From fe25ff2003c9c84cee089b4e651010bd59ce4b38 Mon Sep 17 00:00:00 2001 From: semantic-release Date: Wed, 29 May 2024 16:16:16 +0000 Subject: [PATCH] 1.1.0 Automatically generated by python-semantic-release --- CHANGELOG.md | 7794 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 7794 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..21260281 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,7794 @@ +# CHANGELOG + + + +## v1.1.0 (2024-05-29) + +### Chore + +* chore: bump version ([`58ec67f`](https://github.com/bhklab/med-imagetools/commit/58ec67f1f83eeb1f1ce1b580818f5812e1d04244)) + +### Feature + +* feat: semantic release (#114) + +* feat: semantic release + +* fix: if statement issue ([`23a2d70`](https://github.com/bhklab/med-imagetools/commit/23a2d700772449837672d671873f9db3c544cd37)) + +### Fix + +* fix: add codecov badge ([`f43d042`](https://github.com/bhklab/med-imagetools/commit/f43d04231c76313d86d9e0444a6f1e26ed21b9fc)) + +* fix: explicit module to track for code coverage ([`f15d45d`](https://github.com/bhklab/med-imagetools/commit/f15d45dd43ef2d8956c0e7cbc91eb7741e9830e3)) + +### Unknown + +* Dev (#112) + +* kill bob the builder + +* pip publish without semantic release + +* oops + +* adding checkout to pip-squeak + +* fixed main.yml + +* fixed main.yml + +* fixed main.yml + +* skip autopipeline in pip testing + +* adding code coverage + +* removed pytest-xdist + +* xdist removed, -n flag gone + +* fix: explicit module to track for code coverage + +* chore: bump version + +* removed pytest-xdist + +* xdist removed, -n flag gone + +* fixing main.yml conflict + +--------- + +Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> ([`76cea29`](https://github.com/bhklab/med-imagetools/commit/76cea29325ed28bddee54ca9a326bf8c4017a78c)) + +* Dev (#111) + +* kill bob the builder + +* pip publish without semantic release + +* oops + +* adding checkout to pip-squeak + +* fixed main.yml + +* fixed main.yml + +* fixed main.yml + +* skip autopipeline in pip testing + +* adding code coverage + +* removed pytest-xdist + +* xdist removed, -n flag gone ([`48fcfd0`](https://github.com/bhklab/med-imagetools/commit/48fcfd098ebd25f3391c479873551115135aa0aa)) + +* skip autopipeline in pip testing ([`054d1b4`](https://github.com/bhklab/med-imagetools/commit/054d1b4af42b0d2eba9071509e5f7a73c20ffe2a)) + +* fixed main.yml ([`b5b09e7`](https://github.com/bhklab/med-imagetools/commit/b5b09e7d2ea171bb1da93b75db05e531ea95c190)) + +* fixed main.yml ([`560272f`](https://github.com/bhklab/med-imagetools/commit/560272fb9a147c442377fff2ef25263b66958539)) + +* fixed main.yml ([`535a1c5`](https://github.com/bhklab/med-imagetools/commit/535a1c5dacbdb1009a74108d6839bd8d8856b26e)) + +* adding checkout to pip-squeak ([`da6e006`](https://github.com/bhklab/med-imagetools/commit/da6e006f49f915ad8e367d24422ea8fbde864d07)) + +* oops ([`8291564`](https://github.com/bhklab/med-imagetools/commit/8291564fcc200cf651c56b27806e6c05c076a687)) + +* pip publish without semantic release ([`5e3cc39`](https://github.com/bhklab/med-imagetools/commit/5e3cc39c6be4f3ad32bfde6345f8a2e56da84479)) + +* kill bob the builder ([`5eacc0f`](https://github.com/bhklab/med-imagetools/commit/5eacc0fe4858706f426fe1fda55065e95ceb1342)) + +* Substantial refactoring, linting, CI/CD updates (#107) + +* Switching to poetry + ruff + +* fixed main.yml + +* this will do + +* maybe this? + +* update lock + +* fix: ruff errors + +* fix: python version error + +* all lint checks pass + +* tests should work... + +* update pytest version + +* new poetry install + +* windows ghaction poetry install... work pls + +* yml fix + +* poetry version=1.8.2 + +* still fixing main.yml + +* maybe it's poetry? + +* oh boy! + +* kill old unit test ci/cd + +* update ci/cd badge + +--------- + +Co-authored-by: Jermiah Joseph <jermiahjoseph98@gmail.com> ([`6ddc645`](https://github.com/bhklab/med-imagetools/commit/6ddc645d1ba4ab8b5945c25edbc5d52a172642c2)) + +* New tests, improving code coverage. (#105) + +* new_tests_in_progress + +* Added majority coverage for `imgtools.ops`. + +* updated main-ci.yml with dataset-check.py name change. ([`c2e8ddb`](https://github.com/bhklab/med-imagetools/commit/c2e8ddb55b8379c19f868426f1ffd4c74a0711b4)) + +* Mit lite (#104) + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* added zipfile and request + +* added torch and torchio + +* added missing dep in main-ci + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* updated PyPI push with API key + +* build-pkg pls work + +* pypi changes + +* no egg please + +* hm + +* remove dataset dependency. to be reconciled later + +* 1.2.0.1 hopefully fixed + +* main-ci removed test_dataset + +* readding scikit-learn + +* push to 1.2.0.2 ([`9137965`](https://github.com/bhklab/med-imagetools/commit/9137965b3ee7ef64935bfec36efddb0b7b5898bf)) + +* Mit lite (#103) + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* added zipfile and request + +* added torch and torchio + +* added missing dep in main-ci + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* updated PyPI push with API key + +* build-pkg pls work + +* pypi changes + +* no egg please + +* hm + +* remove dataset dependency. to be reconciled later + +* 1.2.0.1 hopefully fixed + +* main-ci removed test_dataset + +* readding scikit-learn ([`4b06915`](https://github.com/bhklab/med-imagetools/commit/4b06915b08c7aadd3b4cf4ab9ce1487b28549198)) + +* MIT lite (#102) + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* added zipfile and request + +* added torch and torchio + +* added missing dep in main-ci + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* updated PyPI push with API key + +* build-pkg pls work + +* pypi changes + +* no egg please + +* hm + +* remove dataset dependency. to be reconciled later + +* 1.2.0.1 hopefully fixed + +* main-ci removed test_dataset ([`535bff0`](https://github.com/bhklab/med-imagetools/commit/535bff0ff2ce51fc403e3fd2a4bb49f455859e5b)) + +* Mit lite (#101) + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* added zipfile and request + +* added torch and torchio + +* added missing dep in main-ci + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* updated PyPI push with API key + +* build-pkg pls work + +* pypi changes + +* no egg please + +* hm ([`e378eea`](https://github.com/bhklab/med-imagetools/commit/e378eea0d446aa7271f3438ca644a15e8e5cb489)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/3df6f2c723e4b5885793e6d636f46262faa8c045)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/92da3014d01ed337a002b696b949b04dbccc68c7)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/7dfca09192986809b0d86cd00939a9cc115df142)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/07dad6c53f3305bca65e7fbfd124a98ee8a746eb)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/afea6988a804baef20db27e8bd596e367cdf942f)) + +* Detached branch (#94) (#95) + +* Detached branch (#94) + +* v1.2.0 for lighter install. + +* update main-ci.yml + +* fixed test_dataset + +* added zipfile and request ([`88857bf`](https://github.com/bhklab/med-imagetools/commit/88857bf2aea946a5c033088dbbd6545e6523b8d2)) + +* updated actions to new default branch. 'master' branch is DEPRECATED ([`d10b5ba`](https://github.com/bhklab/med-imagetools/commit/d10b5ba32e67117771c138ebe1e457b6304460f8)) + +* updated version and default branch to 'main' ([`8784b5f`](https://github.com/bhklab/med-imagetools/commit/8784b5fb9cc898d8099a4966b8faec8b6150e283)) + +* Flake8 linting fixes (#93) + +* add stop_before_pixels tag and set to True to speed up dcm reads + +* add ct-seg support + +* flake8 linting fixes + +* flake8 linting fixes transforms + +--------- + +Co-authored-by: Umar Yousafzai <umaryousafzai54@gmail.com> ([`43a72fe`](https://github.com/bhklab/med-imagetools/commit/43a72fe108d5ba50559093708c1fdf15402d82b5)) + +* convert to dicom (#89) + +nifti to dicom function ([`ba50037`](https://github.com/bhklab/med-imagetools/commit/ba50037fee4c0c6bc0640d5efdc074ea75944da7)) + +* test break during demo (#81) + +* test break during demo +- changed https://github.com/bhklab/med-imagetools/blob/d99950f4240ec286deeef6d635fe329ca520f2a7/imgtools/modules/datagraph.py#L61 set 2nd half pandas`astype(str)` + +* Update setup.py to 1.1.6 ([`1268cbc`](https://github.com/bhklab/med-imagetools/commit/1268cbc668d2960e3dbb66955ed84b298bb1a651)) + +* add stop_before_pixels tag and set to True to speed up dcm reads (#80) + +AYE AYE ([`bb4dad7`](https://github.com/bhklab/med-imagetools/commit/bb4dad72aa4b1e2ddf9bf521b1bcb5b2f21c01d9)) + +* Dicom seg (#78) + +* DICOM-SEG beta commit + +* dicom-seg update + +* some changes + +* utils for refactoring + +* add attr to reqs + +* fixed attr to attrs + +* update version ([`d99950f`](https://github.com/bhklab/med-imagetools/commit/d99950f4240ec286deeef6d635fe329ca520f2a7)) + +* Dicom seg (#77) + +* DICOM-SEG beta commit + +* dicom-seg update + +* some changes + +* utils for refactoring + +* add attr to reqs + +* fixed attr to attrs ([`7634a6c`](https://github.com/bhklab/med-imagetools/commit/7634a6c671cff6807f10505223c4f83c85e906c7)) + +* DICOM-SEG beta commit (#74) ([`5c4924d`](https://github.com/bhklab/med-imagetools/commit/5c4924d6ebc80791672c7e7608b4fa138877ffdb)) + +* Add docstrings to Segmentation init (#73) ([`223f0b6`](https://github.com/bhklab/med-imagetools/commit/223f0b6e43672d943a7041a9de2bbd94dfbe0ff5)) + +* Add raw roi columns (#72) + +* Change roi_names to roi_indices + +* Add raw_roi_names + +* Add raw_roi_names ([`6327578`](https://github.com/bhklab/med-imagetools/commit/6327578153953e43441bf95b0621d80f86e787c6)) + +* update version ([`52c3a8d`](https://github.com/bhklab/med-imagetools/commit/52c3a8d37402989e4bd0a0855f1eb3cbce94fa47)) + +* Add mr crawls (#71) + +* added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus + +* added SEGMENTATION ReferencedSeriesSequence as ref_ct + +* change pytest version + +* pytest 6.2.2 + +* whoops + +* testing nibabel + +* importlib test + +* iniconfig test + +* sitk 2.2.0 test + +* snumpy21.23test + +* numpy 1.23 test + +* changed deprecated numpy np.int to int + +* deprecated np.warnings + +* fixed problematic autopipeline:612 ([`37e5d8e`](https://github.com/bhklab/med-imagetools/commit/37e5d8ea0e4f8c5feb87d47e73e796f20d7cc949)) + +* 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`](https://github.com/bhklab/med-imagetools/commit/8a95ae7c76f5b1d5834e7aae3df7b5f076698d08)) + +* added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFiel… (#70) + +* added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus + +* added SEGMENTATION ReferencedSeriesSequence as ref_ct + +* change pytest version ([`8f81e40`](https://github.com/bhklab/med-imagetools/commit/8f81e40582af3be5568169d754e5bf2aa835014f)) + +* Delete the labels that are empty (#69) ([`1e25c57`](https://github.com/bhklab/med-imagetools/commit/1e25c573ac2585f3bb1ea0f4dc7228a657092d17)) + +* Autopipeline fix (#68) + +* Added default value for path strings + +* Changed is_nnunet for nnunet ([`9b19076`](https://github.com/bhklab/med-imagetools/commit/9b19076425e0978fb579b9ddab14a08ccc06c957)) + +* Update setup.py ([`b3314d4`](https://github.com/bhklab/med-imagetools/commit/b3314d4d43fa90b7ee5293ee7f4b9e6722ef30cf)) + +* hotfix (#67) ([`f3151a1`](https://github.com/bhklab/med-imagetools/commit/f3151a11f49c71437e0011618b0e53c0bc34cd85)) + +* Crawl orientation (#66) + +* added orientation DICOM tag crawling + +* nnunet flags hotfix (#64) + +* autopipeline.py:164, changed or -> and + +* added orientation DICOM tag crawling + +* more is_nnunet fails ([`ffd6bca`](https://github.com/bhklab/med-imagetools/commit/ffd6bcaf6bb6cd6f19a7f9cf434681974864755e)) + +* added orientation DICOM tag crawling (#65) ([`cc9cea1`](https://github.com/bhklab/med-imagetools/commit/cc9cea185165d4f1d718e13a0377a1dfc0ef3903)) + +* autopipeline.py:164, changed or -> and ([`f41f18d`](https://github.com/bhklab/med-imagetools/commit/f41f18d0e6c8834147c82c380248372377e3e2e1)) + +* nnunet flags hotfix (#64) ([`ecc6939`](https://github.com/bhklab/med-imagetools/commit/ecc6939a10bcf4cca065368a62b5fe900b8c2184)) + +* New flags: --update, --roi_select_first, --roi_separate, better mask_label parsing (#45) + +* added --update flag, needs test. + +* Added --roi_select_first and --roi_separate flags for advanced ROI parsing for contours. + +* mask_label parsing for illegal Windows/Unix characters (Issue #45 resolved) ([`89b715b`](https://github.com/bhklab/med-imagetools/commit/89b715be5d8684ffbb3d1770dfd9eb5125f78235)) + +* Update README.md ([`199071e`](https://github.com/bhklab/med-imagetools/commit/199071e0e2c1572fa6c947c17722d254fb5b2468)) + + +## v1.0.3 (2022-10-14) + +### Unknown + +* Subseries (#61) + +* subseries implementation step 1 + +* Fixes for issues #57, #53. + +* update README. + +* fixed pytest error ([`f8f3606`](https://github.com/bhklab/med-imagetools/commit/f8f3606f4340e57e224bbc1ea0b33398db39b61b)) + +* update github actions ([`4adf148`](https://github.com/bhklab/med-imagetools/commit/4adf148f30fbd0772b514c0a2ae90b2b088037ea)) + +* Update build-pkg.yml ([`ec167b7`](https://github.com/bhklab/med-imagetools/commit/ec167b731df27b245be615105b474d79bd83389f)) + +* Update build-pkg.yml ([`4154d26`](https://github.com/bhklab/med-imagetools/commit/4154d267ef4675a185f5cba520756f7728b65e1d)) + +* Update build-pkg.yml ([`b2ab181`](https://github.com/bhklab/med-imagetools/commit/b2ab18129e24d248c358b9d7127502d176da4ca7)) + +* Update build-pkg.yml ([`be566e8`](https://github.com/bhklab/med-imagetools/commit/be566e8cb568c39ca007844c068b220341f9810f)) + +* Update build-pkg.yml ([`8265aff`](https://github.com/bhklab/med-imagetools/commit/8265aff2ea33f2a94393df5eee5ce60afdc33acd)) + +* Merge pull request #60 from bhklab/sw-fix + +Sw fix ([`91330f0`](https://github.com/bhklab/med-imagetools/commit/91330f063467731bc42c310d58306d5de2a16e65)) + +* Merge branch 'master' of github.com:bhklab/med-imagetools into sw-fix ([`c743a98`](https://github.com/bhklab/med-imagetools/commit/c743a9804382a45ec283d12e34342a48959a7a9b)) + +* Update build-pkg.yml ([`072d597`](https://github.com/bhklab/med-imagetools/commit/072d597dddde90a899a43f0144fc97474478752b)) + +* Skim2257 patch 1 (#59) + +* Update README.md + +* Update setup.py + +* Update build-pkg.yml ([`ce5ee0c`](https://github.com/bhklab/med-imagetools/commit/ce5ee0c0fcf0735407cf8bedbf42aa9e95c4e8e9)) + +* updated dose ([`645aae7`](https://github.com/bhklab/med-imagetools/commit/645aae7fd039bb60798ef48777b407a6e1b2fa78)) + +* Merge branch 'master' of github.com:bhklab/med-imagetools into sw-fix ([`c6f8376`](https://github.com/bhklab/med-imagetools/commit/c6f8376c216a4828c8746eb74e86a8ad8d39e480)) + +* temporary dose fix loading error with Sejin ([`abb452f`](https://github.com/bhklab/med-imagetools/commit/abb452f1a1b3fd4c2ad4f7538116ca39d6adf64f)) + +* Update README.md (#58) ([`edb8612`](https://github.com/bhklab/med-imagetools/commit/edb86123a4eae8394bf08ecee51d0ce68ca95273)) + +* Update build-pkg.yml ([`954b224`](https://github.com/bhklab/med-imagetools/commit/954b22468682f779b89d2ea5ed851eb30b076de9)) + +* multi-modality fix + +* adding test param for better QC + +checking patient_ID error for issue #53 + +* Relative robust fix for issue #53 + +* Update setup.py + +* Update README.md ([`bc43f29`](https://github.com/bhklab/med-imagetools/commit/bc43f29d96b0c4f6de11bc8fb9a57364ca764e55)) + +* Update setup.py ([`56faf21`](https://github.com/bhklab/med-imagetools/commit/56faf21378841d993756194e48857af5edae166b)) + +* Create LICENSE ([`a01891f`](https://github.com/bhklab/med-imagetools/commit/a01891fe9ba76ab3256ef73683126a83e246c6da)) + +* 1.0.0 (#52) + +* Update README.md + +* Update setup.py ([`3ceaf19`](https://github.com/bhklab/med-imagetools/commit/3ceaf19dea6c622fddacee98670114ddcb34d37b)) + + +## v4.4.0 (2022-07-27) + +### Unknown + +* 0.4.4 (#49) + +* Update setup.py + +* Update README.md + +* readme changes + +* Update README.md + +* Delete autopipeline.png + +Co-authored-by: Kevin <qukevin99@gmail.com> ([`2d2079c`](https://github.com/bhklab/med-imagetools/commit/2d2079c8346869588ed3531af86e5ead07ac45d4)) + +* Delete autopipeline.png ([`6a5b7d0`](https://github.com/bhklab/med-imagetools/commit/6a5b7d0fe506abcd2bfb82fdea93e2bca84a8767)) + +* Markdown Report and new CLI options (#48) + +* markdown report generator + +* update version to push to pypi + +* working on changes for nnunet inference + +* update version to push to pypi + +* nnunet inference formatting + +* dry run and continue flags + +* fixed up dry run and continute processing + +* fixing error that scout CT causes + +* dill in requirements + +* isabs for rel path args + +* Update main-ci.yml + +* fixed failing tests + +* another pytest fix + +* error check + +* error check 2 + +* Update test_components.py + +* test if values are working + +* missing values? + +* more ci tests + +* more ci tests 2 + +* ci tests 3 + +* ci tests 4 + +* ci tests 5 + +* ci tests 5 + +* ci tests 6 + +* ci tests 7 + +* ci tests 7 + +* removed debugging prints + +Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> ([`37f89b9`](https://github.com/bhklab/med-imagetools/commit/37f89b9f111b18111674e962f9c3f86733c7833e)) + +* Update main-ci.yml ([`c6851d9`](https://github.com/bhklab/med-imagetools/commit/c6851d97aa4aaeda1d920799519b96998113ed65)) + +* Add files via upload ([`52364da`](https://github.com/bhklab/med-imagetools/commit/52364da5bfb0301f45fdc76270d037210253c2a5)) + +* Add files via upload ([`677221b`](https://github.com/bhklab/med-imagetools/commit/677221b19240f685731f6968082c676e2b441571)) + +* Add files via upload ([`99c90d2`](https://github.com/bhklab/med-imagetools/commit/99c90d252f976a97b454fbc81030e3c94be6edd5)) + +* Delete methodology.png ([`c960771`](https://github.com/bhklab/med-imagetools/commit/c960771c517e85f59f80e38ce337183170b91fa6)) + +* Delete autopipeline.png ([`51944f8`](https://github.com/bhklab/med-imagetools/commit/51944f8818b1eb0e83bbce7fd82943993c990b33)) + +* Add files via upload ([`d5599f1`](https://github.com/bhklab/med-imagetools/commit/d5599f19ea11c76c4a1888efccb065050923b1ec)) + +* Update readme (#43) + +* Update README.md + +* redesigned autopipeline diagram + +* Delete build-ci.yml + +* Delete main.yml + +* Delete manual-test.yml ([`d54d704`](https://github.com/bhklab/med-imagetools/commit/d54d7042e568363c9f664aba5120e0718aa2e3d1)) + +* Markdown report (#42) + +* markdown report generator + +* update version to push to pypi + +Co-authored-by: Kevin <qukevin99@gmail.com> ([`3a2f742`](https://github.com/bhklab/med-imagetools/commit/3a2f7428992e6987cd5c34f99cecc1792d56be85)) + +* Nnunet demo (#41) + +* uncommented one line pytest + + +Former-commit-id: 3dc8cd388da3ab755d979987b36389dd88396801 + +* uncommented one line pytest + + +Former-commit-id: 01fb59285920aaa2fd8c3f355feab86619938568 [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c] [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c [formerly 3dc8cd388da3ab755d979987b36389dd88396801]] +Former-commit-id: fa09db6832e6455d56540ee8e6910cfcb484d27a +Former-commit-id: 652bd34dc69873469e060381ef0d8995d93335b5 + +* uncommented one line pytest + +* uncommented one line pytest + + +Former-commit-id: 2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe + +* uncommented one line pytest + + +Former-commit-id: 7aa572b0b68fa17a57d73a7b5f677af269e19154 [formerly 3f878494e3be177a2784ae665bf110f562422443] [formerly 3f878494e3be177a2784ae665bf110f562422443 [formerly 2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe]] +Former-commit-id: 11196a3f1e9560f82afc8e9d767068628d85a5e7 +Former-commit-id: 2046fb64b2d129db338c3d3f2a70e3640eea80ab + +* uncommented one line pytest + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: f2480c3bd2fba4498c609ef1efc031e1d4f7e2cd + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + + +Former-commit-id: 1cd89845970f294417d95d0792bdcb817b0324d7 + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + + +Former-commit-id: 29118a649d990863cfbf1b059cab862913e2ab30 [formerly 29118a649d990863cfbf1b059cab862913e2ab30 [formerly 1cd89845970f294417d95d0792bdcb817b0324d7]] +Former-commit-id: ea7077819568f350bb9583514acf63338249b0f3 +Former-commit-id: aa2d95a7888dd213554c627c0d76b4237a1967bf + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* Create build-ci.yml + +Former-commit-id: 5a0e9451e6e59de05e5dc2062ccbae6d8632179f + +* Create build-ci.yml + +* Update build-ci.yml + +Former-commit-id: 33a1d6066819f05051f55302f273a77031f70ecb + +* Update build-ci.yml + +* Update requirements.txt + +Former-commit-id: fcd6cb453acf63d6e67bd3066216d33d873f8f8f + +* Update requirements.txt + +* bug fixes_1.0 + + +Former-commit-id: d2556741284260f74609ead96c2e64621af8511a + +* bug fixes_1.0 + + +Former-commit-id: 3344042ddfb1ef709ec4fa02628c0c97a6ebd477 [formerly a27dc3c212327be4058cc374d9b37ae005fe87e0] [formerly a27dc3c212327be4058cc374d9b37ae005fe87e0 [formerly d2556741284260f74609ead96c2e64621af8511a]] +Former-commit-id: 63604aedc9199a01c2601640d6f53c32c1aea195 +Former-commit-id: b7161a48f3fffb445336ea2a3d827cdb5686deab + +* bug fixes_1.0 + +* test and autopipe fixed + + +Former-commit-id: 9cc88b1b402108310dbbc8e09a8b13730aa72102 + +* test and autopipe fixed + + +Former-commit-id: bbd1dc9a718bf69247befc0e1e99d1c75519eeef [formerly 2aca0013e705864697c9df5fa1c574487e307000] [formerly 2aca0013e705864697c9df5fa1c574487e307000 [formerly 9cc88b1b402108310dbbc8e09a8b13730aa72102]] +Former-commit-id: 0784880393713ae5376edb2c75cf1118187e011b +Former-commit-id: a402b01f18507176c1de523fb5e978552ea8f01c + +* test and autopipe fixed + +* bug fixes 2 + + +Former-commit-id: e7f4b424ecf5519ded2352b3d6266a7da07a5b07 + +* bug fixes 2 + + +Former-commit-id: a513f1a9102c236845fa273100bb39112b092bf7 [formerly 374041fceb9f851959a35da4d525a6930aa4837a] [formerly 374041fceb9f851959a35da4d525a6930aa4837a [formerly e7f4b424ecf5519ded2352b3d6266a7da07a5b07]] +Former-commit-id: 15bc9317197f2fcf7bf553596118bff24098a9ff +Former-commit-id: 4dd4c4a0b4238a97d93d3df36268108de9c7fb2a + +* bug fixes 2 + +* bug fixes 2 + + +Former-commit-id: 90732d81ff1873e24cd501283e4cdd2326febd28 + +* bug fixes 2 + + +Former-commit-id: 5ed5f32cea580aab518d28154a9e47c5b344c3c6 [formerly ad812ba0225fb2bff2ca5b49f307dc748ded3efe] [formerly ad812ba0225fb2bff2ca5b49f307dc748ded3efe [formerly 90732d81ff1873e24cd501283e4cdd2326febd28]] +Former-commit-id: 843025f73f358562b1a4fb2cc008e9655c593c3e +Former-commit-id: ab086810cefee5270450561b6db2cfb999416c27 + +* bug fixes 2 + +* added visualizations and some more bug fixes + + +Former-commit-id: 735b26c9de88e0a48b468f8fca490bcc68d4cf6c + +* added visualizations and some more bug fixes + + +Former-commit-id: 68280704e6bdc7afb814166dc4d9ea1c69cc0111 [formerly 2daaf02ec87a1caccd93e18e5a119c9863e940af] [formerly 2daaf02ec87a1caccd93e18e5a119c9863e940af [formerly 735b26c9de88e0a48b468f8fca490bcc68d4cf6c]] +Former-commit-id: 9bdf715e27d3a5aa0a6176b4a033c0015ced1bfc +Former-commit-id: 856e72bf73fef22350f1d53fcad601fe3d76798e + +* added visualizations and some more bug fixes + +* Create manual-test.yml + +Former-commit-id: d0b495ccb195a7cd99f8bb7a4d98e33cbbc1f729 + +* Create manual-test.yml + +* Update build-ci.yml + +Former-commit-id: f77c367df07b7792359edb8434cf4a5f80e328eb + +* Update build-ci.yml + +* Update manual-test.yml + +Former-commit-id: c17f6b55fa2949bb33a5c32cfa57c5d0b192d583 + +* Update manual-test.yml + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5 + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + + +Former-commit-id: 1528efc88ca4952ce570721832a339ff8274b4fa + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + + +Former-commit-id: ab236e55b1de2ca583f4118dec4a250b5801e5b1 [formerly ab236e55b1de2ca583f4118dec4a250b5801e5b1 [formerly 1528efc88ca4952ce570721832a339ff8274b4fa]] +Former-commit-id: 3e374bf83a1c5facaa7e311595c2b6550ec2025e +Former-commit-id: 82e0e186b9d508c398f798469326c643cd6527c2 + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + + +Former-commit-id: 7a27ee36703947cbeae3addb99a86c2c2566d0c0 + +* small bug fix + + +Former-commit-id: 43e3c6b28cecf2b33ea563904a2ac6197fab48b4 [formerly 43e3c6b28cecf2b33ea563904a2ac6197fab48b4 [formerly 7a27ee36703947cbeae3addb99a86c2c2566d0c0]] +Former-commit-id: 9c20b59415a751058a7d40e8ed2c570a3a8ffbd7 +Former-commit-id: 137b961a46c61f43f19f56f0c2564d14992a3d56 + +* small bug fix + +* added demo.py + + +Former-commit-id: b64491943988d84244d64f7d6001be088174e741 + +* added demo.py + + +Former-commit-id: 64a7701af6ea133285259cc40df0f47bcab496ba [formerly 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caad95a251fab60b5a8078bcd60987ba7dbbbd9d + +* fix conflicts + + +Former-commit-id: 3e769f713eead224f382b5abe98f9f90c69fcc65 [formerly c70d9c89cc2dd93f6c820b9b4a84577088fcb239] [formerly c70d9c89cc2dd93f6c820b9b4a84577088fcb239 [formerly caad95a251fab60b5a8078bcd60987ba7dbbbd9d]] +Former-commit-id: c207bb58235d76f7af1439da0adba4b814628926 +Former-commit-id: 0cf3b71107adb75b3ebf4c2babf2ba344e7b91cd + +* fix conflicts + +* fixed test autopipe + + +Former-commit-id: 63b9543e16a615f3cd2023a6e5457a6707835a4d + +* fixed test autopipe + + +Former-commit-id: eb71a6ece7d1b92ce1575fbf38354fde98ccc697 [formerly 3817bbbe40989f26078ead582ef508d58bd22d03] [formerly 3817bbbe40989f26078ead582ef508d58bd22d03 [formerly 63b9543e16a615f3cd2023a6e5457a6707835a4d]] +Former-commit-id: dc5e06511512a251129f80d0d07ccce2a94bb75c +Former-commit-id: 0de4a6d07c1b07618fa0e6ddd0bf5ce4553aa8ca + +* fixed test autopipe + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + + +Former-commit-id: d81a74dfcdcd21f2b9248d197362a6dbaabf901b + +* fix path backslash issues + + +Former-commit-id: c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8 [formerly c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8 [formerly d81a74dfcdcd21f2b9248d197362a6dbaabf901b]] +Former-commit-id: 0dd174dd2b65c959b8f26f41dc4b3ca51d257792 +Former-commit-id: 26d44c87a36a8ed5cd64b5553ac8bf5a1c5e7af3 + +* fix path backslash issues + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 5c6f7b00b440c06a730ff7ee289e0dd0f146a4dd + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +Former-commit-id: c0bf276b327056d7dff1b538492afe2b01438a34 + +* Update main.yml + +* Update main.yml + +Former-commit-id: f5397265d7f844ce7abbf81f9c38349610e5aacd + +* Update main.yml + +* Update README.md + +Former-commit-id: acf8cfbcc193d404fe42befdd9535c1bf42a10aa + +* 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 + +Former-commit-id: 9011025130ba625cf9451d6354a85d8a88d2937c + +* 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 + +Former-commit-id: 2a36b0491645b5b59ab309b1f1eea760d66c36fd + +* Update README.md + +* Update README.md (#19) 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into each contour + +* change kwargs in put for basesubjectwriter + +* still kinda failing... + +* brought back basesubjectwriter + +* .imgtools directory + +* changed absolute paths to relative paths + +* changed os.path.join to pathlib.Path.as_posix() + +* removed unused cv2 import + +* removed cv2 import + +* appened is deprecated, changed to concat + +* debug print + +* removed debug print + +* added sparse mask class and generating function + +* testing out sparse mask + +* funky NaN problem + +* commented sparse mask + +* overwrite all subjects + +* space + +* overwrite false + +* metadata stuffs + +* metadata in dataset.csv + +* added modalities, num rtstruct and pixel size to metadata + +* metadata bugfix + +* a + +* fixed wrong variable names for metadata stuff + +* fixed pathlib float error + +* relative paths and output folder paths for dataset.csv + +* put metadata stuff into a util file + +* deal with empty metadata + +* messing around with sparse mask + +* tried to save sparse mask, did some stuff with nnunet output format + +* compliant with nnunet directory structure + +* CLI Interface, argparse moved to utils + +* fixed formatting problems with folder names + +* train test split + +* train size and random state optional + +* merge conflicts + +* changed warnings to not interrupt + +* changed to warnings.warn for generate_sparse_mask + +* merge + +* resolving conflicts? + +* args + +* changes for roi names as a dict + +* added regex dictionary option for non nnunet runs + +* sparse mask global labelling for contour name: index + +* got rid of file_name_convention stuff + +* conflicts resolved + +* yaml thing + +* added list capabilities for the roi names dictionary + +* dataset.json for nnunet + +* CLI "autonew" + +* changed all mutable defaults to None + +* moved autotest changes to autopipeline and addede a few CLI args + +* getting ready for merge to live + +* test_components, test_modalities works with new AutoPipeline + +* overwrite changes and error fix for nan paths again + +* fixed if statement + +* joblib parallel + +* warnings for missing patients + +* summary messages + +* updated, passing tests. Updated version to 0.4 + +* update test + +* yaml path cli + +* yaml error check + +* pandas error + +* Fixed read_dicom_auto + +* skips series check if seris is None + +* updated readme to reflect v0.4 changes + +* updated readme + +* minor change + +* remove .idea + +* remote .idea + +* git ignore + +* transpose for nnunet + +* skip if no mask for nnunet and nnunet folder names + +* bugs in nnunet folder stuff + +* rename nnunetutil (again) + +* sorting the output streams + +* shell script + +* shell script in autopipeline + +* bug + +* forgot CopyInformation for nnunet + +* ignore deprecation warning + +* moved sh file down one dir + +* set -e for stopping execution if there is an error + +* broken checker for missing labels + +* train test fix for 1 patient + +* fix for broken self.existing_roi_names caused by joblib + +* added autotest to gitignore + +* sorted list for train test split + +* custom train test split + +* custom train test split + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> +Co-authored-by: Sejin Kim <hello@sejin.kim> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> +Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> ([`f3e5307`](https://github.com/bhklab/med-imagetools/commit/f3e5307f9687d070ec848d028bd949996a0d9da0)) + +* Nnunet demo (#40) + +* uncommented one line pytest + + +Former-commit-id: 3dc8cd388da3ab755d979987b36389dd88396801 + +* uncommented one line pytest + + +Former-commit-id: 01fb59285920aaa2fd8c3f355feab86619938568 [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c] [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c [formerly 3dc8cd388da3ab755d979987b36389dd88396801]] +Former-commit-id: fa09db6832e6455d56540ee8e6910cfcb484d27a +Former-commit-id: 652bd34dc69873469e060381ef0d8995d93335b5 + +* uncommented one line pytest + +* uncommented one line 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avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 47f31227269208fc91d4796e0e50816a16a93ea5 + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + 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[formerly 3817bbbe40989f26078ead582ef508d58bd22d03 [formerly 63b9543e16a615f3cd2023a6e5457a6707835a4d]] +Former-commit-id: dc5e06511512a251129f80d0d07ccce2a94bb75c +Former-commit-id: 0de4a6d07c1b07618fa0e6ddd0bf5ce4553aa8ca + +* fixed test autopipe + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 539777cd850404c9f0f85ef90b7508b1979f328c + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + + +Former-commit-id: d81a74dfcdcd21f2b9248d197362a6dbaabf901b + +* fix path backslash issues + + +Former-commit-id: c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8 [formerly c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8 [formerly d81a74dfcdcd21f2b9248d197362a6dbaabf901b]] +Former-commit-id: 0dd174dd2b65c959b8f26f41dc4b3ca51d257792 +Former-commit-id: 26d44c87a36a8ed5cd64b5553ac8bf5a1c5e7af3 + +* fix path backslash issues + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 5c6f7b00b440c06a730ff7ee289e0dd0f146a4dd + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +Former-commit-id: c0bf276b327056d7dff1b538492afe2b01438a34 + +* Update main.yml + +* Update main.yml + +Former-commit-id: f5397265d7f844ce7abbf81f9c38349610e5aacd + +* Update main.yml + +* Update README.md + +Former-commit-id: acf8cfbcc193d404fe42befdd9535c1bf42a10aa + +* 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 + +Former-commit-id: 9011025130ba625cf9451d6354a85d8a88d2937c + +* 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 + +Former-commit-id: 2a36b0491645b5b59ab309b1f1eea760d66c36fd + +* Update README.md + +* Update README.md (#19) + + + +Former-commit-id: bde03e1820874f8884cd4e1f36a19dddfc653e20 + +* Update README.md (#19) + +* Update README.md + +Former-commit-id: edb278febad7d37f8bb987210479319a09fd359e + +* Update README.md + +* added tests for Dataset class + + +Former-commit-id: 8d345fb040a8c6e1725d749d9d8554f35d107013 + +* added tests for Dataset class + + +Former-commit-id: d75ee6e437692650f4a7d62833946161acb12d79 [formerly abfd4dbebccc334866237362629389e79fdcba11] [formerly abfd4dbebccc334866237362629389e79fdcba11 [formerly 8d345fb040a8c6e1725d749d9d8554f35d107013]] +Former-commit-id: d8a5980fdc460c0386d73b5a3e204dbbf70771df +Former-commit-id: 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(#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +Former-commit-id: 5e93381461268785776402061d555ab02b78fda3 + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +Former-commit-id: 5116186cc44acffc828b7983e84ec2db49b628cb [formerly 65d66d20aa91799be74eaeeab91a5f1022d95d70] [formerly 65d66d20aa91799be74eaeeab91a5f1022d95d70 [formerly 5e93381461268785776402061d555ab02b78fda3]] +Former-commit-id: 5b66da423bd0a09f61d0768cf1491bdcdc20a18a +Former-commit-id: 9bbf4aebbf1978a63dd49de045cc91e4893a5237 + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +* quick fixes + + +Former-commit-id: 5e118add39a6796a6d03d9c6729146981da7f44f + +* quick fixes + + +Former-commit-id: d444cb8e2b63900c7747d9a405125066fb67d88e [formerly 8ac1dfd1340ce26440ed165fa7c2b7386034aa7a] [formerly 8ac1dfd1340ce26440ed165fa7c2b7386034aa7a [formerly 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metadata + +* metadata bugfix + +* a + +* fixed wrong variable names for metadata stuff + +* fixed pathlib float error + +* relative paths and output folder paths for dataset.csv + +* put metadata stuff into a util file + +* deal with empty metadata + +* messing around with sparse mask + +* tried to save sparse mask, did some stuff with nnunet output format + +* compliant with nnunet directory structure + +* CLI Interface, argparse moved to utils + +* fixed formatting problems with folder names + +* train test split + +* train size and random state optional + +* merge conflicts + +* changed warnings to not interrupt + +* changed to warnings.warn for generate_sparse_mask + +* merge + +* resolving conflicts? + +* args + +* changes for roi names as a dict + +* added regex dictionary option for non nnunet runs + +* sparse mask global labelling for contour name: index + +* got rid of file_name_convention stuff + +* conflicts resolved + +* yaml thing + +* added list capabilities for the roi names dictionary + +* dataset.json for nnunet + +* CLI "autonew" + +* changed all mutable defaults to None + +* moved autotest changes to autopipeline and addede a few CLI args + +* getting ready for merge to live + +* test_components, test_modalities works with new AutoPipeline + +* overwrite changes and error fix for nan paths again + +* fixed if statement + +* joblib parallel + +* warnings for missing patients + +* summary messages + +* updated, passing tests. Updated version to 0.4 + +* update test + +* yaml path cli + +* yaml error check + +* pandas error + +* Fixed read_dicom_auto + +* skips series check if seris is None + +* updated readme to reflect v0.4 changes + +* updated readme + +* minor change + +* remove .idea + +* remote .idea + +* git ignore + +* transpose for nnunet + +* skip if no mask for nnunet and nnunet folder names + +* bugs in nnunet folder stuff + +* rename nnunetutil (again) + +* sorting the output streams + +* shell script + +* shell script in autopipeline + +* bug + +* forgot CopyInformation for nnunet + +* ignore deprecation warning + +* moved sh file down one dir + +* set -e for stopping execution if there is an error + +* broken checker for missing labels + +* train test fix for 1 patient + +* fix for broken self.existing_roi_names caused by joblib + +* added autotest to gitignore + +* sorted list for train test split + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> +Co-authored-by: Sejin Kim <hello@sejin.kim> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> +Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> ([`31cecbe`](https://github.com/bhklab/med-imagetools/commit/31cecbeb04078bdf97beccc03682cecd0b72d918)) + +* Update README.md ([`c39ffe6`](https://github.com/bhklab/med-imagetools/commit/c39ffe6f4775e4bdd8218ff8b983ad21bc03cee1)) + +* Ci update (#39) + +* new ci/cd actions + +* updated pathing too + +* updated ci/cd actions + +* update + +* update ([`df61201`](https://github.com/bhklab/med-imagetools/commit/df61201ff26765f1f37a3a6c670f57a057eaa764)) + +* Update build-pkg.yml ([`5a314e5`](https://github.com/bhklab/med-imagetools/commit/5a314e5a873f3ec308ef8cb10bc1cceada1bdc2c)) + +* Update build-pkg.yml ([`630c184`](https://github.com/bhklab/med-imagetools/commit/630c1844d0781ba5c6e14065ccdcb6b65a83a5dd)) + +* Update build-pkg.yml ([`1ff1b2b`](https://github.com/bhklab/med-imagetools/commit/1ff1b2ba533640c76b3c12c5e913fc3fc3241a95)) + +* Create build-pkg.yml ([`c9d1f42`](https://github.com/bhklab/med-imagetools/commit/c9d1f4214fa4664c89bccd326cf8195ad00671e9)) + +* post-rebase (#38) + +* removed old structure set code + +* fixed label handling in image statistics computation + +* fixed label handling in image statistics computation + +* [In Progress] Adding documentation to ops.py + +* added support for dynamic path specification in writers + +* image CSV loader now accepts pandas DataFrames + +* fixed indentation error + +* fixed index column handling in ImageCSVLoader + +* Revert "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 + + +Former-commit-id: 03f99572453723e4a3e895acac0996997f090168 + +* PT/RTDOSE metadata to csv + + +Former-commit-id: 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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 + +* Create build-ci.yml + +* Update build-ci.yml + +* Update requirements.txt + +* bug fixes_1.0 + + +Former-commit-id: d2556741284260f74609ead96c2e64621af8511a + +* test and autopipe fixed + + +Former-commit-id: 9cc88b1b402108310dbbc8e09a8b13730aa72102 + +* bug fixes 2 + + +Former-commit-id: e7f4b424ecf5519ded2352b3d6266a7da07a5b07 + +* bug fixes 2 + + +Former-commit-id: 90732d81ff1873e24cd501283e4cdd2326febd28 + +* added visualizations and some more bug fixes + + +Former-commit-id: 735b26c9de88e0a48b468f8fca490bcc68d4cf6c + +* Create manual-test.yml + +* Update build-ci.yml + +* Update manual-test.yml + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + + +Former-commit-id: 1528efc88ca4952ce570721832a339ff8274b4fa + +* small bug fix + + +Former-commit-id: 7a27ee36703947cbeae3addb99a86c2c2566d0c0 + +* added demo.py + + +Former-commit-id: b64491943988d84244d64f7d6001be088174e741 + +* Ready for + +* Create main.yml (#15) + +* Changed dataset class returns + + +Former-commit-id: 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a + +* fix conflicts + + +Former-commit-id: caad95a251fab60b5a8078bcd60987ba7dbbbd9d + +* fixed test autopipe + + +Former-commit-id: 63b9543e16a615f3cd2023a6e5457a6707835a4d + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + + +Former-commit-id: d81a74dfcdcd21f2b9248d197362a6dbaabf901b + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +* Update main.yml + +* Update README.md + +* Update main.yml (#18) + +* Update main.yml + +* Update requirements.txt + +* Update main.yml + +* Update main.yml + +* build binary/dist + +* removed linter + +* Update setup.py + +* Update README.md + +* Update README.md (#19) + +* Update README.md + +* added tests for Dataset class + + +Former-commit-id: 8d345fb040a8c6e1725d749d9d8554f35d107013 + +* added tests for Dataset class + + +Former-commit-id: 7747a81615aa5d913284b22a623ee572ea8b293a + +* Create LICENSE (#20) + +* Create LICENSE + +* Update setup.py + +* Seg.nrrd quick fix + +* Minor bug fixes + + +Former-commit-id: f18aa1bd415fbb25050f6d4f8206492a23a61e54 + +* test fix + + +Former-commit-id: 2fad37ee3a827f831e6f6b3b7e707bc7509c284b + +* Added demo + + +Former-commit-id: 48ea411f5bea9471e83b05248ca95198e2e8a997 + +* Update setup.py (#23) + + + +Former-commit-id: 9e24716cfabf338fa46c4e4a4123bfd003f96918 + +* 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 + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +Former-commit-id: 5e93381461268785776402061d555ab02b78fda3 +Former-commit-id: d83fb0135155c4c94846c23614e75805db63cf37 + +* first commit + + +Former-commit-id: 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handles indexing + +* Fix empty array check in structure set conversion + +* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT + +* Fix slice matching issue when generating binary mask from RTStruct + +* CLI "autonew" + + +Former-commit-id: 8e33cf5a2ee0d285f2f243b72fa1d10ee1a3a77e [formerly 71e5b751d9c83e0be441a52bc314b6def1c8c53a] [formerly c8351e4cf69b47c095dcb6bbe99df634f1d801b0] +Former-commit-id: c818a4c3e204799794b59b2aed4d9d8b82226525 +Former-commit-id: 160208aa5919b57bfb6ea552d8a583919a19feee + +* changed all mutable defaults to None + + +Former-commit-id: e72e1e50633d56cd20ddd6b8e19c56bd650dd20c [formerly f1f225e4551b6d8a728d71b362a0cb0619df07ac] [formerly 41630cdfeeeff8f8a5c12b2924cc01e532dc5bd1] +Former-commit-id: f626aaa8894fd72ac7ec4bc18ec106bac411fe88 +Former-commit-id: a31c31bcfa4e66e9ba60710c7826bd16046af3a7 + +* remote .idea + + +Former-commit-id: 844a85d794b13a74179515b9450cebc6c5a40e9a [formerly aa9eafea5fa992c46cf1bda5ca3f00b5b1ec1f02] [formerly cf18c39521cf0c3466c9443e4e1183a8784debec] +Former-commit-id: abab7e92f5d42e02fc8299c1a28995f9a6df4f41 +Former-commit-id: d18186a612ac3f4c77f2fa6fc5e104b341bc1ab7 + +* git ignore + + +Former-commit-id: f0590a6162204eb487716ea9aac9f398dee837fa [formerly e3a31a1dc0121f146f455773fafa8e791675c49c] [formerly 7d5b46a90b3957255a2ac064eb6fb3864fbdb302] +Former-commit-id: 04668ec3eff07b321baaedeef78adff6f840cf47 +Former-commit-id: 705ae3b7631140cbaf362e853c9c4ceb62233ec8 + +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`](https://github.com/bhklab/med-imagetools/commit/7dcea0612043d0d03b68ac335a3e4ea9e2641b4c)) + +* Update README.md ([`49aa813`](https://github.com/bhklab/med-imagetools/commit/49aa813278f1b295cfc7d539fa7bbdf30af12679)) + +* Update setup.py (#37) + + + +Former-commit-id: e2e44ddd889fd44d0527af944053d9bd127cdf48 +Former-commit-id: b5cc03eb55295facdd85aba570a87e613b30e2dd ([`2fba09d`](https://github.com/bhklab/med-imagetools/commit/2fba09df124bd2ae1fffdfbdf381fdda523436f0)) + +* Kevin branch (#36) + +* simplified loader/writer specification in IO ops + +* updated imports in pipeline + +* improved ops repr + +* minor fixes in IO and segmentation + +* matching roi names in StructureSet.to_segmentation is now case-insensitive + +* fixed segmentation method call in some functional ops + +* fixed typo in pipeline warning message + +* StructureSet now correctly handles ROIs with no contour data + +* fixed error when trying to detect CSV delimiter in MetadataWriter + +* MetadataWriter can now remove existing files from previous runs + +* MetadataWriter can now remove existing files from previous runs + +* Segmentation object now correctly handles indexing + +* fixed segmentation mask handling in image statistics computation + +* removed old structure set code + +* removed old structure set code + +* fixed label handling in image statistics computation + +* fixed label handling in image statistics computation + +* [In Progress] Adding documentation to ops.py + +* added support for dynamic path specification in writers + +* image CSV loader now accepts pandas DataFrames + +* fixed indentation error + +* fixed index column handling in ImageCSVLoader + +* Revert "fixed index column handling in ImageCSVLoader" + +This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33. + +* fixed index column handling in ImageCSVLoader + +* fixed index column handling in ImageCSVLoader + +* ImageCSVLoader now returns correct keys + +* ImageCSVLoader now correctly handles globbing in paths + +* more informative exception handling in pipeline + +* pipeline can now warn on error instead of raising exception + +* [Docs] Cleaned up extra whitespace in ops.py + +* Added convenience method to get all ops in a pipeline + +* Fix empty array check in structure set conversion + +* Fix segmentation to label image conversion + +* Update README.md + +* Fix spurious mixin in ops + +* Fix type error when passing Numpy array to rotate + +* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT + +* Fix crop size issue in crop_to_bounding_box + +* Make imports easier + +* Improved handling of regular expressions in structure set + +* Fix slice matching issue when generating binary mask from RTStruct + +* Fix binary mask generation from RTStruct when missing labels are present + +* little updates + +* added seg.nrrd compatibility + +* supports RTSTRUCT processing without roi_names + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* fixed structureset.py:148 + +* RT dose pipeline completed and tested. Error in segmentation not resolved + +* PET readability added + +* PET readability added + +* Head-Neck-PET-CT pipeline + `read_dicom_auto` + +* final pipeline working for doses and PET + +* corrected the view + +* reading in sitk format from beginning + +* Completed PET overlay + +* Modified RT dose, pipeline working for PET_CT quebec dataset + +* Added DataGraph, now fetching subset of dataset is supported using graph query + +* added crawl.py + +* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes + +* Rectified some bugs, added reference to rtplan in the crawler + +* Now missing RTDOSE references are completed by RTPLAN + +* small change + +* Fixed dataset.csv writing issues + +* major refactoring + +* more refactoring + +* Update radcure_simple.py + +* Update loaders.py + +* Update pet.py + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* ignore .DS_Store + +* Update README.md + +* quick README under ops + +* tcia_sample + +* example bash script with path parsing, fixed reference_frame + +* housekeeping + +* fixed dataset.csv + +* sanity changes before purging dev-20200414 + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + + +Former-commit-id: 941669ee0574c71785fd8eb07e7dbe4e0b07b484 [formerly 03f99572453723e4a3e895acac0996997f090168] + +* PT/RTDOSE metadata to csv + + 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2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe] + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + + +Former-commit-id: 21a8546de909e2d98d23e232643588e9cfb1c956 [formerly 1cd89845970f294417d95d0792bdcb817b0324d7] + +* Create build-ci.yml + +* Update build-ci.yml + +* Update requirements.txt + +* bug fixes_1.0 + + +Former-commit-id: 384794ad0cff9f35b16e01177e16422f96eef8cd [formerly d2556741284260f74609ead96c2e64621af8511a] + +* test and autopipe fixed + + +Former-commit-id: 2ef1bb694da65458e9eae8dea7bfeb9238f652af [formerly 9cc88b1b402108310dbbc8e09a8b13730aa72102] + +* bug fixes 2 + + +Former-commit-id: d523d79396f367bd6c2b634a0602e45df0a595f9 [formerly e7f4b424ecf5519ded2352b3d6266a7da07a5b07] + +* bug fixes 2 + + +Former-commit-id: c0aa46eb71ee640ec4b086e715852b001dbd92fd [formerly 90732d81ff1873e24cd501283e4cdd2326febd28] + +* added visualizations and some more bug fixes + + +Former-commit-id: bfc783954909833e5fea376fcae054b01c30596b [formerly 735b26c9de88e0a48b468f8fca490bcc68d4cf6c] + +* Create manual-test.yml + +* Update build-ci.yml + +* Update manual-test.yml + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + + +Former-commit-id: bf97b7fb25abd156d258a5b22d5f2ad348a382f4 [formerly 1528efc88ca4952ce570721832a339ff8274b4fa] + +* small bug fix + + +Former-commit-id: c5de9faa884b8ac399aed64bfb7c11e65bd7d70f [formerly 7a27ee36703947cbeae3addb99a86c2c2566d0c0] + +* added demo.py + + +Former-commit-id: fcd6610aa6939eeb84965d6aaf7db547d18fec2b [formerly b64491943988d84244d64f7d6001be088174e741] + +* Ready for + +* Create main.yml (#15) + +* Changed dataset class returns + + +Former-commit-id: 40c53e6226ca60dd7b51ba848af5f2f3fb8ce33a [formerly 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a] + +* fix conflicts + + +Former-commit-id: f2304e116f0a487ecea85c362cfac9626e5cda30 [formerly caad95a251fab60b5a8078bcd60987ba7dbbbd9d] + +* fixed test autopipe + + +Former-commit-id: 12f9098d2bf8962679440e58afb67ff1b1d240e7 [formerly 63b9543e16a615f3cd2023a6e5457a6707835a4d] + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + + +Former-commit-id: e62073999fb01b945b5203ab2511e943833f437e [formerly d81a74dfcdcd21f2b9248d197362a6dbaabf901b] + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +* Update main.yml + +* Update README.md + +* Update main.yml (#18) + +* Update main.yml + +* Update requirements.txt + +* Update main.yml + +* Update main.yml + +* build binary/dist + +* removed linter + +* Update setup.py + +* Update README.md + +* Update README.md (#19) + +* Update README.md + +* added tests for Dataset class + + +Former-commit-id: c44cfcd1df0f235eac6032120b8378c43cb670ff [formerly 8d345fb040a8c6e1725d749d9d8554f35d107013] + +* added tests for Dataset class + + +Former-commit-id: 608b9c734ff0f006ede4fce6d5832f5ca0752ccd [formerly 7747a81615aa5d913284b22a623ee572ea8b293a] + +* Create LICENSE (#20) + +* Create LICENSE + +* Update setup.py + +* Seg.nrrd quick fix + +* Minor bug fixes + + +Former-commit-id: 52cf95f0271fbb1cdda186db56cc6cde8a536d5d [formerly f18aa1bd415fbb25050f6d4f8206492a23a61e54] + +* test fix + + +Former-commit-id: 424dc17ce0f3bd9a54c8a3ebb52bab96725d2977 [formerly 2fad37ee3a827f831e6f6b3b7e707bc7509c284b] + +* Added demo + + +Former-commit-id: e8eb00ba173df71ea56ed8accd366e1a015df864 [formerly 48ea411f5bea9471e83b05248ca95198e2e8a997] + +* Update setup.py (#23) + + + +Former-commit-id: a00e8f2ed448fecd0f5b9cccb6e04421e4952e19 [formerly 9e24716cfabf338fa46c4e4a4123bfd003f96918] + +* updated README + + +Former-commit-id: 4757ba85017119f8cda7fb0dea07f4e66a8629b6 [formerly c406bfc9526357e2091e1348d837c68cd5633801] [formerly 0f0414533cb6667b68aa48541feb376226fd5515] + +* Update README.md (#24) + + + +Former-commit-id: 213a9a7d009a2859a36988866fc031158d593b8b [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] [formerly 9aaf51bcb71b28cf062a03d873682b2ff38cee90] + +* preliminary MRI functionality (MR-RTSTRUCT pairs) + + +Former-commit-id: bfaaae9324716a550fcb468e137d9b4a7bfb07b6 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] [formerly 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85] + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +Former-commit-id: e942f7e7dd641efe61faed8a445c7b4abe6da994 [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly 5e93381461268785776402061d555ab02b78fda3] + +* first commit + + +Former-commit-id: 7aa40dd17ac859d599fc8fde8722f52fa9bed9d8 [formerly d8ab6611d1233f9d30cc2b3fcfcd1e5e3ecb6b07] [formerly 971e8d62b3e5dd1afa4cb02578c8f8f1c064e59b] + +* removed test files, changed gitignore + + +Former-commit-id: fe47ed26d1f2ea010d5ab8887a650d91bb04436a [formerly 7eaef9c15385ac64d755c8f95cfdc31c8d1c92e3] [formerly ff42f8af6223ce1bc7e83b308d0149979a523d1b] + +* changed file directory structure for imageautooutput + + +Former-commit-id: acda49e48c463ed67d7f6582a0eb261b26505516 [formerly 77425123598eecd2c3911ca150142b7d3703fd01] [formerly c2d8c680399afa8555636aa1b7ee7da909033fc9] + +* split mask up into each contour + + +Former-commit-id: 9a4509b260b889a7ded360c6289317c5ed85b62d [formerly 3607e0b8a2b74b8ba859b5aeceab6019cf28a620] [formerly 7a8285ce35ac4099a92d0b31ce2bd4029847835e] + +* change kwargs in put for basesubjectwriter + + +Former-commit-id: cd886d2c3d559663f4c79f271654cdb4a08c60ec [formerly e7747e4a255aa0b53f5788d92db01b1ac4df2b32] [formerly a9f093ceb48776f6d9906f572c73f576096b0cf1] + +* still kinda failing... + + +Former-commit-id: 21a47c580db1a7fe76fa7192e8e20286de7ec8fb [formerly 8ea1ca37337271dd77aee5d9f855ee7e10c04e12] [formerly 358df05939e6facbcb7be2df553b3adf944781ea] + +* brought back basesubjectwriter + + +Former-commit-id: a2d4763a775608cff06d1f029099a986c8246012 [formerly ad5abdc9cbb01fb00e95025d55f97d346f35d513] [formerly 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autopipeline and addede a few CLI args + + +Former-commit-id: 3698af5f0f0ab2e83e79d65749415915f1e531dd [formerly 55c91a8afcf22b1c1280103256ebc1c519ad701f] [formerly d8ff8d750f78d12f131b26b7f7e7a6d4e49366a8] + +* getting ready for merge to live + + +Former-commit-id: decd0fe54d13f23a0f0dd190cf812c5a507a182f [formerly 30b981fa409c4e5c7ada6d58418f298b351478d4] [formerly a7867249a9bbdf8ca4dcf2d5dd0bb24a5e75c4e0] + +* test_components, test_modalities works with new AutoPipeline + + +Former-commit-id: fcb3184ce3ff37b02fc030c7fad7b66ab7ececcc [formerly 7c7ab366d00183daa077681d74a16e09c7897e5c] [formerly e51fe82210b07d68dab4d36eddc6f34ed145cc03] + +* overwrite changes and error fix for nan paths again + + +Former-commit-id: 423cd0e71c01feb457ad920904fe2e887c70695e [formerly ecc51505211d6173e6b614232f4980c7b2a3aa76] [formerly b138fe2a09e6e0d18aef9b4b58fe6c3967335864] + +* fixed if statement + + +Former-commit-id: ed57bd69287eab17b7ad3238df652e341729bd0f [formerly 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Updated version to 0.4 + + +Former-commit-id: 4749c41ca0d3ea0acc1552436accc03b8fbc2b46 [formerly 7ff2fc9eab44411dd6083418e1a47da687818d84] [formerly 81d6795885cc1115e6d934a9ec358b544b590285] + +* update test + + +Former-commit-id: 7a2c4fe052aa1cd927c4b1b4ea86b3eddfb44577 [formerly 756c3f15fa10a3d81c721c58a881fe73a89fe6d8] [formerly 7bc3588c525a68284c52e0d697203ca685a21d92] + +* yaml path cli + + +Former-commit-id: eb9b162b497d297909998189840d6599e3dd6a5f [formerly a949496578406d7424559c557b7111ab2a47c4bf] [formerly 67ef10d2091473f96250355b7d8b9e81fd7cd55b] + +* yaml error check + + +Former-commit-id: 2d4df3538d8fc9ff9ae2fbc088481e69ace3c603 [formerly c8d6d77b19dcf488aacc647bbf6f5eaa21e444d3] [formerly fdeabd1746099989fd4de2bbeb5929428cd4e244] + +* pandas error + + +Former-commit-id: 9622190857e20fa17ebae5cb701c278182014a2e [formerly 9dce7c9809282dc6a85d748171a8ff1c412d8c63] [formerly 4745da298ce2fb6d903749c886baf8127ea0914a] + +* Fixed read_dicom_auto + + +Former-commit-id: 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05d7a38d8cfb15806bf732822d0ec928ba77e108 [formerly 94d2ecbf167651819e828eca69445a69ef627fd4] [formerly 8bd0a0f64943b764aed918487b1a11da07d918b5] + +* remote .idea + + +Former-commit-id: 844a85d794b13a74179515b9450cebc6c5a40e9a [formerly aa9eafea5fa992c46cf1bda5ca3f00b5b1ec1f02] [formerly cf18c39521cf0c3466c9443e4e1183a8784debec] + +* git ignore + + +Former-commit-id: f0590a6162204eb487716ea9aac9f398dee837fa [formerly e3a31a1dc0121f146f455773fafa8e791675c49c] [formerly 7d5b46a90b3957255a2ac064eb6fb3864fbdb302] + +* refactor nnunetutils to nnunet + + +Former-commit-id: 6d89ab1ce84d16a9a759f45530fc87eab46962d5 [formerly 8ae957266df825e1687e1d49a6114b6e657240e8] [formerly d996869c596f2c5353254d0cdc73d9f19e97fe69] + +* updated versions + +Former-commit-id: 980b5ea62602c4194a6a3014ce04d34e348bce8f [formerly 66542e225383a7edc3d21e06b728a17ccdf4761a] [formerly 41c8c88d93bb7a625eb9c31e400be8902500f13f] + +Co-authored-by: przebieglykaziu <mkazmierski.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`](https://github.com/bhklab/med-imagetools/commit/4fba9bcf83984e249c8d6eeebc3f5c8b715b32f8)) + +* update to 0.4.1 for new readme (#35) + +* simplified loader/writer specification in IO ops + +* updated imports in pipeline + +* improved ops repr + +* minor fixes in IO and segmentation + +* matching roi names in StructureSet.to_segmentation is now case-insensitive + +* fixed segmentation method call in some functional ops + +* fixed typo in pipeline warning message + +* StructureSet now correctly handles ROIs with no contour data + +* fixed error when trying to detect CSV delimiter in MetadataWriter + +* MetadataWriter can now remove existing files from previous runs + +* MetadataWriter can now remove existing files from previous runs + +* Segmentation object now correctly handles indexing + +* fixed segmentation mask handling in image statistics computation + +* removed old structure set code + +* removed old structure set code + +* fixed label handling in image statistics computation + +* fixed label handling in image statistics computation + +* [In Progress] Adding documentation to ops.py + +* added support for dynamic path specification in writers + +* image CSV loader now accepts pandas DataFrames + +* fixed indentation error + +* fixed index column handling in ImageCSVLoader + +* Revert "fixed index column handling in ImageCSVLoader" + +This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33. + +* fixed index column handling in ImageCSVLoader + +* fixed index column handling in ImageCSVLoader + +* ImageCSVLoader now returns correct keys + +* ImageCSVLoader now correctly handles globbing in paths + +* more informative exception handling in pipeline + +* pipeline can now warn on error instead of raising exception + +* [Docs] Cleaned up extra whitespace in ops.py + +* Added convenience method to get all ops in a pipeline + +* Fix empty array check in structure set conversion + +* Fix segmentation to label image conversion + +* Update README.md + +* Fix spurious mixin in ops + +* Fix type error when passing Numpy array to rotate + +* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT + +* Fix crop size issue in crop_to_bounding_box + +* Make imports easier + +* Improved handling of regular expressions in structure set + +* Fix slice matching issue when generating binary mask from RTStruct + +* Fix binary mask generation from RTStruct when missing labels are present + +* little updates + +* added seg.nrrd compatibility + +* supports RTSTRUCT processing without roi_names + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* fixed structureset.py:148 + +* RT dose pipeline completed and tested. Error in segmentation not resolved + +* PET readability added + +* PET readability added + +* Head-Neck-PET-CT pipeline + `read_dicom_auto` + +* final pipeline working for doses and PET + +* corrected the view + +* reading in sitk format from beginning + +* Completed PET overlay + +* Modified RT dose, pipeline working for PET_CT quebec dataset + +* Added DataGraph, now fetching subset of dataset is supported using graph query + +* added crawl.py + +* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes + +* Rectified some bugs, added reference to rtplan in the crawler + +* Now missing RTDOSE references are completed by RTPLAN + +* small change + +* Fixed dataset.csv writing issues + +* major refactoring + +* more refactoring + +* Update radcure_simple.py + +* Update loaders.py + +* Update pet.py + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* ignore .DS_Store + +* Update README.md + +* quick README under ops + +* tcia_sample + +* example bash script with path parsing, fixed reference_frame + +* housekeeping + +* fixed dataset.csv + +* sanity changes before purging dev-20200414 + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* Create build-ci.yml + +* Update build-ci.yml + +* Update requirements.txt + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* Create manual-test.yml + +* Update build-ci.yml + +* Update manual-test.yml + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Ready for + +* Create main.yml (#15) + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +* Update main.yml + +* Update README.md + +* Update main.yml (#18) + +* Update main.yml + +* Update requirements.txt + +* Update main.yml + +* Update main.yml + +* build binary/dist + +* removed linter + +* Update setup.py + +* Update README.md + +* Update README.md (#19) + +* Update README.md + +* added tests for Dataset class + +* added tests for Dataset class + +* Create LICENSE (#20) + +* Create LICENSE + +* Update setup.py + +* Seg.nrrd quick fix + +* Minor bug fixes + +* test fix + +* Added demo + +* Update setup.py (#23) + +* updated README + +* Update README.md (#24) + +* preliminary MRI functionality (MR-RTSTRUCT pairs) + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +* first commit + +* removed test files, changed gitignore + +* changed file directory structure for imageautooutput + +* split mask up into each contour + +* change kwargs in put for basesubjectwriter + +* still kinda failing... + +* brought back basesubjectwriter + +* .imgtools directory + +* changed absolute paths to relative paths + +* changed os.path.join to pathlib.Path.as_posix() + +* removed unused cv2 import + +* removed cv2 import + +* appened is deprecated, changed to concat + +* debug print + +* removed debug print + +* added sparse mask class and generating function + +* testing out sparse mask + +* funky NaN problem + +* commented sparse mask + +* overwrite all subjects + +* space + +* overwrite false + +* metadata stuffs + +* metadata in dataset.csv + +* added modalities, num rtstruct and pixel size to metadata + +* metadata bugfix + +* a + +* fixed wrong variable names for metadata stuff + +* fixed pathlib float error + +* relative paths and output folder paths for dataset.csv + +* put metadata stuff into a util file + +* deal with empty metadata + +* messing around with sparse mask + +* tried to save sparse mask, did some stuff with nnunet output format + +* compliant with nnunet directory structure + +* CLI Interface, argparse moved to utils + +* fixed formatting problems with folder names + +* train test split + +* train size and random state optional + +* merge conflicts + +* changed warnings to not interrupt + +* changed to warnings.warn for generate_sparse_mask + +* merge + +* resolving conflicts? + +* args + +* changes for roi names as a dict + +* added regex dictionary option for non nnunet runs + +* sparse mask global labelling for contour name: index + +* got rid of file_name_convention stuff + +* conflicts resolved + +* yaml thing + +* added list capabilities for the roi names dictionary + +* dataset.json for nnunet + +* CLI "autonew" + +* changed all mutable defaults to None + +* moved autotest changes to autopipeline and addede a few CLI args + +* getting ready for merge to live + +* test_components, test_modalities works with new AutoPipeline + +* overwrite changes and error fix for nan paths again + +* fixed if statement + +* joblib parallel + +* warnings for missing patients + +* summary messages + +* updated, passing tests. Updated version to 0.4 + +* update test + +* yaml path cli + +* yaml error check + +* pandas error + +* Fixed read_dicom_auto + +* skips series check if seris is None + +* updated readme to reflect v0.4 changes + +* updated readme + +* minor change + +* remove .idea + +* remote .idea + +* git ignore + +* refactor nnunetutils to nnunet + +* updated versions + +Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com> +Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> +Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> +Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> +Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> +Co-authored-by: fishingguy456 <qukevin99@gmail.com> +Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> +Former-commit-id: 4fc74ad7a233bf80dd95219eea058e86d8170e90 +Former-commit-id: be0f5c830268c987ce5b3b921a1a1e0476e1f0ea +Former-commit-id: 1f70cb08fcf0988d42babbed92c6aa53a49de7c2 ([`f0c10b6`](https://github.com/bhklab/med-imagetools/commit/f0c10b660300ab271968ec91815eba63e346263f)) + +* Kevin branch (#34) + +* ops using segmentation masks now accept Segmentation + +* simplified loader/writer specification in IO ops + +* simplified loader/writer specification in IO ops + +* updated imports in pipeline + +* improved ops repr + +* minor fixes in IO and segmentation + +* matching roi names in StructureSet.to_segmentation is now case-insensitive + +* fixed segmentation method call in some functional ops + +* fixed typo in pipeline warning message + +* StructureSet now correctly handles ROIs with no contour data + +* fixed error when trying to detect CSV delimiter in MetadataWriter + +* MetadataWriter can now remove existing files from previous runs + +* MetadataWriter can now remove existing files from previous runs + +* Segmentation object now correctly handles indexing + +* fixed segmentation mask handling in image statistics computation + +* removed old structure set code + +* removed old structure set code + +* fixed label handling in image statistics computation + +* fixed label handling in image statistics computation + +* [In Progress] Adding documentation to ops.py + +* added support for dynamic path specification in writers + +* image CSV loader now accepts pandas DataFrames + +* fixed indentation error + +* fixed index column handling in ImageCSVLoader + +* Revert "fixed index column handling in ImageCSVLoader" + +This reverts commit ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33. + +* fixed index column handling in ImageCSVLoader + +* fixed index column handling in ImageCSVLoader + +* ImageCSVLoader now returns correct keys + +* ImageCSVLoader now correctly handles globbing in paths + +* more informative exception handling in pipeline + +* pipeline can now warn on error instead of raising exception + +* [Docs] Cleaned up extra whitespace in ops.py + +* Added convenience method to get all ops in a pipeline + +* Fix empty array check in structure set conversion + +* Fix segmentation to label image conversion + +* Update README.md + +* Fix spurious mixin in ops + +* Fix type error when passing Numpy array to rotate + +* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT + +* Fix crop size issue in crop_to_bounding_box + +* Make imports easier + +* Improved handling of regular expressions in structure set + +* Fix slice matching issue when generating binary mask from RTStruct + +* Fix binary mask generation from RTStruct when missing labels are present + +* little updates + +* added seg.nrrd compatibility + +* supports RTSTRUCT processing without roi_names + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + +* fixed structureset.py:148 + +* RT dose pipeline completed and tested. Error in segmentation not resolved + +* PET readability added + +* PET readability added + +* Head-Neck-PET-CT pipeline + `read_dicom_auto` + +* final pipeline working for doses and PET + +* corrected the view + +* reading in sitk format from beginning + +* Completed PET overlay + +* Modified RT dose, pipeline working for PET_CT quebec dataset + +* Added DataGraph, now fetching subset of dataset is supported using graph query + +* added crawl.py + +* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes + +* Rectified some bugs, added reference to rtplan in the crawler + +* Now missing RTDOSE references are completed by RTPLAN + +* small change + +* Fixed dataset.csv writing issues + +* major refactoring + +* more refactoring + +* Update radcure_simple.py + +* Update loaders.py + +* Update pet.py + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* Delete .DS_Store + +* ignore .DS_Store + +* Update README.md + +* quick README under ops + +* tcia_sample + +* example bash script with path parsing, fixed reference_frame + +* housekeeping + +* fixed dataset.csv + +* sanity changes before purging dev-20200414 + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* Create build-ci.yml + +* Update build-ci.yml + +* Update requirements.txt + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* Create manual-test.yml + +* Update build-ci.yml + +* Update manual-test.yml + +* PR tests - macos/ubuntu failing (#13) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Ready for + +* Create main.yml (#15) + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* merging new features (#16) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* fix path backslash issues + +* fix path backslashes (#17) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* bug fixes 2 + +* added visualizations and some more bug fixes + +* fixed bugs regarding multiple connections, saving of metadata and loading of metadata + +* small bug fix + +* added demo.py + +* Changed dataset class returns + +* fix conflicts + +* fixed test autopipe + +* fix path backslash issues + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> + +* Update main.yml + +* Update main.yml + +* Update README.md + +* Update main.yml (#18) + +* Update main.yml + +* Update requirements.txt + +* Update main.yml + +* Update main.yml + +* build binary/dist + +* removed linter + +* Update setup.py + +* Update README.md + +* Update README.md (#19) + +* Update README.md + +* added tests for Dataset class + +* added tests for Dataset class + +* Create LICENSE (#20) + +* Create LICENSE + +* Update setup.py + +* Seg.nrrd quick fix + +* Minor bug fixes + +* test fix + +* Added demo + +* Update setup.py (#23) + +* updated README + +* Update README.md (#24) + +* preliminary MRI functionality (MR-RTSTRUCT pairs) + +* Skim2257 quick fix (#26) + +* Updated crawler to force String on all meta fields + +* Update setup.py + +* first commit + +* removed test files, changed gitignore + +* changed file directory structure for imageautooutput + +* split mask up into each contour + +* change kwargs in put for basesubjectwriter + +* still kinda failing... + +* brought back basesubjectwriter + +* .imgtools directory + +* changed absolute paths to relative paths + +* changed os.path.join to pathlib.Path.as_posix() + +* removed unused cv2 import + +* removed cv2 import + +* appened is deprecated, changed to concat + +* debug print + +* removed debug print + +* added sparse mask class and generating function + +* testing out sparse mask + +* funky NaN problem + +* commented sparse mask + +* overwrite all subjects + +* space + +* overwrite false + +* metadata stuffs + +* metadata in dataset.csv + +* added modalities, num rtstruct and pixel size to metadata + +* metadata bugfix + +* a + +* fixed wrong variable names for metadata stuff + +* fixed pathlib float error + +* relative paths and output folder paths for dataset.csv + +* put metadata stuff into a util file + +* deal with empty metadata + +* messing around with sparse mask + +* tried to save sparse mask, did some stuff with nnunet output format + +* compliant with nnunet directory structure + +* CLI Interface, argparse moved to utils + +* fixed formatting problems with folder names + +* train test split + +* train size and random state optional + +* merge conflicts + +* changed warnings to not interrupt + +* changed to warnings.warn for generate_sparse_mask + +* merge + +* resolving conflicts? + +* args + +* changes for roi names as a dict + +* added regex dictionary option for non nnunet runs + +* sparse mask global labelling for contour name: index + +* got rid of file_name_convention stuff + +* conflicts resolved + +* yaml thing + +* added list capabilities for the roi names dictionary + +* dataset.json for nnunet + +* CLI "autonew" + +* changed all mutable defaults to None + +* moved autotest changes to autopipeline and addede a few CLI args + +* getting ready for merge to live + +* test_components, test_modalities works with new AutoPipeline + +* overwrite changes and error fix for nan paths again + +* fixed if statement + +* joblib parallel + +* warnings for missing patients + +* summary messages + +* updated, passing tests. Updated version to 0.4 + +* update test + +* yaml path cli + +* yaml error check + +* pandas error + +* Fixed read_dicom_auto + +* skips series check if seris is None + +* updated readme to reflect v0.4 changes + +* updated readme + +* minor change + +* remove .idea + +* remote .idea + +* git ignore + +* refactor nnunetutils to nnunet + +Co-authored-by: przebieglykaziu <mkazmierski.poznan@gmail.com> +Co-authored-by: Minoru Nakano <minoru.nakano@gmail.com> +Co-authored-by: Sejin Kim <sejinkim@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node88.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node40.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@node97.uhnh4h.cluster> +Co-authored-by: Sejin Kim <sejinkim@h4huhnlogin2.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-Air.uhn.ca> +Co-authored-by: Sejin Kim <sejinkim@node38.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <ramanav@node49.uhnh4h.cluster> +Co-authored-by: Vishwesh Ramanathan <ramanav@node53.uhnh4h.cluster> +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Co-authored-by: Benjamin Haibe-Kains <bhaibeka@bhaibek1.uhn.ca> +Co-authored-by: Sejin Kim <sejinkim@node89.uhnh4h.cluster> +Co-authored-by: Sejin Kim <hello@sejin.kim> +Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> +Co-authored-by: Vishwesh Ramanathan <vishwesh@Vishweshs-MacBook-Air.local> +Co-authored-by: Kevin Qu <kqu@uhnslurmbuildbox.uhnh4h.cluster> +Co-authored-by: Kevin Qu <kqu@node90.uhnh4h.cluster> +Former-commit-id: 8090df83dd6ea23061b5df9e32f46758adcaef7c [formerly c6f2749e73443aac15df901d317eae16b3f9bff4] [formerly 66a85e2f1dd0555b38be3fb9c35de6c2e9b9d188] +Former-commit-id: de87e624140735955a2cab1b1f2074512901495e +Former-commit-id: e872a2d09d3e36f0bd733158685e2cff4b8fa327 ([`208aacd`](https://github.com/bhklab/med-imagetools/commit/208aacdd7cb6d65981a3e5126a3fe3a9ba0605d8)) + +* Merge branch 'master' of github.com:bhklab/med-imagetools + + 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line pytest + +* uncommented one line pytest + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + +* bug fixes_1.0 + +* test and autopipe fixed + +* bug fixes 2 + +* fixed pipeline tests + +* clean tests + +* added workflow + +* yml + +* yml + +* matplotlib + +* trying other patient to avoid memoryerror + +* set roi_names to avoid memoryerror + +* cave + +* indents + +* Update manual-test.yml + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 10a90b47190fb9fcbd372b30a091f56fb38ef703 ([`1de1d92`](https://github.com/bhklab/med-imagetools/commit/1de1d9200f53f84b0b647144da0b331b03a0e645)) + +* Update manual-test.yml + +Former-commit-id: 4ac0c1d1d67d24ee59eee1eab4a1c7d6d3b6d479 ([`2e915fb`](https://github.com/bhklab/med-imagetools/commit/2e915fb33f17f9015245a5d869a7f0eba57a24e1)) + +* Update build-ci.yml + +Former-commit-id: bca2a786b94ed4bb1d04717355dd4fee0f8fc3c8 ([`b00f14d`](https://github.com/bhklab/med-imagetools/commit/b00f14dbfa24e698b0772019842829b28d9c348a)) + +* Create manual-test.yml + +Former-commit-id: fbdb6e0c66ba11d57fcaf6beb0be6e45caebfca8 ([`f820ad4`](https://github.com/bhklab/med-imagetools/commit/f820ad4dcea5389b44afb91ff70d1b0acb1d2163)) + +* added visualizations and some more bug fixes + + +Former-commit-id: 68280704e6bdc7afb814166dc4d9ea1c69cc0111 [formerly 37ca2cff8a3e699a739b1cea0594cf8f9c3f2636 [formerly 37ca2cff8a3e699a739b1cea0594cf8f9c3f2636 [formerly 2daaf02ec87a1caccd93e18e5a119c9863e940af]]] [formerly 37ca2cff8a3e699a739b1cea0594cf8f9c3f2636 [formerly 37ca2cff8a3e699a739b1cea0594cf8f9c3f2636 [formerly 2daaf02ec87a1caccd93e18e5a119c9863e940af]] [formerly bfc783954909833e5fea376fcae054b01c30596b [formerly bfc783954909833e5fea376fcae054b01c30596b [formerly 735b26c9de88e0a48b468f8fca490bcc68d4cf6c]]]] +Former-commit-id: bfc783954909833e5fea376fcae054b01c30596b +Former-commit-id: 856e72bf73fef22350f1d53fcad601fe3d76798e 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([`e152160`](https://github.com/bhklab/med-imagetools/commit/e15216086af12e868ba47264d7f3042b6b1aee28)) + +* test and autopipe fixed + + +Former-commit-id: bbd1dc9a718bf69247befc0e1e99d1c75519eeef [formerly b0b6efa954b4e9cb0eff438efceb60395069c059 [formerly b0b6efa954b4e9cb0eff438efceb60395069c059 [formerly 2aca0013e705864697c9df5fa1c574487e307000]]] [formerly b0b6efa954b4e9cb0eff438efceb60395069c059 [formerly b0b6efa954b4e9cb0eff438efceb60395069c059 [formerly 2aca0013e705864697c9df5fa1c574487e307000]] [formerly 2ef1bb694da65458e9eae8dea7bfeb9238f652af [formerly 2ef1bb694da65458e9eae8dea7bfeb9238f652af [formerly 9cc88b1b402108310dbbc8e09a8b13730aa72102]]]] +Former-commit-id: 2ef1bb694da65458e9eae8dea7bfeb9238f652af +Former-commit-id: a402b01f18507176c1de523fb5e978552ea8f01c +Former-commit-id: c206f6d5c638b50ed3981ac0946d18d3399d0414 [formerly cc2e55235011f73f0ec01ff158ecfcfec21506e2] +Former-commit-id: 834aaa0532513bece9827a6975f9db2e5987103f ([`e321e31`](https://github.com/bhklab/med-imagetools/commit/e321e31c9d69f41d873d94eeaccd2181b33fda74)) + +* test and autopipe fixed + + +Former-commit-id: 2ef1bb694da65458e9eae8dea7bfeb9238f652af [formerly 9cc88b1b402108310dbbc8e09a8b13730aa72102] +Former-commit-id: 2aca0013e705864697c9df5fa1c574487e307000 ([`b0b6efa`](https://github.com/bhklab/med-imagetools/commit/b0b6efa954b4e9cb0eff438efceb60395069c059)) + +* bug fixes_1.0 + + +Former-commit-id: 3344042ddfb1ef709ec4fa02628c0c97a6ebd477 [formerly a047ef65c17b77282b3cf5df8523f4bcaab14a8e [formerly a27dc3c212327be4058cc374d9b37ae005fe87e0]] [formerly a047ef65c17b77282b3cf5df8523f4bcaab14a8e [formerly a27dc3c212327be4058cc374d9b37ae005fe87e0] [formerly 384794ad0cff9f35b16e01177e16422f96eef8cd [formerly d2556741284260f74609ead96c2e64621af8511a]]] +Former-commit-id: 384794ad0cff9f35b16e01177e16422f96eef8cd +Former-commit-id: b7161a48f3fffb445336ea2a3d827cdb5686deab +Former-commit-id: d42919d0a2a4d695018091f5d2ed827dff4bbf96 ([`7bb87b6`](https://github.com/bhklab/med-imagetools/commit/7bb87b6f0eccef842f8aa78552993196fc3758a4)) + +* bug fixes_1.0 + + +Former-commit-id: 384794ad0cff9f35b16e01177e16422f96eef8cd [formerly d2556741284260f74609ead96c2e64621af8511a] +Former-commit-id: a27dc3c212327be4058cc374d9b37ae005fe87e0 ([`a047ef6`](https://github.com/bhklab/med-imagetools/commit/a047ef65c17b77282b3cf5df8523f4bcaab14a8e)) + +* Update requirements.txt + +Former-commit-id: 3f9a7c3be559aba59c69a489ae003b553a2b5f83 ([`e665e21`](https://github.com/bhklab/med-imagetools/commit/e665e21fe6c3ca95dcd23d274baa0c863059dcaa)) + +* Update build-ci.yml + +Former-commit-id: c9a12d274d67ad911a82214a81ae6bcf588f38bf ([`9b519f4`](https://github.com/bhklab/med-imagetools/commit/9b519f4e03c8fa2918b18672168a8ba13c13bc18)) + +* Create build-ci.yml + +Former-commit-id: 6d5d4780b98534abb35c9996646ac41653856355 ([`49f0197`](https://github.com/bhklab/med-imagetools/commit/49f019706b2f950b65a082b07e2a3f2204c1ac30)) + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + + +Former-commit-id: db2e63a8fbf4e0a01a39af862ee916e14d16e445 [formerly 29118a649d990863cfbf1b059cab862913e2ab30] [formerly db2e63a8fbf4e0a01a39af862ee916e14d16e445 [formerly 29118a649d990863cfbf1b059cab862913e2ab30] [formerly 21a8546de909e2d98d23e232643588e9cfb1c956 [formerly 1cd89845970f294417d95d0792bdcb817b0324d7]]] +Former-commit-id: 21a8546de909e2d98d23e232643588e9cfb1c956 +Former-commit-id: aa2d95a7888dd213554c627c0d76b4237a1967bf +Former-commit-id: 2ae58c65d67dce9ed708a3cca2f15e5715f68a5f ([`4408c23`](https://github.com/bhklab/med-imagetools/commit/4408c235ff961b2443e26afd9a91a933a9d22ea6)) + +* Added dataset class which can load from nrrds or directly from the dataset and convert to pytorch dataset + + +Former-commit-id: 21a8546de909e2d98d23e232643588e9cfb1c956 [formerly 1cd89845970f294417d95d0792bdcb817b0324d7] +Former-commit-id: 29118a649d990863cfbf1b059cab862913e2ab30 ([`db2e63a`](https://github.com/bhklab/med-imagetools/commit/db2e63a8fbf4e0a01a39af862ee916e14d16e445)) + +* self.existing, dataset.csv fixed (#10) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + +* PT/RTDOSE metadata to csv + +* fixed some bugs in autopipeline.py + +* now the pipeline saves on exit + +* deleted data + +* now checks for existing subject id + +* uncommented one line pytest + +* uncommented one line pytest + +Co-authored-by: Vishwesh <vishweshramanathan@gmail.com> +Former-commit-id: 8ff5550b971938a3a7ad1f50c68ff606b3b54236 ([`ca98e79`](https://github.com/bhklab/med-imagetools/commit/ca98e7908705922963d88c5c68c99e931870a738)) + +* uncommented one line pytest + + +Former-commit-id: 7aa572b0b68fa17a57d73a7b5f677af269e19154 [formerly 1c37daba97d23ab4b74681c93ac5149f8b50c67a [formerly 3f878494e3be177a2784ae665bf110f562422443]] [formerly 1c37daba97d23ab4b74681c93ac5149f8b50c67a [formerly 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[formerly 6709767dc75f8ef3a15ea704e0464aa3151e858c]] [formerly 412841075771927200c633890319cb084bc2e7c9 [formerly 6709767dc75f8ef3a15ea704e0464aa3151e858c] [formerly faab613797495d5181b01f12f43f41865270f6fc [formerly 66a1ffd5a899d64868216e818fffc97260a42fa1]]] +Former-commit-id: faab613797495d5181b01f12f43f41865270f6fc +Former-commit-id: 19cc853aeaa9544a9f048ce73236af56ff04ed42 +Former-commit-id: 8c2c3af8a054c0a9d80a97f09c773079eeb86ebd ([`1bb0cc4`](https://github.com/bhklab/med-imagetools/commit/1bb0cc40d7ec178d00146117c4a54f12e3f1b7d9)) + +* Merge branch 'add_capabilities' of https://github.com/bhklab/imgtools into add_capabilities + +merging sejin's addition + + +Former-commit-id: faab613797495d5181b01f12f43f41865270f6fc [formerly 66a1ffd5a899d64868216e818fffc97260a42fa1] +Former-commit-id: 6709767dc75f8ef3a15ea704e0464aa3151e858c ([`4128410`](https://github.com/bhklab/med-imagetools/commit/412841075771927200c633890319cb084bc2e7c9)) + +* now checks for existing subject id + + 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4aa150d143e100349f0ca595747fb44734d9617c [formerly 2b9ac7e5ee454d0d4646c81889a3324ef0fb5ed1] [formerly 4aa150d143e100349f0ca595747fb44734d9617c [formerly 2b9ac7e5ee454d0d4646c81889a3324ef0fb5ed1] [formerly 099d6ca41b0beae20c8261942b1d9c2b91e130a2 [formerly 9cd421dd778df1afc6eb3e8a30a032f676f9b3b3]]] +Former-commit-id: 099d6ca41b0beae20c8261942b1d9c2b91e130a2 +Former-commit-id: 0e2e9ada4e52a06692df3ae6120988ef3ce83cf0 +Former-commit-id: fb3560460de9f1be962c40e5a07078983c66074d ([`d4656f0`](https://github.com/bhklab/med-imagetools/commit/d4656f01ae363f050c49bd4dc520662129d94804)) + +* now the pipeline saves on exit + + +Former-commit-id: 099d6ca41b0beae20c8261942b1d9c2b91e130a2 [formerly 9cd421dd778df1afc6eb3e8a30a032f676f9b3b3] +Former-commit-id: 2b9ac7e5ee454d0d4646c81889a3324ef0fb5ed1 ([`4aa150d`](https://github.com/bhklab/med-imagetools/commit/4aa150d143e100349f0ca595747fb44734d9617c)) + +* fixed some bugs in autopipeline.py + + +Former-commit-id: eef51f9391d54edb5f9c1fc60bf9e7fa0991ce5b [formerly ce800b87f646f60a9825903520527e20b6a3a862] [formerly eef51f9391d54edb5f9c1fc60bf9e7fa0991ce5b [formerly ce800b87f646f60a9825903520527e20b6a3a862] [formerly f7a40316af77e38465cb511454d615001936764a [formerly e05ea389216e61ad2231757ddccfe46608535a1d]]] +Former-commit-id: f7a40316af77e38465cb511454d615001936764a +Former-commit-id: eafc72c0a39d04c4b2eab01d2b91af52765000de +Former-commit-id: 4acc42796806ea928d07d381bdc5007bbe65859a ([`c637001`](https://github.com/bhklab/med-imagetools/commit/c63700153e45b96c7ccfa83a492e7e3ce5df8ba2)) + +* fixed some bugs in autopipeline.py + + +Former-commit-id: f7a40316af77e38465cb511454d615001936764a [formerly e05ea389216e61ad2231757ddccfe46608535a1d] +Former-commit-id: ce800b87f646f60a9825903520527e20b6a3a862 ([`eef51f9`](https://github.com/bhklab/med-imagetools/commit/eef51f9391d54edb5f9c1fc60bf9e7fa0991ce5b)) + +* PT/RTDOSE metadata to csv + + +Former-commit-id: 1c25fc0ef604ba983f4af370f5eb27b5e113cf02 [formerly b8e88e61f6bf24971d8e5e81a836b655fa1ea187] [formerly 1c25fc0ef604ba983f4af370f5eb27b5e113cf02 [formerly b8e88e61f6bf24971d8e5e81a836b655fa1ea187] [formerly 34b9b7f6c0c8cc50bcba03067dc70d748a0cbf32 [formerly 08616a5987e08a0e392d6a1b2411a035b9c89722]]] +Former-commit-id: 34b9b7f6c0c8cc50bcba03067dc70d748a0cbf32 +Former-commit-id: 286998f0619dee39a38d8bb1c0bf8dd2cfc0734a +Former-commit-id: 1b2d49097326a58d7c3802988d95218e64556205 ([`fe91a82`](https://github.com/bhklab/med-imagetools/commit/fe91a82c75dffa28fbdc5c00c436abb9021393ca)) + +* PT/RTDOSE metadata to csv + + +Former-commit-id: 34b9b7f6c0c8cc50bcba03067dc70d748a0cbf32 [formerly 08616a5987e08a0e392d6a1b2411a035b9c89722] +Former-commit-id: b8e88e61f6bf24971d8e5e81a836b655fa1ea187 ([`1c25fc0`](https://github.com/bhklab/med-imagetools/commit/1c25fc0ef604ba983f4af370f5eb27b5e113cf02)) + +* uptodate with master, merged + + +Former-commit-id: 7c279256bc5ba6dac6872338e1c77e88392611f6 [formerly 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c53ee623a6f420e5575cbb0b2e97f3630213f52f [formerly 2d72ee4c185d5848277d8d0a52cf4ddd4e664d44] [formerly c53ee623a6f420e5575cbb0b2e97f3630213f52f [formerly 2d72ee4c185d5848277d8d0a52cf4ddd4e664d44] [formerly 941669ee0574c71785fd8eb07e7dbe4e0b07b484 [formerly 03f99572453723e4a3e895acac0996997f090168]]] +Former-commit-id: 941669ee0574c71785fd8eb07e7dbe4e0b07b484 +Former-commit-id: 4705b14fd0bacf2a7524a8d2a4bb13a7320041c2 +Former-commit-id: a843e69e3b38f7c08790bcee5c596402d6be99ba ([`ea4096e`](https://github.com/bhklab/med-imagetools/commit/ea4096e0da4fb7bad0b0d9e4eafff51780e8346e)) + +* Added test autopipeline and modalities, solved some autopipeline bugs, read_dicom_series and pet now supports series_id + + +Former-commit-id: 941669ee0574c71785fd8eb07e7dbe4e0b07b484 [formerly 03f99572453723e4a3e895acac0996997f090168] +Former-commit-id: 2d72ee4c185d5848277d8d0a52cf4ddd4e664d44 ([`c53ee62`](https://github.com/bhklab/med-imagetools/commit/c53ee623a6f420e5575cbb0b2e97f3630213f52f)) + +* sanity changes before purging dev-20200414 + + +Former-commit-id: 91e453c71973a466b8fb5c8b0161e4ffe6a3a61a ([`76a9e88`](https://github.com/bhklab/med-imagetools/commit/76a9e88fb229537fd1035c8aa74d8defbc0672cb)) + +* fixed dataset.csv + + +Former-commit-id: 0ca701119857b9c31c2d8c33d077d0bcc42878d7 ([`1669ba3`](https://github.com/bhklab/med-imagetools/commit/1669ba30407ece9128e840f28e826aca09669397)) + +* housekeeping + + +Former-commit-id: bd4d2d12a67241d9f51d61f2a25a2764e0831618 ([`9962656`](https://github.com/bhklab/med-imagetools/commit/996265630a78b8c130d55508a9ee4165998e5d68)) + +* example bash script with path parsing, fixed reference_frame + + +Former-commit-id: f9d08c6d789f375de7bee0f936a6df557bc8b07f ([`bf4be18`](https://github.com/bhklab/med-imagetools/commit/bf4be1883ef852e6f1e7e6143b6ad7eafe39e609)) + +* Merge pull request #8 from bhklab/tcia_sample + +attached tcia_sample repo + sample autopipeline scripts + +Former-commit-id: 44fe7ced649d25edca4251b82dfdf5b4a43cfc5f ([`7b31dd7`](https://github.com/bhklab/med-imagetools/commit/7b31dd7f6b555889a34c8d4f135f043de68baef7)) + +* tcia_sample + + +Former-commit-id: 08e89f216e028b10e57a2f87192d5c80b08495fa ([`2e14e7a`](https://github.com/bhklab/med-imagetools/commit/2e14e7a0f12f5a21a9fcc8c323ed7faec616dbed)) + +* quick README under ops + + +Former-commit-id: 04076ffb42aeef6e9c9fb75f6193b64807a1e6fe ([`57b5392`](https://github.com/bhklab/med-imagetools/commit/57b5392e9f00f9d6cc4d6c5b167d521e2427e665)) + +* Update README.md + +Former-commit-id: 369152bc8fb397c266b3e8fe81ed8c5919680bc8 ([`548b8c1`](https://github.com/bhklab/med-imagetools/commit/548b8c188c5b8456c4bba895d3873e5bdce12f7f)) + +* ignore .DS_Store + +Former-commit-id: 15e9aa8410a7bf58fe338a75c63afc079e1c34db ([`9d8dd2b`](https://github.com/bhklab/med-imagetools/commit/9d8dd2b827bb61d2b5c285edb4aa7492ab7c764f)) + +* Delete .DS_Store + +Former-commit-id: ff6a34e2b42ddb01c57341b5a24f177071cf4799 ([`85512dc`](https://github.com/bhklab/med-imagetools/commit/85512dc53733403229ddf217d4864f74d39d1b49)) + +* Delete .DS_Store + +Former-commit-id: 3b50f2054f5905f996af525a5400aab02d29b412 ([`09937a5`](https://github.com/bhklab/med-imagetools/commit/09937a50d5f886698cdfbdd893023fd86d38b5e3)) + +* Delete .DS_Store + +Former-commit-id: 64b0a0fd24734f039cb58f2f406fe2e1fb6d6908 ([`558d37a`](https://github.com/bhklab/med-imagetools/commit/558d37acd4c93d743bd30e6526c1139cd25bb116)) + +* Delete .DS_Store + +Former-commit-id: 7cd867db6a1984e445f514413e991d242f0cf2d7 ([`e3b5626`](https://github.com/bhklab/med-imagetools/commit/e3b562663e36b819863442f34a802a4b84093bd4)) + +* Delete .DS_Store + +Former-commit-id: d8377a24db4f85e2336db99a1cebf0b744094c75 ([`fec46e4`](https://github.com/bhklab/med-imagetools/commit/fec46e40c5581bbff97685898c0d15f861722d85)) + +* Delete .DS_Store + +Former-commit-id: 4eb2bd52ff80aa004ccdd4448b6c708dc23f6a68 ([`9bf1264`](https://github.com/bhklab/med-imagetools/commit/9bf1264e71b9e2144e2032f4ca06a203a51808d7)) + +* Delete .DS_Store + +Former-commit-id: c8a704cf0aa2c61d9e856351e04eec63cf6bac4e ([`2e41219`](https://github.com/bhklab/med-imagetools/commit/2e4121977487461a6a3e8343f7d4419bdef273b3)) + +* Update pet.py + +Former-commit-id: 6768c8895b517dcdfb1d402e8e26bfec96b4b6cc ([`7ab9ca1`](https://github.com/bhklab/med-imagetools/commit/7ab9ca1cb474ce2d7308d11f810d2e5782a97b1d)) + +* Update loaders.py + +Former-commit-id: 931a601a998c797dd79d3e8952e9f3794d44a3d2 ([`48f2749`](https://github.com/bhklab/med-imagetools/commit/48f2749d5e1ea37d9af71cdcbdfde745dd59f4d8)) + +* Merge pull request #7 from bhklab/label_save + +merge added features + +Former-commit-id: c30626bf0139333de87aed6e7c4ce1cd3d4f7d19 ([`f3f0371`](https://github.com/bhklab/med-imagetools/commit/f3f037160372e361d1ca86dc75b01ed19976aa23)) + +* Update radcure_simple.py + +Former-commit-id: b3825c217a3e4b67bb6f73fa73e2656fa79b8fbe ([`aeb3cb4`](https://github.com/bhklab/med-imagetools/commit/aeb3cb49be1bae7d1ff0585c50d628a60980e73d)) + +* Merge pull request #6 from bhklab/complete_pipe + +merge into label_save + +Former-commit-id: 9e97512736e5a260e6652f3e84e80c4b06b2f9aa ([`4971b4d`](https://github.com/bhklab/med-imagetools/commit/4971b4deb008045c1591cd61157503e2ec6d7574)) + +* Merge branch 'label_save' of github.com:bhklab/imgtools into complete_pipe + + +Former-commit-id: 0cfa63a989727ff9fe16493c7c0c5adc54fad64e ([`21cda28`](https://github.com/bhklab/med-imagetools/commit/21cda286fd859a68e6d2876817622f214590363b)) + +* more refactoring + + +Former-commit-id: 8820e7c90bb1ca343ac86de716349ac7d1a39c8a ([`2e9ad24`](https://github.com/bhklab/med-imagetools/commit/2e9ad24f6194fc0ad5163a9c717c1389611e335b)) + +* Merge branch 'complete_pipe' of github.com:bhklab/imgtools into complete_pipe + + +Former-commit-id: 35f92d06bec081f3334ccc52841d42ef5c225bc5 ([`16b6abc`](https://github.com/bhklab/med-imagetools/commit/16b6abc3ecc03c9af2075776392ebc61a380cdec)) + +* major refactoring + + +Former-commit-id: 525f5bc85313f8584910407d48b071c029a08542 ([`261229f`](https://github.com/bhklab/med-imagetools/commit/261229f7ef6c58afe347a817000579f54d2bc545)) + +* Fixed dataset.csv writing issues + + +Former-commit-id: 46d8d7d3ca3d822a3c3b0c2afe85f914d4940df2 ([`2bd9245`](https://github.com/bhklab/med-imagetools/commit/2bd924557c8730080eb1ee15dc162ba2326041ab)) + +* small change + + +Former-commit-id: 22cd0254f6792ed848d756ba8dad5f27512eef43 ([`42d93c6`](https://github.com/bhklab/med-imagetools/commit/42d93c676255903449caec52a304db0aab1bb318)) + +* Now missing RTDOSE references are completed by RTPLAN + + +Former-commit-id: 7a45d32f1c07bd330fc946f4e452fa4dbd5ea89d ([`99b6dbe`](https://github.com/bhklab/med-imagetools/commit/99b6dbe3f74f9edadaf858480315c8bbfa0a55e3)) + +* Rectified some bugs, added reference to rtplan in the crawler + + 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Made the pipeline fully general. Made wrapper classes + + +Former-commit-id: bb446096a2315e8c52b2c0d74facebe8b967f7ee ([`8bd3804`](https://github.com/bhklab/med-imagetools/commit/8bd3804d67fc31b6b3fb50f35f443cdd32b1f100)) + +* added crawl.py + + +Former-commit-id: 3d3bf231400a8f8ae5eb2f0b450b0adf511d2911 ([`06f4bf5`](https://github.com/bhklab/med-imagetools/commit/06f4bf50888ca4342cab6fb66cc71f8fc3ce5bf5)) + +* Added DataGraph, now fetching subset of dataset is supported using graph query + + +Former-commit-id: 032e45294efaa8d9d0a39fd97d4eaa50e2a0bb0b ([`dc66a4a`](https://github.com/bhklab/med-imagetools/commit/dc66a4ac31e1750a0ced8ca1c9b34f68e8f9aa41)) + +* Modified RT dose, pipeline working for PET_CT quebec dataset + + +Former-commit-id: e981d7ee6a36e7066efe9bddf8762318a4fde9ca ([`b0ee749`](https://github.com/bhklab/med-imagetools/commit/b0ee74941aa1a5bcd768843263505f6838dcd97d)) + +* Completed PET overlay + + +Former-commit-id: c5a8a4020680a721638a1b820f5485addf712b70 ([`38f1660`](https://github.com/bhklab/med-imagetools/commit/38f16606e5a8af0271a9d1742e6877be27619890)) + +* reading in sitk format from beginning + + +Former-commit-id: e328aa9dd5ad67d9ed7e2fbc1f56c05624703c99 ([`e333c4f`](https://github.com/bhklab/med-imagetools/commit/e333c4f5acd14d097bdb04be19ef46a992dedf9c)) + +* corrected the view + + +Former-commit-id: e4d5d3c311b26021e68370b62cda09d4a9e2e0cb ([`2b20590`](https://github.com/bhklab/med-imagetools/commit/2b20590f2ba641045c5e3dc5a8f623035428599a)) + +* final pipeline working for doses and PET + + +Former-commit-id: c2e2d1ceff9c932e2c210cc305fe2545f239eae8 ([`7991481`](https://github.com/bhklab/med-imagetools/commit/79914814e778c359f2c72af058cfdc69ec071204)) + +* Merge branch 'RTdose' into complete_pipe +RT dose and PET done. Now focusing on the completion of pipeline + + +Former-commit-id: 5725a1ca40cf21162204435f9944d84460712c21 ([`71fc6ac`](https://github.com/bhklab/med-imagetools/commit/71fc6acf309656b8c326b7c5a024627f7d8c11af)) + +* Head-Neck-PET-CT pipeline + `read_dicom_auto` + + +Former-commit-id: fa6408c11a2b9b6bd80279504ba4c79975ad3582 ([`6e6be59`](https://github.com/bhklab/med-imagetools/commit/6e6be592285e808d11798294396d0f20db562060)) + +* PET readability added + + +Former-commit-id: f09b23daa59b1689b393ddc8b6da43ed297dfd68 ([`30ebe63`](https://github.com/bhklab/med-imagetools/commit/30ebe63cc805dda06abcc14077e047e40f00a92c)) + +* PET readability added + + +Former-commit-id: d7b309bb898286e9c4a000511ed2c585df931045 ([`b30508d`](https://github.com/bhklab/med-imagetools/commit/b30508dd7234c1452f6aa13598dac3b41ada91a2)) + +* RT dose pipeline completed and tested. Error in segmentation not resolved + + +Former-commit-id: 716c9f682863f75a1dbcc2bd1956d3c8160757c6 ([`91a9330`](https://github.com/bhklab/med-imagetools/commit/91a9330edfbcfb42370b7cd6c58ce5ae3b7f16ad)) + +* fixed structureset.py:148 + + +Former-commit-id: eabd7eb1b07017713184a81bfb418fd4596025e3 ([`65340cd`](https://github.com/bhklab/med-imagetools/commit/65340cd03d9b25bd79d7c7b90e1c7df30053bd75)) + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + + +Former-commit-id: 3a0d0d98a583d35609ed11a1fccb65e621751ad1 ([`bc1d3c2`](https://github.com/bhklab/med-imagetools/commit/bc1d3c2edcf10979bf4d274f1595895290fd9cbe)) + +* Fixed contour (RTSTRUCT) handling to rasterize multiple contours better. + + +Former-commit-id: bf0a595feb28c2b23dac6d9fd7991ed966678a60 ([`6398fe6`](https://github.com/bhklab/med-imagetools/commit/6398fe6c92f1f657202123b73d8b44b53e04d553)) + +* supports RTSTRUCT processing without roi_names + + +Former-commit-id: f0691ad7086b06f42dc11f4995a248ffbfb8a01c ([`14b0156`](https://github.com/bhklab/med-imagetools/commit/14b0156ec7cd6f2340fa475bf40c9722d11dccf5)) + +* added seg.nrrd compatibility + + +Former-commit-id: f5021ff82a0fd0263568e77fcf17c00af680560e ([`bff822a`](https://github.com/bhklab/med-imagetools/commit/bff822a6bb74e29a6f7ffe8841f85294f9e4abf1)) + +* little updates + + +Former-commit-id: 310406647bdfcbb9bfcc8fef2c2cae320ac2f2ce ([`b5948ab`](https://github.com/bhklab/med-imagetools/commit/b5948ab178f13ce5ef94e5377eb8f65fa428691a)) + +* Fix binary mask generation from RTStruct when missing labels are present + + +Former-commit-id: 7577ad43e4f1d0ffea0ba8b2a8ed6f93959ea47c ([`98bd813`](https://github.com/bhklab/med-imagetools/commit/98bd8134955a852337767910414edd5356dcafd5)) + +* Fix slice matching issue when generating binary mask from RTStruct + + +Former-commit-id: f2b74e91e5c4c191c182033ab77c3e34c10c2908 ([`22abe45`](https://github.com/bhklab/med-imagetools/commit/22abe450cd698a566ca4d01fd0ef330928e9243f)) + +* Improved handling of regular expressions in structure set + + +Former-commit-id: 5532e0e5e8782408b3e562ece27a16d4bfe2af6b ([`e978814`](https://github.com/bhklab/med-imagetools/commit/e978814545502e969ab3c4386eb9b64e2a36a5a6)) + +* Make imports easier + + +Former-commit-id: 184319338f0ba88439f6145726f24903128b75ba ([`ed7918c`](https://github.com/bhklab/med-imagetools/commit/ed7918c171d305072d35808d740da454102d5ed2)) + +* Fix crop size issue in crop_to_bounding_box + + +Former-commit-id: 59c0e92d1f075574113fa5fe7dc7bc2394221d5b ([`97b00ad`](https://github.com/bhklab/med-imagetools/commit/97b00ad5fc467f134568a40fb7c2338df16333dc)) + +* Merge branch 'master' of https://github.com/bhklab/imgtools + + +Former-commit-id: 93ac3245f2e3448a1f7e2b81086fca8b24596fdf ([`1055648`](https://github.com/bhklab/med-imagetools/commit/1055648fe9e80b2bb879625ce0803a7f800b5bb0)) + +* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT + + +Former-commit-id: 919ea491ae01f0e6c87731bcd7ebe4d89a325042 ([`f662f90`](https://github.com/bhklab/med-imagetools/commit/f662f902df7f5de3c696969a71135bdd9976aaca)) + +* Fix type error when passing Numpy array to rotate + + +Former-commit-id: 53223da1c607294a9bc42d94a09a1c35376547fa ([`d043593`](https://github.com/bhklab/med-imagetools/commit/d0435930a8ba39ab821ce48a30304a2318168c0f)) + +* Fix spurious mixin in ops + + +Former-commit-id: 8e19d063d2d59b883aaa8e69da10050047b8c60c ([`61ce543`](https://github.com/bhklab/med-imagetools/commit/61ce543e55daca7d83adceb1bd6d0f76a9e83d05)) + +* Update README.md + +Former-commit-id: 05da815d8189c425200c3ae7aab4a26a1da993ae ([`548dd61`](https://github.com/bhklab/med-imagetools/commit/548dd612a62ea1a6d6fa1bcd7b3c0f6a26708df1)) + +* Fix segmentation to label image conversion + + +Former-commit-id: 404793bb4f835b18529ae24b3fd8e2a2373c59e0 ([`14fe19c`](https://github.com/bhklab/med-imagetools/commit/14fe19c3937b83d9aea986fbfa3140b0f395ea72)) + +* Fix empty array check in structure set conversion + + +Former-commit-id: f28cbdfe65cd988972ab9e7b48c36f13e3cd575d ([`4e361fc`](https://github.com/bhklab/med-imagetools/commit/4e361fc6d175530764067b13758130b5a724bc1a)) + +* Added convenience method to get all ops in a pipeline + + +Former-commit-id: 248e0960a70eea23cc57fc3917cd5014e098ad66 ([`3af305e`](https://github.com/bhklab/med-imagetools/commit/3af305e66a3b3cc4d4967ae4acd5d204782e4d91)) + +* [Docs] Cleaned up extra whitespace in ops.py + + +Former-commit-id: 708a3882a82746642b2254e7ac3b845d1415f1ea ([`efc6eac`](https://github.com/bhklab/med-imagetools/commit/efc6eacc09dab84411fc9713f8af28f60e8eb0f5)) + +* pipeline can now warn on error instead of raising exception + + +Former-commit-id: 35e686dd6d91dda6d39746b68409a3b76d810b88 ([`b1a595e`](https://github.com/bhklab/med-imagetools/commit/b1a595e22fe7b394a4c1d260a38e5fb40e5e87b4)) + +* more informative exception handling in pipeline + + +Former-commit-id: 2d615b2974c4b724fbc07d13a7cb2b5d67c7fb64 ([`3804728`](https://github.com/bhklab/med-imagetools/commit/3804728b2811106fa36a6399370a3c2bd73877d4)) + +* ImageCSVLoader now correctly handles globbing in paths + + +Former-commit-id: 61e31e2acbe1b83169ddc30861435c93ff632ef0 ([`61f162a`](https://github.com/bhklab/med-imagetools/commit/61f162af9aedfc9d1405de7d7e22c035fb4c14d8)) + +* ImageCSVLoader now returns correct keys + + +Former-commit-id: 90009186983e7aa7267ad90e3f934176d8bc76f3 ([`2a67f11`](https://github.com/bhklab/med-imagetools/commit/2a67f1192378847adc5162e5e1f98dc0691cc31c)) + +* fixed index column handling in ImageCSVLoader + + +Former-commit-id: 45af80b94a7343d452970cce620cc0310781766e ([`6eb93ba`](https://github.com/bhklab/med-imagetools/commit/6eb93ba49632654160d958ce6f5d643ec387f791)) + +* fixed index column handling in ImageCSVLoader + + +Former-commit-id: ccb2673a341395a6d13c8c26ffa74a8354a4cff7 ([`9fb9b67`](https://github.com/bhklab/med-imagetools/commit/9fb9b6793a578c7264d4055c48dd17781c0ae595)) + +* Revert "fixed index column handling in ImageCSVLoader" + +This reverts commit 5561121c00024f8ebf72b83b9605a6ffe655eb23 [formerly ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33]. + + +Former-commit-id: 678fc6ea41b8f29fed3c4b0af74e03971526816b ([`e6d66a8`](https://github.com/bhklab/med-imagetools/commit/e6d66a8945f540c85b8ef3a5c695416210286b98)) + +* fixed index column handling in ImageCSVLoader + + +Former-commit-id: ac9b8d1aec53ec3f989cbfbb89fae353d2b94e33 ([`5561121`](https://github.com/bhklab/med-imagetools/commit/5561121c00024f8ebf72b83b9605a6ffe655eb23)) + +* fixed indentation error + + +Former-commit-id: 61cec9cdb9d05bdf9693c33b0a12cac14da31da0 ([`2b5c9f3`](https://github.com/bhklab/med-imagetools/commit/2b5c9f3f7e0e96daa1130944284a23a45ea0a9a6)) + +* Merge branch 'master' of https://github.com/bhklab/imgtools + + +Former-commit-id: aee62cb868378e8437033ae82a422c060d4ff854 ([`5e33ff5`](https://github.com/bhklab/med-imagetools/commit/5e33ff50ff3afd5941cee62a83e248de7b4549eb)) + +* image CSV loader now accepts pandas DataFrames + + +Former-commit-id: 5f25bfdb51761b8bb4d870e682991492c900852a ([`84c7c77`](https://github.com/bhklab/med-imagetools/commit/84c7c77c30cd5802f41b1ae7d139632b36cc9265)) + +* added support for dynamic path specification in writers + + +Former-commit-id: 57b944e8dbd4d74d09f72baac19bd090af220c15 ([`006b352`](https://github.com/bhklab/med-imagetools/commit/006b35282d0360a54ba34b4ab67e0b09eb34fc32)) + +* Merge branch 'master' of https://github.com/bhklab/imgtools + + +Former-commit-id: 1286866b657ff7fd44a10ce8da7f53fac06c1411 ([`673fe68`](https://github.com/bhklab/med-imagetools/commit/673fe68b54312918211389bc128682baedabff05)) + +* [In Progress] Adding documentation to ops.py + + +Former-commit-id: 0463acabdfb879de5467f813d90bae6c537e957f ([`3b706fa`](https://github.com/bhklab/med-imagetools/commit/3b706fabfaaabbe86ed9b4c5ca9801abb3267298)) + +* fixed label handling in image statistics computation + + +Former-commit-id: 12eecd14267a570f5bd7254a5e481e6dbf6afc6c ([`f56d634`](https://github.com/bhklab/med-imagetools/commit/f56d63422a950865287437cfc06e2734b3f9656f)) + +* fixed label handling in image statistics computation + + +Former-commit-id: f9144f000a3c186a2de0c499055ef5915b2657b9 ([`ef0ab45`](https://github.com/bhklab/med-imagetools/commit/ef0ab458fa0ce7d3839697f710a960893831f2d1)) + +* removed old structure set code + + +Former-commit-id: 8383fe62e5c2a59229f4919361bbbfe0cd3a259a ([`0477848`](https://github.com/bhklab/med-imagetools/commit/047784844d5acc308547dfbde2101ea5e868b587)) + +* removed old structure set code + + +Former-commit-id: c73d187e52d14c78789e0beee5ad4b11f8490895 ([`6f3c5b0`](https://github.com/bhklab/med-imagetools/commit/6f3c5b05dfa0028129a1928c6a360452758064d7)) + +* fixed segmentation mask handling in image statistics computation + + +Former-commit-id: e237e89ab03e8ed377023794afc7429e43cd901c ([`bd0e0ca`](https://github.com/bhklab/med-imagetools/commit/bd0e0ca0895d34ee396f5077600bd2a1784af08f)) + +* Segmentation object now correctly handles indexing + + +Former-commit-id: 5cee77d4a553bae602cc019876754130055aad81 ([`107c807`](https://github.com/bhklab/med-imagetools/commit/107c8074d0a00150e15eafb05f206304a674373a)) + +* MetadataWriter can now remove existing files from previous runs + + +Former-commit-id: 4550b0c040d1b7ee21bf20975cc437a17afe080f ([`26328f7`](https://github.com/bhklab/med-imagetools/commit/26328f7d874484e5e08b4d1a8679e2e901c52bbf)) + +* MetadataWriter can now remove existing files from previous runs + + +Former-commit-id: 0b8d94c02e9e49b95db70392574899bbe8f7a50c ([`edc5db2`](https://github.com/bhklab/med-imagetools/commit/edc5db2b795bb89653a2d0fa28958810381e1232)) + +* fixed error when trying to detect CSV delimiter in MetadataWriter + + +Former-commit-id: 4dac32399e9918d6fe41c5e34a834e0307fd54a1 ([`3087492`](https://github.com/bhklab/med-imagetools/commit/30874920ecb010d383c41b7c47401a71b70109d5)) + +* StructureSet now correctly handles ROIs with no contour data + + +Former-commit-id: 0ffaca0302bf3bf1b8c9722f6e7c64b2967018ec ([`bbf6529`](https://github.com/bhklab/med-imagetools/commit/bbf652914c620ae4c8ca3a92ed7e8a39c3337e75)) + +* fixed typo in pipeline warning message + + +Former-commit-id: 9b8d5148a1460f83b5e23c961c752988bed03916 ([`f5cf3c2`](https://github.com/bhklab/med-imagetools/commit/f5cf3c21da5977d9b49ce11c718c019bc22f89c1)) + +* fixed segmentation method call in some functional ops + + +Former-commit-id: cf2d9fc2b9e9f0725cf641ae6633e8f1f69d61d6 ([`4f20f12`](https://github.com/bhklab/med-imagetools/commit/4f20f126413d41602ca2f150b11261242e024ab8)) + +* matching roi names in StructureSet.to_segmentation is now case-insensitive + + +Former-commit-id: 9cf4cb1aea4ee9fbd6b7a9220c0e71e89ef074a0 ([`987457e`](https://github.com/bhklab/med-imagetools/commit/987457eaa88d5d610678c3418f8685034bfb27bf)) + +* minor fixes in IO and segmentation + + +Former-commit-id: ef05b1c3be698e100422f6d0fc6dfa7f30703a14 ([`fb7bb7c`](https://github.com/bhklab/med-imagetools/commit/fb7bb7cf5ef14e491ae0bb85421f05f969b1a7a3)) + +* improved ops repr + + +Former-commit-id: 088485f94ce9f030a50da94743bd7f42542c169a ([`165e59c`](https://github.com/bhklab/med-imagetools/commit/165e59cacac83228addc1a3191aa9297a510e8bf)) + +* updated imports in pipeline + + +Former-commit-id: 7a3539c85f684b178113833104d775f869e91699 ([`becc687`](https://github.com/bhklab/med-imagetools/commit/becc68722267658665ea4990f977103625115fc3)) + +* simplified loader/writer specification in IO ops + + +Former-commit-id: e6f74eccf9ec998fcb4b7339748a73365038ce5d ([`a1d509f`](https://github.com/bhklab/med-imagetools/commit/a1d509f4d321e0719bdfb04588e596fbb5e9b70f)) + +* simplified loader/writer specification in IO ops + + +Former-commit-id: c8221c7104083b99dde0cfddf5b1da09348edcd8 ([`6da2d1d`](https://github.com/bhklab/med-imagetools/commit/6da2d1d5ffae007c25edf819245fd7b1581c8396)) + +* ops using segmentation masks now accept Segmentation + + +Former-commit-id: 7ffbc49381db1d4d7127fc6fc1c61b7df6a10317 ([`81ae38d`](https://github.com/bhklab/med-imagetools/commit/81ae38d92ca9f31dcb978137f42a7d21d2d2f79c)) + +* minor fixes in segmentation module + + +Former-commit-id: 1f5d43894a8978a3e593ae2f4d8afbf0017834c4 ([`056e7ee`](https://github.com/bhklab/med-imagetools/commit/056e7ee4ed1c45de0bbb52b3fb4fc75c7617ba60)) + +* updated examples to use the new Segmentation API + + +Former-commit-id: f7588ed77894f9e64675487a2ee140d6775b0038 ([`5d21a90`](https://github.com/bhklab/med-imagetools/commit/5d21a9049aa1f1860b4dbb57359da3bbba61a32f)) + +* updated method names to reflect usage of Segmentation class + + +Former-commit-id: 6ce2991fb6c2ec7c611baf8211ecb12e35c4c268 ([`f6fb42e`](https://github.com/bhklab/med-imagetools/commit/f6fb42e86b3ba7a6c1b787baac64abc7081c12fd)) + +* loaders will now use the new structureset + + +Former-commit-id: 1b890daa34f6a2ea0273c141cb4653ca50d53a08 ([`d0e7561`](https://github.com/bhklab/med-imagetools/commit/d0e756141a48d324c2a1959e2193d7badb651afc)) + +* new experimental segmentation class + + +Former-commit-id: 63b67517bceea47f526c1c942aaa4e8b04e168b7 ([`afe09aa`](https://github.com/bhklab/med-imagetools/commit/afe09aa4dc4965c15fe7b707f9b6e4dcf2565b97)) + +* moved lower level reading functions to loaders.py + + +Former-commit-id: 395975643db8cf02d6e062ea4761498bf27df113 ([`dc61c81`](https://github.com/bhklab/med-imagetools/commit/dc61c817f3398c92beb4d5fa0449b8244b0ad143)) + +* bounding box is now returned in a frendlier format + + +Former-commit-id: 604ab239c6e391bf6e6874452e0c4e0ce2752c8f ([`48ff0c3`](https://github.com/bhklab/med-imagetools/commit/48ff0c3a96764982e292890735d9d2e71da8aad5)) + +* refactored subdirectory handling into BaseWriter + + +Former-commit-id: d3120792f9a3802616919780360df0cbe2890b55 ([`7eddcc4`](https://github.com/bhklab/med-imagetools/commit/7eddcc414a40c314fd9b03f2654c25f71a9fe828)) + +* fixed typo in ops + + +Former-commit-id: 94c510b56c37f27f6dc5aa7acf3cf2b792acca3a ([`0435ff1`](https://github.com/bhklab/med-imagetools/commit/0435ff1729168f151ed18169a39b761c2fa6e6e0)) + +* structure set now supports passing list of regexes for roi names + + +Former-commit-id: 392ddd81a926af2049ffed96f220080c0a51968f ([`5b5b286`](https://github.com/bhklab/med-imagetools/commit/5b5b2865dadfc825d38a33e70a58630dc036af86)) + +* added a writer for metadata + + +Former-commit-id: de1fa0664fce7a28b9d1385ee2a4e8ce21e3e0dd ([`a3136e6`](https://github.com/bhklab/med-imagetools/commit/a3136e61ff2b5b0358bde63f3607580b5f0b5ac4)) + +* ImageFileWriter now correctly handles subdirectories in filename_format + + +Former-commit-id: b824998eee88ade67538d714c4199437e2faa9fd ([`7b8db79`](https://github.com/bhklab/med-imagetools/commit/7b8db797cf6d61358bf0872764938868dad9137d)) + +* added support for compression in ImageFileWriter + + +Former-commit-id: 302b2a7077a12e6459b4b18d6a6ff1b8d772bb02 ([`623313b`](https://github.com/bhklab/med-imagetools/commit/623313be4b47e3d5a4f2f2e176b42192fd46e2ad)) + +* added example data & updated example pipeline + + +Former-commit-id: 0a86231503f56c579e2ea7dc8e3a97d225effa1a ([`5ebdce5`](https://github.com/bhklab/med-imagetools/commit/5ebdce5c012715014a1203e83f07f38050e4778d)) + +* structureset now correctly handles missing ROIs ([`a2fd796`](https://github.com/bhklab/med-imagetools/commit/a2fd7968926d8d042c52747c44c42aa861d6b04c)) + +* fixed typo in resample ([`cfa1443`](https://github.com/bhklab/med-imagetools/commit/cfa1443d13ba59a0077e7c5c3e544e5333454e27)) + +* updated gitignore ([`bdb9a3e`](https://github.com/bhklab/med-imagetools/commit/bdb9a3e8fb79edc67dbf3fafbebfe2efbdf39aaf)) + +* updated arguments in resample op ([`d5e5268`](https://github.com/bhklab/med-imagetools/commit/d5e5268c42d1130d1958b8573b50acaa2ea7533e)) + +* Merge branch 'master' of https://github.com/bhklab/imgtools ([`ebd0717`](https://github.com/bhklab/med-imagetools/commit/ebd07173f9b8745f6ea750e53a7d15fd57b7badf)) + +* updated readme with development mode installation instructions ([`2fe5e95`](https://github.com/bhklab/med-imagetools/commit/2fe5e956147556de0d6e4ffb369d211efd30d3c6)) + +* [quick fix] removed a syntax error, = that was added with __init__ function's output_directory parameter ([`8657727`](https://github.com/bhklab/med-imagetools/commit/865772722d9c1f2ad582fbe021c23866692dfa6d)) + +* added zoom operation ([`0426d0e`](https://github.com/bhklab/med-imagetools/commit/0426d0edbb6425f6a41f4b557d065539ef11d1c9)) + +* added more pipeline ops from functional module ([`e33c83f`](https://github.com/bhklab/med-imagetools/commit/e33c83fa5683dacd9da1fcc3e50d1f5b06b359c2)) + +* refactored image statistics computation ([`265e19a`](https://github.com/bhklab/med-imagetools/commit/265e19a7ce232f15738f870ba870b1196a58ca23)) + +* minor documentation & type annotation fixes ([`01b5295`](https://github.com/bhklab/med-imagetools/commit/01b5295fb1cd03c8f5cf3957ee8c2786225cfb07)) + +* fixed standard scaling function ([`f74a78f`](https://github.com/bhklab/med-imagetools/commit/f74a78fbea6df123784898692a27e53e9b10454d)) + +* fixed standard scaling function ([`36145fc`](https://github.com/bhklab/med-imagetools/commit/36145fc4a536a8061365b45b8161f5b933d62ceb)) + +* minor style fixes ([`d81f46d`](https://github.com/bhklab/med-imagetools/commit/d81f46df35baec8f8aea73627797f3c21d4c92d6)) + +* fixed type annotations in resample ([`25007be`](https://github.com/bhklab/med-imagetools/commit/25007bee9a14bdf267d0ce6ee8d5848d5dc223cc)) + +* implemented better sigma computation when downsampling ([`feee338`](https://github.com/bhklab/med-imagetools/commit/feee3389c3f7be3b52a5ba89b599f45c959c8a42)) + +* output size can now be specified when resampling ([`f644c26`](https://github.com/bhklab/med-imagetools/commit/f644c263ceb41c19860b7a111eded1b7f0b169b0)) + +* moved examples outside package code ([`a5fd368`](https://github.com/bhklab/med-imagetools/commit/a5fd368455673f328255b5c43c2a83cd42067ba8)) + +* Revert "minor fixes in RADCURE example" + +This reverts commit 3ed090c6554e61eee35d4d3161ca5489a56b49ee. ([`b68c6f4`](https://github.com/bhklab/med-imagetools/commit/b68c6f4b89abc74586f11417fb6b2e8ccb424f75)) + +* Revert "moved examples outside package code" + +This reverts commit 0014e6526bf37062ef6e3bb686f42538d8d075a0. ([`25cf496`](https://github.com/bhklab/med-imagetools/commit/25cf4965c8d9bf293c30c2b7d854b6af46a8a656)) + +* removed datasets directory ([`483f449`](https://github.com/bhklab/med-imagetools/commit/483f4494ac69b169df660d6ffabafd73bf4d3ffe)) + +* support for 3D rotations ([`14f7120`](https://github.com/bhklab/med-imagetools/commit/14f712023a215beec5a157598bf99fd0e72cf6ad)) + +* fixed unbound variable error in ImageFileLoader ([`9100032`](https://github.com/bhklab/med-imagetools/commit/9100032ed8b4d720877a06b2fd0d086b6412c439)) + +* improved documentation and type annotation in ops.functional ([`6c3b04e`](https://github.com/bhklab/med-imagetools/commit/6c3b04e0dcf15c520e8376f90dd4c8de6342248d)) + +* added functions for computing bounding box and centroid ([`a87deb2`](https://github.com/bhklab/med-imagetools/commit/a87deb2a595caafbd097570f04332aa2ea6d40c9)) + +* added intensity statistics functions ([`d9bf8ab`](https://github.com/bhklab/med-imagetools/commit/d9bf8ab38889482361c748e938420f1ed543f36f)) + +* crop function now correctly handles the crop size ([`fa887eb`](https://github.com/bhklab/med-imagetools/commit/fa887eb94c50f042a0b80267ff7f86f20f1d6e7e)) + +* moved examples outside package code ([`0014e65`](https://github.com/bhklab/med-imagetools/commit/0014e6526bf37062ef6e3bb686f42538d8d075a0)) + +* minor fixes in RADCURE example ([`3ed090c`](https://github.com/bhklab/med-imagetools/commit/3ed090c6554e61eee35d4d3161ca5489a56b49ee)) + +* Merge branch 'master' of https://github.com/bhklab/imgtools ([`f617f7e`](https://github.com/bhklab/med-imagetools/commit/f617f7e0330c06b035ace3e503884bea8e5a7ec3)) + +* lazy import matplotlib in imageutils ([`eefaef6`](https://github.com/bhklab/med-imagetools/commit/eefaef6c0fa6520cbe0851c667d3746fa19343db)) + +* fixed BaseOp repr ([`f6a34c4`](https://github.com/bhklab/med-imagetools/commit/f6a34c486097a078681131fd3d68bc6db2650ff2)) + +* minor fixes in RADCURE example ([`f65f050`](https://github.com/bhklab/med-imagetools/commit/f65f050696be761ab637eaede2515f6c44fd9ee3)) + +* clean up variable names in writers ([`8f93220`](https://github.com/bhklab/med-imagetools/commit/8f93220ed69cae206ee097695e6b510f05e936fe)) + +* fixed subject id handling in ImageFileLoader when subdir path is passed ([`0d4d117`](https://github.com/bhklab/med-imagetools/commit/0d4d117fc40ee7667553e28bd0a764319962250b)) + +* updated conda installation instructions ([`8f34ea3`](https://github.com/bhklab/med-imagetools/commit/8f34ea3baddd62dbf333ae8f51717ebdc4261528)) + +* Update README.md ([`1dc8d33`](https://github.com/bhklab/med-imagetools/commit/1dc8d33cde8048e57318ff77a11030ba61e11796)) + +* added README ([`01f04c4`](https://github.com/bhklab/med-imagetools/commit/01f04c49dda61860834111a0cc2d7ed129e27134)) + +* fixed parameter names in RADCURE example ([`8578ef8`](https://github.com/bhklab/med-imagetools/commit/8578ef81364eb6ca45e90acaa636970de688f26e)) + +* added setup.py ([`2720532`](https://github.com/bhklab/med-imagetools/commit/2720532b3347c04efb93edcbbd6a04d5c2f65fa0)) + +* added requirements file ([`ddedcc1`](https://github.com/bhklab/med-imagetools/commit/ddedcc1899aae10b9f13b1408200b3683f338442)) + +* fixed pipeline repr ([`7b95202`](https://github.com/bhklab/med-imagetools/commit/7b95202629a602e8009b578f4350b28e5acf2c8f)) + +* added requirements file ([`a4dcd7d`](https://github.com/bhklab/med-imagetools/commit/a4dcd7db0ce5b0514ce554351d8f945a0312fe39)) + +* pipeline now issues warning for missing data in loaders ([`5530a6a`](https://github.com/bhklab/med-imagetools/commit/5530a6a4d779f22fea34b30867e9fca652c986cf)) + +* improved variable and class names in loaders ([`ba12cb0`](https://github.com/bhklab/med-imagetools/commit/ba12cb0adcdd26dafa65f196ec08ece3dc2adfbb)) + +* changed subject ID naming convention in loaders ([`ddc0e39`](https://github.com/bhklab/med-imagetools/commit/ddc0e3900d82be9d3af899424bce15c6f95114d8)) + +* test pipeline now generates test data on the fly ([`c4022d7`](https://github.com/bhklab/med-imagetools/commit/c4022d758b25401697139b9625c7476f593a616c)) + +* updated gitignore ([`b09cd8d`](https://github.com/bhklab/med-imagetools/commit/b09cd8d484ff80f0ccc99ec854b8a132bba784fb)) + +* fixed multiprocessing issue related to sitk object pickling ([`30c42b4`](https://github.com/bhklab/med-imagetools/commit/30c42b477decb6a25ee803e04093811e6d6e5ffc)) + +* changed RADCURE example to follow current AP ([`fdfb4e6`](https://github.com/bhklab/med-imagetools/commit/fdfb4e6aa7718cefb77fa0c12dda68e28ca795e3)) + +* cleaned up ops ([`d2c1154`](https://github.com/bhklab/med-imagetools/commit/d2c11543ab88d2139620370c7e41124c433fe81f)) + +* cleaned up writers ([`7419f21`](https://github.com/bhklab/med-imagetools/commit/7419f21437fbef4db7a8aa5f5676e64700350129)) + +* cleanup before initial release ([`66183dd`](https://github.com/bhklab/med-imagetools/commit/66183ddc3601a430619467144a6e7b85f472c739)) + +* cleanup before initial release ([`ead8cbf`](https://github.com/bhklab/med-imagetools/commit/ead8cbf68d219b930546cb992e6f6ff7573e35af)) + +* updated gitignore ([`e11ca58`](https://github.com/bhklab/med-imagetools/commit/e11ca58a9f70b8ad4c6b000bcdbc80f9bba16ae7)) + +* demo ([`bd73693`](https://github.com/bhklab/med-imagetools/commit/bd73693a8ee1a59c1491266c389499df391b4c36)) + +* demo ([`5fb8266`](https://github.com/bhklab/med-imagetools/commit/5fb8266c85e41ab0f9211f55567085fc3fd5035d)) + +* demo ([`f4ca619`](https://github.com/bhklab/med-imagetools/commit/f4ca61945b2fba4862bcd24e1e4e888953452071)) + +* demo ([`6e4a93a`](https://github.com/bhklab/med-imagetools/commit/6e4a93ac8ab53eff3c219894266a5edd3f607864)) + +* initial implementation of Image class ([`4288b5b`](https://github.com/bhklab/med-imagetools/commit/4288b5bd8e2f81b31e0eb7f409598aef35bb7f3b)) + +* added docstrings to io functions ([`0037a15`](https://github.com/bhklab/med-imagetools/commit/0037a15c610b442e368b02faf4b6621a4b4a5b53)) + +* implemented cropping and padding transforms ([`2cf5a9c`](https://github.com/bhklab/med-imagetools/commit/2cf5a9cf906bcab5520ca16da30f75430469ef64)) + +* removed mask argument and renamed the resampling transform ([`40e391d`](https://github.com/bhklab/med-imagetools/commit/40e391db5ac7652aa9265a120e9fbfcfacf8ccbe)) + +* improved type annotations in transforms.spatial.resample_image ([`d125e12`](https://github.com/bhklab/med-imagetools/commit/d125e12f4702791bde29c2a22490a8d448f20069)) + +* improved spacing specification for resampling ([`7237ee5`](https://github.com/bhklab/med-imagetools/commit/7237ee5b284b37b745a825dd0c123465aaf86c60)) + +* minor fixes in transforms.spatial.resample_image ([`02d3ed0`](https://github.com/bhklab/med-imagetools/commit/02d3ed001849474a02095c967db43c37125a3cbb)) + +* added documentation and type annotations to transforms.spatial.resample_image ([`d7862f0`](https://github.com/bhklab/med-imagetools/commit/d7862f0f58c8d113a5841cbc7dcc33932b4811eb)) + +* fixed interpolator choice in resample_image ([`d0c80d7`](https://github.com/bhklab/med-imagetools/commit/d0c80d7c426a2967513745a1a63efff6e98a7595)) + +* utility function to check mask geometry ([`4316546`](https://github.com/bhklab/med-imagetools/commit/4316546a8ba421993718f53310c7a141996f88e6)) + +* first implementation of image resampling ([`180f759`](https://github.com/bhklab/med-imagetools/commit/180f759653617dca7054c11fa81db41809420994)) + +* added basic IO functions ([`dfb11dd`](https://github.com/bhklab/med-imagetools/commit/dfb11dd20374659a826cf84657f9df79e3a76f6b)) + +* initial commit ([`2afb431`](https://github.com/bhklab/med-imagetools/commit/2afb43157eaacde0a88d8336ffa59c68ce25a9bf))