SEGMENTATION ReferencedSeriesSequence as ref_ct
change pytest version (8f81e40)
Delete the labels that are empty (#69) (1e25c57)
Autopipeline fix (#68)
Added default value for path strings
Changed is_nnunet for nnunet (9b19076)
Update setup.py (b3314d4)
hotfix (#67) (f3151a1)
Crawl orientation (#66)
added orientation DICOM tag crawling
nnunet flags hotfix (#64)
autopipeline.py:164, changed or -> and
added orientation DICOM tag crawling
more is_nnunet fails (ffd6bca)
added orientation DICOM tag crawling (#65) (cc9cea1)
autopipeline.py:164, changed or -> and (f41f18d)
nnunet flags hotfix (#64) (ecc6939)
New flags: --update, --roi_select_first, --roi_separate, better mask_label parsing (#45)
added --update flag, needs test.
Added --roi_select_first and --roi_separate flags for advanced ROI parsing for contours.
mask_label parsing for illegal Windows/Unix characters (Issue #45 resolved) (89b715b)
Update README.md (199071e)

v1.0.3 (2022-10-14)

Unknown

Subseries (#61)
subseries implementation step 1
Fixes for issues #57, #53.
update README.
fixed pytest error (f8f3606)
update github actions (4adf148)
Update build-pkg.yml (ec167b7)
Update build-pkg.yml (4154d26)
Update build-pkg.yml (b2ab181)
Update build-pkg.yml (be566e8)
Update build-pkg.yml (8265aff)
Merge pull request #60 from bhklab/sw-fix

Sw fix (91330f0)

Merge branch 'master' of github.com:bhklab/med-imagetools into sw-fix (c743a98)
Update build-pkg.yml (072d597)
Skim2257 patch 1 (#59)
Update README.md
Update setup.py
Update build-pkg.yml (ce5ee0c)
updated dose (645aae7)
Merge branch 'master' of github.com:bhklab/med-imagetools into sw-fix (c6f8376)
temporary dose fix loading error with Sejin (abb452f)
Update README.md (#58) (edb8612)
Update build-pkg.yml (954b224)
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)
Update setup.py (56faf21)
Create LICENSE (a01891f)
1.0.0 (#52)
Update README.md
Update setup.py (3ceaf19)
0.4.4 (#49)
Update setup.py
Update README.md
readme changes
Update README.md
Delete autopipeline.png

Co-authored-by: Kevin <qukevin99@gmail.com> (2d2079c)

Delete autopipeline.png (6a5b7d0)
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+skim2257@users.noreply.github.com> (37f89b9)

Update main-ci.yml (c6851d9)
Add files via upload (52364da)
Add files via upload (677221b)
Add files via upload (99c90d2)
Delete methodology.png (c960771)
Delete autopipeline.png (51944f8)
Add files via upload (d5599f1)
Update readme (#43)
Update README.md
redesigned autopipeline diagram
Delete build-ci.yml
Delete main.yml
Delete manual-test.yml (d54d704)
Markdown report (#42)
markdown report generator
update version to push to pypi

Co-authored-by: Kevin <qukevin99@gmail.com> (3a2f742)

Nnunet demo (#41)
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: 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 <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: 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 <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: 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 <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: 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 <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> (f3e5307)

Nnunet demo (#40)
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: 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 <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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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: 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 <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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fix conflicts
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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: 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 <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: 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 <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

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> (31cecbe)

Update README.md (c39ffe6)
Ci update (#39)
new ci/cd actions
updated pathing too
updated ci/cd actions
update
update (df61201)
Update build-pkg.yml (5a314e5)
Update build-pkg.yml (630c184)
Update build-pkg.yml (1ff1b2b)
Create build-pkg.yml (c9d1f42)
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 "fixed index column handling in ImageCSVLoader"

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 <vishweshramanathan@gmail.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

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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 <vishweshramanathan@gmail.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 <vishweshramanathan@gmail.com>

fix path backslash issues

Former-commit-id: d81a74dfcdcd21f2b9248d197362a6dbaabf901b

fix path backslashes (#17)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Changed dataset class returns
fix conflicts
fixed test autopipe
fix path backslash issues

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

Update main.yml
Update main.yml
Update README.md
Update main.yml (#18)
Update main.yml
Update requirements.txt
Update main.yml
Update main.yml
build binary/dist
removed linter
Update setup.py
Update README.md
Update README.md (#19)
Update README.md
added tests for Dataset class

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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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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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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 "autonew"

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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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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 "autonew"

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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.poznan@gmail.com> Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: fishingguy456 <qukevin99@gmail.com> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> (7dcea06)

Update README.md (49aa813)
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 "fixed index column handling in ImageCSVLoader"

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 <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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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 <vishweshramanathan@gmail.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 <vishweshramanathan@gmail.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 <vishweshramanathan@gmail.com>

Update main.yml
Update main.yml
Update README.md
Update main.yml (#18)
Update main.yml
Update requirements.txt
Update main.yml
Update main.yml
build binary/dist
removed linter
Update setup.py
Update README.md
Update README.md (#19)
Update README.md
added tests for Dataset class

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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 "autonew"

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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

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updated versions

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Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com> Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: fishingguy456 <qukevin99@gmail.com> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> Former-commit-id: a17183df96a623e372011e66cc7a8eef287ef497 Former-commit-id: 9535d8f43d2c6437176fe22c7c249481b23c777c (4fba9bc)

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 "fixed index column handling in ImageCSVLoader"

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 <vishweshramanathan@gmail.com>

Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
Create build-ci.yml
Update build-ci.yml
Update requirements.txt
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
Create manual-test.yml
Update build-ci.yml
Update manual-test.yml
PR tests - macos/ubuntu failing (#13)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
fixed pipeline tests
clean tests
added workflow
yml
yml
matplotlib
trying other patient to avoid memoryerror
set roi_names to avoid memoryerror
cave
indents
Update manual-test.yml

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

fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Ready for
Create main.yml (#15)
Changed dataset class returns
fix conflicts
fixed test autopipe
merging new features (#16)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Changed dataset class returns
fix conflicts
fixed test autopipe

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

fix path backslash issues
fix path backslashes (#17)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Changed dataset class returns
fix conflicts
fixed test autopipe
fix path backslash issues

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

Update main.yml
Update main.yml
Update README.md
Update main.yml (#18)
Update main.yml
Update requirements.txt
Update main.yml
Update main.yml
build binary/dist
removed linter
Update setup.py
Update README.md
Update README.md (#19)
Update README.md
added tests for Dataset class
added tests for Dataset class
Create LICENSE (#20)
Create LICENSE
Update setup.py
Seg.nrrd quick fix
Minor bug fixes
test fix
Added demo
Update setup.py (#23)
updated README
Update README.md (#24)
preliminary MRI functionality (MR-RTSTRUCT pairs)
Skim2257 quick fix (#26)
Updated crawler to force String on all meta fields
Update setup.py
first commit
removed test files, changed gitignore
changed file directory structure for imageautooutput
split mask up into each contour
change kwargs in put for basesubjectwriter
still kinda failing...
brought back basesubjectwriter
.imgtools directory
changed absolute paths to relative paths
changed os.path.join to pathlib.Path.as_posix()
removed unused cv2 import
removed cv2 import
appened is deprecated, changed to concat
debug print
removed debug print
added sparse mask class and generating function
testing out sparse mask
funky NaN problem
commented sparse mask
overwrite all subjects
space
overwrite false
metadata stuffs
metadata in dataset.csv
added modalities, num rtstruct and pixel size to metadata
metadata bugfix
a
fixed wrong variable names for metadata stuff
fixed pathlib float error
relative paths and output folder paths for dataset.csv
put metadata stuff into a util file
deal with empty metadata
messing around with sparse mask
tried to save sparse mask, did some stuff with nnunet output format
compliant with nnunet directory structure
CLI Interface, argparse moved to utils
fixed formatting problems with folder names
train test split
train size and random state optional
merge conflicts
changed warnings to not interrupt
changed to warnings.warn for generate_sparse_mask
merge
resolving conflicts?
args
changes for roi names as a dict
added regex dictionary option for non nnunet runs
sparse mask global labelling for contour name: index
got rid of file_name_convention stuff
conflicts resolved
yaml thing
added list capabilities for the roi names dictionary
dataset.json for nnunet
CLI "autonew"
changed all mutable defaults to None
moved autotest changes to autopipeline and addede a few CLI args
getting ready for merge to live
test_components, test_modalities works with new AutoPipeline
overwrite changes and error fix for nan paths again
fixed if statement
joblib parallel
warnings for missing patients
summary messages
updated, passing tests. Updated version to 0.4
update test
yaml path cli
yaml error check
pandas error
Fixed read_dicom_auto
skips series check if seris is None
updated readme to reflect v0.4 changes
updated readme
minor change
remove .idea
remote .idea
git ignore
refactor nnunetutils to nnunet
updated versions

Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com> Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: fishingguy456 <qukevin99@gmail.com> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> Former-commit-id: 4fc74ad7a233bf80dd95219eea058e86d8170e90 Former-commit-id: be0f5c830268c987ce5b3b921a1a1e0476e1f0ea Former-commit-id: 1f70cb08fcf0988d42babbed92c6aa53a49de7c2 (f0c10b6)

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 "fixed index column handling in ImageCSVLoader"

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 <vishweshramanathan@gmail.com>

Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
Create build-ci.yml
Update build-ci.yml
Update requirements.txt
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
Create manual-test.yml
Update build-ci.yml
Update manual-test.yml
PR tests - macos/ubuntu failing (#13)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
fixed pipeline tests
clean tests
added workflow
yml
yml
matplotlib
trying other patient to avoid memoryerror
set roi_names to avoid memoryerror
cave
indents
Update manual-test.yml

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

fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Ready for
Create main.yml (#15)
Changed dataset class returns
fix conflicts
fixed test autopipe
merging new features (#16)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Changed dataset class returns
fix conflicts
fixed test autopipe

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

fix path backslash issues
fix path backslashes (#17)
Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
PT/RTDOSE metadata to csv
fixed some bugs in autopipeline.py
now the pipeline saves on exit
deleted data
now checks for existing subject id
uncommented one line pytest
uncommented one line pytest
Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
bug fixes_1.0
test and autopipe fixed
bug fixes 2
bug fixes 2
added visualizations and some more bug fixes
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
small bug fix
added demo.py
Changed dataset class returns
fix conflicts
fixed test autopipe
fix path backslash issues

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

Update main.yml
Update main.yml
Update README.md
Update main.yml (#18)
Update main.yml
Update requirements.txt
Update main.yml
Update main.yml
build binary/dist
removed linter
Update setup.py
Update README.md
Update README.md (#19)
Update README.md
added tests for Dataset class
added tests for Dataset class
Create LICENSE (#20)
Create LICENSE
Update setup.py
Seg.nrrd quick fix
Minor bug fixes
test fix
Added demo
Update setup.py (#23)
updated README
Update README.md (#24)
preliminary MRI functionality (MR-RTSTRUCT pairs)
Skim2257 quick fix (#26)
Updated crawler to force String on all meta fields
Update setup.py
first commit
removed test files, changed gitignore
changed file directory structure for imageautooutput
split mask up into each contour
change kwargs in put for basesubjectwriter
still kinda failing...
brought back basesubjectwriter
.imgtools directory
changed absolute paths to relative paths
changed os.path.join to pathlib.Path.as_posix()
removed unused cv2 import
removed cv2 import
appened is deprecated, changed to concat
debug print
removed debug print
added sparse mask class and generating function
testing out sparse mask
funky NaN problem
commented sparse mask
overwrite all subjects
space
overwrite false
metadata stuffs
metadata in dataset.csv
added modalities, num rtstruct and pixel size to metadata
metadata bugfix
a
fixed wrong variable names for metadata stuff
fixed pathlib float error
relative paths and output folder paths for dataset.csv
put metadata stuff into a util file
deal with empty metadata
messing around with sparse mask
tried to save sparse mask, did some stuff with nnunet output format
compliant with nnunet directory structure
CLI Interface, argparse moved to utils
fixed formatting problems with folder names
train test split
train size and random state optional
merge conflicts
changed warnings to not interrupt
changed to warnings.warn for generate_sparse_mask
merge
resolving conflicts?
args
changes for roi names as a dict
added regex dictionary option for non nnunet runs
sparse mask global labelling for contour name: index
got rid of file_name_convention stuff
conflicts resolved
yaml thing
added list capabilities for the roi names dictionary
dataset.json for nnunet
CLI "autonew"
changed all mutable defaults to None
moved autotest changes to autopipeline and addede a few CLI args
getting ready for merge to live
test_components, test_modalities works with new AutoPipeline
overwrite changes and error fix for nan paths again
fixed if statement
joblib parallel
warnings for missing patients
summary messages
updated, passing tests. Updated version to 0.4
update test
yaml path cli
yaml error check
pandas error
Fixed read_dicom_auto
skips series check if seris is None
updated readme to reflect v0.4 changes
updated readme
minor change
remove .idea
remote .idea
git ignore
refactor nnunetutils to nnunet

Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com> Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> Co-authored-by: Sejin Kim <hello@sejin.kim> Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> Former-commit-id: 8090df83dd6ea23061b5df9e32f46758adcaef7c [formerly c6f2749e73443aac15df901d317eae16b3f9bff4] [formerly 66a85e2f1dd0555b38be3fb9c35de6c2e9b9d188] Former-commit-id: de87e624140735955a2cab1b1f2074512901495e Former-commit-id: e872a2d09d3e36f0bd733158685e2cff4b8fa327 (208aacd)

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

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Merge branch 'master' 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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updated README

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updated README

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Update setup.py (#23)

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Update setup.py (#23)

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Added demo

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Added demo

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test fix

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test fix

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Merge branch 'add_capabilities'

Conflicts: tests/test_autopipe.py

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Merge branch 'add_capabilities'

Conflicts: tests/test_autopipe.py

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Minor bug fixes

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Minor bug fixes

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Seg.nrrd quick fix

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Create LICENSE (#20)
Create LICENSE
Update setup.py

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added tests for Dataset class

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added tests for Dataset class

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added tests for Dataset class

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Update README.md

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Update README.md (#19)

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Update README.md

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Update main.yml (#18)
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Update setup.py

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Update main.yml

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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 <vishweshramanathan@gmail.com> Former-commit-id: bafe9e56aadbc5e54430757de3ac50374a6433dc (777f935)

fix

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fix

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fix path backslash issues

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fix path backslash issues

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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 <vishweshramanathan@gmail.com> Former-commit-id: bd8625cd37b114b7b26f981b8b8af5159dec9b5b (7833463)

fixed test autopipe

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fixed test autopipe

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fix conflicts

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fix conflicts

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

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

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Changed dataset class returns

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Changed dataset class returns

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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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added demo.py

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small bug fix

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small bug fix

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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

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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 <vishweshramanathan@gmail.com> Former-commit-id: 10a90b47190fb9fcbd372b30a091f56fb38ef703 (1de1d92)

Update manual-test.yml

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Update build-ci.yml

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Create manual-test.yml

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added visualizations and some more bug fixes

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added visualizations and some more bug fixes

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bug fixes 2

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bug fixes 2

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bug fixes 2

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bug fixes 2

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test and autopipe fixed

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test and autopipe fixed

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bug fixes_1.0

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bug fixes_1.0

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Update requirements.txt

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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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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 <vishweshramanathan@gmail.com> Former-commit-id: 8ff5550b971938a3a7ad1f50c68ff606b3b54236 (ca98e79)

uncommented one line pytest

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uncommented one line pytest

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uncommented one line pytest

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

merging sejin's addition

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

merging sejin's addition

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now checks for existing subject id

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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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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 'label_save' of github.com:bhklab/imgtools into complete_pipe

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more refactoring

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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

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Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes

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added crawl.py

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Added DataGraph, now fetching subset of dataset is supported using graph query

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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

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Merge branch 'RTdose' into complete_pipe RT dose and PET done. Now focusing on the completion of pipeline

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Head-Neck-PET-CT pipeline + read_dicom_auto

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PET readability added

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PET readability added

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RT dose pipeline completed and tested. Error in segmentation not resolved

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fixed structureset.py:148

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Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.

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Fixed contour (RTSTRUCT) handling to rasterize multiple contours better.

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supports RTSTRUCT processing without roi_names

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added seg.nrrd compatibility

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little updates

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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

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Fix crop size issue in crop_to_bounding_box

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

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[Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT

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Fix type error when passing Numpy array to rotate

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Fix spurious mixin in ops

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Update README.md

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Fix segmentation to label image conversion

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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

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fixed index column handling in ImageCSVLoader

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Revert "fixed index column handling in ImageCSVLoader"

This reverts commit 5561121c00024f8ebf72b83b9605a6ffe655eb23 [formerly ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33].

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fixed index column handling in ImageCSVLoader

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fixed indentation error

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

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image CSV loader now accepts pandas DataFrames

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added support for dynamic path specification in writers

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

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[In Progress] Adding documentation to ops.py

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fixed label handling in image statistics computation

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fixed label handling in image statistics computation

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removed old structure set code

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removed old structure set code

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fixed segmentation mask handling in image statistics computation

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Segmentation object now correctly handles indexing

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MetadataWriter can now remove existing files from previous runs

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MetadataWriter can now remove existing files from previous runs

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fixed error when trying to detect CSV delimiter in MetadataWriter

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StructureSet now correctly handles ROIs with no contour data

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fixed typo in pipeline warning message

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fixed segmentation method call in some functional ops

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matching roi names in StructureSet.to_segmentation is now case-insensitive

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minor fixes in IO and segmentation

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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

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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)
fixed typo in resample (cfa1443)
updated gitignore (bdb9a3e)
updated arguments in resample op (d5e5268)
Merge branch 'master' of https://github.com/bhklab/imgtools (ebd0717)
updated readme with development mode installation instructions (2fe5e95)
[quick fix] removed a syntax error, = that was added with init function's output_directory parameter (8657727)
added zoom operation (0426d0e)
added more pipeline ops from functional module (e33c83f)
refactored image statistics computation (265e19a)
minor documentation & type annotation fixes (01b5295)
fixed standard scaling function (f74a78f)
fixed standard scaling function (36145fc)
minor style fixes (d81f46d)
fixed type annotations in resample (25007be)
implemented better sigma computation when downsampling (feee338)
output size can now be specified when resampling (f644c26)
moved examples outside package code (a5fd368)
Revert "minor fixes in RADCURE example"

This reverts commit 3ed090c6554e61eee35d4d3161ca5489a56b49ee. (b68c6f4)

Revert "moved examples outside package code"

This reverts commit 0014e6526bf37062ef6e3bb686f42538d8d075a0. (25cf496)

removed datasets directory (483f449)
support for 3D rotations (14f7120)
fixed unbound variable error in ImageFileLoader (9100032)
improved documentation and type annotation in ops.functional (6c3b04e)
added functions for computing bounding box and centroid (a87deb2)
added intensity statistics functions (d9bf8ab)
crop function now correctly handles the crop size (fa887eb)
moved examples outside package code (0014e65)
minor fixes in RADCURE example (3ed090c)
Merge branch 'master' of https://github.com/bhklab/imgtools (f617f7e)
lazy import matplotlib in imageutils (eefaef6)
fixed BaseOp repr (f6a34c4)
minor fixes in RADCURE example (f65f050)
clean up variable names in writers (8f93220)
fixed subject id handling in ImageFileLoader when subdir path is passed (0d4d117)
updated conda installation instructions (8f34ea3)
Update README.md (1dc8d33)
added README (01f04c4)
fixed parameter names in RADCURE example (8578ef8)
added setup.py (2720532)
added requirements file (ddedcc1)
fixed pipeline repr (7b95202)
added requirements file (a4dcd7d)
pipeline now issues warning for missing data in loaders (5530a6a)
improved variable and class names in loaders (ba12cb0)
changed subject ID naming convention in loaders (ddc0e39)
test pipeline now generates test data on the fly (c4022d7)
updated gitignore (b09cd8d)
fixed multiprocessing issue related to sitk object pickling (30c42b4)
changed RADCURE example to follow current AP (fdfb4e6)
cleaned up ops (d2c1154)
cleaned up writers (7419f21)
cleanup before initial release (66183dd)
cleanup before initial release (ead8cbf)
updated gitignore (e11ca58)
demo (bd73693)
demo (5fb8266)
demo (f4ca619)
demo (6e4a93a)
initial implementation of Image class (4288b5b)
added docstrings to io functions (0037a15)
implemented cropping and padding transforms (2cf5a9c)
removed mask argument and renamed the resampling transform (40e391d)
improved type annotations in transforms.spatial.resample_image (d125e12)
improved spacing specification for resampling (7237ee5)
minor fixes in transforms.spatial.resample_image (02d3ed0)
added documentation and type annotations to transforms.spatial.resample_image (d7862f0)
fixed interpolator choice in resample_image (d0c80d7)
utility function to check mask geometry (4316546)
first implementation of image resampling (180f759)
added basic IO functions (dfb11dd)
initial commit (2afb431)

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