Index _ | A | B | C | D | E | F | G | I | J | M | N | P | R | S | T | U | V | W _ _affine() (skoots.train.merged_transform.TransformFromCfg method) _bake_skeleton_torch() (in module skoots.lib.skeleton) _bake_skeleton_triton() (in module skoots.lib.skeleton) _brightness() (skoots.train.merged_transform.TransformFromCfg method) _calculate_skeletons() (in module skoots.train.generate_skeletons) _compiled_affine() (in module skoots.train.merged_transform) _compiled_grid_sample() (in module skoots.train.merged_transform) _compute_zero_padding() (in module skoots.lib.morphology) (in module skoots.train.erosion) _contrast() (skoots.train.merged_transform.TransformFromCfg method) _crop1() (skoots.train.merged_transform.BackgroundTransformFromCfg method) (skoots.train.merged_transform.TransformFromCfg method) _crop2() (skoots.train.merged_transform.TransformFromCfg method) _crop2d() (in module skoots.lib.utils) _crop3d() (in module skoots.lib.utils) _dice() (in module skoots.train.loss) _elastic() (skoots.train.merged_transform.TransformFromCfg method) _elastic_on_skeletons() (in module skoots.train.merged_transform) _flipX() (skoots.train.merged_transform.TransformFromCfg method) _flipY() (skoots.train.merged_transform.TransformFromCfg method) _flipZ() (skoots.train.merged_transform.TransformFromCfg method) _get_affine_matrix() (in module skoots.train.merged_transform) _get_binary_kernel2d() (in module skoots.lib.morphology) _get_binary_kernel3d() (in module skoots.lib.morphology) (in module skoots.train.erosion) _get_box() (in module skoots.train.merged_transform) _get_cached_disk_coords() (in module skoots.lib.utils) _get_gaussian_kernel1d() (in module skoots.lib.morphology) _get_gaussian_kernel2d() (in module skoots.lib.morphology) _get_gaussian_kernel3d() (in module skoots.lib.morphology) _get_inverse_affine_matrix() (in module skoots.train.merged_transform) _identity() (skoots.train.merged_transform.TransformFromCfg method) _in_place_replace() (in module skoots.lib.flood_fill) _invert() (skoots.train.merged_transform.TransformFromCfg method) _iou_instance_dict() (in module skoots.validate.lib) _is_dict() (skoots.train.erosion.erosion method) _is_tensor() (skoots.train.erosion.erosion method) _noise() (skoots.train.merged_transform.TransformFromCfg method) _normalize() (skoots.train.merged_transform.TransformFromCfg method) _skeleton_to_mask() (in module skoots.lib.skeleton) _split_loss() (skoots.train.loss.split static method) _sub_sq_sum() (in module skoots.train.dataloader) _tversky() (skoots.train.loss.tversky static method) _vec2embed2D() (in module skoots.lib.vector_to_embedding) _vec2embed3D() (in module skoots.lib.vector_to_embedding) _vec2embed3D_graphable() (in module skoots.lib.vector_to_embedding) A accuracies_from_iou() (in module skoots.validate.lib) average_baked_skeletons() (in module skoots.lib.skeleton) B BackgroundDataset (class in skoots.train.dataloader) BackgroundTransformFromCfg (class in skoots.train.merged_transform) bake_skeleton() (in module skoots.lib.skeleton) baked_embed_to_prob() (in module skoots.lib.embedding_to_prob) binary_dilation() (in module skoots.lib.morphology) binary_dilation_2d() (in module skoots.lib.morphology) binary_erosion() (in module skoots.lib.morphology) (in module skoots.train.erosion) box_iou() (in module skoots.validate.lib) C calc_centroid() (in module skoots.train.merged_transform) calculate_accuracies_from_bbox() (in module skoots.validate.lib) calculate_indexes() (in module skoots.lib.utils) calculate_skeletons() (in module skoots.train.generate_skeletons) cantor2() (in module skoots.lib.utils) cantor3() (in module skoots.lib.utils) cfg_to_bism_model() (in module skoots.lib.utils) cleanup() (in module skoots.lib.mp_utils) (in module skoots.train.setup) connected_components() (in module skoots.lib.flood_fill) cpu() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) create_gt_skeletons() (in module skoots.train.generate_skeletons) crop_to_identical_size() (in module skoots.lib.utils) cuda() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) D dataset (class in skoots.train.dataloader) dfs() (in module skoots.lib.flood_fill) dice (class in skoots.train.loss) dilate() (in module skoots.lib.morphology) E efficient_flood_fill() (in module skoots.lib.flood_fill) elastic_deform() (in module skoots.train.merged_transform) erosion (class in skoots.train.erosion) F f1_score() (in module skoots.validate.lib) find_free_port() (in module skoots.lib.mp_utils) (in module skoots.train.setup) flood_all() (in module skoots.lib.flood_fill) forward() (skoots.train.loss.dice method) (skoots.train.loss.jaccard method) (skoots.train.loss.soft_cldice method) (skoots.train.loss.soft_dice_cldice method) (skoots.train.loss.split method) (skoots.train.loss.tversky method) (skoots.train.merged_transform.BackgroundTransformFromCfg method) (skoots.train.merged_transform.TransformFromCfg method) G gauss_filter() (in module skoots.lib.morphology) get_adjacent_labels() (in module skoots.lib.flood_fill) (in module skoots.lib.merge) get_batch() (in module skoots.lib.mp_utils) (in module skoots.train.setup) get_cached_ball_coords() (in module skoots.lib.utils) get_cached_disk_coords() (in module skoots.lib.utils) get_dtype_offset() (in module skoots.lib.utils) get_segmentation_errors() (in module skoots.validate.lib) get_vector_mesh() (in module skoots.lib.vector_to_embedding) I identical_rows() (in module skoots.lib.utils) imread() (in module skoots.validate.utils) index_skeleton_by_embed() (in module skoots.lib.skeleton) init_sigma() (in module skoots.train.sigma) J jaccard (class in skoots.train.loss) M map() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) mask_dice() (in module skoots.validate.lib) mask_iou() (in module skoots.validate.lib) mask_overlay() (in module skoots.train.utils) mask_soft_cldice() (in module skoots.validate.lib) mask_to_bbox() (in module skoots.validate.lib) mean() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) mean_filter() (in module skoots.lib.morphology) median_filter() (in module skoots.lib.morphology) module skoots.lib.embedding_to_prob skoots.lib.flood_fill skoots.lib.merge skoots.lib.morphology skoots.lib.mp_utils skoots.lib.skeleton skoots.lib.utils skoots.lib.vector_to_embedding skoots.train.dataloader skoots.train.engine skoots.train.erosion skoots.train.generate_skeletons skoots.train.loss skoots.train.merged_transform skoots.train.setup skoots.train.sigma skoots.train.utils skoots.validate.lib skoots.validate.utils MultiDataset (class in skoots.train.dataloader) N next_power_of_2() (in module skoots.lib.skeleton) numel() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) P pin_memory() (skoots.train.dataloader.dataset method) post_crop_fn() (skoots.train.merged_transform.TransformFromCfg method) post_fn() (skoots.train.merged_transform.TransformFromCfg method) pre_fn() (skoots.train.merged_transform.TransformFromCfg method) R replace() (in module skoots.lib.flood_fill) S save_train_test_split() (in module skoots.train.generate_skeletons) set_dataset_mean() (skoots.train.merged_transform.TransformFromCfg method) set_dataset_std() (skoots.train.merged_transform.TransformFromCfg method) set_sharing_strategy() (in module skoots.lib.mp_utils) (in module skoots.train.setup) setup_process() (in module skoots.lib.mp_utils) (in module skoots.train.setup) show_box_pred() (in module skoots.train.utils) Sigma (class in skoots.train.sigma) skeleton_colate() (in module skoots.train.dataloader) skeleton_to_mask() (in module skoots.lib.skeleton) skoots.lib.embedding_to_prob module skoots.lib.flood_fill module skoots.lib.merge module skoots.lib.morphology module skoots.lib.mp_utils module skoots.lib.skeleton module skoots.lib.utils module skoots.lib.vector_to_embedding module skoots.train.dataloader module skoots.train.engine module skoots.train.erosion module skoots.train.generate_skeletons module skoots.train.loss module skoots.train.merged_transform module skoots.train.setup module skoots.train.sigma module skoots.train.utils module skoots.validate.lib module skoots.validate.utils module soft_cldice (class in skoots.train.loss) soft_dice() (in module skoots.train.loss) soft_dice_cldice (class in skoots.train.loss) soft_dilate() (in module skoots.train.loss) soft_erode() (in module skoots.train.loss) soft_open() (in module skoots.train.loss) soft_skeletonize() (in module skoots.train.loss) sparse_mask_iou() (in module skoots.validate.lib) split (class in skoots.train.loss) std() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) subtract_square_sum() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) sum() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) sum_loss() (in module skoots.train.utils) T test_setup() (in module skoots.lib.mp_utils) (in module skoots.train.setup) to() (skoots.train.dataloader.BackgroundDataset method) (skoots.train.dataloader.dataset method) (skoots.train.dataloader.MultiDataset method) train() (in module skoots.train.engine) TransformFromCfg (class in skoots.train.merged_transform) tversky (class in skoots.train.loss) tversky_graphable() (in module skoots.train.loss) U update_bn() (in module skoots.train.utils) use_file_system_sharing_strategy() (in module skoots.lib.mp_utils) (in module skoots.train.setup) V valid_box_inds() (in module skoots.validate.lib) vec2embedND() (in module skoots.lib.vector_to_embedding) vector_to_embedding() (in module skoots.lib.vector_to_embedding) W write_progress() (in module skoots.train.utils)