[e9500f]: / docs / searchindex.js

Download this file

1 lines (1 with data), 25.9 kB

1
Search.setIndex({docnames:["index"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["index.rst"],objects:{"pathflowai-monitor":{"--version":[0,5,1,"cmdoption-pathflowai-monitor-version"]},"pathflowai-monitor-monitor_usage":{"--delay_time":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-dt"],"--records_output_csv":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-csv"],"--total_time":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-tt"],"-csv":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-csv"],"-dt":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-dt"],"-tt":[0,5,1,"cmdoption-pathflowai-monitor-monitor-usage-tt"]},"pathflowai-preprocess":{"--version":[0,5,1,"cmdoption-pathflowai-preprocess-version"]},"pathflowai-preprocess-alter_masks":{"--from_annotations":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-fr"],"--mask_dir":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-i"],"--output_dir":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-o"],"--to_annotations":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-to"],"-fr":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-fr"],"-i":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-i"],"-o":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-o"],"-to":[0,5,1,"cmdoption-pathflowai-preprocess-alter-masks-to"]},"pathflowai-preprocess-collapse_annotations":{"--from_annotations":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-fr"],"--input_patch_db":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-i"],"--max_background_area":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-ma"],"--output_patch_db":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-o"],"--patch_size":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-ps"],"--remove_background_annotation":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-rb"],"--to_annotations":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-to"],"-fr":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-fr"],"-i":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-i"],"-ma":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-ma"],"-o":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-o"],"-ps":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-ps"],"-rb":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-rb"],"-to":[0,5,1,"cmdoption-pathflowai-preprocess-collapse-annotations-to"]},"pathflowai-preprocess-preprocess_pipeline":{"--adjust_mask":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-am"],"--annotations":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-a"],"--basename":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-b"],"--basic_preprocess":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-bp"],"--generate_finetune_segmentation":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-g"],"--img2npy":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-npy"],"--input_dir":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-i"],"--intensity_threshold":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-it"],"--n_neighbors":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-nn"],"--out_db":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-odb"],"--patch_size":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-ps"],"--patches":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-pa"],"--preprocess":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-pr"],"--target_segmentation_class":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-tc"],"--target_threshold":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-tt"],"--threshold":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-t"],"-a":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-a"],"-am":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-am"],"-b":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-b"],"-bp":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-bp"],"-g":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-g"],"-i":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-i"],"-it":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-it"],"-nn":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-nn"],"-npy":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-npy"],"-odb":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-odb"],"-pa":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-pa"],"-pr":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-pr"],"-ps":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-ps"],"-t":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-t"],"-tc":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-tc"],"-tt":[0,5,1,"cmdoption-pathflowai-preprocess-preprocess-pipeline-tt"]},"pathflowai-preprocess-remove_basename_from_db":{"--basename":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-b"],"--input_patch_db":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-i"],"--output_patch_db":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-o"],"--patch_size":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-ps"],"-b":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-b"],"-i":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-i"],"-o":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-o"],"-ps":[0,5,1,"cmdoption-pathflowai-preprocess-remove-basename-from-db-ps"]},"pathflowai-visualize":{"--version":[0,5,1,"cmdoption-pathflowai-visualize-version"]},"pathflowai-visualize-extract_patch":{"--basename":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-b"],"--custom_segmentation":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-c"],"--input_dir":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-i"],"--n_segmentation_classes":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-sc"],"--outputfname":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-o"],"--patch_info_file":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-p"],"--patch_size":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-ps"],"--segmentation":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-s"],"--x":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-x"],"--y":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-y"],"-b":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-b"],"-c":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-c"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-i"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-o"],"-p":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-p"],"-ps":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-ps"],"-s":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-s"],"-sc":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-sc"],"-x":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-x"],"-y":[0,5,1,"cmdoption-pathflowai-visualize-extract-patch-y"]},"pathflowai-visualize-overlay_new_annotations":{"--annotation_txt":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-a"],"--compression_factor":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-cf"],"--img_file":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-i"],"--original_compression_factor":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-ocf"],"--outputfilename":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-o"],"-a":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-a"],"-cf":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-cf"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-i"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-o"],"-ocf":[0,5,1,"cmdoption-pathflowai-visualize-overlay-new-annotations-ocf"]},"pathflowai-visualize-plot_embeddings":{"--annotations":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-a"],"--basename":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-b"],"--embeddings_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-i"],"--max_background_area":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-ma"],"--n_neighbors":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-nn"],"--plotly_output_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-o"],"--remove_background_annotation":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-rb"],"-a":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-a"],"-b":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-b"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-i"],"-ma":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-ma"],"-nn":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-nn"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-o"],"-rb":[0,5,1,"cmdoption-pathflowai-visualize-plot-embeddings-rb"]},"pathflowai-visualize-plot_image":{"--compression_factor":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-cf"],"--image_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-i"],"--outputfname":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-o"],"-cf":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-cf"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-i"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-o"]},"pathflowai-visualize-plot_image_umap_embeddings":{"--basename":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b"],"--embeddings_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e"],"--input_dir":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i"],"--max_background_area":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma"],"--mpl_scatter":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl"],"--n_neighbors":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn"],"--outputfilename":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o"],"--remove_background_annotation":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb"],"--sort_col":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc"],"--sort_mode":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm"],"--zoom":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z"],"-b":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b"],"-e":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i"],"-ma":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma"],"-mpl":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl"],"-nn":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o"],"-rb":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb"],"-sc":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc"],"-sm":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm"],"-z":[0,5,1,"cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z"]},"pathflowai-visualize-plot_predictions":{"--alpha":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-al"],"--annotation_col":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-ac"],"--annotations":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-an"],"--basename":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-b"],"--compression_factor":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-cf"],"--custom_segmentation":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-c"],"--input_dir":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-i"],"--n_segmentation_classes":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-sc"],"--outputfname":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-o"],"--patch_info_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-p"],"--patch_size":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-ps"],"--scaling_factor":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-sf"],"--segmentation":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-s"],"--tif_file":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-tif"],"-ac":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-ac"],"-al":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-al"],"-an":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-an"],"-b":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-b"],"-c":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-c"],"-cf":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-cf"],"-i":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-i"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-o"],"-p":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-p"],"-ps":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-ps"],"-s":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-s"],"-sc":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-sc"],"-sf":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-sf"],"-tif":[0,5,1,"cmdoption-pathflowai-visualize-plot-predictions-tif"]},"pathflowai-visualize-shapley_plot":{"--batch_size":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-bs"],"--local_smoothing":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-l"],"--method":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-mth"],"--model_pkl":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-m"],"--n_samples":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-ns"],"--outputfilename":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-o"],"--pred_out":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-p"],"-bs":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-bs"],"-l":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-l"],"-m":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-m"],"-mth":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-mth"],"-ns":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-ns"],"-o":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-o"],"-p":[0,5,1,"cmdoption-pathflowai-visualize-shapley-plot-p"]},"pathflowai.datasets":{DynamicImageDataset:[0,1,1,""],RandomRotate90:[0,3,1,""],create_transforms:[0,3,1,""],get_data_transforms:[0,3,1,""],get_normalizer:[0,3,1,""],segmentation_transform:[0,3,1,""]},"pathflowai.datasets.DynamicImageDataset":{binarize_annotations:[0,2,1,""],concat:[0,2,1,""],get_class_weights:[0,2,1,""],retain_ID:[0,2,1,""],split_by_ID:[0,2,1,""],subsample:[0,2,1,""]},"pathflowai.losses":{FocalLoss:[0,1,1,""],GeneralizedDice:[0,1,1,""],GeneralizedDiceLoss:[0,1,1,""],ShapeError:[0,4,1,""],SurfaceLoss:[0,1,1,""],assert_:[0,3,1,""],class2one_hot:[0,3,1,""],eq:[0,3,1,""],flatten_samples:[0,3,1,""],one_hot2dist:[0,3,1,""],one_hot:[0,3,1,""],simplex:[0,3,1,""],sset:[0,3,1,""],uniq:[0,3,1,""]},"pathflowai.losses.FocalLoss":{forward:[0,2,1,""]},"pathflowai.losses.GeneralizedDiceLoss":{forward:[0,2,1,""]},"pathflowai.sampler":{ImbalancedDatasetSampler:[0,1,1,""]},"pathflowai.schedulers":{CosineAnnealingWithRestartsLR:[0,1,1,""],Scheduler:[0,1,1,""]},"pathflowai.schedulers.Scheduler":{get_lr:[0,2,1,""],step:[0,2,1,""]},"pathflowai.utils":{add_purple_mask:[0,3,1,""],adjust_mask:[0,3,1,""],boxes2interior:[0,3,1,""],create_purple_mask:[0,3,1,""],create_sparse_annotation_arrays:[0,3,1,""],create_train_val_test:[0,3,1,""],df2sql:[0,3,1,""],dir2images:[0,3,1,""],extract_patch_information:[0,3,1,""],fix_name:[0,3,1,""],fix_names:[0,3,1,""],generate_patch_pipeline:[0,3,1,""],grab_interior_points:[0,3,1,""],image2coords:[0,3,1,""],images2coord_dict:[0,3,1,""],img2npy_:[0,3,1,""],is_coords_in_box:[0,3,1,""],is_image_in_boxes:[0,3,1,""],is_valid_patch:[0,3,1,""],load_dataset:[0,3,1,""],load_image:[0,3,1,""],load_process_image:[0,3,1,""],load_sql_df:[0,3,1,""],npy2da:[0,3,1,""],parse_coord_return_boxes:[0,3,1,""],process_svs:[0,3,1,""],retain_images:[0,3,1,""],return_image_coord:[0,3,1,""],return_image_in_boxes_dict:[0,3,1,""],run_preprocessing_pipeline:[0,3,1,""],save_all_patch_info:[0,3,1,""],save_dataset:[0,3,1,""],segmentation_predictions2npy:[0,3,1,""],svs2dask_array:[0,3,1,""]},"pathflowai.visualize":{PlotlyPlot:[0,1,1,""],PredictionPlotter:[0,1,1,""],annotation2rgb:[0,3,1,""],blend:[0,3,1,""],plot_image_:[0,3,1,""],plot_shap:[0,3,1,""],plot_umap_images:[0,3,1,""],prob2rbg:[0,3,1,""],seg2rgb:[0,3,1,""],to_pil:[0,3,1,""]},"pathflowai.visualize.PlotlyPlot":{add_plot:[0,2,1,""],plot:[0,2,1,""]},"pathflowai.visualize.PredictionPlotter":{add_custom_segmentation:[0,2,1,""],generate_image:[0,2,1,""],output_image:[0,2,1,""],return_patch:[0,2,1,""]},pathflowai:{datasets:[0,0,0,"-"],losses:[0,0,0,"-"],sampler:[0,0,0,"-"],schedulers:[0,0,0,"-"],utils:[0,0,0,"-"],visualize:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","function","Python function"],"4":["py","exception","Python exception"],"5":["std","cmdoption","program option"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:function","4":"py:exception","5":"std:cmdoption"},terms:{"0561e8a95cde6bfc5e10a3609841b7b0ca5b03ca":0,"0th":0,"break":0,"case":0,"class":0,"default":0,"export":0,"final":0,"float":0,"function":0,"int":0,"new":0,"null":0,"return":0,"short":0,"switch":0,"true":0,"while":0,For:0,SVS:0,The:0,Use:0,Used:0,Using:0,Will:0,a01:0,abov:0,abs:0,access:0,accomplish:0,add:0,add_custom_segment:0,add_plot:0,add_purple_mask:0,add_softmax:0,added:0,addit:0,adj_mask:0,adjust:0,adjust_mask:0,after:0,afterward:0,again:0,against:0,albument:0,all:0,allow:0,allow_unknown_chunks:0,alpha:0,alpha_decai:0,also:0,although:0,amount:0,ani:0,anneal:0,annot:0,annotation2rgb:0,annotation_col:0,annotation_nam:0,annotation_txt:0,anoth:0,appear:0,append:0,appli:0,applic:0,arbitrari:0,area:0,arg:0,argument:0,arr1:0,arr2:0,arr3:0,arr:0,arrai:0,arxiv:0,asc:0,ascend:0,assert:0,assert_:0,assertionerror:0,assign:0,atleast:0,attribut:0,averag:0,axes:0,axes_off:0,axi:0,background:0,backgrund:0,balanc:0,balance_index:0,base:0,basenam:0,basic:0,basic_preprocess:0,batch:0,batch_siz:0,be6123c7ee3b366e333a:0,becaus:0,becom:0,been:0,befor:0,being:0,below:0,benchmark:0,between:0,binar:0,binari:0,binarize_annot:0,binary_threshold:0,blend:0,bool:0,box:0,boxes2interior:0,broken:0,calcul:0,call:0,can:0,care:0,categor:0,certain:0,chang:0,channel:0,channelwis:0,choos:0,chosen:0,chunk:0,class2one_hot:0,classif:0,classifi:0,classify_annot:0,coars:0,color:0,color_col:0,column:0,com:0,come:0,command:0,compar:0,compress:0,compression_factor:0,comput:0,concat:0,concaten:0,condit:0,conduct:0,configur:0,connect:0,consid:0,contain:0,convert:0,coord:0,coordin:0,correspond:0,cos:0,cosin:0,cosineannealingwithrestartslr:0,creat:0,create_purple_mask:0,create_sparse_annotation_arrai:0,create_train_val_test:0,create_transform:0,criteria:0,criterion:0,cross:0,csv:0,cuda:0,cur:0,current:0,custom:0,custom_color:0,custom_segment:0,cv2:0,cval:0,darker:0,dask:0,dask_arr_dict:0,dask_img_array_fil:0,data:0,databas:0,datafram:0,dataset_df:0,dataset_opt:0,datbas:0,deep:0,defin:0,deform:0,degre:0,delay_tim:0,denot:0,dens:0,deprec:0,desc:0,descend:0,descent:0,descript:0,desir:0,detect:0,deviat:0,df2sql:0,dice:0,dict:0,dictionari:0,differ:0,dilat:0,dimens:0,dimi:0,dimx:0,dir2imag:0,dir:0,directli:0,directori:0,don:0,doubl:0,draw:0,dsize:0,dump:0,dure:0,dynamicdataset:0,dynamicimagedataset:0,each:0,elast:0,element:0,embed:0,embeddings_fil:0,empti:0,enter:0,entir:0,entropi:0,epoch:0,eps:0,eros:0,eta_:0,eta_min:0,eta_t:0,etc:0,everi:0,exampl:0,except:0,exception_typ:0,exclus:0,exist:0,exit:0,expect:0,explain:0,extens:0,extract:0,extract_patch_inform:0,factor:0,fals:0,faster:0,file:0,file_dir:0,filenam:0,find:0,finetun:0,first:0,fix:0,fix_nam:0,flatten:0,flatten_sampl:0,flexibl:0,floattensor:0,focal:0,focal_loss:0,focalloss:0,focu:0,follow:0,format:0,former:0,forth:0,forward:0,frac:0,fraction:0,from:0,from_annot:0,gamma:0,gdl:0,gener:0,generalizeddic:0,generalizeddiceloss:0,generate_finetune_segment:0,generate_imag:0,generate_patch_pipelin:0,get:0,get_class_weight:0,get_data_transform:0,get_lr:0,get_norm:0,gist:0,github:0,githubusercont:0,give:0,given:0,grab_interior_point:0,gradient:0,grai:0,graph:0,grayscal:0,greater:0,group:0,groupbi:0,hard:0,has:0,help:0,higher:0,hook:0,hot:0,hous:0,how:0,hsuxu:0,html:0,http:0,ignor:0,illegitim:0,imag:0,image2coord:0,image_coord_dict:0,image_dir:0,image_fil:0,image_r:0,images2coord_dict:0,imbalanc:0,imbalanceddatasetsampl:0,img2npi:0,img2npy_:0,img:0,img_fil:0,img_siz:0,implement:0,in_pkl:0,in_zarr:0,includ:0,inclus:0,incorpor:0,index:0,inferno:0,info:0,inform:0,initi:0,initial_lr:0,input:0,input_:0,input_dir:0,input_info_db:0,input_patch_db:0,inspir:0,instanc:0,instead:0,intens:0,intensity_threshold:0,inter_cub:0,intern:0,interpol:0,intersect:0,interv:0,invers:0,is_coords_in_box:0,is_image_in_box:0,is_valid_patch:0,iter:0,its:0,just:0,kwarg:0,label:0,labelbinar:0,last:0,last_epoch:0,latter:0,learn:0,less:0,level:0,like:0,line:0,list:0,liviaet:0,load:0,load_dataset:0,load_imag:0,load_process_imag:0,load_sql_df:0,local:0,local_smooth:0,locat:0,log:0,logit:0,look:0,loss_toolbox:0,low:0,lr_scheduler_decai:0,lukemetz:0,machin:0,made:0,mai:0,maintain:0,make:0,map:0,marker:0,mask:0,mask_dir:0,mask_fil:0,master:0,match:0,matplotlib:0,max:0,max_background_area:0,maximum:0,mean:0,messag:0,method:0,min:0,minimum:0,minut:0,misclassifi:0,mix:0,mode:0,model:0,model_pkl:0,modifi:0,modify_patch_info:0,modul:0,more:0,mpl:0,mpl_scatter:0,mt_bce:0,mth:0,much:0,multi:0,multipl:0,multipli:0,musn:0,must:0,n_neighbor:0,n_output:0,n_sampl:0,n_segmentation_class:0,name:0,name_col:0,nb_channel:0,nb_class:0,ndarrai:0,nearest:0,need:0,neighbor:0,networkx:0,no_db:0,non:0,none:0,normal:0,normalization_fil:0,now:0,npy2da:0,npy:0,npy_fil:0,npy_mask:0,npy_output:0,num_class:0,num_sampl:0,num_target:0,number:0,numpi:0,object:0,occur:0,ocf:0,odb:0,one:0,one_hot2dist:0,one_hot:0,onli:0,opac:0,open:0,oper:0,opt:0,optim:0,option:0,order:0,org:0,origin:0,original_compression_factor:0,other:0,other_annot:0,other_dataset:0,out:0,out_db:0,out_npi:0,out_pkl:0,out_zarr:0,output:0,output_dir:0,output_embed:0,output_fnam:0,output_imag:0,output_patch_db:0,output_pkl:0,output_point:0,output_zarr:0,outputfilenam:0,outputfnam:0,over:0,overlai:0,overlaid:0,overlap:0,overridden:0,oversampling_factor:0,own:0,page:0,pair:0,palett:0,pallet:0,panda:0,paramet:0,parse_coord_return_box:0,part:0,particular:0,pass:0,patch:0,patch_info:0,patch_info_db:0,patch_info_fil:0,patch_info_input:0,patch_info_output:0,patch_siz:0,patient:0,per:0,perform:0,pickl:0,pil:0,pipelin:0,pixel:0,pkl:0,plot:0,plot_annot:0,plot_image_:0,plot_shap:0,plot_umap_imag:0,plotli:0,plotly_output_fil:0,plotlyplot:0,png:0,point:0,polygon:0,pos_annotation_class:0,posit:0,pred_out:0,predict:0,predictionplott:0,preidict:0,prepar:0,pretrain:0,previou:0,prob2rbg:0,prob:0,probabl:0,process:0,process_sv:0,proport:0,propos:0,purpl:0,purple_mask:0,put:0,pytorch:0,random:0,randomli:0,randomrotate90:0,rate:0,raw:0,read:0,readi:0,receiv:0,recip:0,recommend:0,record:0,records_output_csv:0,reduc:0,region:0,regist:0,regress:0,rel:0,remov:0,remove_background_annot:0,remove_last:0,replac:0,repres:0,resiz:0,resolut:0,respect:0,restart:0,result:0,retain_id:0,retain_imag:0,return_coord:0,return_image_coord:0,return_image_in_boxes_dict:0,return_patch:0,rgb:0,rid:0,rotat:0,run:0,run_preprocessing_pipelin:0,sampl:0,save:0,save_all_patch_info:0,save_dataset:0,scalar:0,scale:0,scaling_factor:0,scatter:0,scheduler_choic:0,scheduler_step_fn:0,score:0,search:0,second:0,see:0,seg2rgb:0,seg:0,segment:0,segmentation_map:0,segmentation_predictions2npi:0,segmentation_transform:0,select:0,self:0,set:0,set_similarity_measur:0,sgdr:0,shap:0,shap_plot:0,shape:0,shapeerror:0,shaplei:0,share_memori:0,should:0,show:0,shrink:0,sigmoid:0,silent:0,similar:0,simplex:0,sinc:0,singl:0,size:0,size_averag:0,slide:0,slide_label:0,slowdown:0,smooth:0,softmax:0,some:0,soon:0,sort:0,sort_col:0,sort_mod:0,sourc:0,spars:0,spatial:0,specif:0,specifi:0,split:0,split_by_id:0,sql:0,sql_file:0,sset:0,standard:0,std:0,stdev:0,step:0,step_n:0,still:0,stochast:0,storag:0,store:0,str:0,sub:0,subclass:0,submodul:0,subsampl:0,subset:0,summari:0,suppli:0,support:0,surfac:0,surfaceloss:0,svs2dask_arrai:0,svs:0,svs_file:0,t_data_df:0,t_max:0,t_mult:0,take:0,target:0,target_class:0,target_nam:0,target_segmentation_class:0,target_threshold:0,task:0,tensor:0,test:0,test_image_nam:0,than:0,them:0,thi:0,thing:0,threshold:0,tif:0,tif_fil:0,tiff:0,tile:0,tile_s:0,time:0,timeout:0,tissu:0,to_annot:0,to_pil:0,togeth:0,tool:0,top:0,torch:0,torch_util:0,total:0,total_tim:0,train:0,train_val_test_pkl:0,trainign:0,transform:0,transform_opt:0,transform_platform:0,tri:0,tupl:0,two:0,txt:0,type:0,ufoym:0,umap:0,uniq:0,updat:0,usag:0,use:0,used:0,using:0,val:0,valid:0,valu:0,variabl:0,version:0,versu:0,via:0,warm:0,weight:0,well:0,what:0,when:0,where:0,whether:0,which:0,white:0,whole:0,wip:0,within:0,work:0,wrap:0,write:0,wsi:0,xml:0,xml_file:0,xyz_col:0,y_pred:0,zarr:0,zoom:0},titles:["Welcome to PathFlowAI\u2019s documentation!"],titleterms:{alter_mask:0,collapse_annot:0,dataset:0,document:0,extract_patch:0,indic:0,loss:0,monitor:0,monitor_usag:0,overlay_new_annot:0,pathflowai:0,plot_embed:0,plot_imag:0,plot_image_umap_embed:0,plot_predict:0,preprocess:0,preprocess_pipelin:0,remove_basename_from_db:0,sampler:0,schedul:0,shapley_plot:0,tabl:0,util:0,visual:0,welcom:0}})