Coverage report: 79%

Files Functions Classes

coverage.py v7.8.0, created at 2025-04-02 00:06 +0000

File function statements missing excluded coverage
src/recon3d/__init__.py (no function) 0 0 0 100%
src/recon3d/command_line.py recon3d 1 1 0 0%
src/recon3d/command_line.py hello 1 0 0 100%
src/recon3d/command_line.py module_version 5 0 0 100%
src/recon3d/command_line.py work_in_progress 1 1 0 0%
src/recon3d/command_line.py (no function) 8 0 0 100%
src/recon3d/constants.py (no function) 19 0 0 100%
src/recon3d/downscale.py apply_bbox 4 0 0 100%
src/recon3d/downscale.py bbox_range 8 0 0 100%
src/recon3d/downscale.py downscale 43 3 0 93%
src/recon3d/downscale.py pad_amount 4 0 0 100%
src/recon3d/downscale.py padded_size 13 1 0 92%
src/recon3d/downscale.py save_downscale_stack 4 0 0 100%
src/recon3d/downscale.py main 5 5 0 0%
src/recon3d/downscale.py (no function) 19 1 0 95%
src/recon3d/grayscale_image_stack_to_segmentation.py validate_recipe 11 11 0 0%
src/recon3d/grayscale_image_stack_to_segmentation.py segment_image_stack_save 10 10 0 0%
src/recon3d/grayscale_image_stack_to_segmentation.py grayscale_image_stack_to_segmentation 23 23 0 0%
src/recon3d/grayscale_image_stack_to_segmentation.py main 6 6 0 0%
src/recon3d/grayscale_image_stack_to_segmentation.py (no function) 18 18 0 0%
src/recon3d/hdf_io.py create_hdf 2 0 0 100%
src/recon3d/hdf_io.py modify_hdf_dataset 21 3 0 86%
src/recon3d/hdf_io.py write_attr_dict 8 1 0 88%
src/recon3d/hdf_io.py write_h5 9 0 0 100%
src/recon3d/hdf_io.py add_to_h5 4 4 0 0%
src/recon3d/hdf_io.py _ 6 0 0 100%
src/recon3d/hdf_io.py _ 10 0 0 100%
src/recon3d/hdf_io.py _ 6 0 0 100%
src/recon3d/hdf_io.py _ 6 0 0 100%
src/recon3d/hdf_io.py _ 8 0 0 100%
src/recon3d/hdf_io.py _ 1 1 0 0%
src/recon3d/hdf_io.py _ 20 0 0 100%
src/recon3d/hdf_io.py _ 14 0 0 100%
src/recon3d/hdf_io.py image_to_voxel 9 0 0 100%
src/recon3d/hdf_io.py image_to_voxel_command_line 5 5 0 0%
src/recon3d/hdf_io.py voxel_to_image 16 1 0 94%
src/recon3d/hdf_io.py voxel_to_image_command_line 6 6 0 0%
src/recon3d/hdf_io.py (no function) 35 0 0 100%
src/recon3d/image_stack_to_array.py save_image_stack_to_array 7 2 0 71%
src/recon3d/image_stack_to_array.py validate_recipe 7 7 0 0%
src/recon3d/image_stack_to_array.py image_to_stack_array 23 23 0 0%
src/recon3d/image_stack_to_array.py main 6 6 0 0%
src/recon3d/image_stack_to_array.py (no function) 16 1 0 94%
src/recon3d/instance_analysis.py calc_moment 7 1 0 86%
src/recon3d/instance_analysis.py center_of_mass 6 0 0 100%
src/recon3d/instance_analysis.py centroid_pix 5 0 0 100%
src/recon3d/instance_analysis.py ellipsoid_surface_area 5 0 0 100%
src/recon3d/instance_analysis.py ellipsoid_volume 4 0 0 100%
src/recon3d/instance_analysis.py equivalent_spherical_diameter 2 0 0 100%
src/recon3d/instance_analysis.py fit_ellipsoid 26 1 0 96%
src/recon3d/instance_analysis.py instance_indices 10 0 0 100%
src/recon3d/instance_analysis.py minimum_size_filter 12 1 0 92%
src/recon3d/instance_analysis.py map_features_to_voxels 0 0 0 100%
src/recon3d/instance_analysis.py nearest_neighbor_distance 11 0 0 100%
src/recon3d/instance_analysis.py num_voxels 4 0 0 100%
src/recon3d/instance_analysis.py process_image_stack 31 3 0 90%
src/recon3d/instance_analysis.py save_instance_images 2 2 0 0%
src/recon3d/instance_analysis.py semantic_to_instance 5 0 0 100%
src/recon3d/instance_analysis.py instance_analysis_included 5 0 0 100%
src/recon3d/instance_analysis.py instance_properties 35 0 0 100%
src/recon3d/instance_analysis.py process 22 22 0 0%
src/recon3d/instance_analysis.py main 6 6 0 0%
src/recon3d/instance_analysis.py (no function) 41 1 0 98%
src/recon3d/static_test_paths.py (no function) 10 0 0 100%
src/recon3d/types.py (no function) 134 0 0 100%
src/recon3d/utility.py binary_with_pores_to_semantic 15 1 0 93%
src/recon3d/utility.py validate_yml 12 2 0 83%
src/recon3d/utility.py binarize 3 0 0 100%
src/recon3d/utility.py semantic_to_binary 6 0 0 100%
src/recon3d/utility.py binary_to_semantic 3 0 0 100%
src/recon3d/utility.py main_binary_to_semantic 6 6 0 0%
src/recon3d/utility.py main_semantic_to_binary 6 6 0 0%
src/recon3d/utility.py hdf_to_instance_properties 23 0 0 100%
src/recon3d/utility.py hdf_to_metadata 18 18 0 0%
src/recon3d/utility.py centroids_to_ndarray 6 0 0 100%
src/recon3d/utility.py ellipsoids_to_ndarray 16 0 0 100%
src/recon3d/utility.py surface_areas_to_ndarray 4 0 0 100%
src/recon3d/utility.py volumes_to_ndarray 4 0 0 100%
src/recon3d/utility.py rmdir 7 0 0 100%
src/recon3d/utility.py compare_files 20 12 0 40%
src/recon3d/utility.py date_time_utc 4 4 0 0%
src/recon3d/utility.py underline 1 1 0 0%
src/recon3d/utility.py in_a_but_not_in_b 5 0 0 100%
src/recon3d/utility.py pairwise 3 0 0 100%
src/recon3d/utility.py pairwise_circular 3 0 0 100%
src/recon3d/utility.py metadata_to_dict 11 0 0 100%
src/recon3d/utility.py yaml_to_dict 17 5 0 71%
src/recon3d/utility.py dict_to_yaml 3 0 0 100%
src/recon3d/utility.py ndarray_to_img 17 2 0 88%
src/recon3d/utility.py read_images 10 2 0 80%
src/recon3d/utility.py (no function) 39 0 0 100%
src/recon3d/voxel_to_mesh.py validate_recipe 14 0 0 100%
src/recon3d/voxel_to_mesh.py voxel_to_mesh 55 12 0 78%
src/recon3d/voxel_to_mesh.py main 6 6 0 0%
src/recon3d/voxel_to_mesh.py (no function) 21 1 0 95%
Total   1189 255 0 79%

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