├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── list_approx_weight.txt ├── mda_train_clinical_info.csv ├── notebooks ├── evaluate_segmentation.ipynb ├── evaluate_segmentation2022.ipynb ├── example_seg_submission.ipynb ├── example_seg_submission2022.ipynb ├── example_surv_submission.ipynb └── example_surv_submission2022.ipynb ├── requirements.txt ├── setup.py ├── src ├── __init__.py ├── aicrowd_evaluator │ ├── .gitignore │ ├── __init__.py │ ├── aicrowd.yaml │ ├── evaluator.py │ ├── requirements.txt │ ├── segmentation_metrics.py │ ├── survival_metrics.py │ └── utils.py ├── data │ ├── .gitkeep │ ├── __init__.py │ ├── bounding_box.py │ ├── cli_get_bb_as_mask.py │ ├── convert_to_nii_interobserver.py │ ├── extract_dicom_info.py │ ├── generate_voi_mapping.py │ ├── generate_voi_mapping_interobserver.py │ ├── make_dataset.py │ ├── make_dataset_2022.py │ ├── qc_parameters.yaml │ ├── quality_control.py │ ├── quality_control_total.py │ ├── sort_cases_per_annotator.py │ └── utils.py ├── evaluation │ ├── __init__.py │ └── scores.py ├── mda │ ├── keep_oropharynx.py │ ├── remove_newer_study.py │ └── sort_mda_train.py ├── nnUNet_baseline │ ├── rename_hecktor.py │ └── resample.py ├── resampling │ ├── __init__.py │ ├── resample_2022.py │ └── resample_with_boundingbox.py └── segmentation_gtvtn │ ├── evaluation │ └── utils.py │ ├── models │ ├── fetch_data_segmentation_gtvtn.py │ ├── losses.py │ └── model.py │ └── train_gtvtn.py ├── studies.pkl └── test_environment.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/README.md -------------------------------------------------------------------------------- /list_approx_weight.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/list_approx_weight.txt -------------------------------------------------------------------------------- /mda_train_clinical_info.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/mda_train_clinical_info.csv -------------------------------------------------------------------------------- /notebooks/evaluate_segmentation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/evaluate_segmentation.ipynb -------------------------------------------------------------------------------- /notebooks/evaluate_segmentation2022.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/evaluate_segmentation2022.ipynb -------------------------------------------------------------------------------- /notebooks/example_seg_submission.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/example_seg_submission.ipynb -------------------------------------------------------------------------------- /notebooks/example_seg_submission2022.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/example_seg_submission2022.ipynb -------------------------------------------------------------------------------- /notebooks/example_surv_submission.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/example_surv_submission.ipynb -------------------------------------------------------------------------------- /notebooks/example_surv_submission2022.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/notebooks/example_surv_submission2022.ipynb -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/setup.py -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/aicrowd_evaluator/.gitignore: -------------------------------------------------------------------------------- 1 | data/ -------------------------------------------------------------------------------- /src/aicrowd_evaluator/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/__init__.py -------------------------------------------------------------------------------- /src/aicrowd_evaluator/aicrowd.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/aicrowd.yaml -------------------------------------------------------------------------------- /src/aicrowd_evaluator/evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/evaluator.py -------------------------------------------------------------------------------- /src/aicrowd_evaluator/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/requirements.txt -------------------------------------------------------------------------------- /src/aicrowd_evaluator/segmentation_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/segmentation_metrics.py -------------------------------------------------------------------------------- /src/aicrowd_evaluator/survival_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/survival_metrics.py -------------------------------------------------------------------------------- /src/aicrowd_evaluator/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/aicrowd_evaluator/utils.py -------------------------------------------------------------------------------- /src/data/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/data/bounding_box.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/bounding_box.py -------------------------------------------------------------------------------- /src/data/cli_get_bb_as_mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/cli_get_bb_as_mask.py -------------------------------------------------------------------------------- /src/data/convert_to_nii_interobserver.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/convert_to_nii_interobserver.py -------------------------------------------------------------------------------- /src/data/extract_dicom_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/extract_dicom_info.py -------------------------------------------------------------------------------- /src/data/generate_voi_mapping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/generate_voi_mapping.py -------------------------------------------------------------------------------- /src/data/generate_voi_mapping_interobserver.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/generate_voi_mapping_interobserver.py -------------------------------------------------------------------------------- /src/data/make_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/make_dataset.py -------------------------------------------------------------------------------- /src/data/make_dataset_2022.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/make_dataset_2022.py -------------------------------------------------------------------------------- /src/data/qc_parameters.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/qc_parameters.yaml -------------------------------------------------------------------------------- /src/data/quality_control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/quality_control.py -------------------------------------------------------------------------------- /src/data/quality_control_total.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/quality_control_total.py -------------------------------------------------------------------------------- /src/data/sort_cases_per_annotator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/sort_cases_per_annotator.py -------------------------------------------------------------------------------- /src/data/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/data/utils.py -------------------------------------------------------------------------------- /src/evaluation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/evaluation/scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/evaluation/scores.py -------------------------------------------------------------------------------- /src/mda/keep_oropharynx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/mda/keep_oropharynx.py -------------------------------------------------------------------------------- /src/mda/remove_newer_study.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/mda/remove_newer_study.py -------------------------------------------------------------------------------- /src/mda/sort_mda_train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/mda/sort_mda_train.py -------------------------------------------------------------------------------- /src/nnUNet_baseline/rename_hecktor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/nnUNet_baseline/rename_hecktor.py -------------------------------------------------------------------------------- /src/nnUNet_baseline/resample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/nnUNet_baseline/resample.py -------------------------------------------------------------------------------- /src/resampling/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/resampling/resample_2022.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/resampling/resample_2022.py -------------------------------------------------------------------------------- /src/resampling/resample_with_boundingbox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/resampling/resample_with_boundingbox.py -------------------------------------------------------------------------------- /src/segmentation_gtvtn/evaluation/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/segmentation_gtvtn/evaluation/utils.py -------------------------------------------------------------------------------- /src/segmentation_gtvtn/models/fetch_data_segmentation_gtvtn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/segmentation_gtvtn/models/fetch_data_segmentation_gtvtn.py -------------------------------------------------------------------------------- /src/segmentation_gtvtn/models/losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/segmentation_gtvtn/models/losses.py -------------------------------------------------------------------------------- /src/segmentation_gtvtn/models/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/segmentation_gtvtn/models/model.py -------------------------------------------------------------------------------- /src/segmentation_gtvtn/train_gtvtn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/src/segmentation_gtvtn/train_gtvtn.py -------------------------------------------------------------------------------- /studies.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/studies.pkl -------------------------------------------------------------------------------- /test_environment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voreille/hecktor/HEAD/test_environment.py --------------------------------------------------------------------------------