Index

Symbols

--version pathflowai-monitor command line option pathflowai-preprocess command line option pathflowai-visualize command line option -a, --annotation_txt <annotation_txt> pathflowai-visualize-overlay_new_annotations command line option -a, --annotations <annotations> pathflowai-preprocess-preprocess_pipeline command line option pathflowai-visualize-plot_embeddings command line option -ac, --annotation_col <annotation_col> pathflowai-visualize-plot_predictions command line option -al, --alpha <alpha> pathflowai-visualize-plot_predictions command line option -am, --adjust_mask pathflowai-preprocess-preprocess_pipeline command line option -an, --annotations pathflowai-visualize-plot_predictions command line option -b, --basename <basename> pathflowai-preprocess-preprocess_pipeline command line option pathflowai-preprocess-remove_basename_from_db command line option pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_embeddings command line option pathflowai-visualize-plot_image_umap_embeddings command line option pathflowai-visualize-plot_predictions command line option -bp, --basic_preprocess pathflowai-preprocess-preprocess_pipeline command line option -bs, --batch_size <batch_size> pathflowai-visualize-shapley_plot command line option -c, --custom_segmentation <custom_segmentation> pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_predictions command line option -cf, --compression_factor <compression_factor> pathflowai-visualize-overlay_new_annotations command line option pathflowai-visualize-plot_image command line option pathflowai-visualize-plot_predictions command line option -csv, --records_output_csv <records_output_csv> pathflowai-monitor-monitor_usage command line option -dt, --delay_time <delay_time> pathflowai-monitor-monitor_usage command line option -e, --embeddings_file <embeddings_file> pathflowai-visualize-plot_image_umap_embeddings command line option -fr, --from_annotations <from_annotations> pathflowai-preprocess-alter_masks command line option pathflowai-preprocess-collapse_annotations command line option -g, --generate_finetune_segmentation pathflowai-preprocess-preprocess_pipeline command line option -i, --embeddings_file <embeddings_file> pathflowai-visualize-plot_embeddings command line option -i, --image_file <image_file> pathflowai-visualize-plot_image command line option -i, --img_file <img_file> pathflowai-visualize-overlay_new_annotations command line option -i, --input_dir <input_dir> pathflowai-preprocess-preprocess_pipeline command line option pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_image_umap_embeddings command line option pathflowai-visualize-plot_predictions command line option -i, --input_patch_db <input_patch_db> pathflowai-preprocess-collapse_annotations command line option pathflowai-preprocess-remove_basename_from_db command line option -i, --mask_dir <mask_dir> pathflowai-preprocess-alter_masks command line option -it, --intensity_threshold <intensity_threshold> pathflowai-preprocess-preprocess_pipeline command line option -l, --local_smoothing <local_smoothing> pathflowai-visualize-shapley_plot command line option -m, --model_pkl <model_pkl> pathflowai-visualize-shapley_plot command line option -ma, --max_background_area <max_background_area> pathflowai-preprocess-collapse_annotations command line option pathflowai-visualize-plot_embeddings command line option pathflowai-visualize-plot_image_umap_embeddings command line option -mpl, --mpl_scatter pathflowai-visualize-plot_image_umap_embeddings command line option -mth, --method <method> pathflowai-visualize-shapley_plot command line option

-nn, --n_neighbors <n_neighbors> pathflowai-preprocess-preprocess_pipeline command line option pathflowai-visualize-plot_embeddings command line option pathflowai-visualize-plot_image_umap_embeddings command line option -npy, --img2npy pathflowai-preprocess-preprocess_pipeline command line option -ns, --n_samples <n_samples> pathflowai-visualize-shapley_plot command line option -o, --output_dir <output_dir> pathflowai-preprocess-alter_masks command line option -o, --output_patch_db <output_patch_db> pathflowai-preprocess-collapse_annotations command line option pathflowai-preprocess-remove_basename_from_db command line option -o, --outputfilename <outputfilename> pathflowai-visualize-overlay_new_annotations command line option pathflowai-visualize-plot_image_umap_embeddings command line option pathflowai-visualize-shapley_plot command line option -o, --outputfname <outputfname> pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_image command line option pathflowai-visualize-plot_predictions command line option -o, --plotly_output_file <plotly_output_file> pathflowai-visualize-plot_embeddings command line option -ocf, --original_compression_factor <original_compression_factor> pathflowai-visualize-overlay_new_annotations command line option -odb, --out_db <out_db> pathflowai-preprocess-preprocess_pipeline command line option -p, --patch_info_file <patch_info_file> pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_predictions command line option -p, --pred_out <pred_out> pathflowai-visualize-shapley_plot command line option -pa, --patches pathflowai-preprocess-preprocess_pipeline command line option -pr, --preprocess pathflowai-preprocess-preprocess_pipeline command line option -ps, --patch_size <patch_size> pathflowai-preprocess-collapse_annotations command line option pathflowai-preprocess-preprocess_pipeline command line option pathflowai-preprocess-remove_basename_from_db command line option pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_predictions command line option -rb, --remove_background_annotation <remove_background_annotation> pathflowai-preprocess-collapse_annotations command line option pathflowai-visualize-plot_embeddings command line option pathflowai-visualize-plot_image_umap_embeddings command line option -s, --segmentation pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_predictions command line option -sc, --n_segmentation_classes <n_segmentation_classes> pathflowai-visualize-extract_patch command line option pathflowai-visualize-plot_predictions command line option -sc, --sort_col <sort_col> pathflowai-visualize-plot_image_umap_embeddings command line option -sf, --scaling_factor <scaling_factor> pathflowai-visualize-plot_predictions command line option -sm, --sort_mode <sort_mode> pathflowai-visualize-plot_image_umap_embeddings command line option -t, --threshold <threshold> pathflowai-preprocess-preprocess_pipeline command line option -tc, --target_segmentation_class <target_segmentation_class> pathflowai-preprocess-preprocess_pipeline command line option -tif, --tif_file pathflowai-visualize-plot_predictions command line option -to, --to_annotations <to_annotations> pathflowai-preprocess-alter_masks command line option pathflowai-preprocess-collapse_annotations command line option -tt, --target_threshold <target_threshold> pathflowai-preprocess-preprocess_pipeline command line option -tt, --total_time <total_time> pathflowai-monitor-monitor_usage command line option -x, --x <x> pathflowai-visualize-extract_patch command line option -y, --y <y> pathflowai-visualize-extract_patch command line option -z, --zoom <zoom> pathflowai-visualize-plot_image_umap_embeddings command line option

A

add_custom_segmentation() (pathflowai.visualize.PredictionPlotter method) add_plot() (pathflowai.visualize.PlotlyPlot method) add_purple_mask() (in module pathflowai.utils)

adjust_mask() (in module pathflowai.utils) annotation2rgb() (in module pathflowai.visualize) assert_() (in module pathflowai.losses)

B

binarize_annotations() (pathflowai.datasets.DynamicImageDataset method)

blend() (in module pathflowai.visualize) boxes2interior() (in module pathflowai.utils)

C

class2one_hot() (in module pathflowai.losses) concat() (pathflowai.datasets.DynamicImageDataset method) CosineAnnealingWithRestartsLR (class in pathflowai.schedulers)

create_purple_mask() (in module pathflowai.utils) create_sparse_annotation_arrays() (in module pathflowai.utils) create_train_val_test() (in module pathflowai.utils) create_transforms() (in module pathflowai.datasets)

D

df2sql() (in module pathflowai.utils)

dir2images() (in module pathflowai.utils) DynamicImageDataset (class in pathflowai.datasets)

E

eq() (in module pathflowai.losses)

extract_patch_information() (in module pathflowai.utils)

F

fix_name() (in module pathflowai.utils) fix_names() (in module pathflowai.utils) flatten_samples() (in module pathflowai.losses)

FocalLoss (class in pathflowai.losses) forward() (pathflowai.losses.FocalLoss method) (pathflowai.losses.GeneralizedDiceLoss method)

G

GeneralizedDice (class in pathflowai.losses) GeneralizedDiceLoss (class in pathflowai.losses) generate_image() (pathflowai.visualize.PredictionPlotter method) generate_patch_pipeline() (in module pathflowai.utils)

get_class_weights() (pathflowai.datasets.DynamicImageDataset method) get_data_transforms() (in module pathflowai.datasets) get_lr() (pathflowai.schedulers.Scheduler method) get_normalizer() (in module pathflowai.datasets) grab_interior_points() (in module pathflowai.utils)

I

image2coords() (in module pathflowai.utils) images2coord_dict() (in module pathflowai.utils) ImbalancedDatasetSampler (class in pathflowai.sampler)

img2npy_() (in module pathflowai.utils) is_coords_in_box() (in module pathflowai.utils) is_image_in_boxes() (in module pathflowai.utils) is_valid_patch() (in module pathflowai.utils)

L

load_dataset() (in module pathflowai.utils) load_image() (in module pathflowai.utils)

load_process_image() (in module pathflowai.utils) load_sql_df() (in module pathflowai.utils)

N

npy2da() (in module pathflowai.utils)

O

one_hot() (in module pathflowai.losses)

one_hot2dist() (in module pathflowai.losses) output_image() (pathflowai.visualize.PredictionPlotter method)

P

parse_coord_return_boxes() (in module pathflowai.utils) pathflowai-monitor command line option --version pathflowai-monitor-monitor_usage command line option -csv, --records_output_csv <records_output_csv> -dt, --delay_time <delay_time> -tt, --total_time <total_time> pathflowai-preprocess command line option --version pathflowai-preprocess-alter_masks command line option -fr, --from_annotations <from_annotations> -i, --mask_dir <mask_dir> -o, --output_dir <output_dir> -to, --to_annotations <to_annotations> pathflowai-preprocess-collapse_annotations command line option -fr, --from_annotations <from_annotations> -i, --input_patch_db <input_patch_db> -ma, --max_background_area <max_background_area> -o, --output_patch_db <output_patch_db> -ps, --patch_size <patch_size> -rb, --remove_background_annotation <remove_background_annotation> -to, --to_annotations <to_annotations> pathflowai-preprocess-preprocess_pipeline command line option -a, --annotations <annotations> -am, --adjust_mask -b, --basename <basename> -bp, --basic_preprocess -g, --generate_finetune_segmentation -i, --input_dir <input_dir> -it, --intensity_threshold <intensity_threshold> -nn, --n_neighbors <n_neighbors> -npy, --img2npy -odb, --out_db <out_db> -pa, --patches -pr, --preprocess -ps, --patch_size <patch_size> -t, --threshold <threshold> -tc, --target_segmentation_class <target_segmentation_class> -tt, --target_threshold <target_threshold> pathflowai-preprocess-remove_basename_from_db command line option -b, --basename <basename> -i, --input_patch_db <input_patch_db> -o, --output_patch_db <output_patch_db> -ps, --patch_size <patch_size> pathflowai-visualize command line option --version pathflowai-visualize-extract_patch command line option -b, --basename <basename> -c, --custom_segmentation <custom_segmentation> -i, --input_dir <input_dir> -o, --outputfname <outputfname> -p, --patch_info_file <patch_info_file> -ps, --patch_size <patch_size> -s, --segmentation -sc, --n_segmentation_classes <n_segmentation_classes> -x, --x <x> -y, --y <y> pathflowai-visualize-overlay_new_annotations command line option -a, --annotation_txt <annotation_txt> -cf, --compression_factor <compression_factor> -i, --img_file <img_file> -o, --outputfilename <outputfilename> -ocf, --original_compression_factor <original_compression_factor>

pathflowai-visualize-plot_embeddings command line option -a, --annotations <annotations> -b, --basename <basename> -i, --embeddings_file <embeddings_file> -ma, --max_background_area <max_background_area> -nn, --n_neighbors <n_neighbors> -o, --plotly_output_file <plotly_output_file> -rb, --remove_background_annotation <remove_background_annotation> pathflowai-visualize-plot_image command line option -cf, --compression_factor <compression_factor> -i, --image_file <image_file> -o, --outputfname <outputfname> pathflowai-visualize-plot_image_umap_embeddings command line option -b, --basename <basename> -e, --embeddings_file <embeddings_file> -i, --input_dir <input_dir> -ma, --max_background_area <max_background_area> -mpl, --mpl_scatter -nn, --n_neighbors <n_neighbors> -o, --outputfilename <outputfilename> -rb, --remove_background_annotation <remove_background_annotation> -sc, --sort_col <sort_col> -sm, --sort_mode <sort_mode> -z, --zoom <zoom> pathflowai-visualize-plot_predictions command line option -ac, --annotation_col <annotation_col> -al, --alpha <alpha> -an, --annotations -b, --basename <basename> -c, --custom_segmentation <custom_segmentation> -cf, --compression_factor <compression_factor> -i, --input_dir <input_dir> -o, --outputfname <outputfname> -p, --patch_info_file <patch_info_file> -ps, --patch_size <patch_size> -s, --segmentation -sc, --n_segmentation_classes <n_segmentation_classes> -sf, --scaling_factor <scaling_factor> -tif, --tif_file pathflowai-visualize-shapley_plot command line option -bs, --batch_size <batch_size> -l, --local_smoothing <local_smoothing> -m, --model_pkl <model_pkl> -mth, --method <method> -ns, --n_samples <n_samples> -o, --outputfilename <outputfilename> -p, --pred_out <pred_out> pathflowai.datasets (module) pathflowai.losses (module) pathflowai.sampler (module) pathflowai.schedulers (module) pathflowai.utils (module) pathflowai.visualize (module) plot() (pathflowai.visualize.PlotlyPlot method) plot_image_() (in module pathflowai.visualize) plot_shap() (in module pathflowai.visualize) plot_umap_images() (in module pathflowai.visualize) PlotlyPlot (class in pathflowai.visualize) PredictionPlotter (class in pathflowai.visualize) prob2rbg() (in module pathflowai.visualize) process_svs() (in module pathflowai.utils)

R

RandomRotate90() (in module pathflowai.datasets) retain_ID() (pathflowai.datasets.DynamicImageDataset method) retain_images() (in module pathflowai.utils)

return_image_coord() (in module pathflowai.utils) return_image_in_boxes_dict() (in module pathflowai.utils) return_patch() (pathflowai.visualize.PredictionPlotter method) run_preprocessing_pipeline() (in module pathflowai.utils)

S

save_all_patch_info() (in module pathflowai.utils) save_dataset() (in module pathflowai.utils) Scheduler (class in pathflowai.schedulers) seg2rgb() (in module pathflowai.visualize) segmentation_predictions2npy() (in module pathflowai.utils) segmentation_transform() (in module pathflowai.datasets) ShapeError

simplex() (in module pathflowai.losses) split_by_ID() (pathflowai.datasets.DynamicImageDataset method) sset() (in module pathflowai.losses) step() (pathflowai.schedulers.Scheduler method) subsample() (pathflowai.datasets.DynamicImageDataset method) SurfaceLoss (class in pathflowai.losses) svs2dask_array() (in module pathflowai.utils)

T

to_pil() (in module pathflowai.visualize)

U

uniq() (in module pathflowai.losses)