├── .coveragerc ├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── AUTHOR ├── CONTRIBUTE.md ├── LICENCE.txt ├── README.md ├── coverage.svg ├── examples ├── __init__.py ├── a_generate_phantoms_for_examples.py ├── caliber_usage_distances_example.py ├── caliber_usage_example.py ├── cleaning_before_after.png ├── manipulator_example.py ├── prototype_check_imperfections.py ├── prototype_clean_a_segmentation.py ├── prototype_open_segmentations_in_freeview.py ├── prototype_segment_an_image.py ├── prototype_symmetrise_a_segmentation.py ├── simple_label_fusion.py └── simple_relabelling_example.py ├── logo_low.png ├── nilabels ├── __init__.py ├── agents │ ├── __init__.py │ ├── agents_controller.py │ ├── checker.py │ ├── fuser.py │ ├── header_controller.py │ ├── intensities_manipulator.py │ ├── labels_manipulator.py │ ├── math.py │ ├── measurer.py │ ├── segmenter.py │ ├── shape_manipulator.py │ └── symmetrizer.py ├── definitions.py └── tools │ ├── __init__.py │ ├── aux_methods │ ├── __init__.py │ ├── label_descriptor_manager.py │ ├── morpological_operations.py │ ├── sanity_checks.py │ ├── utils.py │ ├── utils_nib.py │ ├── utils_path.py │ └── utils_rotations.py │ ├── caliber │ ├── __init__.py │ ├── distances.py │ └── volumes_and_values.py │ ├── cleaning │ ├── __init__.py │ └── labels_cleaner.py │ ├── detections │ ├── __init__.py │ ├── check_imperfections.py │ ├── contours.py │ ├── get_segmentation.py │ └── island_detection.py │ ├── image_colors_manipulations │ ├── __init__.py │ ├── cutter.py │ ├── normaliser.py │ ├── relabeller.py │ └── segmentation_to_rgb.py │ ├── image_shape_manipulations │ ├── __init__.py │ ├── apply_passepartout.py │ ├── merger.py │ └── splitter.py │ └── visualiser │ ├── __init__.py │ ├── graphs_and_stats.py │ ├── see_volume.py │ └── volume_manipulations_for_visualisation.py ├── poetry.lock ├── pyproject.toml ├── requirements.txt └── tests ├── __init__.py ├── agents ├── __init__.py └── test_main_app_agent.py └── tools ├── __init__.py ├── decorators_tools.py ├── test_aux_methods_labels_descriptor_manager.py ├── test_aux_methods_morphological_operations.py ├── test_aux_methods_permutations.py ├── test_aux_methods_sanity_checks.py ├── test_aux_methods_utils.py ├── test_aux_methods_utils_nib.py ├── test_aux_methods_utils_path.py ├── test_aux_methods_utils_rotations.py ├── test_caliber_distances.py ├── test_caliber_volumes_and_values.py ├── test_cleaning_labels_cleaner.py ├── test_detections_check_imperfections.py ├── test_detections_contours.py ├── test_detections_get_segmentation.py ├── test_detections_island_detection.py ├── test_image_colors_manip_cutter.py ├── test_image_colors_manip_normaliser.py ├── test_image_colors_manip_relabeller.py ├── test_image_colors_manip_segm_to_rgb.py ├── test_image_shape_manip_apply_passepartout.py ├── test_image_shape_manip_merger.py ├── test_image_shape_manip_splitter.py └── test_labels_checker.py /.coveragerc: 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