diff --git a/CHANGELOG.md b/CHANGELOG.md index d73ec43..eb52727 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7931 +1,218 @@ # CHANGELOG +## v1.6.0-rc.1 (2024-11-14) + +### Bug Fixes + +- Added linux to pixi + ([`023a111`](https://github.com/bhklab/med-imagetools/commit/023a111d3bf2b83175d971c02641a786de6b91f9)) + +- Explicitly direct location of package code and update pixi in pipeline + ([`6767ced`](https://github.com/bhklab/med-imagetools/commit/6767ced27ed52eb6171243534c1364d91728baf5)) + +### Build System + +- Added coverage to gha + ([`6382dbf`](https://github.com/bhklab/med-imagetools/commit/6382dbfe0c37a031f9017130464f5895e11c792c)) + +### Chores + +- Update GitHub Actions workflow to deploy from both main and devel branches, and refresh + dependencies in pixi.lock + ([`60350d6`](https://github.com/bhklab/med-imagetools/commit/60350d64f287085b2f1489af934702d6ad5e7c15)) + +- Clean up GitHub Actions workflow by removing commented-out jobs and updating dependencies + ([`8274e4d`](https://github.com/bhklab/med-imagetools/commit/8274e4d3d36f461c41698174696d902fb8e1fa45)) + +- Update GitHub Actions workflow for improved deployment process + ([`ddad006`](https://github.com/bhklab/med-imagetools/commit/ddad0067796ed0b8539e21a0e380e6325853f886)) + +### Features + +- Updated test suite for pixi and started refactor of cicd + ([`cc94817`](https://github.com/bhklab/med-imagetools/commit/cc9481735c9ea19dc534973d345042a77ebecafb)) + +- Started port to pixi + ([`0ff9b90`](https://github.com/bhklab/med-imagetools/commit/0ff9b90f1327fee183025ef40c204168fb9810e2)) + + ## v1.5.8 (2024-10-25) ### Bug Fixes -* fix(datagraph): iteration through edge_types wasnt updated for seg (#131) +- **datagraph**: Iteration through edge_types wasnt updated for seg + ([#131](https://github.com/bhklab/med-imagetools/pull/131), + [`e7cca2a`](https://github.com/bhklab/med-imagetools/commit/e7cca2a8a2542e6f82ddae221b298094ebf3c022)) + +* fix(datagraph): update edge_types to 8 and handle new edge type for SEG->CT/MR mapping in final + dataframe processing -* fix(datagraph): update edge_types to 8 and handle new edge type for SEG->CT/MR mapping in final dataframe processing +* fix(pyproject): update attrs version constraint to allow all 23.x versions and above + +### Chores -* fix(pyproject): update attrs version constraint to allow all 23.x versions and above ([`e7cca2a`](https://github.com/bhklab/med-imagetools/commit/e7cca2a8a2542e6f82ddae221b298094ebf3c022)) +- **sem-ver**: 1.5.8 + ([`84aa480`](https://github.com/bhklab/med-imagetools/commit/84aa48014308784eef4314750da708682cea2968)) ## v1.5.7 (2024-10-23) ### Bug Fixes -* fix: ci-cd - add id in release for pypi step ([`7abd175`](https://github.com/bhklab/med-imagetools/commit/7abd175d58894b5ea84448735c4933de4aa156bd)) +- Ci-cd - add id in release for pypi step + ([`7abd175`](https://github.com/bhklab/med-imagetools/commit/7abd175d58894b5ea84448735c4933de4aa156bd)) ### Chores -* chore(sem-ver): 1.5.7 ([`c9a10bb`](https://github.com/bhklab/med-imagetools/commit/c9a10bbbfe7cc0e026c6a1719c07361bb7f3187f)) +- **sem-ver**: 1.5.7 + ([`c9a10bb`](https://github.com/bhklab/med-imagetools/commit/c9a10bbbfe7cc0e026c6a1719c07361bb7f3187f)) ## v1.5.6 (2024-10-23) ### Bug Fixes -* fix: update ci to release to pypi ([`a92a41f`](https://github.com/bhklab/med-imagetools/commit/a92a41f56ab6d86c68d7657104f8c559b1958ffc)) +- Update ci to release to pypi + ([`a92a41f`](https://github.com/bhklab/med-imagetools/commit/a92a41f56ab6d86c68d7657104f8c559b1958ffc)) ### Chores -* chore(sem-ver): 1.5.6 ([`22881f1`](https://github.com/bhklab/med-imagetools/commit/22881f19cabf0b9a096fe3d1822cd0ed26dcb507)) +- **sem-ver**: 1.5.6 + ([`22881f1`](https://github.com/bhklab/med-imagetools/commit/22881f19cabf0b9a096fe3d1822cd0ed26dcb507)) ## v1.5.5 (2024-10-23) ### Bug Fixes -* fix: update ci to use semver bot ([`98e3bd0`](https://github.com/bhklab/med-imagetools/commit/98e3bd0c93fc2be20c31976092047e7a11db57fb)) +- Update ci to use semver bot + ([`98e3bd0`](https://github.com/bhklab/med-imagetools/commit/98e3bd0c93fc2be20c31976092047e7a11db57fb)) -* fix: remove deprecated pydicom.dicomdir.DicomDir variable type option (#130) +- Remove deprecated pydicom.dicomdir.DicomDir variable type option + ([#130](https://github.com/bhklab/med-imagetools/pull/130), + [`56ef37e`](https://github.com/bhklab/med-imagetools/commit/56ef37e492d9a4f287ed9ecb7a1c968caca29726)) * fix: remove deprecated pydicom.dicomdir.DicomDir variable type option * style: removed Union since dicom_data can only be a FileDataset -* refactor: remove Union import for linting ([`56ef37e`](https://github.com/bhklab/med-imagetools/commit/56ef37e492d9a4f287ed9ecb7a1c968caca29726)) +* refactor: remove Union import for linting ### Chores -* chore(sem-ver): 1.5.5 ([`9921fba`](https://github.com/bhklab/med-imagetools/commit/9921fba8c74d5bfb6d914ce7af069df3976acde0)) +- **sem-ver**: 1.5.5 + ([`9921fba`](https://github.com/bhklab/med-imagetools/commit/9921fba8c74d5bfb6d914ce7af069df3976acde0)) -* chore: #126 update docstring for StructureSetToSegmentation (reopen) (#128) +- #126 update docstring for StructureSetToSegmentation (reopen) + ([#128](https://github.com/bhklab/med-imagetools/pull/128), + [`272078c`](https://github.com/bhklab/med-imagetools/commit/272078c937fa62fee20a700150f2ed4da7458720)) * chore: bump artifact action version -* refactor: update StructureSetToSegmentation docstring and remove unused dev group in pyproject.toml +* refactor: update StructureSetToSegmentation docstring and remove unused dev group in + pyproject.toml * chore: fix download action in workflow to use correct artifact version -* chore: correct instantiation reference and update parameter description in StructureSetToSegmentation docstring - -* chore: enhance StructureSetToSegmentation docstring to support None as a roi_names option for loading all ROIs ([`272078c`](https://github.com/bhklab/med-imagetools/commit/272078c937fa62fee20a700150f2ed4da7458720)) - -### Unknown - -* removing old Dataset class (#122) ([`5546cec`](https://github.com/bhklab/med-imagetools/commit/5546cec94f1cfe1e3fb4a2dff28a4c1e5275216e)) - -* Seg support (#121) +* chore: correct instantiation reference and update parameter description in + StructureSetToSegmentation docstring -* fix: License updated to MIT - -* Fixing datagraph module to resolve SEG compatibility issues. ([`4c03f48`](https://github.com/bhklab/med-imagetools/commit/4c03f48ec5d323c9ef0d3a7db28057769f4174c9)) +* chore: enhance StructureSetToSegmentation docstring to support None as a roi_names option for + loading all ROIs ## v1.5.4 (2024-06-12) ### Bug Fixes -* fix: License updated to MIT (#119) ([`6e755dd`](https://github.com/bhklab/med-imagetools/commit/6e755ddc70738da5c7afbced6e061d4e039fbd5f)) +- License updated to MIT ([#119](https://github.com/bhklab/med-imagetools/pull/119), + [`6e755dd`](https://github.com/bhklab/med-imagetools/commit/6e755ddc70738da5c7afbced6e061d4e039fbd5f)) ### Chores -* chore(sem-ver): 1.5.4 ([`464462c`](https://github.com/bhklab/med-imagetools/commit/464462cb1718d96652382f115b2f20ae4d8cbee8)) +- **sem-ver**: 1.5.4 + ([`464462c`](https://github.com/bhklab/med-imagetools/commit/464462cb1718d96652382f115b2f20ae4d8cbee8)) ## v1.5.3 (2024-06-10) ### Bug Fixes -* fix: Clarified license in README.md (#118) ([`a4899ca`](https://github.com/bhklab/med-imagetools/commit/a4899ca15924dc9fa19f2e1f3964b7bd6c2e2d35)) +- Clarified license in README.md ([#118](https://github.com/bhklab/med-imagetools/pull/118), + [`a4899ca`](https://github.com/bhklab/med-imagetools/commit/a4899ca15924dc9fa19f2e1f3964b7bd6c2e2d35)) ### Chores -* chore(sem-ver): 1.5.3 ([`7effcaf`](https://github.com/bhklab/med-imagetools/commit/7effcaffbe054995bb3111d3799bc8b7d9246300)) +- **sem-ver**: 1.5.3 + ([`7effcaf`](https://github.com/bhklab/med-imagetools/commit/7effcaffbe054995bb3111d3799bc8b7d9246300)) ## v1.5.2 (2024-05-29) ### Bug Fixes -* fix: upload latest version to pypi ([`1debad3`](https://github.com/bhklab/med-imagetools/commit/1debad3836732faf1a2e3f992a9f1d76943b076e)) +- Upload latest version to pypi + ([`1debad3`](https://github.com/bhklab/med-imagetools/commit/1debad3836732faf1a2e3f992a9f1d76943b076e)) ### Chores -* chore(sem-ver): 1.5.2 ([`69a651f`](https://github.com/bhklab/med-imagetools/commit/69a651f464b418c92f951be33bb865a04f0c604d)) +- **sem-ver**: 1.5.2 + ([`69a651f`](https://github.com/bhklab/med-imagetools/commit/69a651f464b418c92f951be33bb865a04f0c604d)) ## v1.5.1 (2024-05-29) ### Bug Fixes -* fix: format toml ([`269f55d`](https://github.com/bhklab/med-imagetools/commit/269f55db58322dc31a5c44ee5a5e2eb830ed3e4f)) +- Format toml + ([`269f55d`](https://github.com/bhklab/med-imagetools/commit/269f55db58322dc31a5c44ee5a5e2eb830ed3e4f)) ### Chores -* chore(sem-ver): 1.5.1 ([`7890f36`](https://github.com/bhklab/med-imagetools/commit/7890f3638e76b449f3948ae3c8c4a9532bde10ae)) +- **sem-ver**: 1.5.1 + ([`7890f36`](https://github.com/bhklab/med-imagetools/commit/7890f3638e76b449f3948ae3c8c4a9532bde10ae)) ## v1.5.0 (2024-05-29) ### Chores -* chore(sem-ver): 1.5.0 ([`69626ef`](https://github.com/bhklab/med-imagetools/commit/69626ef244aa26a8c7d5235548651cf4230e2b9a)) +- **sem-ver**: 1.5.0 + ([`69626ef`](https://github.com/bhklab/med-imagetools/commit/69626ef244aa26a8c7d5235548651cf4230e2b9a)) ### Features -* feat: update Lock ([`26590a0`](https://github.com/bhklab/med-imagetools/commit/26590a09f71c9f797d89f6276aef1c1e416f77dc)) - -* feat: update readme ([`7cd808e`](https://github.com/bhklab/med-imagetools/commit/7cd808e954ce8e4e1bd8b3dbf1978ba70b0e6713)) - -### Unknown - -* patch: pushing to 1.4.1 (#116) +- Update Lock + ([`26590a0`](https://github.com/bhklab/med-imagetools/commit/26590a09f71c9f797d89f6276aef1c1e416f77dc)) -* feat: semantic release! - -* patch: pushing versions ([`7b4cf22`](https://github.com/bhklab/med-imagetools/commit/7b4cf22b6a981b8a3706a5034f09d4b48cf83c8c)) +- Update readme + ([`7cd808e`](https://github.com/bhklab/med-imagetools/commit/7cd808e954ce8e4e1bd8b3dbf1978ba70b0e6713)) ## v1.1.0 (2024-05-29) ### Bug Fixes -* fix: add codecov badge ([`f43d042`](https://github.com/bhklab/med-imagetools/commit/f43d04231c76313d86d9e0444a6f1e26ed21b9fc)) +- 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)) +- Explicit module to track for code coverage + ([`f15d45d`](https://github.com/bhklab/med-imagetools/commit/f15d45dd43ef2d8956c0e7cbc91eb7741e9830e3)) ### Chores -* chore: bump version ([`58ec67f`](https://github.com/bhklab/med-imagetools/commit/58ec67f1f83eeb1f1ce1b580818f5812e1d04244)) +- Bump version + ([`58ec67f`](https://github.com/bhklab/med-imagetools/commit/58ec67f1f83eeb1f1ce1b580818f5812e1d04244)) ### Features -* feat: semantic release (#114) +- Semantic release ([#114](https://github.com/bhklab/med-imagetools/pull/114), + [`23a2d70`](https://github.com/bhklab/med-imagetools/commit/23a2d700772449837672d671873f9db3c544cd37)) * feat: semantic release -* fix: if statement issue ([`23a2d70`](https://github.com/bhklab/med-imagetools/commit/23a2d700772449837672d671873f9db3c544cd37)) - -### Unknown - -* 1.1.0 - -Automatically generated by python-semantic-release ([`fe25ff2`](https://github.com/bhklab/med-imagetools/commit/fe25ff2003c9c84cee089b4e651010bd59ce4b38)) - -* 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 ([`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 ([`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 ([`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)) +* fix: if statement issue ## 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)) - -* 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)) - -* temporary dose fix loading error with Sejin ([`abb452f`](https://github.com/bhklab/med-imagetools/commit/abb452f1a1b3fd4c2ad4f7538116ca39d6adf64f)) - -* 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)) - -* 0.4.4 (#49) - -* Update setup.py - -* Update README.md - -* readme changes - -* Update README.md - -* Delete autopipeline.png - -Co-authored-by: Kevin ([`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 ([`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 -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 - -* 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 -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 - -* 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 64a7701af6ea133285259cc40df0f47bcab496ba [formerly b64491943988d84244d64f7d6001be088174e741]] -Former-commit-id: 3b3ca59311c18451bc3cd7bb4a71df90501c66cd -Former-commit-id: 52754c4f09646cc9386b8f2699a2718edb77eaf8 - -* added demo.py - -* Ready for - -Former-commit-id: 9e5d03ad12769efe2f14199d6970cecfa1fac0b1 - -* Ready for - -* Create main.yml (#15) - - - -Former-commit-id: 700fbe6ff316bf36536be5bf6cca67df144096fa - -* Create main.yml (#15) - -* Changed dataset class returns - - -Former-commit-id: 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a - -* Changed dataset class returns - - -Former-commit-id: caa9c4d839ff599f63c9ad68c9bc4e844d96092d [formerly 180fe18d186e8909117afead0b974ecf33c0b632] [formerly 180fe18d186e8909117afead0b974ecf33c0b632 [formerly 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a]] -Former-commit-id: 8a66defe36141d1669874f743d5c0b2294414ec6 -Former-commit-id: 51ff2b743a26bfc2ec123e67a1cf8e77245aa75a - -* Changed dataset class returns - -* fix conflicts - - -Former-commit-id: 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 -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 - -* 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 -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 - -* 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: 3b16fbef699e13a000b61cfcc6a031c455b5abac - -* added tests for Dataset class - -* added tests for Dataset class - - -Former-commit-id: 7747a81615aa5d913284b22a623ee572ea8b293a - -* added tests for Dataset class - - -Former-commit-id: 71334289e578249681a435d7781c8955b6cabe1d [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7] [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7 [formerly 7747a81615aa5d913284b22a623ee572ea8b293a]] -Former-commit-id: bcff97c402b0267463107480002d22d4d9fe4fcf -Former-commit-id: 21f753f606167a4258d70f8ac6f8fc23d3a8d175 - -* added tests for Dataset class - -* Create LICENSE (#20) - -* Create LICENSE - -* Update setup.py - -Former-commit-id: 7ec143e7ef1dff2a849c62d1283b889398cb6b32 - -* Create LICENSE (#20) - -* Create LICENSE - -* Update setup.py - -* Seg.nrrd quick fix - - - -Former-commit-id: 7f3b5c62681d1275b09eb20a9a3218d9ecd16b23 - -* Seg.nrrd quick fix - -* Minor bug fixes - - -Former-commit-id: f18aa1bd415fbb25050f6d4f8206492a23a61e54 - -* Minor bug fixes - - -Former-commit-id: 7162d456ff8468c980c6a720d7100d655dc03288 [formerly 7162d456ff8468c980c6a720d7100d655dc03288 [formerly f18aa1bd415fbb25050f6d4f8206492a23a61e54]] -Former-commit-id: 96c6e3ef4e49b006056e7a8a11ca4e5ceeea6873 -Former-commit-id: 0858b138f03a568de16d582d42509ba40dc40903 - -* Minor bug fixes - -* test fix - - -Former-commit-id: 2fad37ee3a827f831e6f6b3b7e707bc7509c284b - -* test fix - - -Former-commit-id: d55216a0b91076b0b0ec06def53c517a6325587b [formerly d55216a0b91076b0b0ec06def53c517a6325587b [formerly 2fad37ee3a827f831e6f6b3b7e707bc7509c284b]] -Former-commit-id: 5e3f932e77e3bf3999f6b904cdfd0238af7fc27d -Former-commit-id: 37aa5e3e74d6e25b4f8766938462a60601c29ab3 - -* test fix - -* Added demo - - -Former-commit-id: 48ea411f5bea9471e83b05248ca95198e2e8a997 - -* Added demo - - -Former-commit-id: 1ec696602dd46966f5f7e1d4984feab6cc26386b [formerly 1ec696602dd46966f5f7e1d4984feab6cc26386b [formerly 48ea411f5bea9471e83b05248ca95198e2e8a997]] -Former-commit-id: fe9d3f4af7cf608a771fe1094f1e1162f1a92377 -Former-commit-id: a054f7d9cba105a4d40f2605ad6ea5e954b4a1a1 - -* Added demo - -* Update setup.py (#23) - - - -Former-commit-id: 9e24716cfabf338fa46c4e4a4123bfd003f96918 - -* Update setup.py (#23) - - - -Former-commit-id: ce8e287294e44e5aeaba1c12ea31bea801083293 [formerly ce8e287294e44e5aeaba1c12ea31bea801083293 [formerly 9e24716cfabf338fa46c4e4a4123bfd003f96918]] -Former-commit-id: b9fe3637d03e51472706d44e9096c76752517785 -Former-commit-id: 0cb0b099ffa6d3d67738f40e211e566049a109ca - -* Update setup.py (#23) - -* updated README - - -Former-commit-id: 0f0414533cb6667b68aa48541feb376226fd5515 - -* updated README - - -Former-commit-id: e35f91d35180b1217560b7f0bc06280bf07aebb0 [formerly e35f91d35180b1217560b7f0bc06280bf07aebb0 [formerly 0f0414533cb6667b68aa48541feb376226fd5515]] -Former-commit-id: bc9c6a28ef88362f14ed2cfbf8a333b3f0eb3cfc -Former-commit-id: d353efbbdace157b77f9bedf74654b5b96cda5f9 - -* updated README - -* Update README.md (#24) - - - -Former-commit-id: 9aaf51bcb71b28cf062a03d873682b2ff38cee90 - -* Update README.md (#24) - - - -Former-commit-id: 27494c03e4d95c58d6ea887e20597dbbe235c317 [formerly 27494c03e4d95c58d6ea887e20597dbbe235c317 [formerly 9aaf51bcb71b28cf062a03d873682b2ff38cee90]] -Former-commit-id: 84c0753414042535d8cc637bb974373ceed78130 -Former-commit-id: 63106282d3b55f6d008ae03c60c4a32babcb7d1b - -* Update README.md (#24) - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85 - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: 3cdc5eb2ad84488f20323b1933c4285eac78d60d [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310] [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310 [formerly 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85]] -Former-commit-id: b4abcace6ced31dd9b7d08503d31d4ee49d5ee74 -Former-commit-id: 2a0158397a55d783d6b627181a8af123952df3dc - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - -* Skim2257 quick fix (#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 5e118add39a6796a6d03d9c6729146981da7f44f]] -Former-commit-id: b1c528e7b1f32acf42a18cd78f37b462bfa05171 -Former-commit-id: 79e19c892e15d254c60b16b4ee67e9c16ca59f91 - -* first commit - -* removed test files, changed gitignore - -* changed file directory structure for imageautooutput - -* split mask up into each contour - -* change kwargs in put for basesubjectwriter - -* still kinda failing... - -* brought back basesubjectwriter - -* .imgtools directory - -* changed absolute paths to relative paths - -* changed os.path.join to pathlib.Path.as_posix() - -* removed unused cv2 import - -* removed cv2 import - -* appened is deprecated, changed to concat - -* debug print - -* removed debug print - -* added sparse mask class and generating function - -* testing out sparse mask - -* funky NaN problem - -* commented sparse mask - -* overwrite all subjects - -* space - -* overwrite false - -* metadata stuffs - -* metadata in dataset.csv - -* added modalities, num rtstruct and pixel size to metadata - -* metadata bugfix - -* a - -* fixed wrong variable names for metadata stuff - -* fixed pathlib float error - -* relative paths and output folder paths for dataset.csv - -* put metadata stuff into a util file - -* deal with empty metadata - -* messing around with sparse mask - -* tried to save sparse mask, did some stuff with nnunet output format - -* compliant with nnunet directory structure - -* CLI Interface, argparse moved to utils - -* fixed formatting problems with folder names - -* train test split - -* train size and random state optional - -* merge conflicts - -* changed warnings to not interrupt - -* changed to warnings.warn for generate_sparse_mask - -* merge - -* resolving conflicts? - -* args - -* changes for roi names as a dict - -* added regex dictionary option for non nnunet runs - -* sparse mask global labelling for contour name: index - -* got rid of file_name_convention stuff - -* conflicts resolved - -* yaml thing - -* added list capabilities for the roi names dictionary - -* dataset.json for nnunet - -* CLI "autonew" - -* changed all mutable defaults to None - -* moved autotest changes to autopipeline and addede a few CLI args - -* getting ready for merge to live - -* test_components, test_modalities works with new AutoPipeline - -* overwrite changes and error fix for nan paths again - -* fixed if statement - -* joblib parallel - -* warnings for missing patients - -* summary messages - -* updated, passing tests. Updated version to 0.4 - -* update test - -* yaml path cli - -* yaml error check - -* pandas error - -* Fixed read_dicom_auto - -* skips series check if seris is None - -* updated readme to reflect v0.4 changes - -* updated readme - -* minor change - -* remove .idea - -* remote .idea - -* git ignore - -* transpose for nnunet - -* skip if no mask for nnunet and nnunet folder names - -* bugs in nnunet folder stuff - -* rename nnunetutil (again) - -* sorting the output streams - -* shell script - -* shell script in autopipeline - -* bug - -* forgot CopyInformation for nnunet - -* ignore deprecation warning - -* moved sh file down one dir - -* set -e for stopping execution if there is an error - -* broken checker for missing labels - -* train test fix for 1 patient - -* fix for broken self.existing_roi_names caused by joblib - -* added autotest to gitignore - -* sorted list for train test split - -* custom train test split - -* custom train test split - -Co-authored-by: Vishwesh -Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu ([`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 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 -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 - -* 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 - 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-* 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 -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 - -* 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 64a7701af6ea133285259cc40df0f47bcab496ba [formerly b64491943988d84244d64f7d6001be088174e741]] -Former-commit-id: 3b3ca59311c18451bc3cd7bb4a71df90501c66cd -Former-commit-id: 52754c4f09646cc9386b8f2699a2718edb77eaf8 - -* added demo.py - -* Ready for - -Former-commit-id: 9e5d03ad12769efe2f14199d6970cecfa1fac0b1 - -* Ready for - -* Create main.yml (#15) - - - -Former-commit-id: 700fbe6ff316bf36536be5bf6cca67df144096fa - -* Create main.yml (#15) - -* Changed dataset class returns - - -Former-commit-id: 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a - -* Changed dataset class returns - - -Former-commit-id: caa9c4d839ff599f63c9ad68c9bc4e844d96092d [formerly 180fe18d186e8909117afead0b974ecf33c0b632] [formerly 180fe18d186e8909117afead0b974ecf33c0b632 [formerly 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a]] -Former-commit-id: 8a66defe36141d1669874f743d5c0b2294414ec6 -Former-commit-id: 51ff2b743a26bfc2ec123e67a1cf8e77245aa75a - -* Changed dataset class returns - -* fix conflicts - - -Former-commit-id: 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 -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 - -* 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 -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 - -* 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: 3b16fbef699e13a000b61cfcc6a031c455b5abac - -* added tests for Dataset class - -* added tests for Dataset class - - -Former-commit-id: 7747a81615aa5d913284b22a623ee572ea8b293a - -* added tests for Dataset class - - -Former-commit-id: 71334289e578249681a435d7781c8955b6cabe1d [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7] [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7 [formerly 7747a81615aa5d913284b22a623ee572ea8b293a]] -Former-commit-id: bcff97c402b0267463107480002d22d4d9fe4fcf -Former-commit-id: 21f753f606167a4258d70f8ac6f8fc23d3a8d175 - -* added tests for Dataset class - -* Create LICENSE (#20) - -* Create LICENSE - -* Update setup.py - -Former-commit-id: 7ec143e7ef1dff2a849c62d1283b889398cb6b32 - -* Create LICENSE (#20) - -* Create LICENSE - -* Update setup.py - -* Seg.nrrd quick fix - - - -Former-commit-id: 7f3b5c62681d1275b09eb20a9a3218d9ecd16b23 - -* Seg.nrrd quick fix - -* Minor bug fixes - - -Former-commit-id: f18aa1bd415fbb25050f6d4f8206492a23a61e54 - -* Minor bug fixes - - -Former-commit-id: 7162d456ff8468c980c6a720d7100d655dc03288 [formerly 7162d456ff8468c980c6a720d7100d655dc03288 [formerly f18aa1bd415fbb25050f6d4f8206492a23a61e54]] -Former-commit-id: 96c6e3ef4e49b006056e7a8a11ca4e5ceeea6873 -Former-commit-id: 0858b138f03a568de16d582d42509ba40dc40903 - -* Minor bug fixes - -* test fix - - -Former-commit-id: 2fad37ee3a827f831e6f6b3b7e707bc7509c284b - -* test fix - - -Former-commit-id: d55216a0b91076b0b0ec06def53c517a6325587b [formerly d55216a0b91076b0b0ec06def53c517a6325587b [formerly 2fad37ee3a827f831e6f6b3b7e707bc7509c284b]] -Former-commit-id: 5e3f932e77e3bf3999f6b904cdfd0238af7fc27d -Former-commit-id: 37aa5e3e74d6e25b4f8766938462a60601c29ab3 - -* test fix - -* Added demo - - -Former-commit-id: 48ea411f5bea9471e83b05248ca95198e2e8a997 - -* Added demo - - -Former-commit-id: 1ec696602dd46966f5f7e1d4984feab6cc26386b [formerly 1ec696602dd46966f5f7e1d4984feab6cc26386b [formerly 48ea411f5bea9471e83b05248ca95198e2e8a997]] -Former-commit-id: fe9d3f4af7cf608a771fe1094f1e1162f1a92377 -Former-commit-id: a054f7d9cba105a4d40f2605ad6ea5e954b4a1a1 - -* Added demo - -* Update setup.py (#23) - - - -Former-commit-id: 9e24716cfabf338fa46c4e4a4123bfd003f96918 - -* Update setup.py (#23) - - - -Former-commit-id: ce8e287294e44e5aeaba1c12ea31bea801083293 [formerly ce8e287294e44e5aeaba1c12ea31bea801083293 [formerly 9e24716cfabf338fa46c4e4a4123bfd003f96918]] -Former-commit-id: b9fe3637d03e51472706d44e9096c76752517785 -Former-commit-id: 0cb0b099ffa6d3d67738f40e211e566049a109ca - -* Update setup.py (#23) - -* updated README - - -Former-commit-id: 0f0414533cb6667b68aa48541feb376226fd5515 - -* updated README - - -Former-commit-id: e35f91d35180b1217560b7f0bc06280bf07aebb0 [formerly e35f91d35180b1217560b7f0bc06280bf07aebb0 [formerly 0f0414533cb6667b68aa48541feb376226fd5515]] -Former-commit-id: bc9c6a28ef88362f14ed2cfbf8a333b3f0eb3cfc -Former-commit-id: d353efbbdace157b77f9bedf74654b5b96cda5f9 - -* updated README - -* Update README.md (#24) - - - -Former-commit-id: 9aaf51bcb71b28cf062a03d873682b2ff38cee90 - -* Update README.md (#24) - - - -Former-commit-id: 27494c03e4d95c58d6ea887e20597dbbe235c317 [formerly 27494c03e4d95c58d6ea887e20597dbbe235c317 [formerly 9aaf51bcb71b28cf062a03d873682b2ff38cee90]] -Former-commit-id: 84c0753414042535d8cc637bb974373ceed78130 -Former-commit-id: 63106282d3b55f6d008ae03c60c4a32babcb7d1b - -* Update README.md (#24) - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85 - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: 3cdc5eb2ad84488f20323b1933c4285eac78d60d [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310] [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310 [formerly 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85]] -Former-commit-id: b4abcace6ced31dd9b7d08503d31d4ee49d5ee74 -Former-commit-id: 2a0158397a55d783d6b627181a8af123952df3dc - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - -* Skim2257 quick fix (#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 5e118add39a6796a6d03d9c6729146981da7f44f]] -Former-commit-id: b1c528e7b1f32acf42a18cd78f37b462bfa05171 -Former-commit-id: 79e19c892e15d254c60b16b4ee67e9c16ca59f91 - -* first commit - -* removed test files, changed gitignore - -* changed file directory structure for imageautooutput - -* split mask up into each contour - -* change kwargs in put for basesubjectwriter - -* still kinda failing... - -* brought back basesubjectwriter - -* .imgtools directory - -* changed absolute paths to relative paths - -* changed os.path.join to pathlib.Path.as_posix() - -* removed unused cv2 import - -* removed cv2 import - -* appened is deprecated, changed to concat - -* debug print - -* removed debug print - -* added sparse mask class and generating function - -* testing out sparse mask - -* funky NaN problem - -* commented sparse mask - -* overwrite all subjects - -* space - -* overwrite false - -* metadata stuffs - -* metadata in dataset.csv - -* added modalities, num rtstruct and pixel size to metadata - -* metadata bugfix - -* a - -* fixed wrong variable names for metadata stuff - -* fixed pathlib float error - -* relative paths and output folder paths for dataset.csv - -* put metadata stuff into a util file - -* deal with empty metadata - -* messing around with sparse mask - -* tried to save sparse mask, did some stuff with nnunet output format - -* compliant with nnunet directory structure - -* CLI Interface, argparse moved to utils - -* fixed formatting problems with folder names - -* train test split - -* train size and random state optional - -* merge conflicts - -* changed warnings to not interrupt - -* changed to warnings.warn for generate_sparse_mask - -* merge - -* resolving conflicts? - -* args - -* changes for roi names as a dict - -* added regex dictionary option for non nnunet runs - -* sparse mask global labelling for contour name: index - -* got rid of file_name_convention stuff - -* conflicts resolved - -* yaml thing - -* added list capabilities for the roi names dictionary - -* dataset.json for nnunet - -* CLI "autonew" - -* changed all mutable defaults to None - -* moved autotest changes to autopipeline and addede a few CLI args - -* getting ready for merge to live - -* test_components, test_modalities works with new AutoPipeline - -* overwrite changes and error fix for nan paths again - -* fixed if statement - -* joblib parallel - -* warnings for missing patients - -* summary messages - -* updated, passing tests. Updated version to 0.4 - -* update test - -* yaml path cli - -* yaml error check - -* pandas error - -* Fixed read_dicom_auto - -* skips series check if seris is None - -* updated readme to reflect v0.4 changes - -* updated readme - -* minor change - -* remove .idea - -* remote .idea - -* git ignore - -* transpose for nnunet - -* skip if no mask for nnunet and nnunet folder names - -* bugs in nnunet folder stuff - -* rename nnunetutil (again) - -* sorting the output streams - -* shell script - -* shell script in autopipeline - -* bug - -* forgot CopyInformation for nnunet - -* ignore deprecation warning - -* moved sh file down one dir - -* set -e for stopping execution if there is an error - -* broken checker for missing labels - -* train test fix for 1 patient - -* fix for broken self.existing_roi_names caused by joblib - -* added autotest to gitignore - -* sorted list for train test split - -Co-authored-by: Vishwesh -Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu ([`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: 08616a5987e08a0e392d6a1b2411a035b9c89722 - -* fixed some bugs in autopipeline.py - - -Former-commit-id: e05ea389216e61ad2231757ddccfe46608535a1d - -* now the pipeline saves on exit - - -Former-commit-id: 9cd421dd778df1afc6eb3e8a30a032f676f9b3b3 - -* deleted data - - -Former-commit-id: d3e6b6a8d0712dbb1aed49be5c2a00c7b919118f - -* now checks for existing subject id - - -Former-commit-id: bf4de755d0618dd037c32b5365a05d939878067f - -* uncommented one line pytest - - -Former-commit-id: 3dc8cd388da3ab755d979987b36389dd88396801 - -* uncommented one line pytest - - -Former-commit-id: 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 - -* 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 - -* 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 - -* 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 - -* 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: 971e8d62b3e5dd1afa4cb02578c8f8f1c064e59b -Former-commit-id: d8ab6611d1233f9d30cc2b3fcfcd1e5e3ecb6b07 - -* removed test files, changed gitignore - - -Former-commit-id: ff42f8af6223ce1bc7e83b308d0149979a523d1b -Former-commit-id: 7eaef9c15385ac64d755c8f95cfdc31c8d1c92e3 - -* changed file directory structure for imageautooutput - - -Former-commit-id: c2d8c680399afa8555636aa1b7ee7da909033fc9 -Former-commit-id: 77425123598eecd2c3911ca150142b7d3703fd01 - -* split mask up into each contour - - -Former-commit-id: 7a8285ce35ac4099a92d0b31ce2bd4029847835e -Former-commit-id: 3607e0b8a2b74b8ba859b5aeceab6019cf28a620 - -* change kwargs in put for basesubjectwriter - - -Former-commit-id: a9f093ceb48776f6d9906f572c73f576096b0cf1 -Former-commit-id: e7747e4a255aa0b53f5788d92db01b1ac4df2b32 - -* still kinda failing... - - -Former-commit-id: 21a47c580db1a7fe76fa7192e8e20286de7ec8fb [formerly 8ea1ca37337271dd77aee5d9f855ee7e10c04e12] [formerly 358df05939e6facbcb7be2df553b3adf944781ea] -Former-commit-id: 7fc0d0fa059b344f724746d14f47bfec4e5cd6df -Former-commit-id: 12db48c8db444840b5167444d1b59b5479da5f78 - -* brought back basesubjectwriter - - -Former-commit-id: a2d4763a775608cff06d1f029099a986c8246012 [formerly ad5abdc9cbb01fb00e95025d55f97d346f35d513] [formerly 9a8ff65418449a1039f68554810f12221a35e6e6] -Former-commit-id: eb39ab0b2e878fefaaa8f1680624e5807b8c91c4 -Former-commit-id: 0ea8a45b8eea9b0dce87bfe18168fc701470cb86 - -* .imgtools directory - - -Former-commit-id: d1070faf18232b91705990167815d2c312e4ffdb [formerly 4369b67c3ce16519673c1220bb7de9f7c015fc65] [formerly 455c027a1683596532c8db43f190665723886054] -Former-commit-id: 156d5d42d7e2b8dfb6467e1a9178cbfa5f5a4371 -Former-commit-id: 8f0e63df6ef7328d8b06a53ec843daff9dc1bb2e - -* changed absolute paths to relative paths - - -Former-commit-id: 68b465824a1073f135d92ae748f672ca57003e24 [formerly 03fd9c7f758d9e66dc1d5d0c7c52fde8f02b00ba] [formerly e1e5d0d90909200b10dc96b31c47516665f61b6c] -Former-commit-id: a783dcae441fcea5abfc5c59cc1284036306d458 -Former-commit-id: 03cbd17a361f1edf9bfc86cb4c62ecd4ec914467 - -* changed os.path.join to pathlib.Path.as_posix() - - -Former-commit-id: b2a9034d42333aaa7270baad6f35a349ae5bb766 [formerly ff4e77dd83053fe8a8b2b8b538f04ca6c4cbc94b] [formerly 042aa1f6c4f6e6f83f817b61ecbd3b4763e176a7] -Former-commit-id: f10f5798dd16c2532f06930b902f7d14a2e4d276 -Former-commit-id: 51bef1373edac77cfeeaa716c4623f1cef1e8bbd - -* removed unused cv2 import - - -Former-commit-id: d8af3a3194189f95f1d3c51c0ba4c6a3aa15945e [formerly 882c6c10d4c46c3971f145dd9f3feb16cf8ceef1] [formerly 9d5bc56d90e97a443446e3373a365d74c81732fa] -Former-commit-id: 969eb873f71a71b80903eab6809c2681cc739378 -Former-commit-id: 0df09fd29e7dd2562262eda99ed074a8c5b27608 - -* removed cv2 import - 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-* added sparse mask class and generating function - - -Former-commit-id: 5adca740f2073cbd4cf94de9a64fe81368886b2a [formerly d487847771a367bd1af76acec101d3ea92db143e] [formerly 8dab6bc3eca3157eba59da8260a5f95071b24c9f] -Former-commit-id: 85a78afc170b2f066c45b708023836741596a7ae -Former-commit-id: b8e9322ff6fa03be31f632e7ac9a2025cdc74f45 - -* testing out sparse mask - - -Former-commit-id: 936217337105ec1596bdd5b80ac6732f2459272c [formerly 21ce9fe74262426bbc54e5766daea2267d077c62] [formerly 19b0ad5121c590b67b91831d6ddbd6a4f0836471] -Former-commit-id: f7e3987244b8da0ac3a4a33cafaff3c4f8e9879e -Former-commit-id: 6610464a2c049eb5b8a694af6472c4691bc4b753 - -* funky NaN problem - - -Former-commit-id: 49eb88a506755b2d6e3b93e3b12f422c77fa757b [formerly c6c303b9edbca9cac83b6d417e28cca11d763e2f] [formerly 7e96504d2c1945c50524bc01539cedbd6d54f8b7] -Former-commit-id: f36e2030909686fa6fb4f45b17bb4001835add6d -Former-commit-id: fe416d97c27f9946bfa80f0bd95fc0aaf265a1b3 - -* commented sparse mask - - -Former-commit-id: 59a894685fffb3cf9a7637c1b05e45c65e88fc24 [formerly 4857e6d3cbba5ca6e0b7225840a0215c6417abe4] [formerly 915d769405f63fd9dc11fc11df4b5302dcc986f6] -Former-commit-id: 52b5f1599dd4571fcc2dcbc341157e11f3c27359 -Former-commit-id: c398ec700542f754af8fbe989aa9237582cff776 - 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-* fixed wrong variable names for metadata stuff - - -Former-commit-id: 6af5032314885c9fa27ff5d560dafe2b2e682ffe [formerly 716e4631a647d2f9ed74f497ce0de0c4d2d1a8cf] [formerly 67449ca1e24f3cd7b33b242396af5439c2ae82f1] -Former-commit-id: 42047698b69dc799befb156d423bfe95adb8d8d5 -Former-commit-id: c4fa88c9d2de73b652ce996763531e157c2c3026 - -* fixed pathlib float error - - -Former-commit-id: d88e5bdb7353c64e85d303ff09e0305c5ffac02c [formerly b90a56572ed01863a3b7bf82bf738f2408f6153d] [formerly aa36b2dfa79510b56a7ff29b882bbce86637edbc] -Former-commit-id: 31a44daf0faba0189d42ddef541d434823b2b7bb -Former-commit-id: bc0cc74d9f482a067665621789e336007bd3d194 - -* relative paths and output folder paths for dataset.csv - - -Former-commit-id: b263aa4d894fe21adeea7911dc139d601747ed0a [formerly 6d7a0a9cb299b11fac3679c99e1e650919ca7809] [formerly 2ce5ade50b716f2e70118e4b122d0a74f7845a7d] -Former-commit-id: f0fb228cb2778120a9df2c67b09915678ef1f2f0 -Former-commit-id: 33ec41ab8281fe3e94d9afd3fbcf913c7641af6e - -* put metadata stuff into a util file - - -Former-commit-id: 732a68434e6f37d72c65e7cc701b3c5dca6833a1 [formerly cf894ec5e2c312b97b2c3f29abc758b78ac05bd0] [formerly 69f4ee7fa24db731ddda19a76004d042d5bca317] -Former-commit-id: dca3976c425fa89582776b982235372546bf93be -Former-commit-id: e552e35608b00e887a8306a7d2b4820f02c2c6cf - -* deal with empty metadata - - -Former-commit-id: 3c02cba89c72bb66025c0479fb6a6a57ff597316 [formerly 47ac4fc0e2b571d4a618a75475011d0ce8c339e1] [formerly 31d0411767ee71b062fe65d23d8cb75864d2b667] -Former-commit-id: 6271fb43a7bcce3224debeedf893c10efd8e4951 -Former-commit-id: ce01f1128b976f8cf3686be59a5efb19c43c1e14 - -* messing around with sparse mask - - -Former-commit-id: 03e625794f8b717e9ec87145c278e99460d247fb [formerly be555b7876505f07a34bf058bcee177653ca20cc] [formerly a66925c9d1a198ffbe27ddf670f7ea00522e5caa] -Former-commit-id: b432ee15ae4cc17eb628519b8efa5d3cbd830a42 -Former-commit-id: 48ff00677dfb9255046625d3e527d4c51111688e - -* tried to save sparse mask, did some stuff with nnunet output format - 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-* matching roi names in StructureSet.to_segmentation is now case-insensitive - -* StructureSet now correctly handles ROIs with no contour data - -* Segmentation object now correctly handles indexing - -* Fix empty array check in structure set conversion - -* [Bugfix] Fix slice number rounding when generating a mask from RTSTRUCT - -* Fix slice matching issue when generating binary mask from RTStruct - -* CLI "autonew" - - -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 -Co-authored-by: Minoru Nakano -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh -Co-authored-by: Benjamin Haibe-Kains -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: fishingguy456 -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu ([`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 - - -Former-commit-id: 34b9b7f6c0c8cc50bcba03067dc70d748a0cbf32 [formerly 08616a5987e08a0e392d6a1b2411a035b9c89722] - -* fixed some bugs in autopipeline.py - - -Former-commit-id: f7a40316af77e38465cb511454d615001936764a [formerly e05ea389216e61ad2231757ddccfe46608535a1d] - -* now the pipeline saves on exit - - -Former-commit-id: 099d6ca41b0beae20c8261942b1d9c2b91e130a2 [formerly 9cd421dd778df1afc6eb3e8a30a032f676f9b3b3] - -* deleted data - - -Former-commit-id: 8c55bc4187dca3aee5548f17d2cb8887aa45b131 [formerly d3e6b6a8d0712dbb1aed49be5c2a00c7b919118f] - -* now checks for existing subject id - - -Former-commit-id: d65b305856ae37363c742f616a83ee1836ed3dd7 [formerly bf4de755d0618dd037c32b5365a05d939878067f] - -* uncommented one line pytest - - -Former-commit-id: 797c47cbebf0ef9042ea1828f590f01a813c304f [formerly 3dc8cd388da3ab755d979987b36389dd88396801] - -* uncommented one line pytest - - -Former-commit-id: f3ba678d71b569a5d4b574c2d7874c93e488ba8b [formerly 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 - -* 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 - -* 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 - -* 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 - -* 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 9a8ff65418449a1039f68554810f12221a35e6e6] - -* .imgtools directory - - -Former-commit-id: d1070faf18232b91705990167815d2c312e4ffdb [formerly 4369b67c3ce16519673c1220bb7de9f7c015fc65] [formerly 455c027a1683596532c8db43f190665723886054] - -* changed absolute paths to relative paths - - -Former-commit-id: 68b465824a1073f135d92ae748f672ca57003e24 [formerly 03fd9c7f758d9e66dc1d5d0c7c52fde8f02b00ba] [formerly e1e5d0d90909200b10dc96b31c47516665f61b6c] - -* changed os.path.join to pathlib.Path.as_posix() - - -Former-commit-id: b2a9034d42333aaa7270baad6f35a349ae5bb766 [formerly ff4e77dd83053fe8a8b2b8b538f04ca6c4cbc94b] [formerly 042aa1f6c4f6e6f83f817b61ecbd3b4763e176a7] - -* removed unused cv2 import - - -Former-commit-id: d8af3a3194189f95f1d3c51c0ba4c6a3aa15945e [formerly 882c6c10d4c46c3971f145dd9f3feb16cf8ceef1] [formerly 9d5bc56d90e97a443446e3373a365d74c81732fa] - -* removed cv2 import - - -Former-commit-id: 0a84fe41555b3fccf8fbcff8658961d207df155b [formerly 9950ec6ab3da450ca9405bf355d28e0dcfe1f6d2] [formerly 36aab93d080b40ee31c6c4d5262aa0d9b950e0d1] - -* appened is deprecated, changed to concat - - -Former-commit-id: 307386f4c17529ae3e0371bed1187f2d5c6ea561 [formerly 4f57b54d97ff4d624fde93c5d1be2fcfb5dd9f45] [formerly f6d997b892baf1b8eb0e6b397aa5ab2f117343da] - -* debug print - - -Former-commit-id: ddfa47951095cbe61ed5799c3beb8912ae2ff13c [formerly eface1b46d4e4e1400db4eaa6cb03a489520afdb] [formerly 5a6caa5ea8f913643776f90ce6781b87d34247aa] - -* removed debug print - - -Former-commit-id: 8464f70078871772881c0959ed124055886ba012 [formerly 4eed751a5335b4ae84013f6808cd07094282b102] [formerly 49c575adeb7299cf84950f038dff79e2d6bd282f] - -* added sparse mask class and generating function - - -Former-commit-id: 5adca740f2073cbd4cf94de9a64fe81368886b2a [formerly d487847771a367bd1af76acec101d3ea92db143e] [formerly 8dab6bc3eca3157eba59da8260a5f95071b24c9f] - -* testing out sparse mask - - -Former-commit-id: 936217337105ec1596bdd5b80ac6732f2459272c [formerly 21ce9fe74262426bbc54e5766daea2267d077c62] [formerly 19b0ad5121c590b67b91831d6ddbd6a4f0836471] - -* funky NaN problem - - -Former-commit-id: 49eb88a506755b2d6e3b93e3b12f422c77fa757b [formerly c6c303b9edbca9cac83b6d417e28cca11d763e2f] [formerly 7e96504d2c1945c50524bc01539cedbd6d54f8b7] - -* commented sparse mask - - -Former-commit-id: 59a894685fffb3cf9a7637c1b05e45c65e88fc24 [formerly 4857e6d3cbba5ca6e0b7225840a0215c6417abe4] [formerly 915d769405f63fd9dc11fc11df4b5302dcc986f6] - -* overwrite all subjects - - -Former-commit-id: 9a363bc044b845e0eefe4848fe7e1f1b935e0fbd [formerly 0c9dbf7794429d9ae1b07b233b7cc7afab53ff82] [formerly f0ebe6a43efcffeadca6f1f9b8b6b593f4ba7858] - -* space - - -Former-commit-id: 2c29c5240901280de454bdd9bba068cdae4cdb64 [formerly 76e32213006c7e539134d9ff58317e351eb7f9f4] [formerly eb30814d22c023d3bab73b7328e9f7c83dc5e8b7] - -* overwrite false - - -Former-commit-id: a543516b1aaa5c95be63d0742a260621bb3f9565 [formerly ba00389611de0fb57a8600ee91ae2abddda94196] [formerly ff3a1158de34b342094b617ec091b01394de03ec] - -* metadata stuffs - - -Former-commit-id: 1cc883fde3c03e5032b5fff818c0a7477eaa9bf8 [formerly cafb7dd92b568dad012c7a5aff300977545cf806] [formerly c2364085e201cd792e029d6238254f15cf229077] - -* metadata in dataset.csv - - -Former-commit-id: 495be0c7138afc8736d619575cadfa2ad04e3608 [formerly ebe757ba380553f0146ae9863278e6a2d4e90cdb] [formerly ae0982734ee2cc09d2fb07e004c8fe078fe3adc3] - -* added modalities, num rtstruct and pixel size to metadata - - -Former-commit-id: 824dff5edad36be6564032c1d3e8f0c99d7648ff [formerly 8a922f22af15bc03873eb9506f5d6e4251ce87f8] [formerly 51634e6bda0591cac408a11366a60562c780204e] - -* metadata bugfix - - -Former-commit-id: 5b785f868771e591ab99db4453dc433a5f452247 [formerly 2784a5a0e188fd1db91773e911f7f8140a233314] [formerly 0042f14ffb74f9637c5591c4226202cb25cb5c1b] - -* a - 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-* deal with empty metadata - - -Former-commit-id: 3c02cba89c72bb66025c0479fb6a6a57ff597316 [formerly 47ac4fc0e2b571d4a618a75475011d0ce8c339e1] [formerly 31d0411767ee71b062fe65d23d8cb75864d2b667] - -* messing around with sparse mask - - -Former-commit-id: 03e625794f8b717e9ec87145c278e99460d247fb [formerly be555b7876505f07a34bf058bcee177653ca20cc] [formerly a66925c9d1a198ffbe27ddf670f7ea00522e5caa] - -* tried to save sparse mask, did some stuff with nnunet output format - - -Former-commit-id: 72d1a9549f7dfb36efedd35461b437630b9a29f3 [formerly dbde3a7840296a376f8fed58a828d1f261441459] [formerly 6b543052b87b529482d582c1b205f5f252cb497e] - -* compliant with nnunet directory structure - - -Former-commit-id: 9150f3de85f07dfefb14283b5582a91d06037943 [formerly 3b2c07ac39e311f7f906671f8644a8b477e383ab] [formerly 1407e1d4679bbbde6f9b3ec89f5cf15aaadbb941] - -* CLI Interface, argparse moved to utils - - -Former-commit-id: 1b107a2669ac370dd90760faf2952898d88fe4b8 [formerly c13cd8b357c2edae1635254ee4d6159954e6e80e] [formerly 6bf5f4f41f3c63d482e08bc74c91e0ef571a3c79] - -* fixed formatting problems with folder names - - -Former-commit-id: a9eb4b030058a069335a8704e4925f0de2bb0473 [formerly 300ee2d95bc3fcc6545675f24661fb1f416f7895] [formerly 437db52f7a4f53bdccc4f561ba8e3bd0b4712e87] - -* train test split - - -Former-commit-id: db3882971f1f961cec443e449111c71ac665f6e6 [formerly 305005399fb502199817eb435622b4ba4a81de7a] [formerly 15bab7b91897b7b341927adffa12b57300d4b21d] - -* train size and random state optional - - -Former-commit-id: cc03dba021510c01edf76a31d8b70751558876c6 [formerly 3308255c03f05615ccadd0fd931f0d902b2e5b4a] [formerly 3ac4016abc14c441cbe760c9988e50671c11d94c] - -* merge conflicts - - -Former-commit-id: 8ff52b0fd72b316f8be7ac268da9b0a2ea0a61dd [formerly a656be7176df1771f21681d7df59f783e2c2dda5] [formerly f96833db93140609b7bfa3cf93e823d986fd9149] - -* changed warnings to not interrupt - - -Former-commit-id: 1ca7741c16c5b04f851c7921bdc4bf0cfb0a57b4 [formerly f88061e09b4a6d271f778bd5889adbf3536b5e2d] [formerly 154819e34c9df3510e6229b595a43103039d93f7] - -* changed to warnings.warn for generate_sparse_mask - - -Former-commit-id: 1feda712797971e5a36320fd63126ca719a57d77 [formerly 597312fc926e2b97a4e805027e008d45fdf99716] [formerly 1aec56d1bd6cc8f85d2365433815c7f8f27475c4] - -* merge - - -Former-commit-id: ff8ce2b070216cb186f03f482785cfba9afffd22 [formerly 2cef89dbc46edc56252cd2f19aef3140d984a680] [formerly 29bc242fafa9a85977aab594ed69ec5a66a456f8] - -* resolving conflicts? - - -Former-commit-id: 01a1f3fde11fef8535ea0b28e21857c976dbfe05 [formerly 92f19d8a14fe1c239968da5ebd714d3d46c68146] [formerly 0d16b0224e0cb1981e3344922b96cef4238ffa17] - -* args - - -Former-commit-id: c2219aa34ce847e7ef45c5313312468866a12d39 [formerly fb2cfa05a8a4d7d38d00ed577c89f18a1e34d75b] [formerly f4f6d2d70f4575233adbfa700104fb2fba839b6d] - -* changes for roi names as a dict - - -Former-commit-id: 61ca8205f587076868c1f5292df10c7d70223a23 [formerly 63c94a0e2d99a982b4aaab2c4f93b7df46ae6b06] [formerly 0479cb8f0efec335658a59a493f031faea163e90] - -* added regex dictionary option for non nnunet runs - 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-* 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 c0a10ed840cbf71c902edd9b12fe83eb0f03e633] [formerly c6a5f4dce6f75c2e22d67d59e5be9caf480ff6a9] - -* joblib parallel - - -Former-commit-id: 6dc7d86b38520600a7afcf1d1df5f7af08e3834c [formerly 6dd94b9cdb121a1aac22a25084fd893a5e3bfab4] [formerly 7a47740c8b8a2289c9c3e5f85cebed37aa22ff87] - -* warnings for missing patients - - -Former-commit-id: 9a322f23144bde1e9718d2b3eaa882aa26e8838d [formerly df376a9a782322c15b56df52e5c93b5fa7cd16ea] [formerly abc0428675a21d80928c05fb02fccafbec49e911] - -* summary messages - - -Former-commit-id: f762b74fdbd7dcc4ccf8d77115ecd1cb0ce77345 [formerly 4bd68fff72c376be8b4cb149d9a0a9c3c1e77c87] [formerly 6729aa555c85687d9ec76828126bb4dcfa12044c] - -* updated, passing tests. 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-* skips series check if seris is None - - -Former-commit-id: 480d450a1b53de81c0d95ae952cc408c2f132d93 [formerly 34d6e52e16297d89b1fe14a64e18b608d0bbbbbe] [formerly eb8fb653c92acfb87c6c7b6bcebafa786d061f82] - -* updated readme to reflect v0.4 changes - - -Former-commit-id: efb59b2544d0ec8c061eb97387e8862cfd8aa5c4 [formerly 4b5d39c072a9d43c535c6b3770c2cd4095f3e685] [formerly d355cf54f2dc9bd8477c202759720e08f17e6046] - -* updated readme - - -Former-commit-id: 3acbd335dc773c09d5fea9837306082ed60c9c1c [formerly 29ec4759bcb7fec2c930b9e40dd00ed2ed77e8bc] [formerly 84d607ff5ba00c694d6a00be2ccf6e4be4580428] - -* minor change - - -Former-commit-id: 7a14eb65f36888ed3aad61d12d0e00acdbcd8993 [formerly 92f7b812c855b1026f32ee2697e23e70b974c504] [formerly 6a0203622a06805d901c31b12cb6436d42595631] - -* remove .idea - - -Former-commit-id: 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 -Co-authored-by: Minoru Nakano -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh -Co-authored-by: Benjamin Haibe-Kains -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: fishingguy456 -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu -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 - -* 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 - -* 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 - -* 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 - -* 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 -Co-authored-by: Minoru Nakano -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh -Co-authored-by: Benjamin Haibe-Kains -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: fishingguy456 -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu -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 - -* 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 - -* 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 - -* 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 - -* 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 -Co-authored-by: Minoru Nakano -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Sejin Kim -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Vishwesh -Co-authored-by: Benjamin Haibe-Kains -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim -Co-authored-by: Sejin Kim <40668167+skim2257@users.noreply.github.com> -Co-authored-by: Vishwesh Ramanathan -Co-authored-by: Kevin Qu -Co-authored-by: Kevin Qu -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 - - -Former-commit-id: e4e58f13fc3759f5900902914a3662098cda2c75 -Former-commit-id: fbcbbbd93f06c759737503ec437ae96b14844c35 [formerly 87a4a66fe927bb0a4818c74e07f2fb12fe5e3941] [formerly 0cce0ee6666d052d4f76a1b6dc5d088392d309f4] -Former-commit-id: 240701570180ceb222c72360d980dccba4f529b0 -Former-commit-id: daa9ec35a51d952dbe88a2c85c73ca050b32a70e ([`e9665f9`](https://github.com/bhklab/med-imagetools/commit/e9665f9e53c56a84a4479bb463f778d46d1ea636)) - -* quick fixes - - -Former-commit-id: 5e118add39a6796a6d03d9c6729146981da7f44f -Former-commit-id: 8ac1dfd1340ce26440ed165fa7c2b7386034aa7a -Former-commit-id: 8d2a5a0e90105a894e4b7376918500c1c96856e5 ([`97adb0b`](https://github.com/bhklab/med-imagetools/commit/97adb0b95bef6714e3b3b1e0e706ab25474ca9cb)) - -* Skim2257 quick fix (#26) - -* Updated crawler to force String on all meta fields - -* Update setup.py - -Former-commit-id: e942f7e7dd641efe61faed8a445c7b4abe6da994 [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly 5e93381461268785776402061d555ab02b78fda3] -Former-commit-id: 65d66d20aa91799be74eaeeab91a5f1022d95d70 -Former-commit-id: 8a58ea10fb3416e01953eea428dac12e97f2fb8f ([`dd6ca1b`](https://github.com/bhklab/med-imagetools/commit/dd6ca1bd3273ffb2ac586b07441b0607ffedd4b5)) - -* Merge branch 'master' of github.com:bhklab/imgtools - - -Former-commit-id: 3af4b2251549bbca2ea985e982f3c2709b162a67 [formerly d147081d420198769fba57214409b8faa71dd8fb] [formerly eaad718360d2bd12872b13251a5dc7f3e16aa072] -Former-commit-id: 2ed78e51fd7a72c41c43c76168c1e3123c495bb5 -Former-commit-id: 7840154162b9d5801ce3d8d95c7397504e65bf92 ([`b9314ca`](https://github.com/bhklab/med-imagetools/commit/b9314caac62e35d51d0f0e5e246e2e3714b875ec)) - -* Update README.md (#24) - - - -Former-commit-id: 213a9a7d009a2859a36988866fc031158d593b8b [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] [formerly 9aaf51bcb71b28cf062a03d873682b2ff38cee90] -Former-commit-id: 27494c03e4d95c58d6ea887e20597dbbe235c317 -Former-commit-id: d8cd3177cb0a09227a6a19e83fa131b85e597aae ([`c645115`](https://github.com/bhklab/med-imagetools/commit/c645115a7a903116ecab68814f14442e037dcb06)) - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: bfaaae9324716a550fcb468e137d9b4a7bfb07b6 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] [formerly 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85] -Former-commit-id: 11971c8b1f10f60e20d62c85b208031dfa2b8310 -Former-commit-id: 50d9fa66a7bfcdd03e9bdd815b767599c85853ec ([`21edaa0`](https://github.com/bhklab/med-imagetools/commit/21edaa0d9ddbd8f2d80d4229de59e105074a0910)) - -* updated README - - -Former-commit-id: 4757ba85017119f8cda7fb0dea07f4e66a8629b6 [formerly c406bfc9526357e2091e1348d837c68cd5633801] [formerly 0f0414533cb6667b68aa48541feb376226fd5515] -Former-commit-id: e35f91d35180b1217560b7f0bc06280bf07aebb0 -Former-commit-id: 9c1db1c93bdac00429775eadf36066fae99fc5a2 ([`90fb398`](https://github.com/bhklab/med-imagetools/commit/90fb39871dae0b664d7297c19751d5f59c5caa76)) - -* Update setup.py (#23) - - - -Former-commit-id: a00e8f2ed448fecd0f5b9cccb6e04421e4952e19 [formerly 9e24716cfabf338fa46c4e4a4123bfd003f96918] -Former-commit-id: ce8e287294e44e5aeaba1c12ea31bea801083293 ([`5f3182a`](https://github.com/bhklab/med-imagetools/commit/5f3182a717903e245cc5b1d62ec5677921caf340)) - -* Added demo - - -Former-commit-id: e8eb00ba173df71ea56ed8accd366e1a015df864 [formerly 48ea411f5bea9471e83b05248ca95198e2e8a997] -Former-commit-id: 1ec696602dd46966f5f7e1d4984feab6cc26386b ([`63a66c7`](https://github.com/bhklab/med-imagetools/commit/63a66c7821b48391ea087c554744ef1a993febbb)) - -* test fix - - -Former-commit-id: 424dc17ce0f3bd9a54c8a3ebb52bab96725d2977 [formerly 2fad37ee3a827f831e6f6b3b7e707bc7509c284b] -Former-commit-id: d55216a0b91076b0b0ec06def53c517a6325587b ([`464e041`](https://github.com/bhklab/med-imagetools/commit/464e0418154bbc82968ed66209475b1a5ee2c453)) - -* Merge branch 'add_capabilities' - -Conflicts: - tests/test_autopipe.py - -Former-commit-id: b3c4025467c80f37dedb0727d2cb0daf40f0702e [formerly 9931e15e6a565336f8550d951e64b50289783eeb] -Former-commit-id: 68ad7c006edcdbc5013e2ea9e17672722ace3dd4 ([`8833ef3`](https://github.com/bhklab/med-imagetools/commit/8833ef379715c007c76dfc93b513c5eb80eafab6)) - -* Minor bug fixes - - -Former-commit-id: 52cf95f0271fbb1cdda186db56cc6cde8a536d5d [formerly f18aa1bd415fbb25050f6d4f8206492a23a61e54] -Former-commit-id: 7162d456ff8468c980c6a720d7100d655dc03288 ([`24d0618`](https://github.com/bhklab/med-imagetools/commit/24d06189e849822d4c203bb187f39a369f268562)) - -* added tests for Dataset class - - -Former-commit-id: 608b9c734ff0f006ede4fce6d5832f5ca0752ccd [formerly 7747a81615aa5d913284b22a623ee572ea8b293a] -Former-commit-id: 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7 ([`fdbe97d`](https://github.com/bhklab/med-imagetools/commit/fdbe97d0af266cbd964f3aa50957337d39589ffd)) - 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-* fix conflicts - - -Former-commit-id: f2304e116f0a487ecea85c362cfac9626e5cda30 [formerly caad95a251fab60b5a8078bcd60987ba7dbbbd9d] -Former-commit-id: c70d9c89cc2dd93f6c820b9b4a84577088fcb239 ([`08a58b0`](https://github.com/bhklab/med-imagetools/commit/08a58b042beba83df9649c222585f5c626211a3a)) - -* Merge branch 'master' of github.com:bhklab/imgtools - - -Former-commit-id: 974939f0558176087f44ebbd5ce062bc1013fff8 [formerly f169a7e8f31285d19659d78e23a597cb6a3c1951] -Former-commit-id: 42e4a1bb16acdbf64c3c93bb7458acfaceed0fd1 ([`ce2072c`](https://github.com/bhklab/med-imagetools/commit/ce2072c3f528460c32f971363781b211979039fb)) - -* Changed dataset class returns - - -Former-commit-id: 40c53e6226ca60dd7b51ba848af5f2f3fb8ce33a [formerly 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a] -Former-commit-id: 180fe18d186e8909117afead0b974ecf33c0b632 ([`fe4e485`](https://github.com/bhklab/med-imagetools/commit/fe4e485bfa1d7123573563e512794d10639efef4)) - -* added demo.py - - -Former-commit-id: fcd6610aa6939eeb84965d6aaf7db547d18fec2b [formerly b64491943988d84244d64f7d6001be088174e741] -Former-commit-id: 64a7701af6ea133285259cc40df0f47bcab496ba ([`fbb0ef3`](https://github.com/bhklab/med-imagetools/commit/fbb0ef3704ed63314ba57f32525073900b8d5905)) - -* small bug fix - - -Former-commit-id: c5de9faa884b8ac399aed64bfb7c11e65bd7d70f [formerly 7a27ee36703947cbeae3addb99a86c2c2566d0c0] -Former-commit-id: 43e3c6b28cecf2b33ea563904a2ac6197fab48b4 ([`d47f574`](https://github.com/bhklab/med-imagetools/commit/d47f574c4c4afb79d50cbd4557f0ef5bc035dc5c)) - -* fixed bugs regarding multiple connections, saving of metadata and loading of metadata - - -Former-commit-id: bf97b7fb25abd156d258a5b22d5f2ad348a382f4 [formerly 1528efc88ca4952ce570721832a339ff8274b4fa] -Former-commit-id: ab236e55b1de2ca583f4118dec4a250b5801e5b1 ([`9caee64`](https://github.com/bhklab/med-imagetools/commit/9caee64066bd68cc53d80a3efcfeb554c791033c)) - -* added visualizations and some more bug fixes - - -Former-commit-id: bfc783954909833e5fea376fcae054b01c30596b [formerly 735b26c9de88e0a48b468f8fca490bcc68d4cf6c] -Former-commit-id: 2daaf02ec87a1caccd93e18e5a119c9863e940af ([`37ca2cf`](https://github.com/bhklab/med-imagetools/commit/37ca2cff8a3e699a739b1cea0594cf8f9c3f2636)) - -* bug fixes 2 - - -Former-commit-id: c0aa46eb71ee640ec4b086e715852b001dbd92fd [formerly 90732d81ff1873e24cd501283e4cdd2326febd28] -Former-commit-id: ad812ba0225fb2bff2ca5b49f307dc748ded3efe ([`c364fdc`](https://github.com/bhklab/med-imagetools/commit/c364fdc0ead6e9c3dbf398b9127282224e848887)) - -* bug fixes 2 - - -Former-commit-id: d523d79396f367bd6c2b634a0602e45df0a595f9 [formerly e7f4b424ecf5519ded2352b3d6266a7da07a5b07] -Former-commit-id: 374041fceb9f851959a35da4d525a6930aa4837a ([`e152160`](https://github.com/bhklab/med-imagetools/commit/e15216086af12e868ba47264d7f3042b6b1aee28)) - -* 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: 384794ad0cff9f35b16e01177e16422f96eef8cd [formerly d2556741284260f74609ead96c2e64621af8511a] -Former-commit-id: a27dc3c212327be4058cc374d9b37ae005fe87e0 ([`a047ef6`](https://github.com/bhklab/med-imagetools/commit/a047ef65c17b77282b3cf5df8523f4bcaab14a8e)) - -* 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)) - -* uncommented one line pytest - - -Former-commit-id: f3ba678d71b569a5d4b574c2d7874c93e488ba8b [formerly 2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe] -Former-commit-id: 3f878494e3be177a2784ae665bf110f562422443 ([`1c37dab`](https://github.com/bhklab/med-imagetools/commit/1c37daba97d23ab4b74681c93ac5149f8b50c67a)) - -* uncommented one line pytest - - -Former-commit-id: 797c47cbebf0ef9042ea1828f590f01a813c304f [formerly 3dc8cd388da3ab755d979987b36389dd88396801] -Former-commit-id: 6da65ddd48d4d10f0e3ec8244581a598d886f75c ([`1f34ff3`](https://github.com/bhklab/med-imagetools/commit/1f34ff389cc9d8d889d76eb6a529ff13323a44ba)) - -* 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)) - -* deleted data - - -Former-commit-id: 8c55bc4187dca3aee5548f17d2cb8887aa45b131 [formerly d3e6b6a8d0712dbb1aed49be5c2a00c7b919118f] -Former-commit-id: 3d94d8618a834b40c45823ab43f3cca68d44b54e ([`672f541`](https://github.com/bhklab/med-imagetools/commit/672f541966579d7230df9baca69b02fccdd3a89e)) - -* now checks for existing subject id - - -Former-commit-id: d65b305856ae37363c742f616a83ee1836ed3dd7 [formerly bf4de755d0618dd037c32b5365a05d939878067f] -Former-commit-id: 746bd72cc59ddac3d583655e47ab28dcd851aa45 ([`c757682`](https://github.com/bhklab/med-imagetools/commit/c7576821455bf58e27c825282ea58c3265a328a2)) - -* 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: f7a40316af77e38465cb511454d615001936764a [formerly e05ea389216e61ad2231757ddccfe46608535a1d] -Former-commit-id: ce800b87f646f60a9825903520527e20b6a3a862 ([`eef51f9`](https://github.com/bhklab/med-imagetools/commit/eef51f9391d54edb5f9c1fc60bf9e7fa0991ce5b)) - -* 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: 3a16c640a40d9f76f9f7d046724b891fbf8f422c [formerly 4c8b72c078e331cdd2cbd26dadef836dc49129d2] -Former-commit-id: 42a974ec43d270818dbd192e95017af691b83137 ([`7c27925`](https://github.com/bhklab/med-imagetools/commit/7c279256bc5ba6dac6872338e1c77e88392611f6)) - -* 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)) - -* quick fixes - - -Former-commit-id: d444cb8e2b63900c7747d9a405125066fb67d88e [formerly 97adb0b95bef6714e3b3b1e0e706ab25474ca9cb [formerly 8d2a5a0e90105a894e4b7376918500c1c96856e5] [formerly 97adb0b95bef6714e3b3b1e0e706ab25474ca9cb [formerly 8d2a5a0e90105a894e4b7376918500c1c96856e5] [formerly 8ac1dfd1340ce26440ed165fa7c2b7386034aa7a]]] [formerly 97adb0b95bef6714e3b3b1e0e706ab25474ca9cb [formerly 8d2a5a0e90105a894e4b7376918500c1c96856e5] [formerly 97adb0b95bef6714e3b3b1e0e706ab25474ca9cb [formerly 8d2a5a0e90105a894e4b7376918500c1c96856e5] [formerly 8ac1dfd1340ce26440ed165fa7c2b7386034aa7a]] [formerly 5e118add39a6796a6d03d9c6729146981da7f44f]] -Former-commit-id: b1c528e7b1f32acf42a18cd78f37b462bfa05171 -Former-commit-id: 79e19c892e15d254c60b16b4ee67e9c16ca59f91 -Former-commit-id: 5964ad41667871eed607b7da37c2c71be069fc13 [formerly beb6f1acd4eb2ffb37ac380c996d30d5ebadb2fe] [formerly 454bfde56605674af7b01909decbbdd1770a2e2e] -Former-commit-id: a58f185604013d8d7f8f0dad406ba17936f21bbb -Former-commit-id: 5459794e907ea5a13ebd476772fb6d1bdba292f8 ([`ca5d2a7`](https://github.com/bhklab/med-imagetools/commit/ca5d2a717553143df0a0ea347e364395608d0be5)) - -* Skim2257 quick fix (#26) - -* Updated crawler to force String on all meta fields - -* Update setup.py - -Former-commit-id: 5116186cc44acffc828b7983e84ec2db49b628cb [formerly dd6ca1bd3273ffb2ac586b07441b0607ffedd4b5 [formerly 8a58ea10fb3416e01953eea428dac12e97f2fb8f] [formerly dd6ca1bd3273ffb2ac586b07441b0607ffedd4b5 [formerly 8a58ea10fb3416e01953eea428dac12e97f2fb8f] [formerly 65d66d20aa91799be74eaeeab91a5f1022d95d70]]] [formerly dd6ca1bd3273ffb2ac586b07441b0607ffedd4b5 [formerly 8a58ea10fb3416e01953eea428dac12e97f2fb8f] [formerly dd6ca1bd3273ffb2ac586b07441b0607ffedd4b5 [formerly 8a58ea10fb3416e01953eea428dac12e97f2fb8f] [formerly 65d66d20aa91799be74eaeeab91a5f1022d95d70]] [formerly e942f7e7dd641efe61faed8a445c7b4abe6da994 [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly e942f7e7dd641efe61faed8a445c7b4abe6da994 [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly 5e93381461268785776402061d555ab02b78fda3]]]] -Former-commit-id: e942f7e7dd641efe61faed8a445c7b4abe6da994 [formerly d83fb0135155c4c94846c23614e75805db63cf37] -Former-commit-id: 9bbf4aebbf1978a63dd49de045cc91e4893a5237 -Former-commit-id: 6c11e6c37f455f6f26d906ba60354097eb09a8cd [formerly 7792a3d8e92a47a49db7c5fce24ca1d7adbef8e6] [formerly 5c78dbd9d5fea2e2f199242dbad5b1c8bcceda82] -Former-commit-id: ff962a4492773cedad0eea0c54f16c45f52bd8d8 -Former-commit-id: 0be584c76974ccd562a45ce3da7bfbd583c8633f ([`55b0015`](https://github.com/bhklab/med-imagetools/commit/55b001589ab9055699fadd89c4df78bae31aa290)) - -* Merge branch 'master' of github.com:bhklab/imgtools - - -Former-commit-id: e545deea42a3863067169017572b482efa2bdd7e [formerly b9314caac62e35d51d0f0e5e246e2e3714b875ec [formerly 7840154162b9d5801ce3d8d95c7397504e65bf92] [formerly b9314caac62e35d51d0f0e5e246e2e3714b875ec [formerly 7840154162b9d5801ce3d8d95c7397504e65bf92] [formerly 2ed78e51fd7a72c41c43c76168c1e3123c495bb5]]] [formerly b9314caac62e35d51d0f0e5e246e2e3714b875ec [formerly 7840154162b9d5801ce3d8d95c7397504e65bf92] [formerly b9314caac62e35d51d0f0e5e246e2e3714b875ec [formerly 7840154162b9d5801ce3d8d95c7397504e65bf92] [formerly 2ed78e51fd7a72c41c43c76168c1e3123c495bb5]] [formerly 3af4b2251549bbca2ea985e982f3c2709b162a67 [formerly d147081d420198769fba57214409b8faa71dd8fb] [formerly 3af4b2251549bbca2ea985e982f3c2709b162a67 [formerly d147081d420198769fba57214409b8faa71dd8fb] [formerly eaad718360d2bd12872b13251a5dc7f3e16aa072]]]] -Former-commit-id: 3af4b2251549bbca2ea985e982f3c2709b162a67 [formerly d147081d420198769fba57214409b8faa71dd8fb] -Former-commit-id: 3665daabe0430f5fe5b9783c5ea9555099032520 -Former-commit-id: 12c808b8d6169826c1492147910bdb85f1a894e9 [formerly 490393a0e18d3aec6c4647fc4b0489097170ce6a] [formerly 258a2421cae15e0401bf30db46962a6d93c2933b] -Former-commit-id: b0e0ed4eed231ffbefae7e2a8aa60f365f978122 -Former-commit-id: a2f02a0f0b46be3b8343a5690aff142421f6a90a ([`ac90723`](https://github.com/bhklab/med-imagetools/commit/ac907239000666cbae42b5f9cdc163da09edf39f)) - -* Update README.md (#24) - - - -Former-commit-id: c645115a7a903116ecab68814f14442e037dcb06 [formerly d8cd3177cb0a09227a6a19e83fa131b85e597aae] [formerly c645115a7a903116ecab68814f14442e037dcb06 [formerly d8cd3177cb0a09227a6a19e83fa131b85e597aae] [formerly 27494c03e4d95c58d6ea887e20597dbbe235c317]] [formerly c645115a7a903116ecab68814f14442e037dcb06 [formerly d8cd3177cb0a09227a6a19e83fa131b85e597aae] [formerly c645115a7a903116ecab68814f14442e037dcb06 [formerly d8cd3177cb0a09227a6a19e83fa131b85e597aae] [formerly 27494c03e4d95c58d6ea887e20597dbbe235c317]] [formerly 213a9a7d009a2859a36988866fc031158d593b8b [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] [formerly 213a9a7d009a2859a36988866fc031158d593b8b [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] [formerly 9aaf51bcb71b28cf062a03d873682b2ff38cee90]]]] -Former-commit-id: 213a9a7d009a2859a36988866fc031158d593b8b [formerly 4e7335ef07059daa9dd3743e0727d63610e9da62] -Former-commit-id: 63106282d3b55f6d008ae03c60c4a32babcb7d1b -Former-commit-id: b39d3e78478c710b0fd7b011f9d82686db99903a [formerly 73f8debe481b2adf9a92182a8ede3d35d38b1408] [formerly b25dc8d43440dbb2ce92892f96a599e492d7b13b] -Former-commit-id: 03e04faeddd185ab57db82dd19fcc955465c44dd -Former-commit-id: ef3cc2e63c8edcb05d5542f8129ca2c1fbd93a15 ([`0a23f23`](https://github.com/bhklab/med-imagetools/commit/0a23f236fb22c039f260e07dbc394b354dda6775)) - -* preliminary MRI functionality (MR-RTSTRUCT pairs) - - -Former-commit-id: 3cdc5eb2ad84488f20323b1933c4285eac78d60d [formerly 21edaa0d9ddbd8f2d80d4229de59e105074a0910 [formerly 50d9fa66a7bfcdd03e9bdd815b767599c85853ec] [formerly 21edaa0d9ddbd8f2d80d4229de59e105074a0910 [formerly 50d9fa66a7bfcdd03e9bdd815b767599c85853ec] [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310]]] [formerly 21edaa0d9ddbd8f2d80d4229de59e105074a0910 [formerly 50d9fa66a7bfcdd03e9bdd815b767599c85853ec] [formerly 21edaa0d9ddbd8f2d80d4229de59e105074a0910 [formerly 50d9fa66a7bfcdd03e9bdd815b767599c85853ec] [formerly 11971c8b1f10f60e20d62c85b208031dfa2b8310]] [formerly bfaaae9324716a550fcb468e137d9b4a7bfb07b6 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] [formerly bfaaae9324716a550fcb468e137d9b4a7bfb07b6 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] [formerly 3c01806a93d5b7ca9c6d1a1564d2c9630ff0cf85]]]] -Former-commit-id: bfaaae9324716a550fcb468e137d9b4a7bfb07b6 [formerly 12b031d46c1c3ddbd1917b4037d9164ca3402ff2] -Former-commit-id: 2a0158397a55d783d6b627181a8af123952df3dc -Former-commit-id: e00bd3a449f743635c3ff8cdf2720aee53a6c122 [formerly 5e9af8041f53e08272f10df6ee30daada4a523e2] [formerly d24cae90fcb9a583aec2a100932e3da24d27f0ac] -Former-commit-id: c165c02fa691e7bae3714229d17f30ecef98250c -Former-commit-id: 92f5975b3be9b2b5e742ee1c58fbab781541d8c9 ([`6bc8db1`](https://github.com/bhklab/med-imagetools/commit/6bc8db1ff885c594509ab7cf0dc489f909e20661)) - -* updated README - - -Former-commit-id: 90fb39871dae0b664d7297c19751d5f59c5caa76 [formerly 9c1db1c93bdac00429775eadf36066fae99fc5a2] [formerly 90fb39871dae0b664d7297c19751d5f59c5caa76 [formerly 9c1db1c93bdac00429775eadf36066fae99fc5a2] [formerly e35f91d35180b1217560b7f0bc06280bf07aebb0]] [formerly 90fb39871dae0b664d7297c19751d5f59c5caa76 [formerly 9c1db1c93bdac00429775eadf36066fae99fc5a2] [formerly 90fb39871dae0b664d7297c19751d5f59c5caa76 [formerly 9c1db1c93bdac00429775eadf36066fae99fc5a2] [formerly e35f91d35180b1217560b7f0bc06280bf07aebb0]] [formerly a256c35d6eb286e59aa625ee80e9a3201858f0ca [formerly 4757ba85017119f8cda7fb0dea07f4e66a8629b6 [formerly c406bfc9526357e2091e1348d837c68cd5633801]] [formerly 4757ba85017119f8cda7fb0dea07f4e66a8629b6 [formerly c406bfc9526357e2091e1348d837c68cd5633801] [formerly 0f0414533cb6667b68aa48541feb376226fd5515]]]] -Former-commit-id: a256c35d6eb286e59aa625ee80e9a3201858f0ca [formerly 4757ba85017119f8cda7fb0dea07f4e66a8629b6 [formerly c406bfc9526357e2091e1348d837c68cd5633801]] -Former-commit-id: d353efbbdace157b77f9bedf74654b5b96cda5f9 -Former-commit-id: 8baf0623196e9472477e1ed4b5288b626f254156 [formerly a43cc3526d3559a3792ee76a1b840e678b569d27] [formerly d57189a300ff51ce26e08ba49da114a06b6194b1] -Former-commit-id: 8a8fc0086e494077f35dbe5b48325b056a1ba20f -Former-commit-id: 9aab9f3c5a38bd1933b218254a8d79f3cc8cbb18 ([`7e55330`](https://github.com/bhklab/med-imagetools/commit/7e55330ab0ecf661d002556d6bdb4781044b63a4)) - -* Update setup.py (#23) - - - -Former-commit-id: 5f3182a717903e245cc5b1d62ec5677921caf340 [formerly 5f3182a717903e245cc5b1d62ec5677921caf340 [formerly ce8e287294e44e5aeaba1c12ea31bea801083293]] [formerly 5f3182a717903e245cc5b1d62ec5677921caf340 [formerly 5f3182a717903e245cc5b1d62ec5677921caf340 [formerly ce8e287294e44e5aeaba1c12ea31bea801083293]] [formerly a00e8f2ed448fecd0f5b9cccb6e04421e4952e19 [formerly a00e8f2ed448fecd0f5b9cccb6e04421e4952e19 [formerly 9e24716cfabf338fa46c4e4a4123bfd003f96918]]]] -Former-commit-id: a00e8f2ed448fecd0f5b9cccb6e04421e4952e19 -Former-commit-id: 0cb0b099ffa6d3d67738f40e211e566049a109ca -Former-commit-id: 2560f13f6c55e1f8ab80d700941c61f1816da9f6 [formerly 836589be5fc88a6d24e84a559484bae1fdb6438a] -Former-commit-id: 4e4ec332bd594435c814ab30b33e04c776fc2cb1 ([`b74ca17`](https://github.com/bhklab/med-imagetools/commit/b74ca17c3c095d2f671cf0e539a3bd6abb3db927)) - -* Added demo - - -Former-commit-id: 63a66c7821b48391ea087c554744ef1a993febbb [formerly 63a66c7821b48391ea087c554744ef1a993febbb [formerly 1ec696602dd46966f5f7e1d4984feab6cc26386b]] [formerly 63a66c7821b48391ea087c554744ef1a993febbb [formerly 63a66c7821b48391ea087c554744ef1a993febbb [formerly 1ec696602dd46966f5f7e1d4984feab6cc26386b]] [formerly e8eb00ba173df71ea56ed8accd366e1a015df864 [formerly e8eb00ba173df71ea56ed8accd366e1a015df864 [formerly 48ea411f5bea9471e83b05248ca95198e2e8a997]]]] -Former-commit-id: e8eb00ba173df71ea56ed8accd366e1a015df864 -Former-commit-id: a054f7d9cba105a4d40f2605ad6ea5e954b4a1a1 -Former-commit-id: 5a774df68a53105a4c220503d919ec657702f8e4 [formerly f9d8f9a2844ae1dce5ecda564397488db65847fe] -Former-commit-id: 276d4f7631aa9c363eb4c038dbd03c6eeec9cef3 ([`8ad070c`](https://github.com/bhklab/med-imagetools/commit/8ad070cff434b96d44b2952ddcc5d064db58432a)) - -* test fix - - -Former-commit-id: 464e0418154bbc82968ed66209475b1a5ee2c453 [formerly 464e0418154bbc82968ed66209475b1a5ee2c453 [formerly d55216a0b91076b0b0ec06def53c517a6325587b]] [formerly 464e0418154bbc82968ed66209475b1a5ee2c453 [formerly 464e0418154bbc82968ed66209475b1a5ee2c453 [formerly d55216a0b91076b0b0ec06def53c517a6325587b]] [formerly 424dc17ce0f3bd9a54c8a3ebb52bab96725d2977 [formerly 424dc17ce0f3bd9a54c8a3ebb52bab96725d2977 [formerly 2fad37ee3a827f831e6f6b3b7e707bc7509c284b]]]] -Former-commit-id: 424dc17ce0f3bd9a54c8a3ebb52bab96725d2977 -Former-commit-id: 37aa5e3e74d6e25b4f8766938462a60601c29ab3 -Former-commit-id: cd7ca810f38c8c15ac7625280954d96e44d8e4a9 [formerly 6b8c112d4b039544f9fdf42f3efccefe447e2b9d] -Former-commit-id: 08cd744182a5536c6e3aed0c35d75cf0a7643e59 ([`8b13379`](https://github.com/bhklab/med-imagetools/commit/8b133794c5c128cc12d6ed4e40d7da2a249b1200)) - -* Merge branch 'add_capabilities' - -Conflicts: - tests/test_autopipe.py - -Former-commit-id: 8833ef379715c007c76dfc93b513c5eb80eafab6 [formerly 8833ef379715c007c76dfc93b513c5eb80eafab6 [formerly 68ad7c006edcdbc5013e2ea9e17672722ace3dd4]] [formerly 8833ef379715c007c76dfc93b513c5eb80eafab6 [formerly 8833ef379715c007c76dfc93b513c5eb80eafab6 [formerly 68ad7c006edcdbc5013e2ea9e17672722ace3dd4]] [formerly b3c4025467c80f37dedb0727d2cb0daf40f0702e [formerly b3c4025467c80f37dedb0727d2cb0daf40f0702e [formerly 9931e15e6a565336f8550d951e64b50289783eeb]]]] -Former-commit-id: b3c4025467c80f37dedb0727d2cb0daf40f0702e -Former-commit-id: f9ba5f029d40986915fc69014a6445712287c2b3 -Former-commit-id: dd7aa9f8e5495f93b7e23d6b70a8c5da0a40965c [formerly 08265b1a721a74d7c168730bfec5156e575a4aaa] -Former-commit-id: 15ee1ee48dcbeb58e9e5747c27e48e4c348a137f ([`27cdb7f`](https://github.com/bhklab/med-imagetools/commit/27cdb7f4a987da8135c3613a952113c836d30731)) - -* Minor bug fixes - - -Former-commit-id: 24d06189e849822d4c203bb187f39a369f268562 [formerly 24d06189e849822d4c203bb187f39a369f268562 [formerly 7162d456ff8468c980c6a720d7100d655dc03288]] [formerly 24d06189e849822d4c203bb187f39a369f268562 [formerly 24d06189e849822d4c203bb187f39a369f268562 [formerly 7162d456ff8468c980c6a720d7100d655dc03288]] [formerly 52cf95f0271fbb1cdda186db56cc6cde8a536d5d [formerly 52cf95f0271fbb1cdda186db56cc6cde8a536d5d [formerly f18aa1bd415fbb25050f6d4f8206492a23a61e54]]]] -Former-commit-id: 52cf95f0271fbb1cdda186db56cc6cde8a536d5d -Former-commit-id: 0858b138f03a568de16d582d42509ba40dc40903 -Former-commit-id: 8d4b1f7e5534ab660345893b149ced85edef5f15 [formerly a7e482da439dd69fc3a6ceba05b2e47e50adfb4a] -Former-commit-id: 18d8aae8e523ddbe65c74d140bae22e73df24cb2 ([`bef2d63`](https://github.com/bhklab/med-imagetools/commit/bef2d637b1d74f8ca937ffae75edec38c9634b11)) - -* added tests for Dataset class - - -Former-commit-id: 71334289e578249681a435d7781c8955b6cabe1d [formerly fdbe97d0af266cbd964f3aa50957337d39589ffd [formerly fdbe97d0af266cbd964f3aa50957337d39589ffd [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7]]] [formerly fdbe97d0af266cbd964f3aa50957337d39589ffd [formerly fdbe97d0af266cbd964f3aa50957337d39589ffd [formerly 1f9c17c8bc13f52d0f12b1e79085528da1c82ec7]] [formerly dc3711f510abfff00697293617bf0de36cb87e72 [formerly 608b9c734ff0f006ede4fce6d5832f5ca0752ccd] [formerly 608b9c734ff0f006ede4fce6d5832f5ca0752ccd [formerly 7747a81615aa5d913284b22a623ee572ea8b293a]]]] -Former-commit-id: dc3711f510abfff00697293617bf0de36cb87e72 [formerly 608b9c734ff0f006ede4fce6d5832f5ca0752ccd] -Former-commit-id: 21f753f606167a4258d70f8ac6f8fc23d3a8d175 -Former-commit-id: 139f540db88bf778866bafcb59b7be0602e908c9 [formerly d9b6cc340a27e69806b01f4567a04955afe42f03] -Former-commit-id: 42bfc2b2bf889277bc6cda0b6ced59aa7d5d97d5 ([`6802ed3`](https://github.com/bhklab/med-imagetools/commit/6802ed384572010ec71f6a1c9b45f91714ea01ef)) - -* added tests for Dataset class - - -Former-commit-id: d75ee6e437692650f4a7d62833946161acb12d79 [formerly b92645cc522eb99334160bf28e3e361b83d5ed0f [formerly b92645cc522eb99334160bf28e3e361b83d5ed0f [formerly abfd4dbebccc334866237362629389e79fdcba11]]] [formerly b92645cc522eb99334160bf28e3e361b83d5ed0f [formerly b92645cc522eb99334160bf28e3e361b83d5ed0f [formerly abfd4dbebccc334866237362629389e79fdcba11]] [formerly c44cfcd1df0f235eac6032120b8378c43cb670ff [formerly c44cfcd1df0f235eac6032120b8378c43cb670ff [formerly 8d345fb040a8c6e1725d749d9d8554f35d107013]]]] -Former-commit-id: c44cfcd1df0f235eac6032120b8378c43cb670ff -Former-commit-id: 3b16fbef699e13a000b61cfcc6a031c455b5abac -Former-commit-id: bfd93a9c8daf6d7c07bf393db1c5661609f83f14 [formerly 6025ba6a47c32a8c8d20deff172a5c032ecce5ea] -Former-commit-id: 5797d2a714d8fa9566c28214f1e02ea849bfe580 ([`594fb0e`](https://github.com/bhklab/med-imagetools/commit/594fb0ef0e187f010692af66ed3830149dece388)) - -* fix - - -Former-commit-id: 549a41109fc8ccac52945b860e7b1f819e8484cd [formerly 549a41109fc8ccac52945b860e7b1f819e8484cd [formerly a242475a70abd1d5cc6a4f77ccce9051ff5bdb23]] [formerly 549a41109fc8ccac52945b860e7b1f819e8484cd [formerly 549a41109fc8ccac52945b860e7b1f819e8484cd [formerly a242475a70abd1d5cc6a4f77ccce9051ff5bdb23]] [formerly 699c46b9dc49b7af21f81c31fab891568672be3a [formerly 699c46b9dc49b7af21f81c31fab891568672be3a [formerly c152b0890d6bb0e94f39a8a3f855311a12b06037]]]] -Former-commit-id: 699c46b9dc49b7af21f81c31fab891568672be3a -Former-commit-id: 5aae0d2d9dd7bbf3a4fd2cadbf4d3d21bf7ead57 -Former-commit-id: 8420e83ab0d2b7fbd32903dc4851e3f786dea65a [formerly d701d3f274cf2b4babd0065b3027b82d8c5488c5] -Former-commit-id: b62ee632b62ab399e7b3c8ef35283c58998ac090 ([`c91acc9`](https://github.com/bhklab/med-imagetools/commit/c91acc93512907b7d408a1e323273094d957bf57)) - -* fix path backslash issues - - -Former-commit-id: d531414ab1f307d8c451d8ef1f2d4833d5b6290c [formerly d531414ab1f307d8c451d8ef1f2d4833d5b6290c [formerly c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8]] [formerly d531414ab1f307d8c451d8ef1f2d4833d5b6290c [formerly d531414ab1f307d8c451d8ef1f2d4833d5b6290c [formerly c9fcbbebbe082ac2b98d59515fbeb2180c79c0f8]] [formerly e62073999fb01b945b5203ab2511e943833f437e [formerly e62073999fb01b945b5203ab2511e943833f437e [formerly d81a74dfcdcd21f2b9248d197362a6dbaabf901b]]]] -Former-commit-id: e62073999fb01b945b5203ab2511e943833f437e -Former-commit-id: 26d44c87a36a8ed5cd64b5553ac8bf5a1c5e7af3 -Former-commit-id: 28127b6ad933d3b6d0ef12917d83f5faba7d5985 [formerly 0f1542e8b011ff003034520d08f93ddfa00480d2] -Former-commit-id: e5bbd11cdacdca069c9f77397962b56b2a7c1445 ([`3a67d80`](https://github.com/bhklab/med-imagetools/commit/3a67d8017283450c08397388593c7038afce259a)) - -* fixed test autopipe - - -Former-commit-id: eb71a6ece7d1b92ce1575fbf38354fde98ccc697 [formerly 42bb296cdca9060d54fcedb2e9c7ad2d236d2d93 [formerly 42bb296cdca9060d54fcedb2e9c7ad2d236d2d93 [formerly 3817bbbe40989f26078ead582ef508d58bd22d03]]] [formerly 42bb296cdca9060d54fcedb2e9c7ad2d236d2d93 [formerly 42bb296cdca9060d54fcedb2e9c7ad2d236d2d93 [formerly 3817bbbe40989f26078ead582ef508d58bd22d03]] [formerly 12f9098d2bf8962679440e58afb67ff1b1d240e7 [formerly 12f9098d2bf8962679440e58afb67ff1b1d240e7 [formerly 63b9543e16a615f3cd2023a6e5457a6707835a4d]]]] -Former-commit-id: 12f9098d2bf8962679440e58afb67ff1b1d240e7 -Former-commit-id: 0de4a6d07c1b07618fa0e6ddd0bf5ce4553aa8ca -Former-commit-id: fa498b42594e64d80601659e8d408238c13b6e15 [formerly c3fcdd80e7d22950b633d2f813fb02f26312ad7e] -Former-commit-id: 00cea5875102d7cababf34930216fabe1da03bd0 ([`f151d81`](https://github.com/bhklab/med-imagetools/commit/f151d81719678eb92596520cb85e76b3165ac03d)) - -* fix conflicts - - -Former-commit-id: 3e769f713eead224f382b5abe98f9f90c69fcc65 [formerly 08a58b042beba83df9649c222585f5c626211a3a [formerly 08a58b042beba83df9649c222585f5c626211a3a [formerly c70d9c89cc2dd93f6c820b9b4a84577088fcb239]]] [formerly 08a58b042beba83df9649c222585f5c626211a3a [formerly 08a58b042beba83df9649c222585f5c626211a3a [formerly c70d9c89cc2dd93f6c820b9b4a84577088fcb239]] [formerly f2304e116f0a487ecea85c362cfac9626e5cda30 [formerly f2304e116f0a487ecea85c362cfac9626e5cda30 [formerly caad95a251fab60b5a8078bcd60987ba7dbbbd9d]]]] -Former-commit-id: f2304e116f0a487ecea85c362cfac9626e5cda30 -Former-commit-id: 0cf3b71107adb75b3ebf4c2babf2ba344e7b91cd -Former-commit-id: 14320ce590a550b5328fefc31d3d35da023f0d93 [formerly 4136956f2d87593662b3147a8ba5f7d5c3fa7fd4] -Former-commit-id: 4f963f3d0179d2541043ffdd0178814d2aea6592 ([`be816fd`](https://github.com/bhklab/med-imagetools/commit/be816fdee0f899ff961cddc530632976db8e6425)) - -* Merge branch 'master' of github.com:bhklab/imgtools - - -Former-commit-id: 9c843ade89affffbfb224d72f62d2feca6824921 [formerly ce2072c3f528460c32f971363781b211979039fb [formerly ce2072c3f528460c32f971363781b211979039fb [formerly 42e4a1bb16acdbf64c3c93bb7458acfaceed0fd1]]] [formerly ce2072c3f528460c32f971363781b211979039fb [formerly ce2072c3f528460c32f971363781b211979039fb [formerly 42e4a1bb16acdbf64c3c93bb7458acfaceed0fd1]] [formerly 974939f0558176087f44ebbd5ce062bc1013fff8 [formerly 974939f0558176087f44ebbd5ce062bc1013fff8 [formerly f169a7e8f31285d19659d78e23a597cb6a3c1951]]]] -Former-commit-id: 974939f0558176087f44ebbd5ce062bc1013fff8 -Former-commit-id: 8ebdd739eb77f532c453e6786bd2e0a3e062d8fb -Former-commit-id: 515f5ead5e14071c987b5dcf7a668077175f842a [formerly 5a5e3e344dcfb6c862a9951becffd0b134c07980] -Former-commit-id: 17b26985172f1ad27cd4aebc2bd2e94715181233 ([`22bea66`](https://github.com/bhklab/med-imagetools/commit/22bea669f4a70eb4717c9a54daa3165c87555e59)) - -* Changed dataset class returns - - -Former-commit-id: caa9c4d839ff599f63c9ad68c9bc4e844d96092d [formerly fe4e485bfa1d7123573563e512794d10639efef4 [formerly fe4e485bfa1d7123573563e512794d10639efef4 [formerly 180fe18d186e8909117afead0b974ecf33c0b632]]] [formerly fe4e485bfa1d7123573563e512794d10639efef4 [formerly fe4e485bfa1d7123573563e512794d10639efef4 [formerly 180fe18d186e8909117afead0b974ecf33c0b632]] [formerly 40c53e6226ca60dd7b51ba848af5f2f3fb8ce33a [formerly 40c53e6226ca60dd7b51ba848af5f2f3fb8ce33a [formerly 3c6d7f5a59865520a11ac8b0772d454f5b24bd2a]]]] -Former-commit-id: 40c53e6226ca60dd7b51ba848af5f2f3fb8ce33a -Former-commit-id: 51ff2b743a26bfc2ec123e67a1cf8e77245aa75a -Former-commit-id: 114ec0c81679e445eaf722c1a3414e6c7e6661d6 [formerly 3b034311e0c45261c6d58393acda56229a7e9c29] -Former-commit-id: 0daee6f284fffc20332ec7adc7e5f7a0f7530ce8 ([`f901df2`](https://github.com/bhklab/med-imagetools/commit/f901df285189287bf933fb65c0d983d6331a9d8a)) - -* added demo.py - - -Former-commit-id: fbb0ef3704ed63314ba57f32525073900b8d5905 [formerly fbb0ef3704ed63314ba57f32525073900b8d5905 [formerly 64a7701af6ea133285259cc40df0f47bcab496ba]] [formerly fbb0ef3704ed63314ba57f32525073900b8d5905 [formerly fbb0ef3704ed63314ba57f32525073900b8d5905 [formerly 64a7701af6ea133285259cc40df0f47bcab496ba]] [formerly fcd6610aa6939eeb84965d6aaf7db547d18fec2b [formerly fcd6610aa6939eeb84965d6aaf7db547d18fec2b [formerly b64491943988d84244d64f7d6001be088174e741]]]] -Former-commit-id: fcd6610aa6939eeb84965d6aaf7db547d18fec2b -Former-commit-id: 52754c4f09646cc9386b8f2699a2718edb77eaf8 -Former-commit-id: 561db07e6bd2f733abba794630866f1523ecc6e2 [formerly 636f89dfed62c8601d501aec5789643e32016fc8] -Former-commit-id: d532c12f5a5349db8fff620fb358060c8f32ea5c ([`a32738f`](https://github.com/bhklab/med-imagetools/commit/a32738feaf78a29c816d30c06e302af0895bd695)) - -* small bug fix - - -Former-commit-id: d47f574c4c4afb79d50cbd4557f0ef5bc035dc5c [formerly d47f574c4c4afb79d50cbd4557f0ef5bc035dc5c [formerly 43e3c6b28cecf2b33ea563904a2ac6197fab48b4]] [formerly d47f574c4c4afb79d50cbd4557f0ef5bc035dc5c [formerly d47f574c4c4afb79d50cbd4557f0ef5bc035dc5c [formerly 43e3c6b28cecf2b33ea563904a2ac6197fab48b4]] [formerly c5de9faa884b8ac399aed64bfb7c11e65bd7d70f [formerly c5de9faa884b8ac399aed64bfb7c11e65bd7d70f [formerly 7a27ee36703947cbeae3addb99a86c2c2566d0c0]]]] -Former-commit-id: c5de9faa884b8ac399aed64bfb7c11e65bd7d70f -Former-commit-id: 137b961a46c61f43f19f56f0c2564d14992a3d56 -Former-commit-id: 59ebc98aeac291ebc97bc8395f41dc7c1bdfab81 [formerly 5e3d53c0efb77113676ae9f343437e4178704760] -Former-commit-id: bfbecf8e90e70e16fcc6fe2693f733e4a4e78dfd ([`1a99c13`](https://github.com/bhklab/med-imagetools/commit/1a99c13f8830b55146129cc4a86a1056ecf44ae5)) - -* fixed bugs regarding multiple connections, saving of metadata and loading of metadata - - -Former-commit-id: 9caee64066bd68cc53d80a3efcfeb554c791033c [formerly 9caee64066bd68cc53d80a3efcfeb554c791033c [formerly ab236e55b1de2ca583f4118dec4a250b5801e5b1]] [formerly 9caee64066bd68cc53d80a3efcfeb554c791033c [formerly 9caee64066bd68cc53d80a3efcfeb554c791033c [formerly ab236e55b1de2ca583f4118dec4a250b5801e5b1]] [formerly bf97b7fb25abd156d258a5b22d5f2ad348a382f4 [formerly bf97b7fb25abd156d258a5b22d5f2ad348a382f4 [formerly 1528efc88ca4952ce570721832a339ff8274b4fa]]]] -Former-commit-id: bf97b7fb25abd156d258a5b22d5f2ad348a382f4 -Former-commit-id: 82e0e186b9d508c398f798469326c643cd6527c2 -Former-commit-id: 572070569f96d035e7a6f223bddc027a0517a0e0 [formerly a7c15fb8edc416e70f38c58ea5b6a9802db7f0fd] -Former-commit-id: 6fbeafeeed9aca80134c95570b89be420187b7d4 ([`2325d36`](https://github.com/bhklab/med-imagetools/commit/2325d3669f4696623826204113d14ed96ca1bd18)) - -* added visualizations and some more bug fixes - 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-* bug fixes 2 - - -Former-commit-id: a513f1a9102c236845fa273100bb39112b092bf7 [formerly e15216086af12e868ba47264d7f3042b6b1aee28 [formerly e15216086af12e868ba47264d7f3042b6b1aee28 [formerly 374041fceb9f851959a35da4d525a6930aa4837a]]] [formerly e15216086af12e868ba47264d7f3042b6b1aee28 [formerly e15216086af12e868ba47264d7f3042b6b1aee28 [formerly 374041fceb9f851959a35da4d525a6930aa4837a]] [formerly d523d79396f367bd6c2b634a0602e45df0a595f9 [formerly d523d79396f367bd6c2b634a0602e45df0a595f9 [formerly e7f4b424ecf5519ded2352b3d6266a7da07a5b07]]]] -Former-commit-id: d523d79396f367bd6c2b634a0602e45df0a595f9 -Former-commit-id: 4dd4c4a0b4238a97d93d3df36268108de9c7fb2a -Former-commit-id: 98e977ddd59b5270ebb44b56703ad178fd7c970d [formerly 78385cf44365648d5c62ec1f9fcad81e37ba14c7] -Former-commit-id: 606636e4084098804c9354039e053f12418f9057 ([`c060a99`](https://github.com/bhklab/med-imagetools/commit/c060a998a511441a4ce579671e91576da616b9cc)) - -* 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)) - -* 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)) - -* 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)) - -* uncommented one line pytest - - -Former-commit-id: 7aa572b0b68fa17a57d73a7b5f677af269e19154 [formerly 1c37daba97d23ab4b74681c93ac5149f8b50c67a [formerly 3f878494e3be177a2784ae665bf110f562422443]] [formerly 1c37daba97d23ab4b74681c93ac5149f8b50c67a [formerly 3f878494e3be177a2784ae665bf110f562422443] [formerly f3ba678d71b569a5d4b574c2d7874c93e488ba8b [formerly 2b9d6d4813e05e0cec0550a4dfee47bf18b1f5fe]]] -Former-commit-id: f3ba678d71b569a5d4b574c2d7874c93e488ba8b -Former-commit-id: 2046fb64b2d129db338c3d3f2a70e3640eea80ab -Former-commit-id: eb1822dbe215e6185b3ce426ac1a2e9741e9bb42 ([`d54944e`](https://github.com/bhklab/med-imagetools/commit/d54944eb426956db7417c9ac85172823302bc01c)) - -* uncommented one line pytest - - -Former-commit-id: 01fb59285920aaa2fd8c3f355feab86619938568 [formerly 1f34ff389cc9d8d889d76eb6a529ff13323a44ba [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c]] [formerly 1f34ff389cc9d8d889d76eb6a529ff13323a44ba [formerly 6da65ddd48d4d10f0e3ec8244581a598d886f75c] [formerly 797c47cbebf0ef9042ea1828f590f01a813c304f [formerly 3dc8cd388da3ab755d979987b36389dd88396801]]] -Former-commit-id: 797c47cbebf0ef9042ea1828f590f01a813c304f -Former-commit-id: 652bd34dc69873469e060381ef0d8995d93335b5 -Former-commit-id: f7cdcc56dcf9c64b0e7864d5c8bf438c462d215c ([`d7e7d66`](https://github.com/bhklab/med-imagetools/commit/d7e7d6644777da08873677bb343409b2bd611139)) - -* Merge branch 'add_capabilities' of https://github.com/bhklab/imgtools into add_capabilities - -merging sejin's addition - - -Former-commit-id: cb8975d133bc33645b641b13ce6367531dbaef78 [formerly 412841075771927200c633890319cb084bc2e7c9 [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)) - -* deleted data - - -Former-commit-id: 672f541966579d7230df9baca69b02fccdd3a89e [formerly 3d94d8618a834b40c45823ab43f3cca68d44b54e] [formerly 672f541966579d7230df9baca69b02fccdd3a89e [formerly 3d94d8618a834b40c45823ab43f3cca68d44b54e] [formerly 8c55bc4187dca3aee5548f17d2cb8887aa45b131 [formerly d3e6b6a8d0712dbb1aed49be5c2a00c7b919118f]]] -Former-commit-id: 8c55bc4187dca3aee5548f17d2cb8887aa45b131 -Former-commit-id: c568f42b9733ee40c94df2d5ddf5507016534cdb -Former-commit-id: 5967c699c5d7d3a17efc03e1318878391c8609d6 ([`23c543e`](https://github.com/bhklab/med-imagetools/commit/23c543ea5937cca07ba44ab5cd2788e1ec17c141)) - -* now checks for existing subject id - - -Former-commit-id: 61153678fe00f0dc2645cee7174fbb9315a119db [formerly c7576821455bf58e27c825282ea58c3265a328a2 [formerly 746bd72cc59ddac3d583655e47ab28dcd851aa45]] [formerly c7576821455bf58e27c825282ea58c3265a328a2 [formerly 746bd72cc59ddac3d583655e47ab28dcd851aa45] [formerly d65b305856ae37363c742f616a83ee1836ed3dd7 [formerly bf4de755d0618dd037c32b5365a05d939878067f]]] -Former-commit-id: d65b305856ae37363c742f616a83ee1836ed3dd7 -Former-commit-id: 8ce34513b50d29fbdf064ee7ffa008c805329d65 -Former-commit-id: 9a5b436d9259580aa15f25a4c9d8a8ede596c04b ([`a34d702`](https://github.com/bhklab/med-imagetools/commit/a34d7025b62543ab84337d1713c59f8d2c19311d)) - -* now the pipeline saves on exit - - -Former-commit-id: 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)) - -* 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)) - -* 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)) - 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-* Seg.nrrd quick fix - - - -Former-commit-id: d4b4710c9cfe238b56634e409c258ad4d8a2a86f ([`69f33a1`](https://github.com/bhklab/med-imagetools/commit/69f33a116af770dfa8065f4986f4199dfb0cef54)) - -* Create LICENSE (#20) - -* Create LICENSE - -* Update setup.py - -Former-commit-id: 7b9c3da298b4de438603e5f9be8c2a5028868e65 ([`9d21b5a`](https://github.com/bhklab/med-imagetools/commit/9d21b5a80315c1f90057ff9bde504e1cbe6709d6)) - -* Update README.md - -Former-commit-id: 069524d56f710429af0abac363b08116b7b7aee5 ([`b605075`](https://github.com/bhklab/med-imagetools/commit/b605075aefb0d37ab407f4b60346cb67b79f6067)) - -* Update README.md (#19) - - - -Former-commit-id: 56ba095200366aac321c11e3a10d089619ec0a4c ([`cd353e4`](https://github.com/bhklab/med-imagetools/commit/cd353e4838e7bf8ea02254b22a2127d162eeb7aa)) - -* Update README.md - -Former-commit-id: 65600d05f79daab6e22bcda9ec77cdfe7ed54f4a ([`f049331`](https://github.com/bhklab/med-imagetools/commit/f04933100dbeb695db6b82e4eabd8c3cdb51ef1c)) - -* 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: 0612c403c124ce50938cca73ca413cb2122d935b ([`5af436a`](https://github.com/bhklab/med-imagetools/commit/5af436aea5b28cc810c818a13ea7843771d62e2f)) - -* Update README.md - -Former-commit-id: 330a0dcf3692f0075397918381848699b7ad69c8 ([`bf67247`](https://github.com/bhklab/med-imagetools/commit/bf6724739d5a83bbde0174ec9126f7775518eed4)) - -* Update main.yml - -Former-commit-id: ed6902d1bc4f0fe6d7bf5aaabf9efbe0c81fe352 ([`809014e`](https://github.com/bhklab/med-imagetools/commit/809014e9b1e17e5df8958495bd138d8b38dc7f40)) - -* Update main.yml - -Former-commit-id: 6511aea8239973d77f30a11cdd959f8ba55250df ([`a3aa08b`](https://github.com/bhklab/med-imagetools/commit/a3aa08b73746fab4964182216cd8139e4a116e65)) - -* 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 -Former-commit-id: bafe9e56aadbc5e54430757de3ac50374a6433dc ([`777f935`](https://github.com/bhklab/med-imagetools/commit/777f935bbd4a40aeb0fadb1db704dc24d0b4c391)) - -* 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 -Former-commit-id: bd8625cd37b114b7b26f981b8b8af5159dec9b5b ([`7833463`](https://github.com/bhklab/med-imagetools/commit/78334633d640833b0d69adefce0411c9bab5fdc1)) - -* Create main.yml (#15) - - - -Former-commit-id: 38035817f09e7c9a174014cb03753ddb8e96f94b ([`0a8e458`](https://github.com/bhklab/med-imagetools/commit/0a8e4583642952b183ce16f409fb5cba16b80719)) - -* Ready for - -Former-commit-id: 5c3ce559fa5ccbab7518c28a68c3ae8a75d9c33d ([`42c2f7b`](https://github.com/bhklab/med-imagetools/commit/42c2f7b846d42ec6ad02c03ca4105c5abd996c00)) - -* 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 -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)) - -* 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)) - -* 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 -Former-commit-id: 8ff5550b971938a3a7ad1f50c68ff606b3b54236 ([`ca98e79`](https://github.com/bhklab/med-imagetools/commit/ca98e7908705922963d88c5c68c99e931870a738)) - -* 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)) - -* added crawl.py - - -Former-commit-id: 3d3bf231400a8f8ae5eb2f0b450b0adf511d2911 ([`06f4bf5`](https://github.com/bhklab/med-imagetools/commit/06f4bf50888ca4342cab6fb66cc71f8fc3ce5bf5)) - -* 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)) - -* 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)) - -* major refactoring - - -Former-commit-id: 525f5bc85313f8584910407d48b071c029a08542 ([`261229f`](https://github.com/bhklab/med-imagetools/commit/261229f7ef6c58afe347a817000579f54d2bc545)) - -* 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 - - -Former-commit-id: 39b298376295d79beaa0fc003ed3c2c5bd79132c ([`15f958e`](https://github.com/bhklab/med-imagetools/commit/15f958e8cd70e5731d08270f62655899e6a59532)) - -* Introduced changes in DataGraph. Made the pipeline fully general. Made wrapper classes - - -Former-commit-id: bb446096a2315e8c52b2c0d74facebe8b967f7ee ([`8bd3804`](https://github.com/bhklab/med-imagetools/commit/8bd3804d67fc31b6b3fb50f35f443cdd32b1f100)) - -* 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)) - -* 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)) - -* Head-Neck-PET-CT pipeline + `read_dicom_auto` - - -Former-commit-id: fa6408c11a2b9b6bd80279504ba4c79975ad3582 ([`6e6be59`](https://github.com/bhklab/med-imagetools/commit/6e6be592285e808d11798294396d0f20db562060)) - -* 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)) - -* Fix type error when passing Numpy array to rotate - - -Former-commit-id: 53223da1c607294a9bc42d94a09a1c35376547fa ([`d043593`](https://github.com/bhklab/med-imagetools/commit/d0435930a8ba39ab821ce48a30304a2318168c0f)) - -* [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 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)) - -* 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)) - -* 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)) - -* 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)) - -* [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)) - -* updated readme with development mode installation instructions ([`2fe5e95`](https://github.com/bhklab/med-imagetools/commit/2fe5e956147556de0d6e4ffb369d211efd30d3c6)) - -* 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)) - -* Update README.md ([`1dc8d33`](https://github.com/bhklab/med-imagetools/commit/1dc8d33cde8048e57318ff77a11030ba61e11796)) - -* 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)) - -* 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)) diff --git a/setup.py b/setup.py index 2ecde22..8b552c2 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ from setuptools import setup, find_packages -__version__ = "1.5.8" +__version__ = "1.6.0-rc.1" with open("README.md", "r") as fh: long_description = fh.read()