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bhklab / readii

Radiomic Extraction and Analysis for DICOM Images (READII)
MIT License
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feat: remove dicom-parser, update mit, deprecate padSeg #51

Closed jjjermiah closed 3 weeks ago

jjjermiah commented 3 weeks ago

since padSegToMatchCT is only referenced once, in featureextraction, I've left everything the same with a try clause to be informative.

This is somewhat of a big change, but will allow for our packages to work with each other moving forward.

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📥 Commits Reviewing files that changed from the base of the PR and between 415d2179b46ad9f6235dc5e23e57890a51b3b92f and 6e4604110134a955de7c591855da59ab767ca154.

Walkthrough

The changes in this pull request involve modifications to several files, primarily focusing on .gitignore, pyproject.toml, src/readii/feature_extraction.py, and src/readii/image_processing.py. The .gitignore file has been updated to include new entries for ignored files. The pyproject.toml file has seen updates in dependency versions and the commenting out of a dependency. The feature_extraction.py file has improved error handling for a specific function, while the image_processing.py file has adjusted the scope of an import statement.

Changes

File Path Change Summary
.gitignore Added entries for data, trash, and .old (moved to a new line).
pyproject.toml Updated med-imagetools dependency version from >=1.2.0.2,<2 to >=1.5.7; commented out dicom-parser.
src/readii/feature_extraction.py Added try-except block around padSegToMatchCT call for error handling; removed import statement for padSegToMatchCT.
src/readii/image_processing.py Moved import statement for Series from dicom_parser inside padSegToMatchCT function.

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codecov[bot] commented 3 weeks ago

Codecov Report

Attention: Patch coverage is 0% with 9 lines in your changes missing coverage. Please review.

Project coverage is 62.80%. Comparing base (0cf184c) to head (6e46041). Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
src/readii/feature_extraction.py 0.00% 8 Missing :warning:
src/readii/image_processing.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #51 +/- ## ========================================== - Coverage 63.96% 62.80% -1.16% ========================================== Files 9 9 Lines 530 535 +5 ========================================== - Hits 339 336 -3 - Misses 191 199 +8 ```

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