- fix: License updated to MIT (#119) (
6e755dd
)
- chore(sem-ver): 1.5.3 (
7effcaf
)
- fix: Clarified license in README.md (#118) (
a4899ca
)
- chore(sem-ver): 1.5.2 (
69a651f
)
- fix: upload latest version to pypi (
1debad3
)
- chore(sem-ver): 1.5.1 (
7890f36
)
- fix: format toml (
269f55d
)
- chore(sem-ver): 1.5.0 (
69626ef
)
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patch: pushing to 1.4.1 (#116)
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feat: semantic release!
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patch: pushing versions (
7b4cf22
)
- chore: bump version (
58ec67f
)
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feat: semantic release (#114)
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feat: semantic release
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fix: if statement issue (
23a2d70
)
- 1.1.0
Automatically generated by python-semantic-release (fe25ff2
)
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Dev (#112)
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kill bob the builder
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pip publish without semantic release
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oops
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adding checkout to pip-squeak
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fixed main.yml
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fixed main.yml
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fixed main.yml
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skip autopipeline in pip testing
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adding code coverage
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removed pytest-xdist
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xdist removed, -n flag gone
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fix: explicit module to track for code coverage
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chore: bump version
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removed pytest-xdist
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xdist removed, -n flag gone
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fixing main.yml conflict
Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> (76cea29
)
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Dev (#111)
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kill bob the builder
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pip publish without semantic release
-
oops
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adding checkout to pip-squeak
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fixed main.yml
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fixed main.yml
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fixed main.yml
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skip autopipeline in pip testing
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adding code coverage
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removed pytest-xdist
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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)
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Switching to poetry + ruff
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fixed main.yml
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this will do
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maybe this?
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update lock
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fix: ruff errors
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fix: python version error
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all lint checks pass
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tests should work...
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update pytest version
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new poetry install
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windows ghaction poetry install... work pls
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yml fix
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poetry version=1.8.2
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still fixing main.yml
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maybe it's poetry?
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oh boy!
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kill old unit test ci/cd
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update ci/cd badge
Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> (6ddc645
)
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New tests, improving code coverage. (#105)
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new_tests_in_progress
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Added majority coverage for
imgtools.ops
. -
updated main-ci.yml with dataset-check.py name change. (
c2e8ddb
) -
Mit lite (#104)
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Detached branch (#94)
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v1.2.0 for lighter install.
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update main-ci.yml
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fixed test_dataset
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added zipfile and request
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added torch and torchio
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added missing dep in main-ci
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Detached branch (#94)
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v1.2.0 for lighter install.
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update main-ci.yml
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fixed test_dataset
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updated PyPI push with API key
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build-pkg pls work
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pypi changes
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no egg please
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hm
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remove dataset dependency. to be reconciled later
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1.2.0.1 hopefully fixed
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main-ci removed test_dataset
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readding scikit-learn
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push to 1.2.0.2 (
9137965
) -
Mit lite (#103)
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Detached branch (#94)
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v1.2.0 for lighter install.
-
update main-ci.yml
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fixed test_dataset
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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
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readding scikit-learn (
4b06915
) -
MIT lite (#102)
-
Detached branch (#94)
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v1.2.0 for lighter install.
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update main-ci.yml
-
fixed test_dataset
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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
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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
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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
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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
set 2nd half pandas
astype(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
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dicom-seg update
-
some changes
-
utils for refactoring
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add attr to reqs
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fixed attr to attrs
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update version (
d99950f
) -
Dicom seg (#77)
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DICOM-SEG beta commit
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dicom-seg update
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some changes
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utils for refactoring
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add attr to reqs
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fixed attr to attrs (
7634a6c
) -
DICOM-SEG beta commit (#74) (
5c4924d
) -
Add docstrings to Segmentation init (#73) (
223f0b6
) -
Add raw roi columns (#72)
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Change roi_names to roi_indices
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Add raw_roi_names
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Add raw_roi_names (
6327578
) -
update version (
52c3a8d
) -
Add mr crawls (#71)
-
added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus
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added SEGMENTATION ReferencedSeriesSequence as ref_ct
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change pytest version
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pytest 6.2.2
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whoops
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testing nibabel
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importlib test
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iniconfig test
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sitk 2.2.0 test
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snumpy21.23test
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numpy 1.23 test
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changed deprecated numpy np.int to int
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deprecated np.warnings
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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
)
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added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFiel… (#70)
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added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus
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added SEGMENTATION ReferencedSeriesSequence as ref_ct
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change pytest version (
8f81e40
) -
Delete the labels that are empty (#69) (
1e25c57
) -
Autopipeline fix (#68)
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Added default value for path strings
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Changed is_nnunet for nnunet (
9b19076
) -
Update setup.py (
b3314d4
) -
hotfix (#67) (
f3151a1
) -
Crawl orientation (#66)
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added orientation DICOM tag crawling
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nnunet flags hotfix (#64)
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autopipeline.py:164, changed or -> and
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added orientation DICOM tag crawling
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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.
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Added --roi_select_first and --roi_separate flags for advanced ROI parsing for contours.
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mask_label parsing for illegal Windows/Unix characters (Issue #45 resolved) (
89b715b
) -
Update README.md (
199071e
)
-
Subseries (#61)
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subseries implementation step 1
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Fixes for issues #57, #53.
-
update README.
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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)
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Update README.md
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Update setup.py
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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
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Relative robust fix for issue #53
-
Update setup.py
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Update README.md (
bc43f29
) -
Update setup.py (
56faf21
) -
Create LICENSE (
a01891f
) -
1.0.0 (#52)
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Update README.md
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Update setup.py (
3ceaf19
) -
0.4.4 (#49)
-
Update setup.py
-
Update README.md
-
readme changes
-
Update README.md
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Delete autopipeline.png
Co-authored-by: Kevin <qukevin99@gmail.com> (2d2079c
)
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Delete autopipeline.png (
6a5b7d0
) -
Markdown Report and new CLI options (#48)
-
markdown report generator
-
update version to push to pypi
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working on changes for nnunet inference
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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
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isabs for rel path args
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Update main-ci.yml
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fixed failing tests
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another pytest fix
-
error check
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error check 2
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Update test_components.py
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test if values are working
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missing values?
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more ci tests
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more ci tests 2
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ci tests 3
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ci tests 4
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ci tests 5
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ci tests 5
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ci tests 6
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ci tests 7
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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)
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Update README.md
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redesigned autopipeline diagram
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Delete build-ci.yml
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Delete main.yml
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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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self.existing, dataset.csv fixed (#10)
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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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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
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: f2480c3bd2fba4498c609ef1efc031e1d4f7e2cd
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self.existing, dataset.csv fixed (#10)
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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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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
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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Create build-ci.yml
Former-commit-id: 5a0e9451e6e59de05e5dc2062ccbae6d8632179f
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Create build-ci.yml
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Update build-ci.yml
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Update build-ci.yml
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Update requirements.txt
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bug fixes_1.0
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test and autopipe fixed
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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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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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added visualizations and some more bug fixes
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Create manual-test.yml
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Create manual-test.yml
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Update build-ci.yml
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Update manual-test.yml
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PR tests - macos/ubuntu failing (#13)
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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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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
-
deleted data
-
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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5
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PR tests - macos/ubuntu failing (#13)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
-
fixed pipeline tests
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clean tests
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added workflow
-
yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
-
set roi_names to avoid memoryerror
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cave
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indents
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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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Ready for
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Ready for
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fixed test autopipe
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merging new features (#16)
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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c
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merging new features (#16)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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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
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fix path backslashes (#17)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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
-
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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
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fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: 5c6f7b00b440c06a730ff7ee289e0dd0f146a4dd
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fix path backslashes (#17)
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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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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
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uncommented one line pytest
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uncommented one line pytest
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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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bug fixes_1.0
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test and autopipe fixed
-
bug fixes 2
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bug fixes 2
-
added visualizations and some more bug fixes
-
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
-
small bug fix
-
added demo.py
-
Changed dataset class returns
-
fix conflicts
-
fixed test autopipe
-
fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- Update main.yml
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build binary/dist
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removed linter
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build binary/dist
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removed linter
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Update README.md (#19)
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Update README.md (#19)
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added tests for Dataset class
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Seg.nrrd quick fix
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test fix
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preliminary MRI functionality (MR-RTSTRUCT pairs)
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quick fixes
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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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brought back basesubjectwriter
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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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metadata in dataset.csv
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metadata bugfix
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a
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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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fixed formatting problems with folder names
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train size and random state optional
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merge conflicts
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added regex dictionary option for non nnunet runs
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yaml thing
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dataset.json for nnunet
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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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warnings for missing patients
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summary messages
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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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updated readme
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minor change
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remote .idea
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transpose for nnunet
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skip if no mask for nnunet and nnunet folder names
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bugs in nnunet folder stuff
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rename nnunetutil (again)
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sorting the output streams
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shell script
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shell script in autopipeline
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bug
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forgot CopyInformation for nnunet
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ignore deprecation warning
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set -e for stopping execution if there is an error
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broken checker for missing labels
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train test fix for 1 patient
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fix for broken self.existing_roi_names caused by joblib
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added autotest to gitignore
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sorted list for train test split
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custom train test split
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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
)
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Nnunet demo (#40)
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uncommented one line pytest
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self.existing, dataset.csv fixed (#10)
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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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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
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: f2480c3bd2fba4498c609ef1efc031e1d4f7e2cd
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self.existing, dataset.csv fixed (#10)
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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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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
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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bug fixes_1.0
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PR tests - macos/ubuntu failing (#13)
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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5
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PR tests - macos/ubuntu failing (#13)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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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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Ready for
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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c
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merging new features (#16)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- fix path backslash issues
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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
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fix path backslash issues
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fix path backslashes (#17)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
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fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- Update main.yml
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build binary/dist
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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)
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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Update setup.py
Former-commit-id: 5e93381461268785776402061d555ab02b78fda3
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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Update setup.py
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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Update setup.py
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quick fixes
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- quick fixes
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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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transpose for nnunet
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skip if no mask for nnunet and nnunet folder names
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bugs in nnunet folder stuff
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rename nnunetutil (again)
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sorting the output streams
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shell script
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shell script in autopipeline
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bug
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forgot CopyInformation for nnunet
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ignore deprecation warning
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moved sh file down one dir
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set -e for stopping execution if there is an error
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broken checker for missing labels
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train test fix for 1 patient
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fix for broken self.existing_roi_names caused by joblib
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added autotest to gitignore
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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
)
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Update README.md (
c39ffe6
) -
Ci update (#39)
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new ci/cd actions
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updated pathing too
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updated ci/cd actions
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update
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update (
df61201
) -
Update build-pkg.yml (
5a314e5
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Update build-pkg.yml (
630c184
) -
Update build-pkg.yml (
1ff1b2b
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Create build-pkg.yml (
c9d1f42
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post-rebase (#38)
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removed old structure set code
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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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[In Progress] Adding documentation to ops.py
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added support for dynamic path specification in writers
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image CSV loader now accepts pandas DataFrames
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fixed indentation error
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fixed index column handling in ImageCSVLoader
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Revert "fixed index column handling in ImageCSVLoader"
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
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fixed index column handling in ImageCSVLoader
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fixed index column handling in ImageCSVLoader
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ImageCSVLoader now returns correct keys
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ImageCSVLoader now correctly handles globbing in paths
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more informative exception handling in pipeline
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pipeline can now warn on error instead of raising exception
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[Docs] Cleaned up extra whitespace in ops.py
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Added convenience method to get all ops in a pipeline
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Fix empty array check in structure set conversion
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Fix segmentation to label image conversion
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Update README.md
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Fix spurious mixin in ops
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Fix type error when passing Numpy array to rotate
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[Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT
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Fix crop size issue in crop_to_bounding_box
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Make imports easier
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Improved handling of regular expressions in structure set
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Fix slice matching issue when generating binary mask from RTStruct
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Fix binary mask generation from RTStruct when missing labels are present
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little updates
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added seg.nrrd compatibility
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supports RTSTRUCT processing without roi_names
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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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fixed structureset.py:148
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RT dose pipeline completed and tested. Error in segmentation not resolved
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PET readability added
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PET readability added
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Head-Neck-PET-CT pipeline +
read_dicom_auto
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final pipeline working for doses and PET
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corrected the view
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reading in sitk format from beginning
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Completed PET overlay
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Modified RT dose, pipeline working for PET_CT quebec dataset
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Added DataGraph, now fetching subset of dataset is supported using graph query
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added crawl.py
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Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes
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Rectified some bugs, added reference to rtplan in the crawler
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Now missing RTDOSE references are completed by RTPLAN
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small change
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Fixed dataset.csv writing issues
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major refactoring
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more refactoring
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Update radcure_simple.py
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Update loaders.py
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Update pet.py
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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ignore .DS_Store
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Update README.md
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quick README under ops
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tcia_sample
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example bash script with path parsing, fixed reference_frame
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housekeeping
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fixed dataset.csv
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sanity changes before purging dev-20200414
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Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id
Former-commit-id: 03f99572453723e4a3e895acac0996997f090168
- PT/RTDOSE metadata to csv
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- fixed some bugs in autopipeline.py
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- now the pipeline saves on exit
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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)
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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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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
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
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Create build-ci.yml
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Update build-ci.yml
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Update requirements.txt
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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
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Update build-ci.yml
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Update manual-test.yml
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PR tests - macos/ubuntu failing (#13)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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Update manual-test.yml
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- fixed bugs regarding multiple connections, saving of metadata and loading of metadata
Former-commit-id: 1528efc88ca4952ce570721832a339ff8274b4fa
- small bug fix
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- added demo.py
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Ready for
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Create main.yml (#15)
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Changed dataset class returns
Former-commit-id: 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a
- fix conflicts
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- fixed test autopipe
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merging new features (#16)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- fix path backslash issues
Former-commit-id: d81a74dfcdcd21f2b9248d197362a6dbaabf901b
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fix path backslashes (#17)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
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fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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Update main.yml
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Update main.yml
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Update README.md
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Update main.yml (#18)
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Update main.yml
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Update requirements.txt
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Update main.yml
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Update main.yml
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build binary/dist
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removed linter
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Update setup.py
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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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added tests for Dataset class
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- added tests for Dataset class
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Create LICENSE (#20)
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Create LICENSE
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Update setup.py
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Seg.nrrd quick fix
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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
Former-commit-id: 0f0414533cb6667b68aa48541feb376226fd5515 Former-commit-id: c406bfc9526357e2091e1348d837c68cd5633801
- Update README.md (#24)
Former-commit-id: 9aaf51bcb71b28cf062a03d873682b2ff38cee90 Former-commit-id: 4e7335ef07059daa9dd3743e0727d63610e9da62
- preliminary MRI functionality (MR-RTSTRUCT pairs)
Former-commit-id: 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85 Former-commit-id: 12b031d46c1c3ddbd1917b4037d9164ca3402ff2
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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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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- debug print
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- removed debug print
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- added sparse mask class and generating function
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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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new experimental segmentation class
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minor fixes in segmentation module
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matching roi names in StructureSet.to_segmentation is now case-insensitive
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StructureSet now correctly handles ROIs with no contour data
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Segmentation object now correctly handles indexing
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Fix empty array check in structure set conversion
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[Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT
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Fix slice matching issue when generating binary mask from RTStruct
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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
)
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Update README.md (
49aa813
) -
Update setup.py (#37)
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Kevin branch (#36)
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simplified loader/writer specification in IO ops
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updated imports in pipeline
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improved ops repr
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minor fixes in IO and segmentation
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matching roi names in StructureSet.to_segmentation is now case-insensitive
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fixed segmentation method call in some functional ops
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fixed typo in pipeline warning message
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StructureSet now correctly handles ROIs with no contour data
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fixed error when trying to detect CSV delimiter in MetadataWriter
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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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Segmentation object now correctly handles indexing
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fixed segmentation mask 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 label handling in image statistics computation
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fixed label handling in image statistics computation
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[In Progress] Adding documentation to ops.py
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added support for dynamic path specification in writers
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image CSV loader now accepts pandas DataFrames
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fixed indentation error
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fixed index column handling in ImageCSVLoader
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Revert "fixed index column handling in ImageCSVLoader"
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
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fixed index column handling in ImageCSVLoader
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fixed index column handling in ImageCSVLoader
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ImageCSVLoader now returns correct keys
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ImageCSVLoader now correctly handles globbing in paths
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more informative exception handling in pipeline
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pipeline can now warn on error instead of raising exception
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[Docs] Cleaned up extra whitespace in ops.py
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Added convenience method to get all ops in a pipeline
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Fix empty array check in structure set conversion
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Fix segmentation to label image conversion
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Update README.md
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Fix spurious mixin in ops
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Fix type error when passing Numpy array to rotate
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[Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT
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Fix crop size issue in crop_to_bounding_box
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Make imports easier
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Improved handling of regular expressions in structure set
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Fix slice matching issue when generating binary mask from RTStruct
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Fix binary mask generation from RTStruct when missing labels are present
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little updates
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added seg.nrrd compatibility
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supports RTSTRUCT processing without roi_names
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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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fixed structureset.py:148
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RT dose pipeline completed and tested. Error in segmentation not resolved
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PET readability added
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PET readability added
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Head-Neck-PET-CT pipeline +
read_dicom_auto
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final pipeline working for doses and PET
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corrected the view
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reading in sitk format from beginning
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Completed PET overlay
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Modified RT dose, pipeline working for PET_CT quebec dataset
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Added DataGraph, now fetching subset of dataset is supported using graph query
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added crawl.py
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Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes
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Rectified some bugs, added reference to rtplan in the crawler
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Now missing RTDOSE references are completed by RTPLAN
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small change
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Fixed dataset.csv writing issues
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major refactoring
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more refactoring
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Update radcure_simple.py
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Update loaders.py
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Update pet.py
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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Delete .DS_Store
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ignore .DS_Store
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Update README.md
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quick README under ops
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tcia_sample
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example bash script with path parsing, fixed reference_frame
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housekeeping
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fixed dataset.csv
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sanity changes before purging dev-20200414
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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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- 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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self.existing, dataset.csv fixed (#10)
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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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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
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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Update build-ci.yml
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Update requirements.txt
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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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Update build-ci.yml
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Update manual-test.yml
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PR tests - macos/ubuntu failing (#13)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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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
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Create main.yml (#15)
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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)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
- fix path backslash issues
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fix path backslashes (#17)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
-
bug fixes 2
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bug fixes 2
-
added visualizations and some more bug fixes
-
fixed bugs regarding multiple connections, saving of metadata and loading of metadata
-
small bug fix
-
added demo.py
-
Changed dataset class returns
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fix conflicts
-
fixed test autopipe
-
fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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Update main.yml
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Update main.yml
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Update README.md
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Update main.yml (#18)
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Update main.yml
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Update requirements.txt
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Update main.yml
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Update main.yml
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build binary/dist
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removed linter
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Update setup.py
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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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added tests for Dataset class
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- added tests for Dataset class
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Create LICENSE (#20)
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Create LICENSE
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Update setup.py
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Seg.nrrd quick fix
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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)
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Updated crawler to force String on all meta fields
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- first commit
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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
)
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update to 0.4.1 for new readme (#35)
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simplified loader/writer specification in IO ops
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updated imports in pipeline
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improved ops repr
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minor fixes in IO and segmentation
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matching roi names in StructureSet.to_segmentation is now case-insensitive
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fixed segmentation method call in some functional ops
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fixed typo in pipeline warning message
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StructureSet now correctly handles ROIs with no contour data
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fixed error when trying to detect CSV delimiter in MetadataWriter
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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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Segmentation object now correctly handles indexing
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fixed segmentation mask 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 label handling in image statistics computation
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fixed label handling in image statistics computation
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[In Progress] Adding documentation to ops.py
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added support for dynamic path specification in writers
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image CSV loader now accepts pandas DataFrames
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fixed indentation error
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fixed index column handling in ImageCSVLoader
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Revert "fixed index column handling in ImageCSVLoader"
This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33.
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fixed index column handling in ImageCSVLoader
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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>
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- Merge branch 'master' of github.com:bhklab/med-imagetools
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- quick fixes
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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Update setup.py
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Skim2257 quick fix (#26)
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Updated crawler to force String on all meta fields
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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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- 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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- Merge branch 'add_capabilities'
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- Merge branch 'add_capabilities'
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- Minor bug fixes
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Create LICENSE (#20)
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Create LICENSE
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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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- 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 main.yml
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fix path backslashes (#17)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
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fix path backslash issues
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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- 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)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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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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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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Changed dataset class returns
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fix conflicts
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fixed test autopipe
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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- fixed test autopipe
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- fixed test autopipe
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- Merge branch 'master' of github.com:bhklab/imgtools
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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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- small bug fix
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PR tests - macos/ubuntu failing (#13)
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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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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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Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset
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bug fixes_1.0
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test and autopipe fixed
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bug fixes 2
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fixed pipeline tests
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clean tests
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added workflow
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yml
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yml
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matplotlib
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trying other patient to avoid memoryerror
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set roi_names to avoid memoryerror
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cave
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indents
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Update manual-test.yml
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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- Update 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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- bug fixes_1.0
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- bug fixes_1.0
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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)
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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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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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uncommented one line pytest
Co-authored-by: Vishwesh <vishweshramanathan@gmail.com>
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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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merging sejin's addition
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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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- 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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attached tcia_sample repo + sample autopipeline scripts
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- Delete .DS_Store
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- Update pet.py
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- Update loaders.py
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- Merge pull request #7 from bhklab/label_save
merge added features
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- Update radcure_simple.py
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- Merge pull request #6 from bhklab/complete_pipe
merge into label_save
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- Merge branch 'label_save' of github.com:bhklab/imgtools into complete_pipe
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- more refactoring
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- Merge branch 'complete_pipe' of github.com:bhklab/imgtools into complete_pipe
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- major refactoring
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- Fixed dataset.csv writing issues
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- small change
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- Now missing RTDOSE references are completed by RTPLAN
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- Rectified some bugs, added reference to rtplan in the crawler
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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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updated readme with development mode installation instructions (
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fixed standard scaling function (
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minor style fixes (
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fixed type annotations in resample (
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Revert "minor fixes in RADCURE example"
This reverts commit 3ed090c6554e61eee35d4d3161ca5489a56b49ee. (b68c6f4
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- Revert "moved examples outside package code"
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removed datasets directory (
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support for 3D rotations (
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fixed unbound variable error in ImageFileLoader (
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improved documentation and type annotation in ops.functional (
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added functions for computing bounding box and centroid (
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added intensity statistics functions (
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crop function now correctly handles the crop size (
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fixed subject id handling in ImageFileLoader when subdir path is passed (
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added requirements file (
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fixed pipeline repr (
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changed subject ID naming convention in loaders (
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test pipeline now generates test data on the fly (
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updated gitignore (
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fixed multiprocessing issue related to sitk object pickling (
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changed RADCURE example to follow current AP (
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cleaned up ops (
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added documentation and type annotations to transforms.spatial.resample_image (
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initial commit (
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