├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md └── workflows │ ├── linter.yml │ ├── python-publish.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── pyproject.toml ├── spineps ├── .vscode │ └── settings.json ├── __init__.py ├── architectures │ ├── __init__.py │ ├── pl_densenet.py │ ├── pl_unet.py │ ├── read_labels.py │ └── unet3D.py ├── entrypoint.py ├── example │ ├── figures │ │ ├── example_semantic.png │ │ └── pipeline_processflow.png │ ├── get_gpu.py │ ├── helper_parallel.py │ └── template_roll_out.py ├── get_models.py ├── lab_model.py ├── phase_instance.py ├── phase_labeling.py ├── phase_post.py ├── phase_pre.py ├── phase_semantic.py ├── seg_enums.py ├── seg_model.py ├── seg_pipeline.py ├── seg_run.py ├── seg_utils.py └── utils │ ├── __init__.py │ ├── auto_download.py │ ├── citation_reminder.py │ ├── compat.py │ ├── data_iterators.py │ ├── default_preprocessor.py │ ├── export_prediction.py │ ├── filepaths.py │ ├── find_min_cost_path.py │ ├── generate_disc_labels.py │ ├── get_network_from_plans.py │ ├── image.py │ ├── inference_api.py │ ├── plans_handler.py │ ├── predictor.py │ ├── proc_functions.py │ ├── seg_modelconfig.py │ └── sliding_window_prediction.py └── unit_tests ├── test_architectures.py ├── test_compat.py ├── test_disc_labels.py ├── test_entrypoint.py ├── test_enums.py ├── test_filepaths.py ├── test_modelconfig.py ├── test_models.py ├── test_path.py ├── test_postproc.py ├── test_proc_functions.py └── test_semantic.py /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Hendrik-code/spineps/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- 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