├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md └── workflows │ ├── autoformat.yml │ ├── pr-lint.yml │ ├── release.yml │ └── tests.yml ├── .gitignore ├── .readthedocs.yaml ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── conf.py │ ├── index.rst │ ├── panoptica.core.rst │ ├── panoptica.metrics.rst │ ├── panoptica.rst │ ├── panoptica.utils.rst │ └── preprocess_readme.py ├── examples ├── example_spine_instance.py ├── example_spine_instance_config.py ├── example_spine_semantic.py ├── example_spine_statistics.py ├── figures │ ├── matched_instance.png │ ├── semantic.png │ ├── unmatched_instance.png │ └── workflow.png └── spine_seg │ ├── matched_instance │ ├── pred.nii.gz │ └── ref.nii.gz │ ├── semantic │ ├── pred.nii.gz │ └── ref.nii.gz │ └── unmatched_instance │ ├── pred.nii.gz │ └── ref.nii.gz ├── main.go ├── metrics.md ├── panoptica ├── __init__.py ├── _functionals.py ├── cli.py ├── configs │ ├── SegmentationClassGroups_example_unmatchedinstancepair.yaml │ ├── panoptica_evaluator_BRATS.yaml │ ├── panoptica_evaluator_ISLES.yaml │ ├── panoptica_evaluator_VERSE.yaml │ ├── panoptica_evaluator_default.yaml │ └── panoptica_evaluator_unmatched_instance.yaml ├── instance_approximator.py ├── instance_evaluator.py ├── instance_matcher.py ├── metrics │ ├── __init__.py │ ├── assd.py │ ├── center_distance.py │ ├── cldice.py │ ├── dice.py │ ├── hausdorff_distance.py │ ├── iou.py │ ├── metrics.py │ ├── normalized_surface_dice.py │ ├── relative_absolute_volume_error.py │ └── relative_volume_difference.py ├── panoptica_aggregator.py ├── panoptica_evaluator.py ├── panoptica_result.py ├── panoptica_statistics.py └── utils │ ├── __init__.py │ ├── citation_reminder.py │ ├── config.py │ ├── constants.py │ ├── edge_case_handling.py │ ├── filepath.py │ ├── input_check_and_conversion │ ├── check_nibabel_image.py │ ├── check_nrrd_image.py │ ├── check_numpy_array.py │ ├── check_sitk_image.py │ ├── check_torch_image.py │ ├── input_data_type_checker.py │ └── sanity_checker.py │ ├── instancelabelmap.py │ ├── label_group.py │ ├── numpy_utils.py │ ├── parallel_processing.py │ ├── processing_pair.py │ ├── segmentation_class.py │ └── timing.py ├── poetry.lock ├── pyproject.toml ├── unit_tests ├── test_cli.py ├── test_config.py ├── test_datatype.py ├── test_edgecasehandler.py ├── test_input_sanity_checker.py ├── test_labelgroup.py ├── test_matcher_variations.py ├── test_metrics.py ├── test_panoptic_aggregator.py ├── test_panoptic_evaluator.py ├── test_panoptic_pipeline.py ├── test_panoptic_result.py ├── test_panoptic_statistics.py ├── test_part_metrics.py ├── test_spatial_caching.py ├── test_unittest_file.tsv ├── test_utils.py └── unit_test_utils.py └── unit_tests_visual └── test_part_metrics.ipynb /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 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