Index

A

abline() (in module tumourkit.classification.evaluate) AccumulateRawOutput (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) add_matrices() (in module tumourkit.segmentation.evaluate) add_node() (in module tumourkit.utils.preprocessing) add_probability() (in module tumourkit.postprocessing.join_hovprob_graph)

add_to_brightness() (in module tumourkit.segmentation.hovernet.dataloader.augs) add_to_contrast() (in module tumourkit.segmentation.hovernet.dataloader.augs) add_to_hue() (in module tumourkit.segmentation.hovernet.dataloader.augs) add_to_saturation() (in module tumourkit.segmentation.hovernet.dataloader.augs) append_results() (in module tumourkit.classification.train_graphs) apply_mask() (in module tumourkit.utils.preprocessing)

B

BaseCallbacks (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base)

C

calibration_error() (in module tumourkit.utils.calibration_error) center_pad_to_shape() (in module tumourkit.segmentation.hovernet.misc.utils) centroids2png() (in module tumourkit.preprocessing.centroids2png) centroidspng2csv() (in module tumourkit.preprocessing.centroidspng2csv) check_imbalance() (in module tumourkit.utils.classification) check_log_dir() (in module tumourkit.segmentation.hovernet.run_utils.utils) check_manual_seed() (in module tumourkit.segmentation.hovernet.run_utils.utils) check_order() (in module tumourkit.utils.postprocessing) check_same_num() (in module tumourkit.utils.pipes) check_training() (in module tumourkit.utils.pipes) check_void() (in module tumourkit.utils.pipes) color_deconvolution() (in module tumourkit.segmentation.hovernet.misc.utils) colorize() (in module tumourkit.segmentation.hovernet.misc.viz_utils) compute_ece() (in module tumourkit.eval_pipe) compute_f1_score_from_matrix() (in module tumourkit.segmentation.evaluate) compute_graph_distance_matrix() (in module tumourkit.postprocessing.draw_rips) compute_matrix_persistence() (in module tumourkit.utils.tda) compute_metrics() (in module tumourkit.classification.evaluate) compute_metrics_from_matrix() (in module tumourkit.segmentation.evaluate) compute_neural_persistence() (in module tumourkit.classification.train_graphs) compute_perc_error_bkgr() (in module tumourkit.segmentation.evaluate)

compute_perimeter() (in module tumourkit.utils.preprocessing) compute_wasserstein_distance() (in module tumourkit.postprocessing.compare_barcodes) ConditionalSaver (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) Config (class in tumourkit.segmentation.hovernet.config) convert_pytorch_checkpoint() (in module tumourkit.segmentation.hovernet.run_utils.utils) create_comparator() (in module tumourkit.utils.postprocessing) create_confs() (in module tumourkit.classification.train_xgboost) create_dir() (in module tumourkit.utils.preprocessing) create_edges() (tumourkit.classification.read_graph.GraphDataset static method) create_geojson() (in module tumourkit.utils.preprocessing) create_id_map() (in module tumourkit.postprocessing.merge_cells) create_mask() (in module tumourkit.preprocessing.pngcsv2geojson) create_model() (in module tumourkit.segmentation.hovernet.models.hovernet.net_desc) create_node_splits() (in module tumourkit.utils.read_nodes) create_results_file() (in module tumourkit.classification.train_graphs) create_splits() (in module tumourkit.segmentation.hovernet.extract_patches) create_subfolders() (in module tumourkit.make_dirs) crop_op() (in module tumourkit.segmentation.hovernet.models.hovernet.utils) crop_to_shape() (in module tumourkit.segmentation.hovernet.models.hovernet.utils) cropping_center() (in module tumourkit.segmentation.hovernet.misc.utils) cross_validate() (in module tumourkit.classification.train_xgboost)

D

DenseBlock (class in tumourkit.segmentation.hovernet.models.hovernet.net_utils) dice_loss() (in module tumourkit.segmentation.hovernet.models.hovernet.utils) draw_barcode() (in module tumourkit.postprocessing.draw_barcode)

draw_cells() (in module tumourkit.postprocessing.draw_cells) draw_graph() (in module tumourkit.postprocessing.draw_graph) draw_reliability_diagram() (in module tumourkit.classification.evaluate) draw_rips() (in module tumourkit.postprocessing.draw_rips)

E

evaluate() (in module tumourkit.classification.train_graphs) (in module tumourkit.classification.train_xgboost) evaluate_hovernet_with_shape() (in module tumourkit.research_pipe) Events (class in tumourkit.segmentation.hovernet.run_utils.engine)

extract_all_scalars() (in module tumourkit.postprocessing.extract_tensorboard) extract_centroids() (in module tumourkit.preprocessing.centroidspng2csv) (in module tumourkit.preprocessing.pngcsv2centroids) extract_features() (in module tumourkit.utils.preprocessing) extract_scalar_from_tb() (in module tumourkit.postprocessing.extract_tensorboard)

F

fig2data() (in module tumourkit.segmentation.hovernet.run_utils.callbacks.serialize) FileLoader (class in tumourkit.segmentation.hovernet.dataloader.train_loader) find_nearest() (in module tumourkit.utils.nearest) find_nearest_dist_idx() (in module tumourkit.utils.nearest) fit_column_normalizer() (in module tumourkit.utils.classification) fix_mirror_padding() (in module tumourkit.segmentation.hovernet.dataloader.augs) fix_shape() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc) format_contour() (in module tumourkit.utils.preprocessing) forward() (tumourkit.classification.models.gat.GAT method) (tumourkit.classification.models.gcn.GCN method) (tumourkit.classification.models.gin.GIN method) (tumourkit.classification.models.graphsage.GraphSAGE method) (tumourkit.classification.models.hgao.HardGAO method) (tumourkit.classification.models.hgao.HardGAT method) (tumourkit.classification.models.norm.Norm method) (tumourkit.segmentation.hovernet.models.hovernet.net_desc.HoVerNet method) (tumourkit.segmentation.hovernet.models.hovernet.net_utils.DenseBlock method) (tumourkit.segmentation.hovernet.models.hovernet.net_utils.Net method) (tumourkit.segmentation.hovernet.models.hovernet.net_utils.ResidualBlock method) (tumourkit.segmentation.hovernet.models.hovernet.net_utils.TFSamepaddingLayer method) (tumourkit.segmentation.hovernet.models.hovernet.net_utils.UpSample2x method)

fuse_loaders() (in module tumourkit.classification.train_graphs)

G

GAT (class in tumourkit.classification.models.gat) gaussian_blur() (in module tumourkit.segmentation.hovernet.dataloader.augs) GCN (class in tumourkit.classification.models.gcn) gen_figure() (in module tumourkit.segmentation.hovernet.misc.viz_utils) gen_instance_hv_map() (in module tumourkit.segmentation.hovernet.models.hovernet.targets) gen_targets() (in module tumourkit.segmentation.hovernet.models.hovernet.targets) generate_configurations() (in module tumourkit.classification.train_graphs) generate_labels() (in module tumourkit.segmentation.hovernet.extract_patches) generate_tree() (in module tumourkit.utils.nearest) geojson2pngcsv() (in module tumourkit.preprocessing.geojson2pngcsv) get_bounding_box() (in module tumourkit.segmentation.hovernet.misc.utils) get_centroid_by_id() (in module tumourkit.utils.preprocessing) get_colors() (in module tumourkit.postprocessing.draw_graph) get_config() (in module tumourkit.segmentation.hovernet.models.hovernet.opt) get_confusion_matrix() (in module tumourkit.segmentation.evaluate) get_dice_1() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) get_dice_2() (in module tumourkit.segmentation.hovernet.metrics.stats_utils)

get_fast_aji() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) get_fast_aji_plus() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) get_fast_dice_2() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) get_fast_pq() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) get_gradient() (in module tumourkit.postprocessing.merge_cells) get_greatest_connected_component() (in module tumourkit.utils.postprocessing) get_inst_centroid() (in module tumourkit.segmentation.hovernet.misc.utils) get_mask() (in module tumourkit.utils.preprocessing) get_model_summary() (in module tumourkit.segmentation.hovernet.run_utils.utils) get_N_closest_pairs_dists() (in module tumourkit.utils.nearest) get_N_closest_pairs_idx() (in module tumourkit.utils.nearest) get_names() (in module tumourkit.utils.preprocessing) get_normalizers() (tumourkit.classification.read_graph.GraphDataset method) get_pairs() (in module tumourkit.segmentation.evaluate) GIN (class in tumourkit.classification.models.gin) graph2centroids() (in module tumourkit.preprocessing.graph2centroids) GraphDataset (class in tumourkit.classification.read_graph) GraphSAGE (class in tumourkit.classification.models.graphsage)

H

HardGAO (class in tumourkit.classification.models.hgao) HardGAT (class in tumourkit.classification.models.hgao)

HoVerNet (class in tumourkit.segmentation.hovernet.models.hovernet.net_desc) hovernet_preproc_with_shape() (in module tumourkit.research_pipe) HovernetNotFoundError

I

infer_hovernet_with_shape() (in module tumourkit.research_pipe) infer_step() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc)

InferManager (class in tumourkit.segmentation.hovernet.infer.base) (class in tumourkit.segmentation.hovernet.infer.tile) initialize_normalizers() (tumourkit.classification.read_graph.GraphDataset method)

J

join() (in module tumourkit.utils.postprocessing)

join_dictionaries() (in module tumourkit.classification.evaluate)

L

load_dataset() (in module tumourkit.classification.train_graphs) load_model() (in module tumourkit.classification.train_graphs) load_normalizer() (in module tumourkit.classification.infer) load_saved_model() (in module tumourkit.classification.infer)

log_debug() (in module tumourkit.segmentation.hovernet.misc.utils) log_info() (in module tumourkit.segmentation.hovernet.misc.utils) LoggingEpochOutput (class in tumourkit.segmentation.hovernet.run_utils.callbacks.logging) LoggingGradient (class in tumourkit.segmentation.hovernet.run_utils.callbacks.logging)

M

main() (in module tumourkit.classification.evaluate) (in module tumourkit.classification.infer) (in module tumourkit.classification.train_graphs) (in module tumourkit.classification.train_xgboost) (in module tumourkit.eval_pipe) (in module tumourkit.infer_pipe) (in module tumourkit.make_dirs) (in module tumourkit.postprocessing.compare_barcodes) (in module tumourkit.postprocessing.draw_barcode) (in module tumourkit.postprocessing.draw_cells) (in module tumourkit.postprocessing.draw_graph) (in module tumourkit.postprocessing.draw_rips) (in module tumourkit.postprocessing.extract_tensorboard) (in module tumourkit.postprocessing.join_graph_gt) (in module tumourkit.postprocessing.join_hovprob_graph) (in module tumourkit.postprocessing.merge_cells) (in module tumourkit.postprocessing.plot_logs) (in module tumourkit.postprocessing.summarize_logs) (in module tumourkit.preprocessing.centroids2png) (in module tumourkit.preprocessing.centroidspng2csv) (in module tumourkit.preprocessing.geojson2pngcsv) (in module tumourkit.preprocessing.graph2centroids) (in module tumourkit.preprocessing.hovernet2centroids) (in module tumourkit.preprocessing.hovernet2geojson) (in module tumourkit.preprocessing.png2graph) (in module tumourkit.preprocessing.pngcsv2centroids) (in module tumourkit.preprocessing.pngcsv2geojson) (in module tumourkit.preprocessing.pngcsv2graph) (in module tumourkit.preprocessing.remove_uncertain) (in module tumourkit.research_pipe) (in module tumourkit.segmentation.evaluate) (in module tumourkit.segmentation.hovernet.extract_patches) (in module tumourkit.segmentation.hovernet.run_infer) (in module tumourkit.segmentation.hovernet.train) (in module tumourkit.train_pipe) main_subthread() (in module tumourkit.postprocessing.draw_barcode) (in module tumourkit.postprocessing.draw_graph) (in module tumourkit.postprocessing.draw_rips) (in module tumourkit.preprocessing.png2graph) (in module tumourkit.preprocessing.pngcsv2graph) main_with_args() (in module tumourkit.classification.evaluate) (in module tumourkit.classification.infer) (in module tumourkit.classification.train_graphs) (in module tumourkit.classification.train_xgboost) (in module tumourkit.postprocessing.compare_barcodes) (in module tumourkit.postprocessing.draw_barcode) (in module tumourkit.postprocessing.draw_cells) (in module tumourkit.postprocessing.draw_graph) (in module tumourkit.postprocessing.draw_rips) (in module tumourkit.postprocessing.join_graph_gt) (in module tumourkit.postprocessing.join_hovprob_graph) (in module tumourkit.postprocessing.summarize_logs) (in module tumourkit.preprocessing.centroids2png) (in module tumourkit.preprocessing.centroidspng2csv) (in module tumourkit.preprocessing.geojson2pngcsv) (in module tumourkit.preprocessing.graph2centroids) (in module tumourkit.preprocessing.hovernet2centroids) (in module tumourkit.preprocessing.hovernet2geojson) (in module tumourkit.preprocessing.png2graph) (in module tumourkit.preprocessing.pngcsv2centroids) (in module tumourkit.preprocessing.pngcsv2geojson) (in module tumourkit.preprocessing.pngcsv2graph) (in module tumourkit.preprocessing.remove_uncertain) (in module tumourkit.segmentation.evaluate) (in module tumourkit.segmentation.hovernet.extract_patches) (in module tumourkit.segmentation.hovernet.run_infer) (in module tumourkit.segmentation.hovernet.train) median_blur() (in module tumourkit.segmentation.hovernet.dataloader.augs) merge_cells() (in module tumourkit.postprocessing.merge_cells) (in module tumourkit.utils.postprocessing) merge_labels() (in module tumourkit.postprocessing.join_graph_gt) metrics_from_predictions() (in module tumourkit.utils.classification) mkdir() (in module tumourkit.segmentation.hovernet.misc.utils) module tumourkit tumourkit.classification tumourkit.classification.compute_imbalance tumourkit.classification.evaluate tumourkit.classification.infer tumourkit.classification.models tumourkit.classification.models.gat tumourkit.classification.models.gcn tumourkit.classification.models.gin tumourkit.classification.models.graphsage tumourkit.classification.models.hgao tumourkit.classification.models.norm tumourkit.classification.read_graph tumourkit.classification.train_graphs tumourkit.classification.train_xgboost tumourkit.eval_pipe tumourkit.infer_pipe tumourkit.make_dirs tumourkit.postprocessing tumourkit.postprocessing.compare_barcodes tumourkit.postprocessing.draw_barcode tumourkit.postprocessing.draw_cells tumourkit.postprocessing.draw_graph tumourkit.postprocessing.draw_rips tumourkit.postprocessing.extract_tensorboard tumourkit.postprocessing.join_graph_gt tumourkit.postprocessing.join_hovprob_graph tumourkit.postprocessing.merge_cells tumourkit.postprocessing.plot_logs tumourkit.postprocessing.rswoosh tumourkit.postprocessing.summarize_logs tumourkit.preprocessing tumourkit.preprocessing.centroids2png tumourkit.preprocessing.centroidspng2csv tumourkit.preprocessing.geojson2pngcsv tumourkit.preprocessing.graph2centroids tumourkit.preprocessing.hovernet2centroids tumourkit.preprocessing.hovernet2geojson tumourkit.preprocessing.png2graph tumourkit.preprocessing.pngcsv2centroids tumourkit.preprocessing.pngcsv2geojson tumourkit.preprocessing.pngcsv2graph tumourkit.preprocessing.remove_uncertain tumourkit.research_pipe tumourkit.segmentation tumourkit.segmentation.evaluate tumourkit.segmentation.hovernet tumourkit.segmentation.hovernet.config tumourkit.segmentation.hovernet.dataloader tumourkit.segmentation.hovernet.dataloader.augs tumourkit.segmentation.hovernet.dataloader.infer_loader tumourkit.segmentation.hovernet.dataloader.train_loader tumourkit.segmentation.hovernet.extract_patches tumourkit.segmentation.hovernet.infer tumourkit.segmentation.hovernet.infer.base tumourkit.segmentation.hovernet.infer.tile tumourkit.segmentation.hovernet.metrics tumourkit.segmentation.hovernet.metrics.stats_utils tumourkit.segmentation.hovernet.misc tumourkit.segmentation.hovernet.misc.patch_extractor tumourkit.segmentation.hovernet.misc.utils tumourkit.segmentation.hovernet.misc.viz_utils tumourkit.segmentation.hovernet.models tumourkit.segmentation.hovernet.models.hovernet tumourkit.segmentation.hovernet.models.hovernet.net_desc tumourkit.segmentation.hovernet.models.hovernet.net_utils tumourkit.segmentation.hovernet.models.hovernet.opt tumourkit.segmentation.hovernet.models.hovernet.post_proc tumourkit.segmentation.hovernet.models.hovernet.run_desc tumourkit.segmentation.hovernet.models.hovernet.targets tumourkit.segmentation.hovernet.models.hovernet.utils tumourkit.segmentation.hovernet.run_infer tumourkit.segmentation.hovernet.run_utils tumourkit.segmentation.hovernet.run_utils.callbacks tumourkit.segmentation.hovernet.run_utils.callbacks.base tumourkit.segmentation.hovernet.run_utils.callbacks.logging tumourkit.segmentation.hovernet.run_utils.callbacks.serialize tumourkit.segmentation.hovernet.run_utils.engine tumourkit.segmentation.hovernet.run_utils.utils tumourkit.segmentation.hovernet.train tumourkit.train_pipe tumourkit.utils tumourkit.utils.calibration_error tumourkit.utils.classification tumourkit.utils.folder2txt tumourkit.utils.nearest tumourkit.utils.pipes tumourkit.utils.postprocessing tumourkit.utils.preprocessing tumourkit.utils.read_nodes tumourkit.utils.tda

mse_loss() (in module tumourkit.segmentation.hovernet.models.hovernet.utils) msge_loss() (in module tumourkit.segmentation.hovernet.models.hovernet.utils)

N

name_from_conf() (in module tumourkit.classification.train_graphs) Net (class in tumourkit.segmentation.hovernet.models.hovernet.net_utils) noop() (in module tumourkit.segmentation.hovernet.models.hovernet.post_proc)

Norm (class in tumourkit.classification.models.norm) normalize() (in module tumourkit.segmentation.hovernet.misc.utils) (in module tumourkit.utils.classification)

P

pair_coordinates() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) parse_centroids() (in module tumourkit.preprocessing.hovernet2centroids) parse_centroids_probs() (in module tumourkit.postprocessing.join_hovprob_graph) parse_contours() (in module tumourkit.preprocessing.hovernet2geojson) parse_path() (in module tumourkit.utils.preprocessing) PatchExtractor (class in tumourkit.segmentation.hovernet.misc.patch_extractor) percentage_error() (in module tumourkit.utils.classification) PeriodicSaver (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) plot_vis() (in module tumourkit.postprocessing.plot_logs)

png2graph() (in module tumourkit.preprocessing.png2graph) pngcsv2features() (in module tumourkit.preprocessing.pngcsv2geojson) pngcsv2geojson() (in module tumourkit.preprocessing.pngcsv2geojson) pngcsv2graph() (in module tumourkit.preprocessing.pngcsv2graph) prep_sample() (in module tumourkit.segmentation.hovernet.models.hovernet.targets) proc_valid_step_output() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc) process() (in module tumourkit.segmentation.hovernet.models.hovernet.post_proc) process_file_list() (tumourkit.segmentation.hovernet.infer.tile.InferManager method) process_gson() (in module tumourkit.preprocessing.remove_uncertain) ProcessAccumulatedRawOutput (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base)

R

random_colors() (in module tumourkit.segmentation.hovernet.misc.viz_utils) read_all_nodes() (in module tumourkit.utils.read_nodes) read_centroids() (in module tumourkit.utils.preprocessing) read_csv() (in module tumourkit.utils.preprocessing) read_diagram_from_csv() (in module tumourkit.postprocessing.compare_barcodes) read_files() (in module tumourkit.utils.folder2txt) read_graph() (in module tumourkit.utils.preprocessing) read_gson() (in module tumourkit.utils.preprocessing) read_image() (in module tumourkit.utils.preprocessing) read_json() (in module tumourkit.utils.preprocessing) read_labels() (in module tumourkit.utils.preprocessing) read_names() (in module tumourkit.utils.preprocessing) read_node_matrix() (in module tumourkit.utils.read_nodes) read_png() (in module tumourkit.utils.preprocessing) remap_label() (in module tumourkit.segmentation.hovernet.metrics.stats_utils) remove_coordinates() (in module tumourkit.utils.folder2txt) remove_idx() (in module tumourkit.utils.postprocessing) remove_lost_ids() (in module tumourkit.postprocessing.merge_cells) remove_small_objects() (in module tumourkit.segmentation.hovernet.misc.utils) ResidualBlock (class in tumourkit.segmentation.hovernet.models.hovernet.net_utils)

rm_n_mkdir() (in module tumourkit.segmentation.hovernet.misc.utils) rswoosh() (in module tumourkit.postprocessing.rswoosh) run_early_topo() (in module tumourkit.research_pipe) run_evaluation() (in module tumourkit.eval_pipe) run_graph_pipe() (in module tumourkit.train_pipe) run_graphs() (in module tumourkit.infer_pipe) run_hov_pipe() (in module tumourkit.train_pipe) run_hovernet() (in module tumourkit.infer_pipe) run_inference() (in module tumourkit.classification.infer) run_once() (tumourkit.segmentation.hovernet.train.TrainManager method) run_postgraphs() (in module tumourkit.infer_pipe) run_posthov() (in module tumourkit.infer_pipe) run_postproc_pipe() (in module tumourkit.train_pipe) run_postprocessing_with_shape() (in module tumourkit.research_pipe) run_preproc_pipe() (in module tumourkit.train_pipe) run_preprocessing() (in module tumourkit.eval_pipe) (in module tumourkit.research_pipe) run_scaling() (in module tumourkit.research_pipe) run_void() (in module tumourkit.research_pipe) run_xgb() (in module tumourkit.research_pipe) RunEngine (class in tumourkit.segmentation.hovernet.run_utils.engine)

S

save() (in module tumourkit.classification.train_xgboost) save_batch() (in module tumourkit.segmentation.hovernet.extract_patches) save_centroids() (in module tumourkit.utils.preprocessing) save_contours() (in module tumourkit.preprocessing.hovernet2geojson) save_csv() (in module tumourkit.segmentation.evaluate) (in module tumourkit.utils.preprocessing) save_debug_matrix() (in module tumourkit.segmentation.evaluate) save_geojson() (in module tumourkit.utils.preprocessing) save_graph() (in module tumourkit.utils.preprocessing) save_imgs() (in module tumourkit.segmentation.hovernet.extract_patches) save_metrics() (in module tumourkit.classification.evaluate) save_model() (in module tumourkit.classification.train_graphs)

save_npy() (in module tumourkit.segmentation.hovernet.extract_patches) save_png() (in module tumourkit.utils.preprocessing) save_pngcsv() (in module tumourkit.utils.preprocessing) save_probs() (in module tumourkit.classification.infer) save_txt() (in module tumourkit.utils.folder2txt) ScalarMovingAverage (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) ScheduleLr (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) serialize() (in module tumourkit.segmentation.hovernet.run_utils.callbacks.serialize) SerializeArray (class in tumourkit.segmentation.hovernet.dataloader.infer_loader) SerializeFileList (class in tumourkit.segmentation.hovernet.dataloader.infer_loader) set_best_configuration() (in module tumourkit.infer_pipe) State (class in tumourkit.segmentation.hovernet.run_utils.engine)

T

TFSamepaddingLayer (class in tumourkit.segmentation.hovernet.models.hovernet.net_utils) to4dim() (in module tumourkit.segmentation.hovernet.extract_patches) to5dim() (in module tumourkit.segmentation.hovernet.extract_patches) to_long_format() (in module tumourkit.postprocessing.extract_tensorboard) TrackLr (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) train() (in module tumourkit.classification.train_graphs) (in module tumourkit.classification.train_xgboost) train_hovernet_with_shape() (in module tumourkit.research_pipe) train_one_conf() (in module tumourkit.classification.train_graphs) train_one_iter() (in module tumourkit.classification.train_graphs) train_step() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc) TrainManager (class in tumourkit.segmentation.hovernet.train) TriggerEngine (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) tumourkit module tumourkit.classification module tumourkit.classification.compute_imbalance module tumourkit.classification.evaluate module tumourkit.classification.infer module tumourkit.classification.models module tumourkit.classification.models.gat module tumourkit.classification.models.gcn module tumourkit.classification.models.gin module tumourkit.classification.models.graphsage module tumourkit.classification.models.hgao module tumourkit.classification.models.norm module tumourkit.classification.read_graph module tumourkit.classification.train_graphs module tumourkit.classification.train_xgboost module tumourkit.eval_pipe module tumourkit.infer_pipe module tumourkit.make_dirs module tumourkit.postprocessing module tumourkit.postprocessing.compare_barcodes module tumourkit.postprocessing.draw_barcode module tumourkit.postprocessing.draw_cells module tumourkit.postprocessing.draw_graph module tumourkit.postprocessing.draw_rips module tumourkit.postprocessing.extract_tensorboard module tumourkit.postprocessing.join_graph_gt module tumourkit.postprocessing.join_hovprob_graph module tumourkit.postprocessing.merge_cells module tumourkit.postprocessing.plot_logs module tumourkit.postprocessing.rswoosh module tumourkit.postprocessing.summarize_logs module tumourkit.preprocessing module tumourkit.preprocessing.centroids2png module tumourkit.preprocessing.centroidspng2csv module tumourkit.preprocessing.geojson2pngcsv module tumourkit.preprocessing.graph2centroids module tumourkit.preprocessing.hovernet2centroids module tumourkit.preprocessing.hovernet2geojson module tumourkit.preprocessing.png2graph module tumourkit.preprocessing.pngcsv2centroids module tumourkit.preprocessing.pngcsv2geojson module tumourkit.preprocessing.pngcsv2graph module

tumourkit.preprocessing.remove_uncertain module tumourkit.research_pipe module tumourkit.segmentation module tumourkit.segmentation.evaluate module tumourkit.segmentation.hovernet module tumourkit.segmentation.hovernet.config module tumourkit.segmentation.hovernet.dataloader module tumourkit.segmentation.hovernet.dataloader.augs module tumourkit.segmentation.hovernet.dataloader.infer_loader module tumourkit.segmentation.hovernet.dataloader.train_loader module tumourkit.segmentation.hovernet.extract_patches module tumourkit.segmentation.hovernet.infer module tumourkit.segmentation.hovernet.infer.base module tumourkit.segmentation.hovernet.infer.tile module tumourkit.segmentation.hovernet.metrics module tumourkit.segmentation.hovernet.metrics.stats_utils module tumourkit.segmentation.hovernet.misc module tumourkit.segmentation.hovernet.misc.patch_extractor module tumourkit.segmentation.hovernet.misc.utils module tumourkit.segmentation.hovernet.misc.viz_utils module tumourkit.segmentation.hovernet.models module tumourkit.segmentation.hovernet.models.hovernet module tumourkit.segmentation.hovernet.models.hovernet.net_desc module tumourkit.segmentation.hovernet.models.hovernet.net_utils module tumourkit.segmentation.hovernet.models.hovernet.opt module tumourkit.segmentation.hovernet.models.hovernet.post_proc module tumourkit.segmentation.hovernet.models.hovernet.run_desc module tumourkit.segmentation.hovernet.models.hovernet.targets module tumourkit.segmentation.hovernet.models.hovernet.utils module tumourkit.segmentation.hovernet.run_infer module tumourkit.segmentation.hovernet.run_utils module tumourkit.segmentation.hovernet.run_utils.callbacks module tumourkit.segmentation.hovernet.run_utils.callbacks.base module tumourkit.segmentation.hovernet.run_utils.callbacks.logging module tumourkit.segmentation.hovernet.run_utils.callbacks.serialize module tumourkit.segmentation.hovernet.run_utils.engine module tumourkit.segmentation.hovernet.run_utils.utils module tumourkit.segmentation.hovernet.train module tumourkit.train_pipe module tumourkit.utils module tumourkit.utils.calibration_error module tumourkit.utils.classification module tumourkit.utils.folder2txt module tumourkit.utils.nearest module tumourkit.utils.pipes module tumourkit.utils.postprocessing module tumourkit.utils.preprocessing module tumourkit.utils.read_nodes module tumourkit.utils.tda module

U

UpSample2x (class in tumourkit.segmentation.hovernet.models.hovernet.net_utils)

V

valid_step() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc) visualize_instances_dict() (in module tumourkit.segmentation.hovernet.misc.viz_utils)

visualize_instances_map() (in module tumourkit.segmentation.hovernet.misc.viz_utils) VisualizeOutput (class in tumourkit.segmentation.hovernet.run_utils.callbacks.base) viz_step_output() (in module tumourkit.segmentation.hovernet.models.hovernet.run_desc)

W

worker_init_fn() (in module tumourkit.segmentation.hovernet.train) write_to_file() (in module tumourkit.postprocessing.extract_tensorboard)

WrongConfigurationError wsi_cli (in module tumourkit.segmentation.hovernet.run_infer)

X

xentropy_loss() (in module tumourkit.segmentation.hovernet.models.hovernet.utils)