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--- a +++ b/docs/genindex.html @@ -0,0 +1,1265 @@ + + + +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>Index — PathFlowAI 0.1 documentation</title> + + + + + + + + + <script type="text/javascript" src="_static/js/modernizr.min.js"></script> + + + <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="_static/language_data.js"></script> + <script async="async" type="text/javascript" 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class="genindex-jumpbox"> + <a href="#Symbols"><strong>Symbols</strong></a> + | <a href="#A"><strong>A</strong></a> + | <a href="#B"><strong>B</strong></a> + | <a href="#C"><strong>C</strong></a> + | <a href="#D"><strong>D</strong></a> + | <a href="#E"><strong>E</strong></a> + | <a href="#F"><strong>F</strong></a> + | <a href="#G"><strong>G</strong></a> + | <a href="#I"><strong>I</strong></a> + | <a href="#L"><strong>L</strong></a> + | <a href="#N"><strong>N</strong></a> + | <a href="#O"><strong>O</strong></a> + | <a href="#P"><strong>P</strong></a> + | <a href="#R"><strong>R</strong></a> + | <a href="#S"><strong>S</strong></a> + | <a href="#T"><strong>T</strong></a> + | <a href="#U"><strong>U</strong></a> + +</div> +<h2 id="Symbols">Symbols</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li> + --version + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-version">pathflowai-monitor command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-version">pathflowai-preprocess command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-version">pathflowai-visualize command line option</a> +</li> + </ul></li> + <li> + -a, --annotation_txt <annotation_txt> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-a">pathflowai-visualize-overlay_new_annotations command line option</a> +</li> + </ul></li> + <li> + -a, --annotations <annotations> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-a">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-a">pathflowai-visualize-plot_embeddings command line option</a> +</li> + </ul></li> + <li> + -ac, --annotation_col <annotation_col> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ac">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -al, --alpha <alpha> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-al">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -am, --adjust_mask + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-am">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -an, --annotations + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-an">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -b, --basename <basename> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-b">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-b">pathflowai-preprocess-remove_basename_from_db command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-b">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-b">pathflowai-visualize-plot_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-b">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -bp, --basic_preprocess + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-bp">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -bs, --batch_size <batch_size> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-bs">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -c, --custom_segmentation <custom_segmentation> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-c">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-c">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -cf, --compression_factor <compression_factor> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-cf">pathflowai-visualize-overlay_new_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-cf">pathflowai-visualize-plot_image command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-cf">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -csv, --records_output_csv <records_output_csv> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-csv">pathflowai-monitor-monitor_usage command line option</a> +</li> + </ul></li> + <li> + -dt, --delay_time <delay_time> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-dt">pathflowai-monitor-monitor_usage command line option</a> +</li> + </ul></li> + <li> + -e, --embeddings_file <embeddings_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -fr, --from_annotations <from_annotations> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-fr">pathflowai-preprocess-alter_masks command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-fr">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + </ul></li> + <li> + -g, --generate_finetune_segmentation + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-g">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -i, --embeddings_file <embeddings_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-i">pathflowai-visualize-plot_embeddings command line option</a> +</li> + </ul></li> + <li> + -i, --image_file <image_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-i">pathflowai-visualize-plot_image command line option</a> +</li> + </ul></li> + <li> + -i, --img_file <img_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-i">pathflowai-visualize-overlay_new_annotations command line option</a> +</li> + </ul></li> + <li> + -i, --input_dir <input_dir> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-i">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-i">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-i">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -i, --input_patch_db <input_patch_db> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-i">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-i">pathflowai-preprocess-remove_basename_from_db command line option</a> +</li> + </ul></li> + <li> + -i, --mask_dir <mask_dir> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-i">pathflowai-preprocess-alter_masks command line option</a> +</li> + </ul></li> + <li> + -it, --intensity_threshold <intensity_threshold> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-it">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -l, --local_smoothing <local_smoothing> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-l">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -m, --model_pkl <model_pkl> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-m">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -ma, --max_background_area <max_background_area> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ma">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-ma">pathflowai-visualize-plot_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -mpl, --mpl_scatter + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -mth, --method <method> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-mth">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li> + -nn, --n_neighbors <n_neighbors> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-nn">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-nn">pathflowai-visualize-plot_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -npy, --img2npy + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-npy">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -ns, --n_samples <n_samples> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-ns">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -o, --output_dir <output_dir> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-o">pathflowai-preprocess-alter_masks command line option</a> +</li> + </ul></li> + <li> + -o, --output_patch_db <output_patch_db> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-o">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-o">pathflowai-preprocess-remove_basename_from_db command line option</a> +</li> + </ul></li> + <li> + -o, --outputfilename <outputfilename> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-o">pathflowai-visualize-overlay_new_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-o">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -o, --outputfname <outputfname> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-o">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-o">pathflowai-visualize-plot_image command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-o">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -o, --plotly_output_file <plotly_output_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-o">pathflowai-visualize-plot_embeddings command line option</a> +</li> + </ul></li> + <li> + -ocf, --original_compression_factor <original_compression_factor> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-ocf">pathflowai-visualize-overlay_new_annotations command line option</a> +</li> + </ul></li> + <li> + -odb, --out_db <out_db> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-odb">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -p, --patch_info_file <patch_info_file> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-p">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-p">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -p, --pred_out <pred_out> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-p">pathflowai-visualize-shapley_plot command line option</a> +</li> + </ul></li> + <li> + -pa, --patches + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pa">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -pr, --preprocess + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pr">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -ps, --patch_size <patch_size> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ps">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-ps">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-ps">pathflowai-preprocess-remove_basename_from_db command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-ps">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ps">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -rb, --remove_background_annotation <remove_background_annotation> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-rb">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-rb">pathflowai-visualize-plot_embeddings command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -s, --segmentation + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-s">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-s">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -sc, --n_segmentation_classes <n_segmentation_classes> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-sc">pathflowai-visualize-extract_patch command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sc">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -sc, --sort_col <sort_col> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -sf, --scaling_factor <scaling_factor> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sf">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -sm, --sort_mode <sort_mode> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + <li> + -t, --threshold <threshold> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-t">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -tc, --target_segmentation_class <target_segmentation_class> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tc">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -tif, --tif_file + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-tif">pathflowai-visualize-plot_predictions command line option</a> +</li> + </ul></li> + <li> + -to, --to_annotations <to_annotations> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-to">pathflowai-preprocess-alter_masks command line option</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-to">pathflowai-preprocess-collapse_annotations command line option</a> +</li> + </ul></li> + <li> + -tt, --target_threshold <target_threshold> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tt">pathflowai-preprocess-preprocess_pipeline command line option</a> +</li> + </ul></li> + <li> + -tt, --total_time <total_time> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-tt">pathflowai-monitor-monitor_usage command line option</a> +</li> + </ul></li> + <li> + -x, --x <x> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-x">pathflowai-visualize-extract_patch command line option</a> +</li> + </ul></li> + <li> + -y, --y <y> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-y">pathflowai-visualize-extract_patch command line option</a> +</li> + </ul></li> + <li> + -z, --zoom <zoom> + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z">pathflowai-visualize-plot_image_umap_embeddings command line option</a> +</li> + </ul></li> + </ul></td> +</tr></table> + +<h2 id="A">A</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.visualize.PredictionPlotter.add_custom_segmentation">add_custom_segmentation() (pathflowai.visualize.PredictionPlotter method)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PlotlyPlot.add_plot">add_plot() (pathflowai.visualize.PlotlyPlot method)</a> +</li> + <li><a href="index.html#pathflowai.utils.add_purple_mask">add_purple_mask() (in module pathflowai.utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.adjust_mask">adjust_mask() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.visualize.annotation2rgb">annotation2rgb() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.losses.assert_">assert_() (in module pathflowai.losses)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="B">B</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.binarize_annotations">binarize_annotations() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.visualize.blend">blend() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.utils.boxes2interior">boxes2interior() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="C">C</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.class2one_hot">class2one_hot() (in module pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.concat">concat() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + <li><a href="index.html#pathflowai.schedulers.CosineAnnealingWithRestartsLR">CosineAnnealingWithRestartsLR (class in pathflowai.schedulers)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.create_purple_mask">create_purple_mask() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.create_sparse_annotation_arrays">create_sparse_annotation_arrays() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.create_train_val_test">create_train_val_test() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.datasets.create_transforms">create_transforms() (in module pathflowai.datasets)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="D">D</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.df2sql">df2sql() (in module pathflowai.utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.dir2images">dir2images() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset">DynamicImageDataset (class in pathflowai.datasets)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="E">E</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.eq">eq() (in module pathflowai.losses)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.extract_patch_information">extract_patch_information() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="F">F</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.fix_name">fix_name() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.fix_names">fix_names() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.losses.flatten_samples">flatten_samples() (in module pathflowai.losses)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.FocalLoss">FocalLoss (class in pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.losses.FocalLoss.forward">forward() (pathflowai.losses.FocalLoss method)</a> + + <ul> + <li><a href="index.html#pathflowai.losses.GeneralizedDiceLoss.forward">(pathflowai.losses.GeneralizedDiceLoss method)</a> +</li> + </ul></li> + </ul></td> +</tr></table> + +<h2 id="G">G</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.GeneralizedDice">GeneralizedDice (class in pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.losses.GeneralizedDiceLoss">GeneralizedDiceLoss (class in pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PredictionPlotter.generate_image">generate_image() (pathflowai.visualize.PredictionPlotter method)</a> +</li> + <li><a href="index.html#pathflowai.utils.generate_patch_pipeline">generate_patch_pipeline() (in module pathflowai.utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.get_class_weights">get_class_weights() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + <li><a href="index.html#pathflowai.datasets.get_data_transforms">get_data_transforms() (in module pathflowai.datasets)</a> +</li> + <li><a href="index.html#pathflowai.schedulers.Scheduler.get_lr">get_lr() (pathflowai.schedulers.Scheduler method)</a> +</li> + <li><a href="index.html#pathflowai.datasets.get_normalizer">get_normalizer() (in module pathflowai.datasets)</a> +</li> + <li><a href="index.html#pathflowai.utils.grab_interior_points">grab_interior_points() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="I">I</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.image2coords">image2coords() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.images2coord_dict">images2coord_dict() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.sampler.ImbalancedDatasetSampler">ImbalancedDatasetSampler (class in pathflowai.sampler)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.img2npy_">img2npy_() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.is_coords_in_box">is_coords_in_box() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.is_image_in_boxes">is_image_in_boxes() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.is_valid_patch">is_valid_patch() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="L">L</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.load_dataset">load_dataset() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.load_image">load_image() (in module pathflowai.utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.load_process_image">load_process_image() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.load_sql_df">load_sql_df() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="N">N</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.npy2da">npy2da() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="O">O</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.one_hot">one_hot() (in module pathflowai.losses)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.one_hot2dist">one_hot2dist() (in module pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PredictionPlotter.output_image">output_image() (pathflowai.visualize.PredictionPlotter method)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="P">P</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.parse_coord_return_boxes">parse_coord_return_boxes() (in module pathflowai.utils)</a> +</li> + <li> + pathflowai-monitor command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-version">--version</a> +</li> + </ul></li> + <li> + pathflowai-monitor-monitor_usage command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-csv">-csv, --records_output_csv <records_output_csv></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-dt">-dt, --delay_time <delay_time></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-monitor-monitor-usage-tt">-tt, --total_time <total_time></a> +</li> + </ul></li> + <li> + pathflowai-preprocess command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-version">--version</a> +</li> + </ul></li> + <li> + pathflowai-preprocess-alter_masks command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-fr">-fr, --from_annotations <from_annotations></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-i">-i, --mask_dir <mask_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-o">-o, --output_dir <output_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-alter-masks-to">-to, --to_annotations <to_annotations></a> +</li> + </ul></li> + <li> + pathflowai-preprocess-collapse_annotations command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-fr">-fr, --from_annotations <from_annotations></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-i">-i, --input_patch_db <input_patch_db></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ma">-ma, --max_background_area <max_background_area></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-o">-o, --output_patch_db <output_patch_db></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-ps">-ps, --patch_size <patch_size></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-rb">-rb, --remove_background_annotation <remove_background_annotation></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-collapse-annotations-to">-to, --to_annotations <to_annotations></a> +</li> + </ul></li> + <li> + pathflowai-preprocess-preprocess_pipeline command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-a">-a, --annotations <annotations></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-am">-am, --adjust_mask</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-bp">-bp, --basic_preprocess</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-g">-g, --generate_finetune_segmentation</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-i">-i, --input_dir <input_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-it">-it, --intensity_threshold <intensity_threshold></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-nn">-nn, --n_neighbors <n_neighbors></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-npy">-npy, --img2npy</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-odb">-odb, --out_db <out_db></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pa">-pa, --patches</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-pr">-pr, --preprocess</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-ps">-ps, --patch_size <patch_size></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-t">-t, --threshold <threshold></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tc">-tc, --target_segmentation_class <target_segmentation_class></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-preprocess-pipeline-tt">-tt, --target_threshold <target_threshold></a> +</li> + </ul></li> + <li> + pathflowai-preprocess-remove_basename_from_db command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-i">-i, --input_patch_db <input_patch_db></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-o">-o, --output_patch_db <output_patch_db></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-preprocess-remove-basename-from-db-ps">-ps, --patch_size <patch_size></a> +</li> + </ul></li> + <li> + pathflowai-visualize command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-version">--version</a> +</li> + </ul></li> + <li> + pathflowai-visualize-extract_patch command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-c">-c, --custom_segmentation <custom_segmentation></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-i">-i, --input_dir <input_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-o">-o, --outputfname <outputfname></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-p">-p, --patch_info_file <patch_info_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-ps">-ps, --patch_size <patch_size></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-s">-s, --segmentation</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-sc">-sc, --n_segmentation_classes <n_segmentation_classes></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-x">-x, --x <x></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-extract-patch-y">-y, --y <y></a> +</li> + </ul></li> + <li> + pathflowai-visualize-overlay_new_annotations command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-a">-a, --annotation_txt <annotation_txt></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-cf">-cf, --compression_factor <compression_factor></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-i">-i, --img_file <img_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-o">-o, --outputfilename <outputfilename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-overlay-new-annotations-ocf">-ocf, --original_compression_factor <original_compression_factor></a> +</li> + </ul></li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li> + pathflowai-visualize-plot_embeddings command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-a">-a, --annotations <annotations></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-i">-i, --embeddings_file <embeddings_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-ma">-ma, --max_background_area <max_background_area></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-nn">-nn, --n_neighbors <n_neighbors></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-o">-o, --plotly_output_file <plotly_output_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-embeddings-rb">-rb, --remove_background_annotation <remove_background_annotation></a> +</li> + </ul></li> + <li> + pathflowai-visualize-plot_image command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-cf">-cf, --compression_factor <compression_factor></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-i">-i, --image_file <image_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-o">-o, --outputfname <outputfname></a> +</li> + </ul></li> + <li> + pathflowai-visualize-plot_image_umap_embeddings command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-e">-e, --embeddings_file <embeddings_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-i">-i, --input_dir <input_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-ma">-ma, --max_background_area <max_background_area></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-mpl">-mpl, --mpl_scatter</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-nn">-nn, --n_neighbors <n_neighbors></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-o">-o, --outputfilename <outputfilename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-rb">-rb, --remove_background_annotation <remove_background_annotation></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sc">-sc, --sort_col <sort_col></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-sm">-sm, --sort_mode <sort_mode></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-image-umap-embeddings-z">-z, --zoom <zoom></a> +</li> + </ul></li> + <li> + pathflowai-visualize-plot_predictions command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ac">-ac, --annotation_col <annotation_col></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-al">-al, --alpha <alpha></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-an">-an, --annotations</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-b">-b, --basename <basename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-c">-c, --custom_segmentation <custom_segmentation></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-cf">-cf, --compression_factor <compression_factor></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-i">-i, --input_dir <input_dir></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-o">-o, --outputfname <outputfname></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-p">-p, --patch_info_file <patch_info_file></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-ps">-ps, --patch_size <patch_size></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-s">-s, --segmentation</a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sc">-sc, --n_segmentation_classes <n_segmentation_classes></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-sf">-sf, --scaling_factor <scaling_factor></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-plot-predictions-tif">-tif, --tif_file</a> +</li> + </ul></li> + <li> + pathflowai-visualize-shapley_plot command line option + + <ul> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-bs">-bs, --batch_size <batch_size></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-l">-l, --local_smoothing <local_smoothing></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-m">-m, --model_pkl <model_pkl></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-mth">-mth, --method <method></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-ns">-ns, --n_samples <n_samples></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-o">-o, --outputfilename <outputfilename></a> +</li> + <li><a href="index.html#cmdoption-pathflowai-visualize-shapley-plot-p">-p, --pred_out <pred_out></a> +</li> + </ul></li> + <li><a href="index.html#module-pathflowai.datasets">pathflowai.datasets (module)</a> +</li> + <li><a href="index.html#module-pathflowai.losses">pathflowai.losses (module)</a> +</li> + <li><a href="index.html#module-pathflowai.sampler">pathflowai.sampler (module)</a> +</li> + <li><a href="index.html#module-pathflowai.schedulers">pathflowai.schedulers (module)</a> +</li> + <li><a href="index.html#module-pathflowai.utils">pathflowai.utils (module)</a> +</li> + <li><a href="index.html#module-pathflowai.visualize">pathflowai.visualize (module)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PlotlyPlot.plot">plot() (pathflowai.visualize.PlotlyPlot method)</a> +</li> + <li><a href="index.html#pathflowai.visualize.plot_image_">plot_image_() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.visualize.plot_shap">plot_shap() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.visualize.plot_umap_images">plot_umap_images() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PlotlyPlot">PlotlyPlot (class in pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PredictionPlotter">PredictionPlotter (class in pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.visualize.prob2rbg">prob2rbg() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.utils.process_svs">process_svs() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="R">R</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.datasets.RandomRotate90">RandomRotate90() (in module pathflowai.datasets)</a> +</li> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.retain_ID">retain_ID() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + <li><a href="index.html#pathflowai.utils.retain_images">retain_images() (in module pathflowai.utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.return_image_coord">return_image_coord() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.return_image_in_boxes_dict">return_image_in_boxes_dict() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.visualize.PredictionPlotter.return_patch">return_patch() (pathflowai.visualize.PredictionPlotter method)</a> +</li> + <li><a href="index.html#pathflowai.utils.run_preprocessing_pipeline">run_preprocessing_pipeline() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.utils.save_all_patch_info">save_all_patch_info() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.utils.save_dataset">save_dataset() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.schedulers.Scheduler">Scheduler (class in pathflowai.schedulers)</a> +</li> + <li><a href="index.html#pathflowai.visualize.seg2rgb">seg2rgb() (in module pathflowai.visualize)</a> +</li> + <li><a href="index.html#pathflowai.utils.segmentation_predictions2npy">segmentation_predictions2npy() (in module pathflowai.utils)</a> +</li> + <li><a href="index.html#pathflowai.datasets.segmentation_transform">segmentation_transform() (in module pathflowai.datasets)</a> +</li> + <li><a href="index.html#pathflowai.losses.ShapeError">ShapeError</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.simplex">simplex() (in module pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.split_by_ID">split_by_ID() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + <li><a href="index.html#pathflowai.losses.sset">sset() (in module pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.schedulers.Scheduler.step">step() (pathflowai.schedulers.Scheduler method)</a> +</li> + <li><a href="index.html#pathflowai.datasets.DynamicImageDataset.subsample">subsample() (pathflowai.datasets.DynamicImageDataset method)</a> +</li> + <li><a href="index.html#pathflowai.losses.SurfaceLoss">SurfaceLoss (class in pathflowai.losses)</a> +</li> + <li><a href="index.html#pathflowai.utils.svs2dask_array">svs2dask_array() (in module pathflowai.utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="T">T</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.visualize.to_pil">to_pil() (in module pathflowai.visualize)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="U">U</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="index.html#pathflowai.losses.uniq">uniq() (in module pathflowai.losses)</a> +</li> + </ul></td> +</tr></table> + + + + </div> + + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2019, Joshua Levy + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + + </div> + </div> + + </section> + + </div> + + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + + + + + + +</body> +</html> \ No newline at end of file