Coverage report: 6%

Files Functions Classes

coverage.py v7.9.2, created at 2025-07-16 16:14 -0700

File function statements missing excluded branches partial coverage
copick_torch/__init__.py (no function) 8 0 0 0 0 100%
copick_torch/_version.py (no function) 1 0 0 0 0 100%
copick_torch/augmentations.py MixupTransform.__init__ 4 0 0 0 0 100%
copick_torch/augmentations.py MixupTransform.randomize 7 2 0 4 2 64%
copick_torch/augmentations.py MixupTransform.__call__ 9 1 0 4 1 85%
copick_torch/augmentations.py MixupTransform.mixup_criterion 1 1 0 0 0 0%
copick_torch/augmentations.py FourierAugment3D.__init__ 7 7 0 0 0 0%
copick_torch/augmentations.py FourierAugment3D.randomize 8 8 0 4 0 0%
copick_torch/augmentations.py FourierAugment3D.__call__ 17 17 0 10 0 0%
copick_torch/augmentations.py FourierAugment3D._apply_fourier_aug 18 18 0 4 0 0%
copick_torch/augmentations.py (no function) 18 0 0 0 0 100%
copick_torch/copick.py CopickDataset.__init__ 37 37 0 10 0 0%
copick_torch/copick.py CopickDataset._set_random_seed 6 6 0 4 0 0%
copick_torch/copick.py CopickDataset._compute_sample_weights 4 4 0 0 0 0%
copick_torch/copick.py CopickDataset._get_cache_path 19 19 0 12 0 0%
copick_torch/copick.py CopickDataset._load_or_process_data 25 25 0 14 0 0%
copick_torch/copick.py CopickDataset._load_from_pickle 8 8 0 2 0 0%
copick_torch/copick.py CopickDataset._save_to_pickle 2 2 0 0 0 0%
copick_torch/copick.py CopickDataset._load_from_parquet 27 27 0 14 0 0%
copick_torch/copick.py CopickDataset._save_to_parquet 20 20 0 6 0 0%
copick_torch/copick.py CopickDataset._extract_subvolume_with_validation 35 35 0 10 0 0%
copick_torch/copick.py CopickDataset._load_data 58 58 0 20 0 0%
copick_torch/copick.py CopickDataset._sample_background_points 22 22 0 8 0 0%
copick_torch/copick.py CopickDataset._augment_subvolume 46 46 0 38 0 0%
copick_torch/copick.py CopickDataset._brightness 2 2 0 0 0 0%
copick_torch/copick.py CopickDataset._gaussian_blur 2 2 0 0 0 0%
copick_torch/copick.py CopickDataset._intensity_scaling 2 2 0 0 0 0%
copick_torch/copick.py CopickDataset._flip 3 3 0 2 0 0%
copick_torch/copick.py CopickDataset._rotate 8 8 0 6 0 0%
copick_torch/copick.py CopickDataset._rotate_z 18 18 0 2 0 0%
copick_torch/copick.py CopickDataset._apply_mixup 11 11 0 6 0 0%
copick_torch/copick.py CopickDataset.__len__ 1 1 0 0 0 0%
copick_torch/copick.py CopickDataset.__getitem__ 37 37 0 30 0 0%
copick_torch/copick.py CopickDataset.get_sample_weights 1 1 0 0 0 0%
copick_torch/copick.py CopickDataset.keys 1 1 0 0 0 0%
copick_torch/copick.py CopickDataset.examples 31 31 0 16 0 0%
copick_torch/copick.py CopickDataset.get_class_distribution 9 9 0 6 0 0%
copick_torch/copick.py CopickDataset.stratified_split 29 29 0 12 0 0%
copick_torch/copick.py CopickDataset.balance_classes 71 71 0 36 0 0%
copick_torch/copick.py CopickDataset.extract_grid_patches 58 58 0 30 0 0%
copick_torch/copick.py CopickDataset.extract_from_region 32 32 0 12 0 0%
copick_torch/copick.py (no function) 46 0 0 0 0 100%
copick_torch/dataset.py SimpleDatasetMixin.__getitem__ 7 7 0 2 0 0%
copick_torch/dataset.py SimpleCopickDataset.__init__ 33 33 0 4 0 0%
copick_torch/dataset.py SimpleCopickDataset._set_random_seed 6 6 0 4 0 0%
copick_torch/dataset.py SimpleCopickDataset._compute_sample_weights 4 4 0 0 0 0%
copick_torch/dataset.py SimpleCopickDataset._get_cache_path 19 19 0 12 0 0%
copick_torch/dataset.py SimpleCopickDataset._load_or_process_data 25 25 0 14 0 0%
copick_torch/dataset.py SimpleCopickDataset._load_from_pickle 8 8 0 2 0 0%
copick_torch/dataset.py SimpleCopickDataset._save_to_pickle 2 2 0 0 0 0%
copick_torch/dataset.py SimpleCopickDataset._load_from_parquet 27 27 0 14 0 0%
copick_torch/dataset.py SimpleCopickDataset._save_to_parquet 20 20 0 6 0 0%
copick_torch/dataset.py SimpleCopickDataset._extract_subvolume_with_validation 35 35 0 10 0 0%
copick_torch/dataset.py SimpleCopickDataset._load_data 58 58 0 20 0 0%
copick_torch/dataset.py SimpleCopickDataset._sample_background_points 22 22 0 8 0 0%
copick_torch/dataset.py SimpleCopickDataset._augment_subvolume 20 20 0 12 0 0%
copick_torch/dataset.py SimpleCopickDataset.__len__ 1 1 0 0 0 0%
copick_torch/dataset.py SimpleCopickDataset.get_sample_weights 1 1 0 0 0 0%
copick_torch/dataset.py SimpleCopickDataset.keys 1 1 0 0 0 0%
copick_torch/dataset.py SimpleCopickDataset.get_class_distribution 9 9 0 6 0 0%
copick_torch/dataset.py SplicedMixupDataset.__init__ 14 14 0 0 0 0%
copick_torch/dataset.py SplicedMixupDataset._generate_synthetic_samples 35 35 0 10 0 0%
copick_torch/dataset.py SplicedMixupDataset._load_copick_roots 17 17 0 4 0 0%
copick_torch/dataset.py SplicedMixupDataset._ensure_zarr_loaded 6 6 0 2 0 0%
copick_torch/dataset.py SplicedMixupDataset._load_experimental_zarr 12 12 0 2 0 0%
copick_torch/dataset.py SplicedMixupDataset._load_synthetic_zarr 12 12 0 2 0 0%
copick_torch/dataset.py SplicedMixupDataset._get_available_tomograms 19 19 0 12 0 0%
copick_torch/dataset.py SplicedMixupDataset._load_segmentation_masks 16 16 0 6 0 0%
copick_torch/dataset.py SplicedMixupDataset._get_segmentation_masks 20 20 0 14 0 0%
copick_torch/dataset.py SplicedMixupDataset._extract_random_crop 14 14 0 2 0 0%
copick_torch/dataset.py SplicedMixupDataset._extract_bounding_box 38 38 0 14 0 0%
copick_torch/dataset.py SplicedMixupDataset._splice_volumes 12 12 0 2 0 0%
copick_torch/dataset.py SplicedMixupDataset.__getitem__ 18 18 0 8 0 0%
copick_torch/dataset.py (no function) 52 0 0 0 0 100%
copick_torch/logging.py setup_logging 4 4 0 0 0 0%
copick_torch/logging.py (no function) 3 0 0 0 0 100%
copick_torch/minimal_dataset.py MinimalCopickDataset.__init__ 20 20 0 4 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset._extract_name_to_label 5 5 0 2 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset._load_data 126 126 0 36 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset._preload_data 15 15 0 6 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset._print_class_distribution 14 14 0 10 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset._sample_background_points 25 25 0 8 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.extract_subvolume 28 28 0 4 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.__len__ 1 1 0 0 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.__getitem__ 10 10 0 4 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.keys 4 4 0 2 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.get_class_distribution 9 9 0 8 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.get_sample_weights 7 7 0 2 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.save 33 33 0 8 0 0%
copick_torch/minimal_dataset.py MinimalCopickDataset.load 57 57 0 16 0 0%
copick_torch/minimal_dataset.py (no function) 28 0 0 0 0 100%
copick_torch/samplers.py ClassBalancedSampler.__init__ 8 8 0 0 0 0%
copick_torch/samplers.py ClassBalancedSampler.__iter__ 2 2 0 0 0 0%
copick_torch/samplers.py ClassBalancedSampler.__len__ 1 1 0 0 0 0%
copick_torch/samplers.py (no function) 8 0 0 0 0 100%
tests/__init__.py (no function) 0 0 0 0 0 100%
tests/setup_test_env.py setup_test_env 11 11 0 0 0 0%
tests/setup_test_env.py (no function) 5 5 2 0 0 0%
tests/test_augmentations.py test_mixup_transform 24 9 0 2 0 65%
tests/test_augmentations.py test_mixup_transform.dummy_criterion 1 1 0 0 0 0%
tests/test_augmentations.py test_fourier_augment3d 11 11 0 0 0 0%
tests/test_augmentations.py test_fourier_augment3d_channel_first 12 12 0 4 0 0%
tests/test_augmentations.py test_zero_probability 9 9 0 0 0 0%
tests/test_augmentations.py (no function) 8 0 0 0 0 100%
tests/test_background_sampling.py TestBackgroundSampling.setUp 5 5 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.tearDown 1 1 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_points 13 13 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_points.mock_extract 1 1 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_points_no_particles 8 8 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_fails_validation 10 10 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_fails_validation.mock_extract 1 1 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_distance_constraint 10 10 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_sample_background_distance_constraint.mock_extract 1 1 0 0 0 0%
tests/test_background_sampling.py TestBackgroundSampling.test_include_background_in_load_data 17 17 0 0 0 0%
tests/test_background_sampling.py (no function) 19 19 2 0 0 0%
tests/test_copick_data_portal_distribution.py TestCopickDataPortalDistribution.setUpClass 9 9 0 0 0 0%
tests/test_copick_data_portal_distribution.py TestCopickDataPortalDistribution.tearDownClass 1 1 0 0 0 0%
tests/test_copick_data_portal_distribution.py TestCopickDataPortalDistribution.test_pickable_object_distribution 51 51 0 26 0 0%
tests/test_copick_data_portal_distribution.py (no function) 17 17 2 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.setUp 6 6 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.tearDown 1 1 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.test_init_basic 6 6 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.test_dataset_empty 8 8 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.test_augmentations 12 12 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.test_getitem_no_augment 11 11 0 0 0 0%
tests/test_copick_dataset.py TestCopickDataset.test_stratified_split 24 24 0 6 0 0%
tests/test_copick_dataset.py (no function) 20 20 2 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.setUp 10 10 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.tearDown 1 1 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_get_cache_path_pickle 4 4 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_get_cache_path_parquet 4 4 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_get_cache_path_with_copick_root 8 8 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_save_load_pickle 19 19 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_save_load_parquet_basics 10 10 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_parquet_metadata 8 8 0 2 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_load_or_process_data_with_cache 6 6 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_load_or_process_data_without_cache 2 2 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_load_or_process_data_no_cache_dir 2 2 0 0 0 0%
tests/test_dataset_caching.py TestDatasetCaching.test_max_samples_limit 12 12 0 2 0 0%
tests/test_dataset_caching.py (no function) 33 33 2 0 0 0%
tests/test_dataset_examples.py TestDatasetExamples.setUpClass 9 9 0 2 0 0%
tests/test_dataset_examples.py TestDatasetExamples.tearDownClass 6 6 0 2 0 0%
tests/test_dataset_examples.py TestDatasetExamples.test_class_name_to_filename_consistency 55 55 0 10 0 0%
tests/test_dataset_examples.py TestDatasetExamples.test_class_name_to_filename_consistency.patched_init 4 4 0 2 0 0%
tests/test_dataset_examples.py (no function) 20 20 2 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.setUp 6 6 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.tearDown 1 1 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.test_extract_center_valid 7 7 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.test_extract_edge_padded 6 6 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.test_extract_near_edge 6 6 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.test_random_strategy 8 8 0 0 0 0%
tests/test_dataset_extraction.py TestDatasetExtraction.test_jittered_strategy 13 13 0 0 0 0%
tests/test_dataset_extraction.py (no function) 20 20 2 0 0 0%
tests/test_integration.py TestIntegration.setUp 2 2 0 0 0 0%
tests/test_integration.py TestIntegration.test_dataset_with_real_data 13 13 0 6 0 0%
tests/test_integration.py TestIntegration.test_examples_method 11 11 0 6 0 0%
tests/test_integration.py (no function) 12 12 2 0 0 0%
tests/test_logging.py TestLogging.test_setup_logging 5 5 0 0 0 0%
tests/test_logging.py (no function) 5 5 2 0 0 0%
tests/test_minimal_dataset.py TestMinimalCopickDataset.test_dataset_initialization 47 47 0 8 0 0%
tests/test_minimal_dataset.py TestMinimalCopickDataset.test_class_to_label_consistency 37 37 0 8 0 0%
tests/test_minimal_dataset.py (no function) 15 15 2 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.setUp 1 1 0 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.test_init 9 9 0 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.test_init_with_custom_samples 4 4 0 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.test_init_with_no_replacement 2 2 0 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.test_iter 11 11 0 0 0 0%
tests/test_samplers.py TestClassBalancedSampler.test_len 5 5 0 0 0 0%
tests/test_samplers.py (no function) 12 12 2 0 0 0%
tests/test_simple_dataset.py TestSimpleDatasetMixin.setUp 4 4 0 0 0 0%
tests/test_simple_dataset.py TestSimpleDatasetMixin.test_getitem 5 5 0 0 0 0%
tests/test_simple_dataset.py TestSimpleDatasetMixin.test_getitem_with_augmentation 4 4 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.setUp 6 6 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.tearDown 1 1 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_init_basic 6 6 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_init_with_options 14 14 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_dataset_empty 8 8 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_compute_sample_weights 5 5 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_get_sample_weights 4 4 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_keys 4 4 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_get_class_distribution 7 7 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_validation_logic_missing_config 2 2 0 0 0 0%
tests/test_simple_dataset.py TestSimpleCopickDataset.test_extract_subvolume_strategies 12 12 0 0 0 0%
tests/test_simple_dataset.py (no function) 34 34 2 0 0 0%
tests/test_simple_dataset_docs.py TestSimpleDatasetDocs.setUpClass 9 9 0 2 0 0%
tests/test_simple_dataset_docs.py TestSimpleDatasetDocs.tearDownClass 6 6 0 2 0 0%
tests/test_simple_dataset_docs.py TestSimpleDatasetDocs.test_class_name_to_filename_consistency 55 55 0 10 0 0%
tests/test_simple_dataset_docs.py TestSimpleDatasetDocs.test_class_name_to_filename_consistency.patched_init 4 4 0 2 0 0%
tests/test_simple_dataset_docs.py (no function) 20 20 2 0 0 0%
tests/test_spliced_mixup_dataset.py TestSplicedMixupDataset.setUp 17 17 0 0 0 0%
tests/test_spliced_mixup_dataset.py TestSplicedMixupDataset.test_splice_volumes_gaussian_blending 18 18 0 0 0 0%
tests/test_spliced_mixup_dataset.py TestSplicedMixupDataset.test_gaussian_blending_vs_no_blending 14 14 0 0 0 0%
tests/test_spliced_mixup_dataset.py (no function) 9 9 2 0 0 0%
Total   2832 2628 28 726 3 6%

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