quicktest update & merge CerebNet.utils.metrics into FastSurferCNN.utils.metrics #590
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taha-abdullah
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Oct 8, 2024
taha-abdullah
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- Deleted CerebNet.utils.metrics.py and merged all functionality into FastSurferCNN.utils.metrics.py
- refactoring usage across files
- changed dice score implementation to numpy (tried MONAI and Ignite, didn't work out)
- added support for multiple images in test_images
- nested parameterization (subjects and test files) in test_images and test_stats
dkuegler
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…ferCNN.utils.metrics.py - Deleting CerebNet.utils.metrics.py - refactoring usage across files - Changing back to numpy dice score implementation - removing CerebNet.utils.metrics.py from docs - Parameterized tests in test_images.py and test_stats.py - also added test configuration files for new filetypes - rebased pytest-feture onto merge-metrics - adding support for multiple images in test_images.py
- quicktest.yaml: commenting out trigger on pull request - FastSurferCNN.utils.metrics.py: docstring changes
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- Add author to github actions - Fix strings in quicktest workflow - Add parameter options pr/**** for docker-image parameters (in addition to build-cached), which allows for building from prs via manually triggered actions - Merge run and test of quicktest into one job to reduce clutter in reported checks - Add cleanup option for run-fastsurfer action - Add annotation with test results job to the quicktest workflow - Clean up some formatting - some minor bugfixes to FastSurferCNN.utils.common.SubjectDirectory - Add overloads to FastSurferCNN.utils.mapper.Mapper.__call__ and some minor bugfixes to the Mapper class to make it a bit more straighforward to use - Make the interface to FastSurferCNN.utils.mapper.TSVLookupTable by default more compatible with LUT.tsv and LUT.txt files (automatically detecting the correct format to read the file). - Add dataframe_to_table (reverse to table_to_dataframe) and read_statsfile to FastSurferCNN.segstats (as importable functions that may be used to handling stats files and stats data) - Update and rework the full quicktest pipeline including fixtures, required environment variables for configuration and data files with thresholds
Move thresholds files into data (instead of thresholds) and remove thresholds folder
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