diff --git a/CHANGELOG.md b/CHANGELOG.md index d1e7d3f..1bff062 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,14 @@ # CHANGELOG +## v1.17.0 (2024-11-22) + +### Features + +- Replace get_logger with imgtools inherited logging instance across modules + ([`01bd13f`](https://github.com/bhklab/readii/commit/01bd13f3321463d627f50254948cc85fd42235a2)) + + ## v1.16.0 (2024-11-13) @@ -8,16 +16,20 @@ ### Bug Fixes -* fix: add readii cli entry point to pyproject (#58) ([`1710b72`](https://github.com/bhklab/readii/commit/1710b7294b7e36273a7cc239b97593c676638463)) +- Add readii cli entry point to pyproject ([#58](https://github.com/bhklab/readii/pull/58), + [`1710b72`](https://github.com/bhklab/readii/commit/1710b7294b7e36273a7cc239b97593c676638463)) ## v1.14.0 (2024-11-01) ### Features -* feat: remove dicom-parser, update mit, deprecate padSeg (#51) +- Remove dicom-parser, update mit, deprecate padSeg + ([#51](https://github.com/bhklab/readii/pull/51), + [`a6658e7`](https://github.com/bhklab/readii/commit/a6658e7fa137b94329ba0dc303d25eab4be4c2f2)) -* fix: Update med-imagetools dependency and handle deprecated padSegToMatchCT function in feature_extraction.py with error logging +* fix: Update med-imagetools dependency and handle deprecated padSegToMatchCT function in + feature_extraction.py with error logging * chore: Update .gitignore to exclude .old, data, and trash directories for working dir @@ -31,1099 +43,1049 @@ Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.git --------- -Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> ([`a6658e7`](https://github.com/bhklab/readii/commit/a6658e7fa137b94329ba0dc303d25eab4be4c2f2)) +Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> ## v1.13.2 (2024-10-22) ### Bug Fixes -* fix: Remove hatch config and streamline build settings in pyproject.toml for better package management and deployment ([`0cf184c`](https://github.com/bhklab/readii/commit/0cf184ce2eca672918b669559c1b47bb53913e55)) +- Remove hatch config and streamline build settings in pyproject.toml for better package management + and deployment + ([`0cf184c`](https://github.com/bhklab/readii/commit/0cf184ce2eca672918b669559c1b47bb53913e55)) ## v1.13.1 (2024-10-22) ### Bug Fixes -* fix: Update CI/CD workflow for PyPI publishing; enhance publish step, remove TestPyPI, and configure pixi.lock sha256 ([`743ea52`](https://github.com/bhklab/readii/commit/743ea526a09bf442af79903a84b06c679ec76215)) +- Update CI/CD workflow for PyPI publishing; enhance publish step, remove TestPyPI, and configure + pixi.lock sha256 + ([`743ea52`](https://github.com/bhklab/readii/commit/743ea526a09bf442af79903a84b06c679ec76215)) ## v1.13.0 (2024-10-22) ### Bug Fixes -* fix: update CI/CD workflow to trigger only on pushes to main branch ([`2cc686f`](https://github.com/bhklab/readii/commit/2cc686f88d5270a21b97e4e85ea524222cdf77f8)) +- Update CI/CD workflow to trigger only on pushes to main branch + ([`2cc686f`](https://github.com/bhklab/readii/commit/2cc686f88d5270a21b97e4e85ea524222cdf77f8)) -* fix: correct version location in pyproject.toml configuration ([`bdb49ea`](https://github.com/bhklab/readii/commit/bdb49ea83ac6676248cb864e3ab45e95629e9aad)) +- Correct version location in pyproject.toml configuration + ([`bdb49ea`](https://github.com/bhklab/readii/commit/bdb49ea83ac6676248cb864e3ab45e95629e9aad)) -* fix: improve modality handling in loadSegmentation by reinforcing RTSTRUCT validation and simplifying modality checks ([`5d1fef6`](https://github.com/bhklab/readii/commit/5d1fef65288f57e39c40ecb35ac2d81a5d07d31a)) +- Improve modality handling in loadSegmentation by reinforcing RTSTRUCT validation and simplifying + modality checks + ([`5d1fef6`](https://github.com/bhklab/readii/commit/5d1fef65288f57e39c40ecb35ac2d81a5d07d31a)) -* fix: update ruff configuration and linting rules, switch docstring style to numpy, and enhance loader type annotations ([`0142860`](https://github.com/bhklab/readii/commit/0142860bf572b5e3ff7c3f0132deeabdcd611482)) +- Update ruff configuration and linting rules, switch docstring style to numpy, and enhance loader + type annotations + ([`0142860`](https://github.com/bhklab/readii/commit/0142860bf572b5e3ff7c3f0132deeabdcd611482)) ### Chores -* chore: refine CI-CD workflow for Publish-To-PyPi and update pixi.lock SHA for dependency consistency ([`3c904e1`](https://github.com/bhklab/readii/commit/3c904e17ada58031cd10ab37f28ef7ec28aac56f)) +- Refine CI-CD workflow for Publish-To-PyPi and update pixi.lock SHA for dependency consistency + ([`3c904e1`](https://github.com/bhklab/readii/commit/3c904e17ada58031cd10ab37f28ef7ec28aac56f)) -* chore: add Ruff linter to CI-CD workflow and update project config for linting and formatting tasks ([`ecebe9a`](https://github.com/bhklab/readii/commit/ecebe9a6f0ff3333102fb08a7bb4c63f9d2f6175)) +- Add Ruff linter to CI-CD workflow and update project config for linting and formatting tasks + ([`ecebe9a`](https://github.com/bhklab/readii/commit/ecebe9a6f0ff3333102fb08a7bb4c63f9d2f6175)) -* chore: adjust CI-CD workflow to trigger on any branch for pull requests and comment out previous push configuration ([`3c77975`](https://github.com/bhklab/readii/commit/3c779750af8b68940236d725264acb4df2e5313c)) +- Adjust CI-CD workflow to trigger on any branch for pull requests and comment out previous push + configuration + ([`3c77975`](https://github.com/bhklab/readii/commit/3c779750af8b68940236d725264acb4df2e5313c)) -* chore: add Codecov badge to README for improved visibility of test coverage ([`9472ab6`](https://github.com/bhklab/readii/commit/9472ab686f61e990ec85f1023ae1c71ee0a781f2)) +- Add Codecov badge to README for improved visibility of test coverage + ([`9472ab6`](https://github.com/bhklab/readii/commit/9472ab686f61e990ec85f1023ae1c71ee0a781f2)) -* chore: add Codecov step in CI/CD workflow to track coverage and report using coverage.xml ([`fcbe561`](https://github.com/bhklab/readii/commit/fcbe561ce0c6adec16d06eba6f01b1558c7b9eac)) +- Add Codecov step in CI/CD workflow to track coverage and report using coverage.xml + ([`fcbe561`](https://github.com/bhklab/readii/commit/fcbe561ce0c6adec16d06eba6f01b1558c7b9eac)) ### Continuous Integration -* ci: clean up .github/workflows/ci-cd.yml by removing unnecessary whitespace and ensuring proper formatting at end of file ([`a6298ab`](https://github.com/bhklab/readii/commit/a6298ab30d7fcb1ead133ef3fbbe31f143a5d36f)) +- Clean up .github/workflows/ci-cd.yml by removing unnecessary whitespace and ensuring proper + formatting at end of file + ([`a6298ab`](https://github.com/bhklab/readii/commit/a6298ab30d7fcb1ead133ef3fbbe31f143a5d36f)) -* ci: update CI-CD workflow to include Ruff as a dependency for the Unit-Tests job before deployment to PyPI ([`5d6a7f3`](https://github.com/bhklab/readii/commit/5d6a7f3a055120a67eb0ac95dd44c59e7e08e1f4)) +- Update CI-CD workflow to include Ruff as a dependency for the Unit-Tests job before deployment to + PyPI + ([`5d6a7f3`](https://github.com/bhklab/readii/commit/5d6a7f3a055120a67eb0ac95dd44c59e7e08e1f4)) ### Documentation -* docs: update README with installation + badges ([`7bdf5d3`](https://github.com/bhklab/readii/commit/7bdf5d3a27fad5fa70b92f9fbd63053be7158e29)) +- Update README with installation + badges + ([`7bdf5d3`](https://github.com/bhklab/readii/commit/7bdf5d3a27fad5fa70b92f9fbd63053be7158e29)) ### Features -* feat: enhance segmentation loading by adding validation for unsupported modalities in loadSegmentation function ([`9ee6931`](https://github.com/bhklab/readii/commit/9ee69315703135ae2951196cb17281a5c2567732)) +- Enhance segmentation loading by adding validation for unsupported modalities in loadSegmentation + function + ([`9ee6931`](https://github.com/bhklab/readii/commit/9ee69315703135ae2951196cb17281a5c2567732)) -* feat: rename job to Publish-To-Test-PyPi and add Test-TestPypi-Installation steps for verifying package deployment ([`336185f`](https://github.com/bhklab/readii/commit/336185fb4486de95abe99ad099dd2f714fb42559)) +- Rename job to Publish-To-Test-PyPi and add Test-TestPypi-Installation steps for verifying package + deployment + ([`336185f`](https://github.com/bhklab/readii/commit/336185fb4486de95abe99ad099dd2f714fb42559)) -* feat: update CI-CD workflow to include publishing to TestPyPI with new environment variables for authentication ([`d645af1`](https://github.com/bhklab/readii/commit/d645af141f1d47fac296c0952c86b71bd0c85a9c)) +- Update CI-CD workflow to include publishing to TestPyPI with new environment variables for + authentication + ([`d645af1`](https://github.com/bhklab/readii/commit/d645af141f1d47fac296c0952c86b71bd0c85a9c)) -* feat: expand pyproject.toml with publish-test command for deploying to test PyPI and add description for build task ([`f309346`](https://github.com/bhklab/readii/commit/f3093465bdcd079ec403324b9a5f3eb29b8aa967)) - -### Unknown - -* Merge pull request #42 from bhklab/jjjermiah/refactor/main - -feat: Enhance CI/CD Workflow with TestPyPI Publishing, Linting Improvements, and minor docs update ([`376b414`](https://github.com/bhklab/readii/commit/376b4140feb49c1470f7f3b639824e08f7c8e046)) - -* doc: enhance docstrings in loaders.py, providing clearer descriptions and improving module documentation for DICOM and RTSTRUCT functions ([`249238c`](https://github.com/bhklab/readii/commit/249238ca60ef8e7ebaff65d85c5eaf755e7d5616)) +- Expand pyproject.toml with publish-test command for deploying to test PyPI and add description for + build task + ([`f309346`](https://github.com/bhklab/readii/commit/f3093465bdcd079ec403324b9a5f3eb29b8aa967)) ## v1.12.0 (2024-10-22) ### Chores -* chore: update CI/CD workflow to use actions/checkout@v3, fix semantic-release task, and update pixi.lock ([`790ae04`](https://github.com/bhklab/readii/commit/790ae04da36e50fd6f7a9087f6f7b7e99c57326f)) +- Update CI/CD workflow to use actions/checkout@v3, fix semantic-release task, and update pixi.lock + ([`790ae04`](https://github.com/bhklab/readii/commit/790ae04da36e50fd6f7a9087f6f7b7e99c57326f)) -* chore: refactor CI/CD workflow with enhanced job structure and add basic config files for coverage and linting ([`994fd75`](https://github.com/bhklab/readii/commit/994fd754e489c95ef044714a9b966aec645ead58)) +- Refactor CI/CD workflow with enhanced job structure and add basic config files for coverage and + linting + ([`994fd75`](https://github.com/bhklab/readii/commit/994fd754e489c95ef044714a9b966aec645ead58)) ### Features -* feat: add semantic-release workflow for automated versioning and update readii version to 1.11.0 with new author email ([`92bc4d4`](https://github.com/bhklab/readii/commit/92bc4d4d3d6bc56bf7a92b88d8b876182fdc0197)) - -* feat: update to use pixi and pyradiomics-bhklab ([`6a67be4`](https://github.com/bhklab/readii/commit/6a67be4ace53c10d4bb98082978ed4bd7413681f)) +- Add semantic-release workflow for automated versioning and update readii version to 1.11.0 with + new author email + ([`92bc4d4`](https://github.com/bhklab/readii/commit/92bc4d4d3d6bc56bf7a92b88d8b876182fdc0197)) -### Unknown - -* Merge pull request #40 from bhklab/jjjermiah/add-pixi - -feat: Use Pixi, pyradiomics fork ([`fd582a5`](https://github.com/bhklab/readii/commit/fd582a5db16b3474df798f948c7f533bbb23dc86)) +- Update to use pixi and pyradiomics-bhklab + ([`6a67be4`](https://github.com/bhklab/readii/commit/6a67be4ace53c10d4bb98082978ed4bd7413681f)) ## v1.11.0 (2024-09-25) ### Bug Fixes -* fix(feature_extraction): actually raise an exception for negative control creation ([`e1a9888`](https://github.com/bhklab/readii/commit/e1a98884308e16055db04846932ce133c34779e0)) +- **feature_extraction**: Actually raise an exception for negative control creation + ([`e1a9888`](https://github.com/bhklab/readii/commit/e1a98884308e16055db04846932ce133c34779e0)) ### Features -* feat(feature_extraction): add logging for error raised when cropping CT and segmentation ([`d9d8069`](https://github.com/bhklab/readii/commit/d9d80695a7e28038389aa0caace5b95295aab479)) - -### Unknown - -* Merge pull request #39 from bhklab/negative_control_error_handling - -Negative control error handling ([`2bac7db`](https://github.com/bhklab/readii/commit/2bac7db3d88c24af8b24233b59ec4a62ee5dacaa)) - -* Merge branch 'main' of github.com:bhklab/yarea into main ([`556178e`](https://github.com/bhklab/readii/commit/556178ed18e9507f25dfd896cb68567298918323)) +- **feature_extraction**: Add logging for error raised when cropping CT and segmentation + ([`d9d8069`](https://github.com/bhklab/readii/commit/d9d80695a7e28038389aa0caace5b95295aab479)) ## v1.10.0 (2024-09-25) ### Bug Fixes -* fix(feature_extraction): actually raise the error for the negative control creation Exception ([`f17fbbc`](https://github.com/bhklab/readii/commit/f17fbbc6074ca68e3378ff4d9ac5865a75b04822)) +- **feature_extraction**: Actually raise the error for the negative control creation Exception + ([`f17fbbc`](https://github.com/bhklab/readii/commit/f17fbbc6074ca68e3378ff4d9ac5865a75b04822)) ### Features -* feat(feature_extraction): add try catch around cropping image step ([`fedf881`](https://github.com/bhklab/readii/commit/fedf88197582e59644da5e9d2974d1e0828bb672)) - -### Unknown - -* Revert "1.9.0" ([`c4d265c`](https://github.com/bhklab/readii/commit/c4d265c02e9b49fd806d3f7c4e05ef665db9453e)) - -* Revert "1.9.0" - -This reverts commit 50794f4f143cd980421ee3099ea11fa7900976af. ([`cd37991`](https://github.com/bhklab/readii/commit/cd3799167091f6960dd4e14b3cc77a081e9af905)) +- **feature_extraction**: Add try catch around cropping image step + ([`fedf881`](https://github.com/bhklab/readii/commit/fedf88197582e59644da5e9d2974d1e0828bb672)) ## v1.9.0 (2024-09-25) ### Documentation -* docs: clean up angular commit formatting in README ([`1f16ad1`](https://github.com/bhklab/readii/commit/1f16ad11c9de5771bc32f3eac399bc30698178ba)) +- Clean up angular commit formatting in README + ([`1f16ad1`](https://github.com/bhklab/readii/commit/1f16ad11c9de5771bc32f3eac399bc30698178ba)) -* docs: add angular commit syntax to README ([`c9f76df`](https://github.com/bhklab/readii/commit/c9f76df9b9d10fc7e37cf4738c9f897816fcef2d)) +- Add angular commit syntax to README + ([`c9f76df`](https://github.com/bhklab/readii/commit/c9f76df9b9d10fc7e37cf4738c9f897816fcef2d)) ### Features -* feat(feature_extraction): add catch and logging around negative control creation ([`a90efac`](https://github.com/bhklab/readii/commit/a90efac732c7fe474cf15885c59ba32c6a8f9b3c)) - -### Unknown - -* Merge pull request #38 from bhklab/add_logging - -Negative control error catching and angular commit syntax ([`8646cf0`](https://github.com/bhklab/readii/commit/8646cf03f77a50ecd4f0ae66997379093f6719f9)) - -* Merge pull request #37 from bhklab/keep_running_flag - -Created keep_running flag ([`0c95c80`](https://github.com/bhklab/readii/commit/0c95c8025567c47e2b98bdfb98d069e645edb765)) - -* Added logging ([`f666b4d`](https://github.com/bhklab/readii/commit/f666b4d6be906122636dde727016c7583203f3d9)) - -* Created keep_running flag, which keeps pipeline running even if a single patient fails. ([`c1fe170`](https://github.com/bhklab/readii/commit/c1fe17097809977fc16b495eb1ec3016a262c8a1)) +- **feature_extraction**: Add catch and logging around negative control creation + ([`a90efac`](https://github.com/bhklab/readii/commit/a90efac732c7fe474cf15885c59ba32c6a8f9b3c)) ## v1.8.0 (2024-09-17) ### Features -* feat: make output directory and parents as needed before saving radiomic output ([`bf7600c`](https://github.com/bhklab/readii/commit/bf7600ce681e08eca55fcf4ef6ece028a99ae430)) +- Make output directory and parents as needed before saving radiomic output + ([`bf7600c`](https://github.com/bhklab/readii/commit/bf7600ce681e08eca55fcf4ef6ece028a99ae430)) ### Refactoring -* refactor: change output file from feature extraction without negative control to be radiomicfeatures_original_datasetname.csv ([`7663ce8`](https://github.com/bhklab/readii/commit/7663ce8de4266a29e857d86e6fad0d32cf4dc87a)) +- Change output file from feature extraction without negative control to be + radiomicfeatures_original_datasetname.csv + ([`7663ce8`](https://github.com/bhklab/readii/commit/7663ce8de4266a29e857d86e6fad0d32cf4dc87a)) ### Testing -* test(test_feature_extraction): updated for new original image feature extraction output ([`2e53bc8`](https://github.com/bhklab/readii/commit/2e53bc8916c53795d96db00057fa108f9f9422db)) - -### Unknown - -* Merge pull request #36 from bhklab/change-original-image-output-name-convention - -Change original image output name convention ([`d6af655`](https://github.com/bhklab/readii/commit/d6af65553f97b8f7b7939a1660d75c6404ce313f)) +- **test_feature_extraction**: Updated for new original image feature extraction output + ([`2e53bc8`](https://github.com/bhklab/readii/commit/2e53bc8916c53795d96db00057fa108f9f9422db)) ## v1.7.7 (2024-09-12) ### Bug Fixes -* fix: Remove coloredlogs dependency and logging configuration from the project ([`ba8208f`](https://github.com/bhklab/readii/commit/ba8208fc1925533cda8dfccc165c887fc58bc67d)) +- Remove coloredlogs dependency and logging configuration from the project + ([`ba8208f`](https://github.com/bhklab/readii/commit/ba8208fc1925533cda8dfccc165c887fc58bc67d)) ### Chores -* chore: update lockfile ([`9c5fa18`](https://github.com/bhklab/readii/commit/9c5fa18fd2b4c53d24a66f12d8987b2c4d7a3f28)) - -### Unknown - -* Merge pull request #35 from bhklab/remove_colored_logs - -fix: Remove coloredlogs dependency and logging configuration from the project ([`7616d88`](https://github.com/bhklab/readii/commit/7616d882119e8d608846ab80e875d58f16973aba)) +- Update lockfile + ([`9c5fa18`](https://github.com/bhklab/readii/commit/9c5fa18fd2b4c53d24a66f12d8987b2c4d7a3f28)) ## v1.7.6 (2024-08-27) ### Bug Fixes -* fix: Update ci-cd.yml ([`13cc197`](https://github.com/bhklab/readii/commit/13cc197546d81be42c3ba4c72c476ba2ad1895a7)) +- Update ci-cd.yml + ([`13cc197`](https://github.com/bhklab/readii/commit/13cc197546d81be42c3ba4c72c476ba2ad1895a7)) ## v1.7.5 (2024-08-20) -### Unknown - -* Merge pull request #34 from bhklab/add_logging - -fix(feature_extraction): add try except around actual feature extract… ([`3e6f211`](https://github.com/bhklab/readii/commit/3e6f211055fd8bcf9a80f8b8dffeb05d60ce88bf)) - -* Merge branch 'main' into add_logging ([`e36ac1b`](https://github.com/bhklab/readii/commit/e36ac1b610f45822652ccd5d517dfa44d800bc44)) - ## v1.7.4 (2024-08-19) ### Bug Fixes -* fix: use Optional for pyradiomicsParamFilePath in feature extraction functions for older python versions ([`a9aa977`](https://github.com/bhklab/readii/commit/a9aa977dcb78e24bdbbf2cc7fa4c92dbd9c755e7)) +- Use Optional for pyradiomicsParamFilePath in feature extraction functions for older python + versions + ([`a9aa977`](https://github.com/bhklab/readii/commit/a9aa977dcb78e24bdbbf2cc7fa4c92dbd9c755e7)) -* fix: filter out None values and ensure feature results are properly formatted as lists in radiomicFeatureExtraction function ([`53c68ff`](https://github.com/bhklab/readii/commit/53c68ffc7adc02176e12f78dc1c8a0fd4e2a6283)) +- Filter out None values and ensure feature results are properly formatted as lists in + radiomicFeatureExtraction function + ([`53c68ff`](https://github.com/bhklab/readii/commit/53c68ffc7adc02176e12f78dc1c8a0fd4e2a6283)) ### Refactoring -* refactor: simplify negative control region handling by removing unnecessary elif and raising ValueError in negative_controls.py ([`17ad253`](https://github.com/bhklab/readii/commit/17ad2532f9c5dfdb84b2b91a2b071ff1133d543c)) - -* refactor: update logging format for better clarity in log messages, put the function name at the end of message in brackets to make it easier to read ([`bb8aa14`](https://github.com/bhklab/readii/commit/bb8aa14a5c525030663dbace9fe86e8db39c2b9c)) - -* refactor: address some type annotation errors, and add logging ([`79f342e`](https://github.com/bhklab/readii/commit/79f342ef92d9943a08c495946c48d1aa9a6b01ba)) +- Simplify negative control region handling by removing unnecessary elif and raising ValueError in + negative_controls.py + ([`17ad253`](https://github.com/bhklab/readii/commit/17ad2532f9c5dfdb84b2b91a2b071ff1133d543c)) -### Unknown +- Update logging format for better clarity in log messages, put the function name at the end of + message in brackets to make it easier to read + ([`bb8aa14`](https://github.com/bhklab/readii/commit/bb8aa14a5c525030663dbace9fe86e8db39c2b9c)) -* Merge pull request #33 from bhklab/feature_extraction_typeannt - -fix: type annotations & refactor typing issues ([`b1ce1ed`](https://github.com/bhklab/readii/commit/b1ce1ed6c618d506305fc5bdff778fec80a3646e)) +- Address some type annotation errors, and add logging + ([`79f342e`](https://github.com/bhklab/readii/commit/79f342ef92d9943a08c495946c48d1aa9a6b01ba)) ## v1.7.3 (2024-08-19) ### Bug Fixes -* fix: update CI/CD workflow to specify supported platforms for Docker build, removing unsupported macOS entries ([`d19bf9b`](https://github.com/bhklab/readii/commit/d19bf9b79840b0921bf6d60be212b2947f7dbb47)) +- Update CI/CD workflow to specify supported platforms for Docker build, removing unsupported macOS + entries + ([`d19bf9b`](https://github.com/bhklab/readii/commit/d19bf9b79840b0921bf6d60be212b2947f7dbb47)) ## v1.7.2 (2024-08-19) ### Bug Fixes -* fix: update base image in Dockerfile to python:3.11-slim to fix docker image errors ([`0e2cd3a`](https://github.com/bhklab/readii/commit/0e2cd3a2e7ef29b445ae9d81520739d44672f938)) +- Update base image in Dockerfile to python:3.11-slim to fix docker image errors + ([`0e2cd3a`](https://github.com/bhklab/readii/commit/0e2cd3a2e7ef29b445ae9d81520739d44672f938)) ## v1.7.1 (2024-08-19) ### Bug Fixes -* fix: using correct pyradiomics in pyproject ([`980cdda`](https://github.com/bhklab/readii/commit/980cdda937ee07333d14d80454e3818a4757b556)) +- Using correct pyradiomics in pyproject + ([`980cdda`](https://github.com/bhklab/readii/commit/980cdda937ee07333d14d80454e3818a4757b556)) ## v1.7.0 (2024-08-19) ### Bug Fixes -* fix(feature_extraction): add try except around actual feature extraction call, add logging to end of feature extraction and file saving ([`ba119ad`](https://github.com/bhklab/readii/commit/ba119adde76c32b9bf04d2199b0c09bbcb07349e)) +- **feature_extraction**: Add try except around actual feature extraction call, add logging to end + of feature extraction and file saving + ([`ba119ad`](https://github.com/bhklab/readii/commit/ba119adde76c32b9bf04d2199b0c09bbcb07349e)) -* fix(logging): enhance metadata file logging output with update flag details and adjust logging level to INFO ([`3705110`](https://github.com/bhklab/readii/commit/370511086ab57bb7fa92fcd341b01d9aacdcc855)) +- **logging**: Enhance metadata file logging output with update flag details and adjust logging + level to INFO + ([`3705110`](https://github.com/bhklab/readii/commit/370511086ab57bb7fa92fcd341b01d9aacdcc855)) ### Chores -* chore(deps): update dependencies ([`0296dbd`](https://github.com/bhklab/readii/commit/0296dbdc687f7e06caed3ef2e2edff16a7cae004)) +- **deps**: Update dependencies + ([`0296dbd`](https://github.com/bhklab/readii/commit/0296dbdc687f7e06caed3ef2e2edff16a7cae004)) ### Features -* feat(logging): integrate logging for feature extraction and pipeline; replace print statements with logger calls ([`ed6aed4`](https://github.com/bhklab/readii/commit/ed6aed499fd8d50ca34218e8cfd0b67b4d4b822a)) +- **logging**: Integrate logging for feature extraction and pipeline; replace print statements with + logger calls + ([`ed6aed4`](https://github.com/bhklab/readii/commit/ed6aed499fd8d50ca34218e8cfd0b67b4d4b822a)) ### Refactoring -* refactor(metadata): add createImageMetadataFile function with logging for segmentation; improve error handling and directory creation ([`7e3d07f`](https://github.com/bhklab/readii/commit/7e3d07f86cd9464e6e146e3bee7968ba5f1d3ba7)) - -### Unknown - -* Merge pull request #31 from bhklab/add_logging - -feat: Add_logging ([`1255e97`](https://github.com/bhklab/readii/commit/1255e97a97b06a231ab70e69f8f6d09dfc940b03)) +- **metadata**: Add createImageMetadataFile function with logging for segmentation; improve error + handling and directory creation + ([`7e3d07f`](https://github.com/bhklab/readii/commit/7e3d07f86cd9464e6e146e3bee7968ba5f1d3ba7)) ## v1.6.4 (2024-08-14) ### Bug Fixes -* fix(feature_extraction): missed variable name change for non-cropped negative control ([`8d0d7bd`](https://github.com/bhklab/readii/commit/8d0d7bd91bb60f669086ef2ef85bf5e210e4ce7d)) +- **feature_extraction**: Missed variable name change for non-cropped negative control + ([`8d0d7bd`](https://github.com/bhklab/readii/commit/8d0d7bd91bb60f669086ef2ef85bf5e210e4ce7d)) ### Refactoring -* refactor(feature_extraction): move cropping to after negative control creation ([`f6e840b`](https://github.com/bhklab/readii/commit/f6e840b5f4b813334a5ec7fb050ac2cb82472564)) - -### Unknown - -* Merge pull request #30 from bhklab/development_katy - -fix(feature_extraction): missed variable name change for non-cropped … ([`ffe6e47`](https://github.com/bhklab/readii/commit/ffe6e4751ed18fb9175db45ea2647d941895a6c4)) - -* Merge pull request #29 from bhklab/development_katy - -refactor(feature_extraction): move cropping to after negative control… ([`f8db5b0`](https://github.com/bhklab/readii/commit/f8db5b06c47c68d6c1759541b59856b0f5354a3d)) +- **feature_extraction**: Move cropping to after negative control creation + ([`f6e840b`](https://github.com/bhklab/readii/commit/f6e840b5f4b813334a5ec7fb050ac2cb82472564)) ## v1.6.3 (2024-08-08) ### Bug Fixes -* fix(feature_extraction): update negative control component splitting for non_roi options to properly separate the type and region in singleRadiomicFeatureExtraction ([`3bb250e`](https://github.com/bhklab/readii/commit/3bb250e138f7886461bd15613d1bac168c54f3b6)) - -### Unknown - -* Merge pull request #28 from bhklab/development_katy - -fix(feature_extraction): update negative control component splitting … ([`fc6d13d`](https://github.com/bhklab/readii/commit/fc6d13d4b14b6f299bb46f24585a58f86ce5d3ef)) +- **feature_extraction**: Update negative control component splitting for non_roi options to + properly separate the type and region in singleRadiomicFeatureExtraction + ([`3bb250e`](https://github.com/bhklab/readii/commit/3bb250e138f7886461bd15613d1bac168c54f3b6)) ## v1.6.2 (2024-08-07) ### Bug Fixes -* fix(feature_extraction): negative control component split wouldn't work for randomized_sampled_non_roi, so added specific fix for it for now until readii input is updated ([`241b202`](https://github.com/bhklab/readii/commit/241b2028f34fd66c0b349c4dbe6e574370a37ecd)) - -### Unknown - -* Merge pull request #27 from bhklab/development_katy - -fix(feature_extraction): negative control component split wouldn't wo… ([`55dac25`](https://github.com/bhklab/readii/commit/55dac2572bf2ff1e8373169d88c0105359693baf)) +- **feature_extraction**: Negative control component split wouldn't work for + randomized_sampled_non_roi, so added specific fix for it for now until readii input is updated + ([`241b202`](https://github.com/bhklab/readii/commit/241b2028f34fd66c0b349c4dbe6e574370a37ecd)) ## v1.6.1 (2024-08-06) ### Performance Improvements -* perf(negative_controls): improved efficiency for ROI and Non-ROI negative control generation ([`00f3ab2`](https://github.com/bhklab/readii/commit/00f3ab266b16b820a8d92bed52e444ded1feb566)) +- **negative_controls**: Improved efficiency for ROI and Non-ROI negative control generation + ([`00f3ab2`](https://github.com/bhklab/readii/commit/00f3ab266b16b820a8d92bed52e444ded1feb566)) ### Refactoring -* refactor(feature_extraction): update for new negative control functions, remove unnecessary imports, add print statement when starting feature extraction to differentiate from negative control creation ([`5669919`](https://github.com/bhklab/readii/commit/566991945fc4c8ff079149ff6c54759f84fa7920)) +- **feature_extraction**: Update for new negative control functions, remove unnecessary imports, add + print statement when starting feature extraction to differentiate from negative control creation + ([`5669919`](https://github.com/bhklab/readii/commit/566991945fc4c8ff079149ff6c54759f84fa7920)) ### Testing -* test(test_negative_controls): updated test functions to match new negative control generation functions ([`fa78177`](https://github.com/bhklab/readii/commit/fa781775c2de8a887464836a526fe770580446ad)) - -### Unknown - -* Merge pull request #26 from bhklab/development_katy - -Improved efficiency negative control functions ([`8d9bcb6`](https://github.com/bhklab/readii/commit/8d9bcb65813f9a158395f684c0236af05f8c2265)) - -* notebook(optimize_negative_controls): code to develop improved negative control functions ([`d5c396b`](https://github.com/bhklab/readii/commit/d5c396be1217de08df5991fa3c5e9d860059fb34)) - -* Coded up improved speed functions for ROI and Non-ROI negative control generation using matrix math ([`bc825cd`](https://github.com/bhklab/readii/commit/bc825cdee4b6970abd453ab2b761a2f52554e4e9)) +- **test_negative_controls**: Updated test functions to match new negative control generation + functions + ([`fa78177`](https://github.com/bhklab/readii/commit/fa781775c2de8a887464836a526fe770580446ad)) ## v1.6.0 (2024-07-31) ### Bug Fixes -* fix(metadata): drop _CT suffix from patient ID column in output of getCTWithSegmentation ([`5e31b73`](https://github.com/bhklab/readii/commit/5e31b739e74edab76d4a2d248098e68fed8c2f52)) +- **metadata**: Drop _CT suffix from patient ID column in output of getCTWithSegmentation + ([`5e31b73`](https://github.com/bhklab/readii/commit/5e31b739e74edab76d4a2d248098e68fed8c2f52)) ### Features -* feat(metadata.py): add saving out samples with segmentations to getCTWithSegmentation ([`b575f31`](https://github.com/bhklab/readii/commit/b575f3110f1b3be64e635cbe2252c668a6725382)) +- **metadata.py**: Add saving out samples with segmentations to getCTWithSegmentation + ([`b575f31`](https://github.com/bhklab/readii/commit/b575f3110f1b3be64e635cbe2252c668a6725382)) ### Refactoring -* refactor(pipeline.py): use new getCTWithSegmentation function, utilizes imgtools edges output ([`f1dd879`](https://github.com/bhklab/readii/commit/f1dd8792692dff0dbaa132a47f47bf39e0d53d6a)) +- **pipeline.py**: Use new getCTWithSegmentation function, utilizes imgtools edges output + ([`f1dd879`](https://github.com/bhklab/readii/commit/f1dd8792692dff0dbaa132a47f47bf39e0d53d6a)) -* refactor(metdata.py): in matchCTtoSegmentation change outputDir to outputFilePath ([`4219a1a`](https://github.com/bhklab/readii/commit/4219a1ac90673ce7fbfc71c907c6101da8928f97)) +- **metdata.py**: In matchCTtoSegmentation change outputDir to outputFilePath + ([`4219a1a`](https://github.com/bhklab/readii/commit/4219a1ac90673ce7fbfc71c907c6101da8928f97)) ### Testing -* test(test_metadata): fix outputFilePath argument for matchCTtoSegmentation, add output test for getCTWithSegmentation ([`a9fec18`](https://github.com/bhklab/readii/commit/a9fec1876d649e02c5097f80cf9f37d8d6d9eea0)) - -* test(test_metadata): added tests for getCTWithSegmentation ([`a7d3fc7`](https://github.com/bhklab/readii/commit/a7d3fc7d7181eab5d539eda46fda38a38d51e116)) - -### Unknown - -* Merge pull request #25 from bhklab/development_katy +- **test_metadata**: Fix outputFilePath argument for matchCTtoSegmentation, add output test for + getCTWithSegmentation + ([`a9fec18`](https://github.com/bhklab/readii/commit/a9fec1876d649e02c5097f80cf9f37d8d6d9eea0)) -New get CT with RTSTRUCTs function ([`5c31b26`](https://github.com/bhklab/readii/commit/5c31b26dbb7400b90620dbf2f79ad4f52eaa103b)) - -* getCTWithSegmentation works for RTSTRUCT ([`6c69b8a`](https://github.com/bhklab/readii/commit/6c69b8a6c5a9123af6b5695ee7baba4523ead50c)) - -* getCTWithSegmentation works for RTSTRUCT ([`bd8d0a0`](https://github.com/bhklab/readii/commit/bd8d0a074db517b84434bb523df956782adf45df)) +- **test_metadata**: Added tests for getCTWithSegmentation + ([`a7d3fc7`](https://github.com/bhklab/readii/commit/a7d3fc7d7181eab5d539eda46fda38a38d51e116)) ## v1.5.0 (2024-07-31) ### Code Style -* style(metadata): Update error message to say READII instead of YAREA ([`d6fc791`](https://github.com/bhklab/readii/commit/d6fc7917140bafb645fc07f8a77d582d73dd3410)) +- **metadata**: Update error message to say READII instead of YAREA + ([`d6fc791`](https://github.com/bhklab/readii/commit/d6fc7917140bafb645fc07f8a77d582d73dd3410)) ### Features -* feat(metadata.py): using imgtools edges crawl output to get matched CT to RTSTRUCT list ([`dce17fc`](https://github.com/bhklab/readii/commit/dce17fc4b353a7f3971f5eebaffd79ac5da5a522)) - -### Unknown - -* Merge pull request #24 from bhklab/development_katy - -New CT to RTSTRUCT matching method and start of testing new negative control generation method ([`c3533a0`](https://github.com/bhklab/readii/commit/c3533a0c21b02d32187fa375505fded3a6741ebb)) - -* notebooks: create general notebook for debugging ([`9df7b73`](https://github.com/bhklab/readii/commit/9df7b734a0ff6a871cccb593a486b91eb661af6b)) - -* notebooks: working on improving efficiency of negative control generation ([`bccb4f5`](https://github.com/bhklab/readii/commit/bccb4f5676df90a690e6846e5f04849e512b8884)) +- **metadata.py**: Using imgtools edges crawl output to get matched CT to RTSTRUCT list + ([`dce17fc`](https://github.com/bhklab/readii/commit/dce17fc4b353a7f3971f5eebaffd79ac5da5a522)) ## v1.4.4 (2024-05-30) ### Bug Fixes -* fix: update docker image reference ([`91b3c05`](https://github.com/bhklab/readii/commit/91b3c057507e316df375a5fab34428cc47622922)) +- Update docker image reference + ([`91b3c05`](https://github.com/bhklab/readii/commit/91b3c057507e316df375a5fab34428cc47622922)) ## v1.4.3 (2024-05-30) ### Bug Fixes -* fix: force build ([`45cab79`](https://github.com/bhklab/readii/commit/45cab79004e661b955157d7c4284351d532d50b4)) +- Force build + ([`45cab79`](https://github.com/bhklab/readii/commit/45cab79004e661b955157d7c4284351d532d50b4)) ### Chores -* chore: update dependencies and workflow for continuous deployment ([`d400520`](https://github.com/bhklab/readii/commit/d4005204a85adacceea20cf00ceb22f51f684df4)) +- Update dependencies and workflow for continuous deployment + ([`d400520`](https://github.com/bhklab/readii/commit/d4005204a85adacceea20cf00ceb22f51f684df4)) ## v1.4.2 (2024-05-30) ### Bug Fixes -* fix: tag version in dockerfile ([`1b06ed8`](https://github.com/bhklab/readii/commit/1b06ed8a4c196f1e794c34717c700fff75a93f48)) +- Tag version in dockerfile + ([`1b06ed8`](https://github.com/bhklab/readii/commit/1b06ed8a4c196f1e794c34717c700fff75a93f48)) ## v1.4.1 (2024-05-30) ### Bug Fixes -* fix: add auto build docker ([`e1a58cd`](https://github.com/bhklab/readii/commit/e1a58cd94c2a2a99b0d71f9a536451b734f4f718)) +- Add auto build docker + ([`e1a58cd`](https://github.com/bhklab/readii/commit/e1a58cd94c2a2a99b0d71f9a536451b734f4f718)) ## v1.4.0 (2024-05-29) ### Features -* feat(pipeline): added random seed command line argument for negative control creation ([`405fa74`](https://github.com/bhklab/readii/commit/405fa74f80c257c8e616d838dcc64b3865ac5bc9)) - -* feat(feature_extraction): added argument random seed for negative control creation ([`053d542`](https://github.com/bhklab/readii/commit/053d54266781863a2c5f285e3aec77a831aa1d28)) - -### Unknown - -* Merge pull request #23 from bhklab/development_katy +- **pipeline**: Added random seed command line argument for negative control creation + ([`405fa74`](https://github.com/bhklab/readii/commit/405fa74f80c257c8e616d838dcc64b3865ac5bc9)) -Adding negative control to main pipeline and feature extraction functions ([`0afc838`](https://github.com/bhklab/readii/commit/0afc83833fcb80f2e158712bc1c8fd91e3b070e1)) +- **feature_extraction**: Added argument random seed for negative control creation + ([`053d542`](https://github.com/bhklab/readii/commit/053d54266781863a2c5f285e3aec77a831aa1d28)) ## v1.3.4 (2024-05-16) ### Bug Fixes -* fix: poetry lock ([`0632d5a`](https://github.com/bhklab/readii/commit/0632d5ae3aa619387f2e3c8ff064c243dd5b3ee4)) +- Poetry lock + ([`0632d5a`](https://github.com/bhklab/readii/commit/0632d5ae3aa619387f2e3c8ff064c243dd5b3ee4)) -* fix: pyradiomics original ([`4ab6aa7`](https://github.com/bhklab/readii/commit/4ab6aa7f7562a34c4ddf91a2697058fc796ee8a8)) +- Pyradiomics original + ([`4ab6aa7`](https://github.com/bhklab/readii/commit/4ab6aa7f7562a34c4ddf91a2697058fc796ee8a8)) -* fix: pyradiomics original ([`9513427`](https://github.com/bhklab/readii/commit/9513427f2cf7a9d7a59adb250d8d1a76d5e45773)) +- Pyradiomics original + ([`9513427`](https://github.com/bhklab/readii/commit/9513427f2cf7a9d7a59adb250d8d1a76d5e45773)) ## v1.3.3 (2024-05-16) ### Bug Fixes -* fix: install poetry ([`c1a905a`](https://github.com/bhklab/readii/commit/c1a905a7c3304d31e6edddb8332d98701b1ede18)) +- Install poetry + ([`c1a905a`](https://github.com/bhklab/readii/commit/c1a905a7c3304d31e6edddb8332d98701b1ede18)) ## v1.3.2 (2024-05-16) ### Bug Fixes -* fix: update lock ([`18054bd`](https://github.com/bhklab/readii/commit/18054bdadda30253b29eb06839dccaca356fbf1f)) +- Update lock + ([`18054bd`](https://github.com/bhklab/readii/commit/18054bdadda30253b29eb06839dccaca356fbf1f)) -* fix: no docker buils ([`e0a8e63`](https://github.com/bhklab/readii/commit/e0a8e63c584d0fcedbd5fcba42523d5d52a22a4d)) +- No docker buils + ([`e0a8e63`](https://github.com/bhklab/readii/commit/e0a8e63c584d0fcedbd5fcba42523d5d52a22a4d)) ## v1.3.1 (2024-05-16) ### Bug Fixes -* fix: update readme with docker link +- Update readme with docker link + ([`4584af7`](https://github.com/bhklab/readii/commit/4584af76e908708e9af1edc4fba0622c8a0ad30c)) -fix: update readme with docker link ([`4584af7`](https://github.com/bhklab/readii/commit/4584af76e908708e9af1edc4fba0622c8a0ad30c)) +fix: update readme with docker link -* fix: update readme with docker link ([`2f9a437`](https://github.com/bhklab/readii/commit/2f9a43707510154f207ff1b1ba31ddb879fb6e2d)) +- Update readme with docker link + ([`2f9a437`](https://github.com/bhklab/readii/commit/2f9a43707510154f207ff1b1ba31ddb879fb6e2d)) ## v1.3.0 (2024-05-16) ### Bug Fixes -* fix(negative_controls): set random generated pixel value to int to work with SetPixel ([`8d9b071`](https://github.com/bhklab/readii/commit/8d9b0717428231ff8e8b96c5150953e487ce6038)) +- **negative_controls**: Set random generated pixel value to int to work with SetPixel + ([`8d9b071`](https://github.com/bhklab/readii/commit/8d9b0717428231ff8e8b96c5150953e487ce6038)) -* fix(negative_controls): cast result from randNumGen.integers to int for sitk SetPixel function to fix type error ([`257c498`](https://github.com/bhklab/readii/commit/257c49873ebd73b0829b1b4d940e214c3a9192fe)) +- **negative_controls**: Cast result from randNumGen.integers to int for sitk SetPixel function to + fix type error + ([`257c498`](https://github.com/bhklab/readii/commit/257c49873ebd73b0829b1b4d940e214c3a9192fe)) -* fix(image_processing): correctedROIImage was assigned to unused variabel, changed to segImage ([`453402e`](https://github.com/bhklab/readii/commit/453402ed269cf7ec796a7337eae6fedabf07adc4)) +- **image_processing**: Correctedroiimage was assigned to unused variabel, changed to segImage + ([`453402e`](https://github.com/bhklab/readii/commit/453402ed269cf7ec796a7337eae6fedabf07adc4)) -* fix(test_negative_controls): makeRandomImage test was using incorrect function (shuffleImage) ([`143712a`](https://github.com/bhklab/readii/commit/143712a7885d957bbd63552a716b51ecbb4a9704)) +- **test_negative_controls**: Makerandomimage test was using incorrect function (shuffleImage) + ([`143712a`](https://github.com/bhklab/readii/commit/143712a7885d957bbd63552a716b51ecbb4a9704)) ### Build System -* build(poetry.lock): updated package versions ([`811b748`](https://github.com/bhklab/readii/commit/811b748184992b090fb96b0ec10ae5768cd6fa1d)) +- **poetry.lock**: Updated package versions + ([`811b748`](https://github.com/bhklab/readii/commit/811b748184992b090fb96b0ec10ae5768cd6fa1d)) ### Code Style -* style(feature_extraction): fix typo in randomizeImageFromDistributionSampling import ([`79dc539`](https://github.com/bhklab/readii/commit/79dc539c6802bc235347e16ba4025c39e3cfef4f)) +- **feature_extraction**: Fix typo in randomizeImageFromDistributionSampling import + ([`79dc539`](https://github.com/bhklab/readii/commit/79dc539c6802bc235347e16ba4025c39e3cfef4f)) -* style(negative_controls): fix spelling of distribution in randomizeImageFromDistributionSampling ([`4a01f5c`](https://github.com/bhklab/readii/commit/4a01f5cb6eb448429d3cdac236ab06a3c6441282)) +- **negative_controls**: Fix spelling of distribution in randomizeImageFromDistributionSampling + ([`4a01f5c`](https://github.com/bhklab/readii/commit/4a01f5cb6eb448429d3cdac236ab06a3c6441282)) ### Documentation -* docs(negative_controls): add random seed description to shuffleImage function header ([`df9a7d3`](https://github.com/bhklab/readii/commit/df9a7d3fa3cc9992a965e670a0474a19b9291cd2)) +- **negative_controls**: Add random seed description to shuffleImage function header + ([`df9a7d3`](https://github.com/bhklab/readii/commit/df9a7d3fa3cc9992a965e670a0474a19b9291cd2)) -* docs(example.ipynb): update notebook to use med-imagetools CT DICOM loader ([`e6339b7`](https://github.com/bhklab/readii/commit/e6339b738f8cf05c04f12d5ae88b0e7baabc8685)) +- **example.ipynb**: Update notebook to use med-imagetools CT DICOM loader + ([`e6339b7`](https://github.com/bhklab/readii/commit/e6339b738f8cf05c04f12d5ae88b0e7baabc8685)) ### Features -* feat(negative_controls): added random seed to all random functions and the apply negative control function ([`280b465`](https://github.com/bhklab/readii/commit/280b46578b6320dd8c9e66ee822dc0ffb7ac9d98)) +- **negative_controls**: Added random seed to all random functions and the apply negative control + function + ([`280b465`](https://github.com/bhklab/readii/commit/280b46578b6320dd8c9e66ee822dc0ffb7ac9d98)) -* feat(negative_controls): add random seed to shuffleNonROI ([`a402ee5`](https://github.com/bhklab/readii/commit/a402ee57b9300558cd796bffe3ed3d8afa1e1654)) +- **negative_controls**: Add random seed to shuffleNonROI + ([`a402ee5`](https://github.com/bhklab/readii/commit/a402ee57b9300558cd796bffe3ed3d8afa1e1654)) -* feat(negative_controls): add random seed to shuffleROI ([`826b00d`](https://github.com/bhklab/readii/commit/826b00ddd92ae7fa1e4441426970066de66f8af4)) +- **negative_controls**: Add random seed to shuffleROI + ([`826b00d`](https://github.com/bhklab/readii/commit/826b00ddd92ae7fa1e4441426970066de66f8af4)) -* feat(negative_controls): added random seed to shuffleImage function, now using numpy RNG and shuffle function ([`a2556ae`](https://github.com/bhklab/readii/commit/a2556aef0afe87f162bf3f6d12c572af23f9a9dc)) +- **negative_controls**: Added random seed to shuffleImage function, now using numpy RNG and shuffle + function + ([`a2556ae`](https://github.com/bhklab/readii/commit/a2556aef0afe87f162bf3f6d12c572af23f9a9dc)) ### Testing -* test(negative_controls): added tests for no roiLabel input for ROI and non-ROI negative control functions ([`c083878`](https://github.com/bhklab/readii/commit/c083878e86f8196ccbf2cf15eecb8b6c01f42754)) +- **negative_controls**: Added tests for no roiLabel input for ROI and non-ROI negative control + functions + ([`c083878`](https://github.com/bhklab/readii/commit/c083878e86f8196ccbf2cf15eecb8b6c01f42754)) -* test(negative_controls): removed redundant random pixel checks and added some checks for any change in the negative controls, updated some assertion failure messages ([`4ca434b`](https://github.com/bhklab/readii/commit/4ca434b34eebaf71064d3cc34f758d1bb6321556)) +- **negative_controls**: Removed redundant random pixel checks and added some checks for any change + in the negative controls, updated some assertion failure messages + ([`4ca434b`](https://github.com/bhklab/readii/commit/4ca434b34eebaf71064d3cc34f758d1bb6321556)) -* test(negative_controls): update whole image pixel checks and remove random pixel checks in shuffleNonROI and makeRandomRoi ([`b970cbe`](https://github.com/bhklab/readii/commit/b970cbe72a2dc66262a3d3bdac8869a5dd160a59)) +- **negative_controls**: Update whole image pixel checks and remove random pixel checks in + shuffleNonROI and makeRandomRoi + ([`b970cbe`](https://github.com/bhklab/readii/commit/b970cbe72a2dc66262a3d3bdac8869a5dd160a59)) -* test(negative_controls): update assertion comment in shuffle ROI ([`0c542f4`](https://github.com/bhklab/readii/commit/0c542f48ff07294e504713e51d6a171dbfb70d1c)) +- **negative_controls**: Update assertion comment in shuffle ROI + ([`0c542f4`](https://github.com/bhklab/readii/commit/0c542f48ff07294e504713e51d6a171dbfb70d1c)) -* test(negative_controls): fix the shuffle check that the same values exist in the new image in shuffleROI ([`6de291d`](https://github.com/bhklab/readii/commit/6de291d5c7595a31cfb22869784c6183ab4207ef)) +- **negative_controls**: Fix the shuffle check that the same values exist in the new image in + shuffleROI + ([`6de291d`](https://github.com/bhklab/readii/commit/6de291d5c7595a31cfb22869784c6183ab4207ef)) -* test(negative_controls): in makeRandomImage, added ROI voxel check, removed random pixel check as its covered by the randomSeed checks ([`17ca738`](https://github.com/bhklab/readii/commit/17ca7386daf7cb5d3437deb1d5dcca9b665b2d57)) +- **negative_controls**: In makeRandomImage, added ROI voxel check, removed random pixel check as + its covered by the randomSeed checks + ([`17ca738`](https://github.com/bhklab/readii/commit/17ca7386daf7cb5d3437deb1d5dcca9b665b2d57)) -* test(negative_controls): Added pixel check for centre of ROI, updated failed assertion message for randomSeed pixel checks ([`ed3bb17`](https://github.com/bhklab/readii/commit/ed3bb17768842339c5661fcfafebbd1c6efc786f)) +- **negative_controls**: Added pixel check for centre of ROI, updated failed assertion message for + randomSeed pixel checks + ([`ed3bb17`](https://github.com/bhklab/readii/commit/ed3bb17768842339c5661fcfafebbd1c6efc786f)) -* test(negative_controls): updated shuffle pixel check that values are the same as original ([`52dda33`](https://github.com/bhklab/readii/commit/52dda337b321b71b61922bbcb20363cea05c23eb)) +- **negative_controls**: Updated shuffle pixel check that values are the same as original + ([`52dda33`](https://github.com/bhklab/readii/commit/52dda337b321b71b61922bbcb20363cea05c23eb)) -* test(negative_controls): added random seed to rest of functions, changed conversion to pixels to include whole image not just region that's been altered ([`28db728`](https://github.com/bhklab/readii/commit/28db7280944c3e99dffa56e99fb297e27710d563)) +- **negative_controls**: Added random seed to rest of functions, changed conversion to pixels to + include whole image not just region that's been altered + ([`28db728`](https://github.com/bhklab/readii/commit/28db7280944c3e99dffa56e99fb297e27710d563)) -* test(negative_controls): added random seed to shuffleROI and randomROI tests, updated negative control image variable to be clearer ([`e09c142`](https://github.com/bhklab/readii/commit/e09c14282427a2c854d06e25b69556b3ae6351ef)) +- **negative_controls**: Added random seed to shuffleROI and randomROI tests, updated negative + control image variable to be clearer + ([`e09c142`](https://github.com/bhklab/readii/commit/e09c14282427a2c854d06e25b69556b3ae6351ef)) -* test(negative_controls): add random seed in shuffleROI test ([`d12ac25`](https://github.com/bhklab/readii/commit/d12ac25ba7cfb050017d365ef5d93825469e9a0c)) +- **negative_controls**: Add random seed in shuffleROI test + ([`d12ac25`](https://github.com/bhklab/readii/commit/d12ac25ba7cfb050017d365ef5d93825469e9a0c)) -* test(negative_controls): updated nsclcCropped fixture to use getCroppedImages function ([`24dafff`](https://github.com/bhklab/readii/commit/24dafff25aeddd0bfded9b7dfbac4bf588ac7870)) +- **negative_controls**: Updated nsclcCropped fixture to use getCroppedImages function + ([`24dafff`](https://github.com/bhklab/readii/commit/24dafff25aeddd0bfded9b7dfbac4bf588ac7870)) -* test(negative_controls): add random seed to make random image ([`6979ac6`](https://github.com/bhklab/readii/commit/6979ac6b72ac9a33aaa2f9178bf52ff711770478)) +- **negative_controls**: Add random seed to make random image + ([`6979ac6`](https://github.com/bhklab/readii/commit/6979ac6b72ac9a33aaa2f9178bf52ff711770478)) -* test(negative_controls): add random seed to shuffle image test ([`c07c50e`](https://github.com/bhklab/readii/commit/c07c50e857d2dd3c1fff4a25d6f59f4074a2a784)) - -### Unknown - -* Merge pull request #19 from bhklab/add_random_seed - -Adding random seed to all negative controls for reproducible results ([`26d8cbc`](https://github.com/bhklab/readii/commit/26d8cbcd74aa0343634332de60dab3ca3b3a2cd6)) +- **negative_controls**: Add random seed to shuffle image test + ([`c07c50e`](https://github.com/bhklab/readii/commit/c07c50e857d2dd3c1fff4a25d6f59f4074a2a784)) ## v1.2.1 (2024-03-27) ### Bug Fixes -* fix: no development branch ([`e3349db`](https://github.com/bhklab/readii/commit/e3349dbc68dd3f8c4f72afe351148f8af2ef846f)) +- No development branch + ([`e3349db`](https://github.com/bhklab/readii/commit/e3349dbc68dd3f8c4f72afe351148f8af2ef846f)) ### Build System -* build: Update pytest command to run tests in parallel ([`e8f67b9`](https://github.com/bhklab/readii/commit/e8f67b9108f254431c0542a2812c674578db0794)) +- Update pytest command to run tests in parallel + ([`e8f67b9`](https://github.com/bhklab/readii/commit/e8f67b9108f254431c0542a2812c674578db0794)) -* build: update poetry lock ([`6999f20`](https://github.com/bhklab/readii/commit/6999f208f33132e53f6ba42037387ae41070bf07)) +- Update poetry lock + ([`6999f20`](https://github.com/bhklab/readii/commit/6999f208f33132e53f6ba42037387ae41070bf07)) -* build: Fix formatting in ci-cd.yml and add back unit tests. Rename jobs for better clarity ([`b4d49d5`](https://github.com/bhklab/readii/commit/b4d49d53fcccaa63e0e0d0b720da39f9f1dda3fb)) +- Fix formatting in ci-cd.yml and add back unit tests. Rename jobs for better clarity + ([`b4d49d5`](https://github.com/bhklab/readii/commit/b4d49d53fcccaa63e0e0d0b720da39f9f1dda3fb)) -* build: add pytest-xdist for development parallel tests ([`d52a5a3`](https://github.com/bhklab/readii/commit/d52a5a3189cef9fc7599687f6dc1558378d87506)) +- Add pytest-xdist for development parallel tests + ([`d52a5a3`](https://github.com/bhklab/readii/commit/d52a5a3189cef9fc7599687f6dc1558378d87506)) ### Code Style -* style(feature_extraction.py): changed some function call spacing ([`09331a3`](https://github.com/bhklab/readii/commit/09331a3d7f9b6459ab151b9b3611877c04f4d265)) +- **feature_extraction.py**: Changed some function call spacing + ([`09331a3`](https://github.com/bhklab/readii/commit/09331a3d7f9b6459ab151b9b3611877c04f4d265)) ### Refactoring -* refactor: format with black, explicit imports, and update type annotations ([`04bada5`](https://github.com/bhklab/readii/commit/04bada5a9d1933f840d647c4ef383329a6e9d2e7)) - -* refactor: Fixes, updates, formatting - -refactor: Fixes, updates, formatting ([`998f299`](https://github.com/bhklab/readii/commit/998f299cfb3d29b95afde4f371508da2c6c142b6)) +- Format with black, explicit imports, and update type annotations + ([`04bada5`](https://github.com/bhklab/readii/commit/04bada5a9d1933f840d647c4ef383329a6e9d2e7)) -* refactor: format with black ([`07d04d8`](https://github.com/bhklab/readii/commit/07d04d8f1b8bacea29a896557971468446e22bf8)) +- Fixes, updates, formatting + ([`998f299`](https://github.com/bhklab/readii/commit/998f299cfb3d29b95afde4f371508da2c6c142b6)) -* refactor: explicit imports from readii.metadata module for performance ([`f91afa4`](https://github.com/bhklab/readii/commit/f91afa43e63daeb06be8d9276c9607453d7fe71c)) +refactor: Fixes, updates, formatting -* refactor: Refactor type check in test_radiomicFeatureExtraction ([`bc0d18d`](https://github.com/bhklab/readii/commit/bc0d18da89907ca82e30eb81fbed1ab1ae475cfe)) +- Format with black + ([`07d04d8`](https://github.com/bhklab/readii/commit/07d04d8f1b8bacea29a896557971468446e22bf8)) -* refactor: Refactor saveDataframeCSV and matchCTtoSegmentation functions, add type hints, and improve error handling, format with black ([`16a83b9`](https://github.com/bhklab/readii/commit/16a83b9541d717f132f6a32afbeb89db02653c63)) +- Explicit imports from readii.metadata module for performance + ([`f91afa4`](https://github.com/bhklab/readii/commit/f91afa43e63daeb06be8d9276c9607453d7fe71c)) -* refactor: Update version variables in pyproject.toml ([`5776e5f`](https://github.com/bhklab/readii/commit/5776e5f0f618c3634d01fb86c685e012bc073a08)) +- Refactor type check in test_radiomicFeatureExtraction + ([`bc0d18d`](https://github.com/bhklab/readii/commit/bc0d18da89907ca82e30eb81fbed1ab1ae475cfe)) -* refactor: explicitly import all, nested import * can lead to performance issues ([`8054799`](https://github.com/bhklab/readii/commit/80547997d7d2c4c852a0f4f43b61d3c49ebe1f51)) +- Refactor saveDataframeCSV and matchCTtoSegmentation functions, add type hints, and improve error + handling, format with black + ([`16a83b9`](https://github.com/bhklab/readii/commit/16a83b9541d717f132f6a32afbeb89db02653c63)) -* refactor: update type annotations. ([`c6ee885`](https://github.com/bhklab/readii/commit/c6ee885422df735b3230c5541936d3f71ab17f6c)) +- Update version variables in pyproject.toml + ([`5776e5f`](https://github.com/bhklab/readii/commit/5776e5f0f618c3634d01fb86c685e012bc073a08)) -* refactor: update type annotations to handle optional parameters, format with black for readability, refactor applyNegativeControl function to raise AssertionErrror for optional baseROI, handle edge case and raise error if none of the nc_types. ([`11f0d92`](https://github.com/bhklab/readii/commit/11f0d92a3f86e1c1db328172d338b92b09654f46)) +- Explicitly import all, nested import * can lead to performance issues + ([`8054799`](https://github.com/bhklab/readii/commit/80547997d7d2c4c852a0f4f43b61d3c49ebe1f51)) -### Unknown +- Update type annotations. + ([`c6ee885`](https://github.com/bhklab/readii/commit/c6ee885422df735b3230c5541936d3f71ab17f6c)) -* Merge pull request #15 from bhklab/dockerfile - -Refactor: Add dockerfile, fix some type errors, update type annotations, add some error-handling, formatting ([`20f8d54`](https://github.com/bhklab/readii/commit/20f8d543cfd27125ca21bb467acad13d556be284)) - -* fixed wrong docker repo ([`8ca1a93`](https://github.com/bhklab/readii/commit/8ca1a9349c7e0ac3bf13da572aa13d691d1cb56d)) - -* Merge branch 'dockerfile' of github.com:bhklab/readii into dockerfile ([`6bb042d`](https://github.com/bhklab/readii/commit/6bb042de6bf31a5869f0bfa016b7f38b229e5249)) +- Update type annotations to handle optional parameters, format with black for readability, refactor + applyNegativeControl function to raise AssertionErrror for optional baseROI, handle edge case and + raise error if none of the nc_types. + ([`11f0d92`](https://github.com/bhklab/readii/commit/11f0d92a3f86e1c1db328172d338b92b09654f46)) ## v1.2.0 (2024-03-15) ### Bug Fixes -* fix: wrong group in toml ([`b55baab`](https://github.com/bhklab/readii/commit/b55baabb4800e074f0f08684874947052ecb9195)) +- Wrong group in toml + ([`b55baab`](https://github.com/bhklab/readii/commit/b55baabb4800e074f0f08684874947052ecb9195)) -* fix: test builds and update toml to include this branch ([`af61beb`](https://github.com/bhklab/readii/commit/af61beba9a677a86695268a55bd2887138fb2c59)) +- Test builds and update toml to include this branch + ([`af61beb`](https://github.com/bhklab/readii/commit/af61beba9a677a86695268a55bd2887138fb2c59)) -* fix: test deployment ([`aa1dcb4`](https://github.com/bhklab/readii/commit/aa1dcb479720f8eec295071ad0b45aedaaf275d2)) +- Test deployment + ([`aa1dcb4`](https://github.com/bhklab/readii/commit/aa1dcb479720f8eec295071ad0b45aedaaf275d2)) ### Features -* feat: adding dockerfile and gha to build and deploy ([`b7d6b73`](https://github.com/bhklab/readii/commit/b7d6b734ef6b955e5b61ff2d980a08893dc2dddb)) - -### Unknown - -* Update ci-cd.yml and pyproject.toml ([`fa35141`](https://github.com/bhklab/readii/commit/fa35141d0d9b1772ac4d6242d942f4ad9c0061d3)) +- Adding dockerfile and gha to build and deploy + ([`b7d6b73`](https://github.com/bhklab/readii/commit/b7d6b734ef6b955e5b61ff2d980a08893dc2dddb)) ## v1.1.3 (2024-03-06) ### Bug Fixes -* fix(pipeline): need to exit when catching the no segmentation type error ([`bd1a93b`](https://github.com/bhklab/readii/commit/bd1a93bf0ac9d1104d3df2a46988b14b3401622b)) +- **pipeline**: Need to exit when catching the no segmentation type error + ([`bd1a93b`](https://github.com/bhklab/readii/commit/bd1a93bf0ac9d1104d3df2a46988b14b3401622b)) ### Build System -* build: updating package versions ([`3f3a593`](https://github.com/bhklab/readii/commit/3f3a59358eaa7b5a81b12b8b45589d17f117df9c)) - -### Unknown - -* Merge pull request #14 from bhklab/development_katy - -Another fix for catching no segmentation type error ([`6e3e8fc`](https://github.com/bhklab/readii/commit/6e3e8fc8486334e7e3c1c438fc5ce757eb8a5585)) +- Updating package versions + ([`3f3a593`](https://github.com/bhklab/readii/commit/3f3a59358eaa7b5a81b12b8b45589d17f117df9c)) ## v1.1.2 (2024-03-06) ### Documentation -* docs: update README with randomized sampled negative controls, add description of negative controls ([`eaff95d`](https://github.com/bhklab/readii/commit/eaff95df12d71af2dd7d69e59565cf00c3bc3e4e)) - -### Unknown - -* Merge pull request #13 from bhklab/development_katy - -fix (pipeline): catch error when there are no suitable segmentation types in the imgtools csv ([`f7f9904`](https://github.com/bhklab/readii/commit/f7f990465bef3f0b1124fb3052352a8f7e9e56af)) - -* fix (pipeline): catch error when there are no suitable segmentation types in the imgtools csv ([`6d475c9`](https://github.com/bhklab/readii/commit/6d475c978125496eaad62a2f49885da7fa964dc1)) - -* Merge pull request #12 from bhklab/development_mogtaba - -Added ROI Name Quality Check for Negative Controls ([`308ceaf`](https://github.com/bhklab/readii/commit/308ceafe882fb15fb0bc9a75638ab20da464411a)) - -* Added function to manually check for roi name if it is missing when calling negative control. Fixed output file checking ([`2810b59`](https://github.com/bhklab/readii/commit/2810b5971c39ed85b97f11d17f477d444a73e37e)) - -* Merge pull request #11 from bhklab/development_katy - -docs: update README with randomized sampled negative controls, add de… ([`0c90846`](https://github.com/bhklab/readii/commit/0c908463559da5f8cd0a4a0fcc59eaa294ab4dd6)) +- Update README with randomized sampled negative controls, add description of negative controls + ([`eaff95d`](https://github.com/bhklab/readii/commit/eaff95df12d71af2dd7d69e59565cf00c3bc3e4e)) ## v1.1.1 (2024-02-08) ### Bug Fixes -* fix: update version number ([`3b90606`](https://github.com/bhklab/readii/commit/3b9060652fa39f8480691c5e5edc9e77c61131e9)) +- Update version number + ([`3b90606`](https://github.com/bhklab/readii/commit/3b9060652fa39f8480691c5e5edc9e77c61131e9)) ### Build System -* build: add pyarrow as dependency for pandas ([`0050dc1`](https://github.com/bhklab/readii/commit/0050dc156940aaab895a367c57307764d580c7d6)) - -* build: updated pyradiomics dependency tp 3.0.1a3 ([`d780b27`](https://github.com/bhklab/readii/commit/d780b27c7fcb4e05343f8575d63b3b5b4b0ae430)) - -* build: updated med-imagetools dependency ([`ed58b9c`](https://github.com/bhklab/readii/commit/ed58b9cfe726ac0d92d165c2e05bdb32753285a7)) - -* build: changed pyradiomics dependency to 3.0.1 as 3.1.0 has installation issues ([`9c89227`](https://github.com/bhklab/readii/commit/9c89227c7c97dadcacd94b7f450668c046c955a1)) - -* build: update dependencies versions ([`8b1af18`](https://github.com/bhklab/readii/commit/8b1af187f9e55dea34685b3a03c0abc80b318035)) +- Add pyarrow as dependency for pandas + ([`0050dc1`](https://github.com/bhklab/readii/commit/0050dc156940aaab895a367c57307764d580c7d6)) -### Unknown +- Updated pyradiomics dependency tp 3.0.1a3 + ([`d780b27`](https://github.com/bhklab/readii/commit/d780b27c7fcb4e05343f8575d63b3b5b4b0ae430)) -* Merge pull request #10 from bhklab/development_katy +- Updated med-imagetools dependency + ([`ed58b9c`](https://github.com/bhklab/readii/commit/ed58b9cfe726ac0d92d165c2e05bdb32753285a7)) -fix: update version number ([`2923f7a`](https://github.com/bhklab/readii/commit/2923f7aff3139c6eeae956fca1db7246d5d1f64a)) +- Changed pyradiomics dependency to 3.0.1 as 3.1.0 has installation issues + ([`9c89227`](https://github.com/bhklab/readii/commit/9c89227c7c97dadcacd94b7f450668c046c955a1)) -* fix version number ([`36e8ff8`](https://github.com/bhklab/readii/commit/36e8ff8f94389913bed1583bc87add3fb7bfdd92)) - -* patch: use pyradiomics 3.0.1a3 ([`98d5e91`](https://github.com/bhklab/readii/commit/98d5e9145ab8642ddb81c68e8fdf3e8b55f01eed)) - -* Merge pull request #9 from bhklab/development_katy - -Development katy ([`0f1cc66`](https://github.com/bhklab/readii/commit/0f1cc665d27bd458a9d7f0f4e95577c4890b175b)) - -* bug(image_processing): force ROI voxel label to int to be compatible with pyradiomics 3.0.1a3 ([`38e7653`](https://github.com/bhklab/readii/commit/38e76532853573b1de204760a11f2833a235001a)) +- Update dependencies versions + ([`8b1af18`](https://github.com/bhklab/readii/commit/8b1af187f9e55dea34685b3a03c0abc80b318035)) ## v1.1.0 (2024-01-31) ### Bug Fixes -* fix(pipeline): fixed check for existing radiomic features file, had incorrect file name ([`1819d3d`](https://github.com/bhklab/readii/commit/1819d3d1e45132c195fed8e06c301005d05e18bf)) +- **pipeline**: Fixed check for existing radiomic features file, had incorrect file name + ([`1819d3d`](https://github.com/bhklab/readii/commit/1819d3d1e45132c195fed8e06c301005d05e18bf)) -* fix(negative_controls): fixed function call for randomized_sample_full in applyNegativeControl ([`06a2f9c`](https://github.com/bhklab/readii/commit/06a2f9cf14be028ea46e8f29c371fbc7770791e6)) +- **negative_controls**: Fixed function call for randomized_sample_full in applyNegativeControl + ([`06a2f9c`](https://github.com/bhklab/readii/commit/06a2f9cf14be028ea46e8f29c371fbc7770791e6)) -* fix(image_processing): moved crop to top of displayOverlay function to get correct centre slice index and array conversion happens after crop ([`c1037d9`](https://github.com/bhklab/readii/commit/c1037d9c7a353ab689b5688780a872d18184e2cd)) +- **image_processing**: Moved crop to top of displayOverlay function to get correct centre slice + index and array conversion happens after crop + ([`c1037d9`](https://github.com/bhklab/readii/commit/c1037d9c7a353ab689b5688780a872d18184e2cd)) ### Features -* feat(image_processing): made cropping CT and segmentation its own function ([`5202cc2`](https://github.com/bhklab/readii/commit/5202cc2113f392a0fce92c555bf58ff3085d3d97)) - -* feat(image_processing): add option to display CT and segmentation cropped to ROI ([`120524c`](https://github.com/bhklab/readii/commit/120524c17d89d3a2cee0c168b16243b385217cc2)) +- **image_processing**: Made cropping CT and segmentation its own function + ([`5202cc2`](https://github.com/bhklab/readii/commit/5202cc2113f392a0fce92c555bf58ff3085d3d97)) -### Unknown - -* Merge pull request #8 from bhklab/development_katy - -Added display functions for CT and CT with segmentation overlaid -Fixed function call for randomized sample full image -Fixed check for existing radiomic features file ([`ba4a9fe`](https://github.com/bhklab/readii/commit/ba4a9fe1d80fad9a9f407ec0e36185af400584e9)) - -* Merge pull request #7 from bhklab/development_mogtaba - -Fixed CTtoSegmentation merge issue and fixed negative control settings ([`7bbf3b7`](https://github.com/bhklab/readii/commit/7bbf3b7ff835df15ffea1e5cb561d2c1a15b168e)) - -* fixed merge between SEGs and CTs, in matchCTtoSegmentation ([`fc1dda1`](https://github.com/bhklab/readii/commit/fc1dda13ded85440c7d2b4ced3ccb86f9f028649)) - -* added new negative controls to --negative_control flag ([`9aaf76c`](https://github.com/bhklab/readii/commit/9aaf76c9c1f5edc968734fde5d03e86f2aa988c3)) +- **image_processing**: Add option to display CT and segmentation cropped to ROI + ([`120524c`](https://github.com/bhklab/readii/commit/120524c17d89d3a2cee0c168b16243b385217cc2)) ## v1.0.0 (2024-01-26) -### Unknown - -* Merge pull request #6 from bhklab/name_change - -Name change from yarea to readii ([`2374af4`](https://github.com/bhklab/readii/commit/2374af46b6522ef617f6366a5b4d4d7e442a5d2c)) - -* Merge branch 'main' into name_change ([`480b596`](https://github.com/bhklab/readii/commit/480b59601294bd1a298fda026b6ebaecd570dfd1)) - -* Merge pull request #5 from bhklab/development_mogtaba - -Created 3 new negative controls by sampling original image and tests ([`2f95cf7`](https://github.com/bhklab/readii/commit/2f95cf7d82c334e34611325c36ea0c1f0a881fbe)) - -* Created 3 new negative controls by sampling original image and added tests for them ([`ec3dd21`](https://github.com/bhklab/readii/commit/ec3dd21f3100ea22bcccd846020f55c052e204ad)) - -* merged changes ([`db63a6c`](https://github.com/bhklab/readii/commit/db63a6c766b1bd6e98dd10369336128038c2b7a1)) - ## v0.6.0 (2024-01-19) -### Breaking +### Build System -* build: changed package name from YAREA to READII +- Changed package name from YAREA to READII + ([`3bcb4f9`](https://github.com/bhklab/readii/commit/3bcb4f9d9b1666f4fb3c3f66b4e4913358db25d7)) -BREAKING CHANGE: yarea name no longer used ([`3bcb4f9`](https://github.com/bhklab/readii/commit/3bcb4f9d9b1666f4fb3c3f66b4e4913358db25d7)) +BREAKING CHANGE: yarea name no longer used ### Documentation -* docs(README): update package headline for READII acronym ([`1294d44`](https://github.com/bhklab/readii/commit/1294d44ed87a45567e6a957db77f9738817b37b4)) +- **README**: Update package headline for READII acronym + ([`1294d44`](https://github.com/bhklab/readii/commit/1294d44ed87a45567e6a957db77f9738817b37b4)) ### Features -* feat(pipeline): change parallel input argument to be false by default ([`3f8c46a`](https://github.com/bhklab/readii/commit/3f8c46ade25b16a77cc1ee6175bda039b811561f)) - -### Unknown - -* Merge pull request #4 from bhklab/development_katy - -feat(pipeline): change parallel input argument to be false by default ([`8d0626d`](https://github.com/bhklab/readii/commit/8d0626d08acad7f9e2ca3d31560ea4d532f86e2e)) - -* Removed test that doesn't take into account shuffling edge case. ([`28ab19e`](https://github.com/bhklab/readii/commit/28ab19e652531095338935d9b6b655f7c3508d02)) +- **pipeline**: Change parallel input argument to be false by default + ([`3f8c46a`](https://github.com/bhklab/readii/commit/3f8c46ade25b16a77cc1ee6175bda039b811561f)) ## v0.5.0 (2024-01-17) ### Bug Fixes -* fix(image_processing): fixed remaining instances of imgArray variable ([`84de500`](https://github.com/bhklab/readii/commit/84de5003d65c8726d925108f087cdba3be9288ad)) +- **image_processing**: Fixed remaining instances of imgArray variable + ([`84de500`](https://github.com/bhklab/readii/commit/84de5003d65c8726d925108f087cdba3be9288ad)) -* fix(image_processing): fixed image vs. imgArray variable mixup in displayImageSlice ([`c9ea3d6`](https://github.com/bhklab/readii/commit/c9ea3d6f1ae6637139c41651a3c66d133b6d6c5f)) +- **image_processing**: Fixed image vs. imgArray variable mixup in displayImageSlice + ([`c9ea3d6`](https://github.com/bhklab/readii/commit/c9ea3d6f1ae6637139c41651a3c66d133b6d6c5f)) ### Build System -* build: updated dependency versions ([`44de606`](https://github.com/bhklab/readii/commit/44de60655fef29716ef5d4edbd6e1e18f8e508d1)) +- Updated dependency versions + ([`44de606`](https://github.com/bhklab/readii/commit/44de60655fef29716ef5d4edbd6e1e18f8e508d1)) ### Documentation -* docs(pipeline): indicate whether flags are true or false by default in help message of parallel and update ([`311dd5e`](https://github.com/bhklab/readii/commit/311dd5e4f946ba78caaf7c1f0d1ed6dceecd5dcb)) +- **pipeline**: Indicate whether flags are true or false by default in help message of parallel and + update + ([`311dd5e`](https://github.com/bhklab/readii/commit/311dd5e4f946ba78caaf7c1f0d1ed6dceecd5dcb)) -* docs(image_processing): wrote docstring for displayCTSegOverlay ([`2f69dab`](https://github.com/bhklab/readii/commit/2f69dab8f8d7b7b46f7fbe2175b356a4fb28baf7)) +- **image_processing**: Wrote docstring for displayCTSegOverlay + ([`2f69dab`](https://github.com/bhklab/readii/commit/2f69dab8f8d7b7b46f7fbe2175b356a4fb28baf7)) -* docs: require python 3.9 in conda env setup ([`480b199`](https://github.com/bhklab/readii/commit/480b1997788be447a53a2699a952df076b7b5262)) +- Require python 3.9 in conda env setup + ([`480b199`](https://github.com/bhklab/readii/commit/480b1997788be447a53a2699a952df076b7b5262)) ### Features -* feat(image_processing): add function to display CT slice with segmentation overlaid ([`73342ef`](https://github.com/bhklab/readii/commit/73342efbd24757ac349124ba332dc26f89544ae9)) +- **image_processing**: Add function to display CT slice with segmentation overlaid + ([`73342ef`](https://github.com/bhklab/readii/commit/73342efbd24757ac349124ba332dc26f89544ae9)) -* feat(image_processing): add function to find center slice and coordinates of ROI in image ([`78d69b2`](https://github.com/bhklab/readii/commit/78d69b227ab1e2006ce46badd2b0a37384f45f40)) +- **image_processing**: Add function to find center slice and coordinates of ROI in image + ([`78d69b2`](https://github.com/bhklab/readii/commit/78d69b227ab1e2006ce46badd2b0a37384f45f40)) ### Testing -* test(test_image_processing): added test for getROICenterCoords ([`8745fe7`](https://github.com/bhklab/readii/commit/8745fe752a27204eed7359aed4525c962481d2db)) - -### Unknown - -* Merge pull request #3 from bhklab/development_katy - -Added some new functions focused on displaying the CT with a segmentation overlaid and fixed a variable name in image_processing ([`04f42a4`](https://github.com/bhklab/readii/commit/04f42a40c7475499094e65ec55639a91b0da629f)) - -* Merge pull request #2 from bhklab/development_katy - -docs: require python 3.9 in conda env setup ([`390d6e6`](https://github.com/bhklab/readii/commit/390d6e6f094968d0d19191484e14da16294e046e)) +- **test_image_processing**: Added test for getROICenterCoords + ([`8745fe7`](https://github.com/bhklab/readii/commit/8745fe752a27204eed7359aed4525c962481d2db)) ## v0.4.0 (2024-01-17) ### Documentation -* docs: add installation and usage details to README ([`4281620`](https://github.com/bhklab/readii/commit/4281620f5f791030a020cb4fe91b08318d63426b)) +- Add installation and usage details to README + ([`4281620`](https://github.com/bhklab/readii/commit/4281620f5f791030a020cb4fe91b08318d63426b)) ### Features -* feat: added command line example runs to notebook ([`48d8d40`](https://github.com/bhklab/readii/commit/48d8d40e24796491cb6491046b3f12f2424df128)) - -### Unknown - -* add tests/output/ to gitignore to not commit output files ([`fa713ff`](https://github.com/bhklab/readii/commit/fa713ff38977b1d2758aae32bde5fa07f0500931)) - -* Merge branch 'main' of github.com:bhklab/yarea into main ([`1327e22`](https://github.com/bhklab/readii/commit/1327e22ab994212e24e4658313897791bef39c82)) - -* Fixed error with the path for CT and SEG files in the tests for negative controls ([`5ea6e2c`](https://github.com/bhklab/readii/commit/5ea6e2caa601f3aa3eefd806c1c09cdbef0c6e23)) - -* Fixed feature_extraction error where padSegToMatchCT function was being called incorrectly ([`82ad022`](https://github.com/bhklab/readii/commit/82ad0228bae60a5d800e15f77a9e6cad487e8c23)) - -* Add ci pass requirement back in ([`b678d4a`](https://github.com/bhklab/readii/commit/b678d4afb2c9818c07d0f8165f8b5baf3426e11c)) - -* Merge pull request #1 from bhklab/negative_control_tests - -Created testing suite for negative controls and fixed errors in image_processing.py and negative_controls.py ([`f0fdd02`](https://github.com/bhklab/readii/commit/f0fdd028e167d78b371fc2ff73bff1328a271e54)) - -* merged conflicts ([`d78fb5f`](https://github.com/bhklab/readii/commit/d78fb5f101d3532b656a63f5134ac05d281f0bcf)) - -* Merge branch 'main' into negative_control_tests ([`c6ff12e`](https://github.com/bhklab/readii/commit/c6ff12ea94eb70691a71a9fb9fda7b655f272669)) - -* Finished testing suite for the negative controls ([`6d81739`](https://github.com/bhklab/readii/commit/6d81739841318c201508eb787f46d1024f78039b)) - -* Fixed issue with shuffleROI and shuffleNonROI, where some pixels with duplicate values were ignored ([`e812bcc`](https://github.com/bhklab/readii/commit/e812bccacaf5ad9f37d62811e6644dc2f6128159)) - -* Fixed error with wrong variable names, for CT folder path ([`302a284`](https://github.com/bhklab/readii/commit/302a284b904ceee539fee64b52b22c1e03f28fe1)) - -* Merge branch 'main' of github.com:bhklab/yarea into main ([`cee3c0f`](https://github.com/bhklab/readii/commit/cee3c0fe50b35d8ac491704d09d9a85e7ddbf2c4)) +- Added command line example runs to notebook + ([`48d8d40`](https://github.com/bhklab/readii/commit/48d8d40e24796491cb6491046b3f12f2424df128)) ## v0.3.0 (2023-12-21) ### Bug Fixes -* fix(test_feature_extraction): fixed expected output path for radiomicFeatureExtraction ([`53c9db3`](https://github.com/bhklab/readii/commit/53c9db3bc31a35e332f9eeda35b82f42c84f5ab1)) +- **test_feature_extraction**: Fixed expected output path for radiomicFeatureExtraction + ([`53c9db3`](https://github.com/bhklab/readii/commit/53c9db3bc31a35e332f9eeda35b82f42c84f5ab1)) -* fix(image_processing): fixed usage of ctDirPath variable in padSegToMatchCT ([`892c8d7`](https://github.com/bhklab/readii/commit/892c8d7629595ce89f2893b004f6f7bc585bab21)) +- **image_processing**: Fixed usage of ctDirPath variable in padSegToMatchCT + ([`892c8d7`](https://github.com/bhklab/readii/commit/892c8d7629595ce89f2893b004f6f7bc585bab21)) -* fix: move size mismatch handling back to radiomicFeatureExtraction because image file paths are available in that function ([`ccbe852`](https://github.com/bhklab/readii/commit/ccbe8524fa69a2334b499512a541c3afa13b430a)) +- Move size mismatch handling back to radiomicFeatureExtraction because image file paths are + available in that function + ([`ccbe852`](https://github.com/bhklab/readii/commit/ccbe8524fa69a2334b499512a541c3afa13b430a)) -* fix(feature_extraction): moved error handling into singleRadiomicFeatureExtraction and added catch for wrong pyradiomics parameter file ([`41a3901`](https://github.com/bhklab/readii/commit/41a39018becde60091ffb113640e180a162d536f)) +- **feature_extraction**: Moved error handling into singleRadiomicFeatureExtraction and added catch + for wrong pyradiomics parameter file + ([`41a3901`](https://github.com/bhklab/readii/commit/41a39018becde60091ffb113640e180a162d536f)) -* fix: change radiomic features file output name ([`ea0b963`](https://github.com/bhklab/readii/commit/ea0b963c7c7caa0a39ab6149fa86d8783717bc32)) +- Change radiomic features file output name + ([`ea0b963`](https://github.com/bhklab/readii/commit/ea0b963c7c7caa0a39ab6149fa86d8783717bc32)) -* fix(feature_extraction): add check for None in pyradiomics parameter file spot, use default if that's the case ([`5340f57`](https://github.com/bhklab/readii/commit/5340f57c8ab18818e6bb45cecda96fcb7aba4f5a)) +- **feature_extraction**: Add check for None in pyradiomics parameter file spot, use default if + that's the case + ([`5340f57`](https://github.com/bhklab/readii/commit/5340f57c8ab18818e6bb45cecda96fcb7aba4f5a)) -* fix(yarea): renamed this file because it had import issues being named the same as the package ([`833c5b4`](https://github.com/bhklab/readii/commit/833c5b460140783d0292b7a1991bca7cbd0e5c64)) +- **yarea**: Renamed this file because it had import issues being named the same as the package + ([`833c5b4`](https://github.com/bhklab/readii/commit/833c5b460140783d0292b7a1991bca7cbd0e5c64)) ### Build System -* build: add publish to PyPI back in ([`e7f182e`](https://github.com/bhklab/readii/commit/e7f182e6b2da527ca9e0a747557bff1bc9dc0b6b)) +- Add publish to PyPI back in + ([`e7f182e`](https://github.com/bhklab/readii/commit/e7f182e6b2da527ca9e0a747557bff1bc9dc0b6b)) -* build: updated semantic release variables ([`5e24044`](https://github.com/bhklab/readii/commit/5e240446bc561cc34640a24d315edaf376cd244f)) +- Updated semantic release variables + ([`5e24044`](https://github.com/bhklab/readii/commit/5e240446bc561cc34640a24d315edaf376cd244f)) -* build: updated semantic release and added package build steps ([`5a51e07`](https://github.com/bhklab/readii/commit/5a51e078a8fbf3c0f14c7d0b429d14b830097142)) +- Updated semantic release and added package build steps + ([`5a51e07`](https://github.com/bhklab/readii/commit/5a51e078a8fbf3c0f14c7d0b429d14b830097142)) -* build: remove publish to PyPI ([`f276b76`](https://github.com/bhklab/readii/commit/f276b767ae452eb7aceb702f607100e1c925c1c8)) +- Remove publish to PyPI + ([`f276b76`](https://github.com/bhklab/readii/commit/f276b767ae452eb7aceb702f607100e1c925c1c8)) ### Code Style -* style(feature_extraction): changed ctFolderPath to ctDirPath for consistency ([`b7b452e`](https://github.com/bhklab/readii/commit/b7b452ea2d0c6f930cc727ec026b03de5d539121)) +- **feature_extraction**: Changed ctFolderPath to ctDirPath for consistency + ([`b7b452e`](https://github.com/bhklab/readii/commit/b7b452ea2d0c6f930cc727ec026b03de5d539121)) ### Documentation -* docs(pipeline): fixed typo in data directory help message ([`7a19b5a`](https://github.com/bhklab/readii/commit/7a19b5a3d53ff24a6a800a7bcd75add2aff2d741)) +- **pipeline**: Fixed typo in data directory help message + ([`7a19b5a`](https://github.com/bhklab/readii/commit/7a19b5a3d53ff24a6a800a7bcd75add2aff2d741)) ### Features -* feat: add ability to run pipeline using poetry run ([`ced5e67`](https://github.com/bhklab/readii/commit/ced5e6771e3f7b688f2f394f0ec0f8b4ff92bf7a)) +- Add ability to run pipeline using poetry run + ([`ced5e67`](https://github.com/bhklab/readii/commit/ced5e6771e3f7b688f2f394f0ec0f8b4ff92bf7a)) -* feat(gitignore): ignore vscode directory with configurations ([`7e30be2`](https://github.com/bhklab/readii/commit/7e30be22e0a56c6f5f438e7ff51ebc9ba2b900f3)) +- **gitignore**: Ignore vscode directory with configurations + ([`7e30be2`](https://github.com/bhklab/readii/commit/7e30be22e0a56c6f5f438e7ff51ebc9ba2b900f3)) -* feat(pipeline): main pipeline function to run radiomic feature extraction ([`929573d`](https://github.com/bhklab/readii/commit/929573d50a22746fae29beceacd8d0169cd3dde3)) +- **pipeline**: Main pipeline function to run radiomic feature extraction + ([`929573d`](https://github.com/bhklab/readii/commit/929573d50a22746fae29beceacd8d0169cd3dde3)) -* feat(metadata): added check for csv type on imgFileListPath argument ([`ac09625`](https://github.com/bhklab/readii/commit/ac09625fd36622e5a0388ce8e4e74209ed4c9c4c)) +- **metadata**: Added check for csv type on imgFileListPath argument + ([`ac09625`](https://github.com/bhklab/readii/commit/ac09625fd36622e5a0388ce8e4e74209ed4c9c4c)) -* feat(metadata): made function to find the segmentation type from the list of image files ([`8dd4ddf`](https://github.com/bhklab/readii/commit/8dd4ddf858c47377d6bac0e9853282772d15dd43)) +- **metadata**: Made function to find the segmentation type from the list of image files + ([`8dd4ddf`](https://github.com/bhklab/readii/commit/8dd4ddf858c47377d6bac0e9853282772d15dd43)) ### Testing -* test(test_metadata): testing for getSegmentationType function ([`57768cf`](https://github.com/bhklab/readii/commit/57768cfe22fa0a7a3a59b65e25fe768848025ce0)) - -### Unknown - -* remove files from tutorial ([`5afac9a`](https://github.com/bhklab/readii/commit/5afac9af90c7112c18acf2c3ce6f22a617c1cf86)) - -* updated version ([`3a063cf`](https://github.com/bhklab/readii/commit/3a063cf057fdfe3c056ca86af325f060c3c65cf3)) +- **test_metadata**: Testing for getSegmentationType function + ([`57768cf`](https://github.com/bhklab/readii/commit/57768cfe22fa0a7a3a59b65e25fe768848025ce0)) ## v0.2.0 (2023-12-19) ### Bug Fixes -* fix: need to see test outputs for actions ([`6e95d0e`](https://github.com/bhklab/readii/commit/6e95d0e287a105c9f71d2f245fcdf10719913daf)) +- Need to see test outputs for actions + ([`6e95d0e`](https://github.com/bhklab/readii/commit/6e95d0e287a105c9f71d2f245fcdf10719913daf)) -* fix: fixed default Pyradiomics parameter file path ([`84f16db`](https://github.com/bhklab/readii/commit/84f16db1d0032fa81dbf7b30422a74a0ec386984)) +- Fixed default Pyradiomics parameter file path + ([`84f16db`](https://github.com/bhklab/readii/commit/84f16db1d0032fa81dbf7b30422a74a0ec386984)) -* fix: fixed inconsistencies and mistakes in variable names ([`7dd0d30`](https://github.com/bhklab/readii/commit/7dd0d3050916b4c2b1945ca772342f9599cc1b03)) +- Fixed inconsistencies and mistakes in variable names + ([`7dd0d30`](https://github.com/bhklab/readii/commit/7dd0d3050916b4c2b1945ca772342f9599cc1b03)) -* fix: incorrect indent in saveDataframeCSV ([`dd6d2f5`](https://github.com/bhklab/readii/commit/dd6d2f51bb55ae5bf5940b511862a7800c4a4fe1)) +- Incorrect indent in saveDataframeCSV + ([`dd6d2f5`](https://github.com/bhklab/readii/commit/dd6d2f51bb55ae5bf5940b511862a7800c4a4fe1)) -* fix: forgot to import pytest ([`6e978ca`](https://github.com/bhklab/readii/commit/6e978ca088971fe2ef80be629dcc6d7556c7cbd7)) +- Forgot to import pytest + ([`6e978ca`](https://github.com/bhklab/readii/commit/6e978ca088971fe2ef80be629dcc6d7556c7cbd7)) -* fix: fixed pyradiomics parameter file path and moved print statement of which ROI is processed back to radiomicFeatureExtraction ([`427eff7`](https://github.com/bhklab/readii/commit/427eff77663c66f919cfe239ae10b9080e4b0ef1)) +- Fixed pyradiomics parameter file path and moved print statement of which ROI is processed back to + radiomicFeatureExtraction + ([`427eff7`](https://github.com/bhklab/readii/commit/427eff77663c66f919cfe239ae10b9080e4b0ef1)) -* fix: missing pytest import and passing flattened SEG to alignImages ([`bab47e4`](https://github.com/bhklab/readii/commit/bab47e48a1f71d2ad8cde43ab9640c83b1337e00)) +- Missing pytest import and passing flattened SEG to alignImages + ([`bab47e4`](https://github.com/bhklab/readii/commit/bab47e48a1f71d2ad8cde43ab9640c83b1337e00)) -* fix: was missing pytest import ([`b38e7a4`](https://github.com/bhklab/readii/commit/b38e7a492a2bfd435ce21c4755268006cb226c44)) +- Was missing pytest import + ([`b38e7a4`](https://github.com/bhklab/readii/commit/b38e7a492a2bfd435ce21c4755268006cb226c44)) -* fix: updated image file paths ([`588ba46`](https://github.com/bhklab/readii/commit/588ba465ce459c64a62857ca97830def18a8f4cf)) +- Updated image file paths + ([`588ba46`](https://github.com/bhklab/readii/commit/588ba465ce459c64a62857ca97830def18a8f4cf)) -* fix: RTSTRUCT loader had incorrect variable for baseImageDirPath ([`6cfb08c`](https://github.com/bhklab/readii/commit/6cfb08cb52314931e98a71e3e9de5e0906debeb3)) +- Rtstruct loader had incorrect variable for baseImageDirPath + ([`6cfb08c`](https://github.com/bhklab/readii/commit/6cfb08cb52314931e98a71e3e9de5e0906debeb3)) ### Build System -* build: add PSR as dev dependency ([`17cb2da`](https://github.com/bhklab/readii/commit/17cb2da3352995c9e716733c79fb1bb8f09de23f)) +- Add PSR as dev dependency + ([`17cb2da`](https://github.com/bhklab/readii/commit/17cb2da3352995c9e716733c79fb1bb8f09de23f)) -* build: add pyradiomics dependency ([`cb11289`](https://github.com/bhklab/readii/commit/cb11289446aad3d1f0b7d874af0b17189fce0959)) +- Add pyradiomics dependency + ([`cb11289`](https://github.com/bhklab/readii/commit/cb11289446aad3d1f0b7d874af0b17189fce0959)) -* build: add med-imagetools as a dependency ([`84aef0f`](https://github.com/bhklab/readii/commit/84aef0fe589a1177e8145e30f7b6df15b79de140)) +- Add med-imagetools as a dependency + ([`84aef0f`](https://github.com/bhklab/readii/commit/84aef0fe589a1177e8145e30f7b6df15b79de140)) ### Features -* feat: changed outputFilePath to outputDirPath so output files can be standardized ([`d3ad8e8`](https://github.com/bhklab/readii/commit/d3ad8e8312dacb2315aace95722da777c3013e14)) +- Changed outputFilePath to outputDirPath so output files can be standardized + ([`d3ad8e8`](https://github.com/bhklab/readii/commit/d3ad8e8312dacb2315aace95722da777c3013e14)) -* feat: changed input variable to outputDirPath to have consistent output file name ([`a0b3336`](https://github.com/bhklab/readii/commit/a0b33368c983b5f62993d46e0a06f295ac9951a4)) +- Changed input variable to outputDirPath to have consistent output file name + ([`a0b3336`](https://github.com/bhklab/readii/commit/a0b33368c983b5f62993d46e0a06f295ac9951a4)) -* feat: check that output file is a csv before starting any feature extraction ([`d2390f5`](https://github.com/bhklab/readii/commit/d2390f50c0bd0f14b13e1eda1729f20c0ca4f9b4)) +- Check that output file is a csv before starting any feature extraction + ([`d2390f5`](https://github.com/bhklab/readii/commit/d2390f50c0bd0f14b13e1eda1729f20c0ca4f9b4)) -* feat: ignore unit test output files ([`a3fd21e`](https://github.com/bhklab/readii/commit/a3fd21eaacc43d7d1b8571c71f91b4bde0e8a530)) +- Ignore unit test output files + ([`a3fd21e`](https://github.com/bhklab/readii/commit/a3fd21eaacc43d7d1b8571c71f91b4bde0e8a530)) -* feat: added check for input not being a dataframe for saveDataframeCSV ([`69a0d84`](https://github.com/bhklab/readii/commit/69a0d84c1ab83487b059cf72d3d523d22cc37dc9)) +- Added check for input not being a dataframe for saveDataframeCSV + ([`69a0d84`](https://github.com/bhklab/readii/commit/69a0d84c1ab83487b059cf72d3d523d22cc37dc9)) -* feat: function for extraction of radiomic features from a single CT and segmentation pair ([`ecb5d5b`](https://github.com/bhklab/readii/commit/ecb5d5bd4c5ba143622f4db9bfff350a5dc70e05)) +- Function for extraction of radiomic features from a single CT and segmentation pair + ([`ecb5d5b`](https://github.com/bhklab/readii/commit/ecb5d5bd4c5ba143622f4db9bfff350a5dc70e05)) -* feat: added example pyradiomics config ([`2dee2eb`](https://github.com/bhklab/readii/commit/2dee2eb6ad5c355dec80ec8a72de7ff988077dbb)) +- Added example pyradiomics config + ([`2dee2eb`](https://github.com/bhklab/readii/commit/2dee2eb6ad5c355dec80ec8a72de7ff988077dbb)) -* feat: function to run radiomic feature extraction, including negative control and parallel options ([`aeb6efd`](https://github.com/bhklab/readii/commit/aeb6efdcdea607738efe33437e443d5bc92d59c7)) +- Function to run radiomic feature extraction, including negative control and parallel options + ([`aeb6efd`](https://github.com/bhklab/readii/commit/aeb6efdcdea607738efe33437e443d5bc92d59c7)) -* feat: add negative control generator functions ([`da6d9c0`](https://github.com/bhklab/readii/commit/da6d9c01275d399cb27191dc5eff21165107336b)) +- Add negative control generator functions + ([`da6d9c0`](https://github.com/bhklab/readii/commit/da6d9c01275d399cb27191dc5eff21165107336b)) -* feat: add function to match CTs and segmentations in medimagetools output and function to save out dataframe as csv ([`2f169e9`](https://github.com/bhklab/readii/commit/2f169e9eadae4f6a8fb73d34c48f03c7e652f991)) +- Add function to match CTs and segmentations in medimagetools output and function to save out + dataframe as csv + ([`2f169e9`](https://github.com/bhklab/readii/commit/2f169e9eadae4f6a8fb73d34c48f03c7e652f991)) -* feat: add seg label finder function ([`d575dee`](https://github.com/bhklab/readii/commit/d575dee223c8908eaedaa41312d361f113c9f768)) +- Add seg label finder function + ([`d575dee`](https://github.com/bhklab/readii/commit/d575dee223c8908eaedaa41312d361f113c9f768)) ### Testing -* test: check output from radiomicFeatureExtraction ([`c525247`](https://github.com/bhklab/readii/commit/c525247f88029b70f17b1249fd2fdedfa6eb3ddf)) - -* test: test output saving for matchCTtoSegmentation ([`995726d`](https://github.com/bhklab/readii/commit/995726dbff3a8e6e2a74de3e0e12e9f35e11a7a6)) +- Check output from radiomicFeatureExtraction + ([`c525247`](https://github.com/bhklab/readii/commit/c525247f88029b70f17b1249fd2fdedfa6eb3ddf)) -* test: updated test for radiomicFeatureExtraction to use default pyradiomics parameter file ([`617abbc`](https://github.com/bhklab/readii/commit/617abbcbf732433c08475652242830b6592fa321)) +- Test output saving for matchCTtoSegmentation + ([`995726d`](https://github.com/bhklab/readii/commit/995726dbff3a8e6e2a74de3e0e12e9f35e11a7a6)) -* test: added test for full radiomicFeatureExtraction function ([`ade890c`](https://github.com/bhklab/readii/commit/ade890cb2a1c8fd90f4fac433ade2c31e15f42a2)) +- Updated test for radiomicFeatureExtraction to use default pyradiomics parameter file + ([`617abbc`](https://github.com/bhklab/readii/commit/617abbcbf732433c08475652242830b6592fa321)) -* test: added incorrect object passed to saveDataframeCSV and fixed outputFilePath error test function call ([`281637b`](https://github.com/bhklab/readii/commit/281637b073dec5b1317a9d1bba627f036e552b64)) +- Added test for full radiomicFeatureExtraction function + ([`ade890c`](https://github.com/bhklab/readii/commit/ade890cb2a1c8fd90f4fac433ade2c31e15f42a2)) -* test: test csv error in saveDataframeCSV ([`3a9929a`](https://github.com/bhklab/readii/commit/3a9929a53b67291b0da46b4f53a82515d4df364b)) +- Added incorrect object passed to saveDataframeCSV and fixed outputFilePath error test function + call + ([`281637b`](https://github.com/bhklab/readii/commit/281637b073dec5b1317a9d1bba627f036e552b64)) -* test: functions for singleRadiomicFeatureExtraction ([`37ec5d6`](https://github.com/bhklab/readii/commit/37ec5d6e587642895a5f59faf773b305ad02480e)) +- Test csv error in saveDataframeCSV + ([`3a9929a`](https://github.com/bhklab/readii/commit/3a9929a53b67291b0da46b4f53a82515d4df364b)) -* test: started writing tests for radiomic feature extraction functions ([`cd31b86`](https://github.com/bhklab/readii/commit/cd31b86fda9bbca1c86111fcd9bd6ea0ff824daf)) +- Functions for singleRadiomicFeatureExtraction + ([`37ec5d6`](https://github.com/bhklab/readii/commit/37ec5d6e587642895a5f59faf773b305ad02480e)) -* test: added tests for matchCTtoSegmentation function ([`c66d24c`](https://github.com/bhklab/readii/commit/c66d24c77910aaa8af515cb0ece7dcf283de7628)) +- Started writing tests for radiomic feature extraction functions + ([`cd31b86`](https://github.com/bhklab/readii/commit/cd31b86fda9bbca1c86111fcd9bd6ea0ff824daf)) -* test: add getROIVoxelLabel test ([`2571cea`](https://github.com/bhklab/readii/commit/2571cea7c363f86716eb986588f746430502fb24)) +- Added tests for matchCTtoSegmentation function + ([`c66d24c`](https://github.com/bhklab/readii/commit/c66d24c77910aaa8af515cb0ece7dcf283de7628)) -* test: added image_processing unit tests ([`587eb2a`](https://github.com/bhklab/readii/commit/587eb2affeff25a4dfa59a2532029ec7989c9ecb)) +- Add getROIVoxelLabel test + ([`2571cea`](https://github.com/bhklab/readii/commit/2571cea7c363f86716eb986588f746430502fb24)) -* test: added image path fixtures and error check test ([`2b69fa1`](https://github.com/bhklab/readii/commit/2b69fa132e9f38868cfe895b6d29606ca6735d4f)) +- Added image_processing unit tests + ([`587eb2a`](https://github.com/bhklab/readii/commit/587eb2affeff25a4dfa59a2532029ec7989c9ecb)) -* test: add load segmentation module tests ([`6137f61`](https://github.com/bhklab/readii/commit/6137f6199628de184fc0b914871f0f1ee1059a07)) +- Added image path fixtures and error check test + ([`2b69fa1`](https://github.com/bhklab/readii/commit/2b69fa132e9f38868cfe895b6d29606ca6735d4f)) -### Unknown - -* data: changed naming convention for matchCTtoSeg output ([`0937fb5`](https://github.com/bhklab/readii/commit/0937fb538ec693eeef1212b18888ec682b2b1960)) - -* data: image metadata file for NSCLC_Radiogenomics, used in testing feature extraction ([`287349c`](https://github.com/bhklab/readii/commit/287349cfe0cbb33b0232aa865f29f81a2666b180)) - -* renamed file for consistency ([`39f969c`](https://github.com/bhklab/readii/commit/39f969c1b8f08fa8f1560b09bc380a270d2dc15a)) - -* data: imgtools output for test data for metadata tests ([`739c6e0`](https://github.com/bhklab/readii/commit/739c6e0a15fda507ed8a60cf76d03e462add5bac)) - -* Moved SEG example to named dataset directory ([`9f31b0c`](https://github.com/bhklab/readii/commit/9f31b0c42bf6d27e777be76a8638e77575d88002)) - -* updated dependencies ([`d42aec8`](https://github.com/bhklab/readii/commit/d42aec8b568d1cc745b644fe8aa3357cf314a2e5)) - -* Added test sample with RTSTRUCT segmentation ([`5124203`](https://github.com/bhklab/readii/commit/5124203b945b11ee64a659bd912b1661ac292835)) - -* Moved to named dataset folder ([`5077821`](https://github.com/bhklab/readii/commit/50778219cbffa6d86241a3e4bd28855606a24609)) - -* "feat: add example data and datasets module" ([`aaeded7`](https://github.com/bhklab/readii/commit/aaeded70258a8704df66994d0174a425050f8071)) - -* More renaming fixes ([`0776f25`](https://github.com/bhklab/readii/commit/0776f2564493315d54752ff6a0c17f3da6e20d88)) - -* test change in new repo ([`32aed17`](https://github.com/bhklab/readii/commit/32aed17a11048787d0b536210322918e9e5b3dc5)) - -* Renamed package to yarea ([`7519c43`](https://github.com/bhklab/readii/commit/7519c43e3950f907e6774a35095124ce4a2d630d)) +- Add load segmentation module tests + ([`6137f61`](https://github.com/bhklab/readii/commit/6137f6199628de184fc0b914871f0f1ee1059a07)) ## v0.1.0 (2023-11-23) ### Bug Fixes -* fix: correct conversion of sitk Image to array ([`34ddb65`](https://github.com/bhklab/readii/commit/34ddb6525983e69996671940e9f13f5107c69369)) +- Correct conversion of sitk Image to array + ([`34ddb65`](https://github.com/bhklab/readii/commit/34ddb6525983e69996671940e9f13f5107c69369)) -* fix: updated segImagePath variable ([`166831c`](https://github.com/bhklab/readii/commit/166831ccfb0c37b4e057dde254cc387e6a016fc6)) +- Updated segImagePath variable + ([`166831c`](https://github.com/bhklab/readii/commit/166831ccfb0c37b4e057dde254cc387e6a016fc6)) ### Build System -* build: added dev dependencies for docs ([`0e87a13`](https://github.com/bhklab/readii/commit/0e87a13807786bfb59aad4e5be9e9812033274fb)) +- Added dev dependencies for docs + ([`0e87a13`](https://github.com/bhklab/readii/commit/0e87a13807786bfb59aad4e5be9e9812033274fb)) -* build: add pytest and pytest-cov as dev dependencies ([`152b825`](https://github.com/bhklab/readii/commit/152b825929a8c0982dd6d5210a14fb891d5b6396)) +- Add pytest and pytest-cov as dev dependencies + ([`152b825`](https://github.com/bhklab/readii/commit/152b825929a8c0982dd6d5210a14fb891d5b6396)) -* build: remove upper bound on dependency versions ([`62ba9f8`](https://github.com/bhklab/readii/commit/62ba9f8f0ec84e8270083f7e82ffcecd30b8dd99)) +- Remove upper bound on dependency versions + ([`62ba9f8`](https://github.com/bhklab/readii/commit/62ba9f8f0ec84e8270083f7e82ffcecd30b8dd99)) -* build: add loading and image processing dependencies ([`96fd62f`](https://github.com/bhklab/readii/commit/96fd62f9794c3a97d84d7b5e1c112c1f8a32cbd0)) +- Add loading and image processing dependencies + ([`96fd62f`](https://github.com/bhklab/readii/commit/96fd62f9794c3a97d84d7b5e1c112c1f8a32cbd0)) ### Documentation -* docs: updated example ([`794530e`](https://github.com/bhklab/readii/commit/794530e2309a448aea4e3775957dcd2e1f95f0ce)) +- Updated example + ([`794530e`](https://github.com/bhklab/readii/commit/794530e2309a448aea4e3775957dcd2e1f95f0ce)) -* docs: updated docstrings for all functions ([`dbe6b84`](https://github.com/bhklab/readii/commit/dbe6b84ac9ecec6a5e5c2282d10ead56085de197)) +- Updated docstrings for all functions + ([`dbe6b84`](https://github.com/bhklab/readii/commit/dbe6b84ac9ecec6a5e5c2282d10ead56085de197)) ### Features -* feat: added image processing functions ([`b0ac044`](https://github.com/bhklab/readii/commit/b0ac04443cdf39addc601678cea5f49f44f1f89f)) +- Added image processing functions + ([`b0ac044`](https://github.com/bhklab/readii/commit/b0ac04443cdf39addc601678cea5f49f44f1f89f)) -* feat: add image loader functions ([`73f67f5`](https://github.com/bhklab/readii/commit/73f67f55dbb59c5967f0d70cd7d7d146118e634e)) +- Add image loader functions + ([`73f67f5`](https://github.com/bhklab/readii/commit/73f67f55dbb59c5967f0d70cd7d7d146118e634e)) ### Testing -* test: add unit test for loadDicomSITK ([`bef39f7`](https://github.com/bhklab/readii/commit/bef39f731363d1693f859ffbcdd6686540c1e98d)) - -### Unknown - -* Changed segImagePath to be optional input ([`cd36ce8`](https://github.com/bhklab/readii/commit/cd36ce833d5ee2c4cdc031ca68df0d446b760a92)) - -* remove incorrect RTSTRUCT from tests ([`0350329`](https://github.com/bhklab/readii/commit/0350329703480f2511d114658618e9dc6880ad29)) - -* Added NSCLC_Radiogenomics sample for testing ([`8df5fbb`](https://github.com/bhklab/readii/commit/8df5fbb2ccca773d60d7a59588a6da56173abc1d)) - -* renamed for loader functions ([`8009a37`](https://github.com/bhklab/readii/commit/8009a374aaaa12fe1b875866724b93496e83d474)) - -* Added dependency imports ([`f4394dc`](https://github.com/bhklab/readii/commit/f4394dc69378bd85e142f1cb412eb2fac756c735)) - -* updated variable names to be consistent ([`d74a455`](https://github.com/bhklab/readii/commit/d74a455e5e8ceab8344e814dab76645685107623)) - -* initial package setup ([`18c743b`](https://github.com/bhklab/readii/commit/18c743be0ba4f15c121834ccf16f9e70bcc5ec09)) +- Add unit test for loadDicomSITK + ([`bef39f7`](https://github.com/bhklab/readii/commit/bef39f731363d1693f859ffbcdd6686540c1e98d)) diff --git a/pyproject.toml b/pyproject.toml index 49b7213..13b5e32 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "readii" -version = "1.16.0" +version = "1.17.0" description = "A package to extract radiomic features!" authors = [{ name = "Katy Scott", email = "Katy.Scott@uhn.ca" }] diff --git a/src/readii/__init__.py b/src/readii/__init__.py index 3155a18..96049ac 100644 --- a/src/readii/__init__.py +++ b/src/readii/__init__.py @@ -1,4 +1,4 @@ # read version from installed package from importlib.metadata import version -__version__ = "1.16.0" +__version__ = "1.17.0"