├── .github └── workflows │ └── github_actions.yml ├── README.md ├── pyproject.toml ├── setup.sh ├── test_assets ├── box_metrics │ ├── cow-roi.json │ ├── test_ROI-1_Metadata.txt │ ├── test_crop_gt_and_pred.txt │ ├── test_iou_dict_from_files_hollow_6x3x3_4x3x3_box_1.JSON │ ├── test_iou_dict_from_files_hollow_6x3x3_4x3x3_box_2.TXT │ ├── test_iou_dict_from_files_hollow_6x3x3_4x7x3_box_1.TXT │ ├── test_iou_dict_from_files_hollow_6x3x3_4x7x3_box_2.JSON │ ├── test_iou_dict_from_files_hollow_6x3x3_shifted_box_1.json │ ├── test_iou_dict_from_files_hollow_6x3x3_shifted_box_2.txt │ ├── test_iou_dict_from_files_tiny_vs_small_box_1.json │ └── test_iou_dict_from_files_tiny_vs_small_box_2.txt ├── edg_metrics │ ├── antpos_np_arr_pred.json │ ├── cow-ant-post-classification_gt.JSON │ ├── cow-ant-post-classification_pred.yml │ └── topcow_ct_003.yml ├── seg_metrics │ ├── 2D │ │ ├── shape_11x11_2D_Fig10_bin_gt.nii.gz │ │ ├── shape_11x11_2D_Fig10_bin_pred.nii.gz │ │ ├── shape_11x11_2D_Fig50_large_bin_gt.nii.gz │ │ ├── shape_11x11_2D_Fig50_large_bin_pred_1.nii.gz │ │ ├── shape_11x11_2D_Fig50_large_bin_pred_2.nii.gz │ │ ├── shape_14x14_Fig63_bin_gt.nii.gz │ │ ├── shape_14x14_Fig63_bin_pred.nii.gz │ │ ├── shape_5x5_2D_RBY_pred.nii.gz │ │ ├── shape_5x5_2D_RGB_gt.nii.gz │ │ ├── shape_5x5_2D_clDice_Tshaped_gt.nii.gz │ │ ├── shape_5x5_2D_clDice_Tshaped_multiclass_gt.nii.gz │ │ ├── shape_5x5_2D_clDice_Tshaped_multiclass_pred.nii.gz │ │ ├── shape_5x5_2D_clDice_Tshaped_pred.nii.gz │ │ ├── shape_5x5_2D_label15_11_pred.nii.gz │ │ ├── shape_5x5_2D_label15_12_11_gt.nii.gz │ │ ├── shape_5x5_2D_label64_ring_gt.nii.gz │ │ ├── shape_5x5_2D_label64_ring_pred.nii.gz │ │ ├── shape_5x5_2D_zigzag_gt.nii.gz │ │ ├── shape_5x5_2D_zigzag_label5_gt.nii.gz │ │ ├── shape_5x5_2D_zigzag_label5_pred.nii.gz │ │ ├── shape_5x5_2D_zigzag_pred.nii.gz │ │ ├── shape_6x3_2D.nii.gz │ │ ├── shape_6x3_2D_clDice_Fig51_gt.nii.gz │ │ ├── shape_6x3_2D_clDice_Fig51_pred_1.nii.gz │ │ ├── shape_6x3_2D_clDice_Fig51_pred_2.nii.gz │ │ ├── shape_6x3_2D_clDice_elong_gt.nii.gz │ │ ├── shape_6x3_2D_clDice_elong_pred.nii.gz │ │ ├── shape_7x7_Fig59_bin_gt.nii.gz │ │ ├── shape_7x7_Fig59_bin_pred_1top.nii.gz │ │ └── shape_7x7_Fig59_bin_pred_2top.nii.gz │ ├── 3D │ │ ├── betti_num_singleBlob_2x2x2_gt.nii.gz │ │ ├── betti_num_singleBlob_2x2x2_pred.nii.gz │ │ ├── detection_label8910_gt_squareL4.nii.gz │ │ ├── detection_label8910_pred_squareL4.nii.gz │ │ ├── expected_1donut_gt_crop.nii.gz │ │ ├── expected_1donut_pred_crop.nii.gz │ │ ├── scaled_image_label_123_gt.nii.gz │ │ ├── scaled_image_label_123_pred.nii.gz │ │ ├── shape_11x11x5_3D_Fig54_label1-5_gt.nii.gz │ │ ├── shape_11x11x5_3D_Fig54_label1-5_pred.nii.gz │ │ ├── shape_2x2x2_3D_Fig50_label15_10_gt.nii.gz │ │ ├── shape_2x2x2_3D_Fig50_label15_10_pred.nii.gz │ │ ├── shape_3x4x2_3D_cross.nii.gz │ │ ├── shape_3x4x2_3D_twoIslands.nii.gz │ │ ├── shape_3x4x2_3D_twoIslands_multiclass.nii.gz │ │ ├── shape_5x6x4_3D_cross_padded.nii.gz │ │ ├── shape_5x6x4_3D_twoIslands_padded.nii.gz │ │ ├── shape_5x7x9_3D_1donut.nii.gz │ │ ├── shape_5x7x9_3D_1donut_multiclass.nii.gz │ │ ├── shape_8x8x8_3D_8Cubes_gt.nii.gz │ │ └── shape_8x8x8_3D_8Cubes_pred.nii.gz │ └── topcow_roi │ │ ├── LPS_ACA_flipped.nii.gz │ │ ├── LPS_ICA_PCA_flipped.nii.gz │ │ ├── topcow_ct_roi_003.nii.gz │ │ ├── topcow_ct_roi_014.nii.gz │ │ ├── topcow_ct_roi_023.nii.gz │ │ ├── topcow_mr_roi_003.nii.gz │ │ ├── topcow_mr_roi_014.nii.gz │ │ └── topcow_mr_roi_023.nii.gz ├── task_1_seg_ground-truth │ ├── shape_5x7x9_3D_1donut.nii.gz │ └── shape_8x8x8_3D_8Cubes_gt.nii.gz ├── task_1_seg_output │ └── expected_e2e_test_metrics.json ├── task_1_seg_predictions │ ├── shape_5x7x9_3D_1donut_multiclass.mha │ └── shape_8x8x8_3D_8Cubes_pred.mha ├── task_1_seg_roi-metadata │ ├── shap_5x7x9_3D_1donut_.txt │ └── shape_8x8x8_3D_8Cubes.txt ├── task_2_box_ground-truth │ ├── test_iou_dict_from_files_hollow_6x3x3_4x3x3_box_2.TXT │ ├── test_iou_dict_from_files_hollow_6x3x3_shifted_box_2.txt │ └── test_iou_dict_from_files_tiny_vs_small_box_2.txt ├── task_2_box_output │ └── expected_e2e_test_metrics.json ├── task_2_box_predictions │ ├── hollow_6x3x3_4x3x3 │ │ └── output │ │ │ └── cow-roi.json │ ├── hollow_6x3x3_shifted │ │ └── output │ │ │ └── cow-roi.json │ └── tiny_vs_small │ │ └── output │ │ └── cow-roi.json ├── task_3_edg_ground-truth │ ├── cow-ant-post-classification_gt.JSON │ └── topcow_ct_003.yml ├── task_3_edg_output │ └── expected_e2e_test_metrics.json └── task_3_edg_predictions │ ├── graph_0 │ └── output │ │ └── cow-ant-post-classification.yml │ └── graph_1 │ └── output │ └── cow-ant-post-classification.json └── topcow24_eval ├── __init__.py ├── aggregate ├── aggregate_all_detection_dicts.py ├── aggregate_all_graph_dicts.py ├── aggregate_all_topo_dicts.py ├── edge_list_to_variant_str.py ├── test_aggregate_all_detection_dicts.py ├── test_aggregate_all_graph_dicts.py ├── test_aggregate_all_topo_dicts.py └── test_edge_list_to_variant_str.py ├── base_algorithm.py ├── configs.py ├── constants.py ├── evaluation.py ├── for_gc_docker.py ├── metrics ├── box_metrics │ ├── __init__.py │ ├── boundary_iou_from_tuple.py │ ├── boundary_points_with_distances.py │ ├── iou_dict_from_files.py │ ├── test_boundary_iou_from_tuple.py │ ├── test_boundary_points_with_distances.py │ └── test_iou_dict_from_files.py ├── edg_metrics │ ├── edge_dict_to_list.py │ ├── graph_dict_from_files.py │ ├── test_edge_dict_to_list.py │ └── test_graph_dict_from_files.py └── seg_metrics │ ├── clDice.py │ ├── cls_avg_b0.py │ ├── cls_avg_dice.py │ ├── cls_avg_hd95.py │ ├── detection_grp2_labels.py │ ├── generate_cls_avg_dict.py │ ├── graph_classification │ ├── __init__.py │ ├── edge_criteria.py │ ├── generate_edgelist.py │ ├── graph_classification.py │ ├── test_edge_criteria.py │ ├── test_generate_edgelist.py │ └── test_graph_classification.py │ ├── test_clDice.py │ ├── test_cls_avg_b0.py │ ├── test_cls_avg_dice.py │ ├── test_cls_avg_hd95.py │ ├── test_detection_grp2_labels.py │ ├── test_generate_cls_avg_dict.py │ └── topology_matching │ ├── __init__.py │ ├── check_LR_flip.py │ ├── test_check_LR_flip.py │ ├── test_topology_matching.py │ └── topology_matching.py ├── score_case_task_1_seg.py ├── score_case_task_2_box.py ├── score_case_task_3_edg.py ├── test_evaluation_task_1_seg.py ├── test_evaluation_task_2_box.py ├── test_evaluation_task_3_edg.py ├── test_score_case.py └── utils ├── crop_gt_and_pred.py ├── crop_sitk.py ├── test_crop_gt_and_pred.py ├── test_crop_sitk.py ├── test_utils_box.py ├── test_utils_edge.py ├── test_utils_mask.py ├── test_utils_neighborhood.py ├── tree_view_dir.py ├── utils_box.py ├── utils_edge.py ├── utils_mask.py ├── utils_neighborhood.py └── utils_nii_mha_sitk.py /.github/workflows/github_actions.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CoWBenchmark/TopCoW_Eval_Metrics/HEAD/.github/workflows/github_actions.yml 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