spacr

• spacr package
  • Submodules
  • spacr.app_annotate module
    • initiate_annotation_app()
    • start_annotate_app()
  • spacr.app_classify module
    • start_classify_app()
  • spacr.app_make_masks module
    • initiate_make_mask_app()
    • start_make_mask_app()
  • spacr.app_mask module
    • start_mask_app()
  • spacr.app_measure module
    • start_measure_app()
  • spacr.app_sequencing module
    • start_seq_app()
  • spacr.app_umap module
    • start_umap_app()
  • spacr.core module
    • all_elements_match()
    • analyze_data_reg()
    • analyze_plaques()
    • analyze_recruitment()
    • annotate_results()
    • apply_model()
    • apply_model_to_tar()
    • check_cellpose_models()
    • check_index()
    • compare_cellpose_masks()
    • compare_mask()
    • find_optimal_threshold()
    • generate_cellpose_masks()
    • generate_dataset()
    • generate_dataset_from_lists()
    • generate_image_umap()
    • generate_loaders()
    • generate_masks_from_imgs()
    • generate_ml_scores()
    • generate_training_data_file_list()
    • generate_training_dataset()
    • identify_masks_finetune()
    • jitterplot_by_annotation()
    • join_measurments_and_annotation()
    • map_condition()
    • merge_pred_mes()
    • ml_analysis()
    • prepare_batch_for_cellpose()
    • preprocess_generate_masks()
    • process_reads()
    • reducer_hyperparameter_search()
    • regression_analasys()
    • save_results_and_figure()
    • shap_analysis()
    • train_cellpose()
    • training_dataset_from_annotation()
  • spacr.deep_spacr module
    • SmoothGrad
      • SmoothGrad.compute_smooth_grad()
    • deep_spacr()
    • evaluate_model_performance()
    • test_model_core()
    • test_model_performance()
    • train_model()
    • train_test_model()
    • visualize_classes()
    • visualize_grad_cam()
    • visualize_integrated_gradients()
    • visualize_saliency_map()
    • visualize_smooth_grad()
  • spacr.graph_learning module
    • Decoder
      • Decoder.forward()
    • Encoder
      • Encoder.forward()
    • GraphTransformer
      • GraphTransformer.forward()
    • analyze_associations()
    • apply_model()
    • construct_well_graph()
    • create_graphs_for_wells()
    • extract_metadata_from_path()
    • generate_synthetic_grna_data()
    • load_images()
    • load_mnist_data()
    • normalize_sequencing_data()
    • preprocess_image()
    • process_sequencing_df()
    • train()
    • train_graph_transformer()
  • spacr.gui module
    • MainApp
      • MainApp.clear_description()
      • MainApp.clear_frame()
      • MainApp.create_startup_screen()
      • MainApp.create_widgets()
      • MainApp.load_app()
      • MainApp.show_description()
      • MainApp.update_description()
    • gui_app()
  • spacr.gui_core module
    • clear_unused_figures()
    • display_figure()
    • import_settings()
    • initiate_abort()
    • initiate_root()
    • main_thread_update_function()
    • process_console_queue()
    • process_fig_queue()
    • set_globals()
    • setup_button_section()
    • setup_console()
    • setup_plot_section()
    • setup_progress_frame()
    • setup_settings_panel()
    • setup_usage_panel()
    • show_next_figure()
    • show_previous_figure()
    • start_process()
    • toggle_settings()
  • spacr.gui_elements module
    • AnnotateApp
      • AnnotateApp.add_colored_border()
      • AnnotateApp.calculate_grid_dimensions()
      • AnnotateApp.filter_channels()
      • AnnotateApp.get_on_image_click()
      • AnnotateApp.load_images()
      • AnnotateApp.load_single_image()
      • AnnotateApp.next_page()
      • AnnotateApp.normalize_image()
      • AnnotateApp.prefilter_paths_annotations()
      • AnnotateApp.previous_page()
      • AnnotateApp.shutdown()
      • AnnotateApp.update_database_worker()
      • AnnotateApp.update_gui_text()
      • AnnotateApp.update_html()
    • ModifyMaskApp
      • ModifyMaskApp.apply_brush()
      • ModifyMaskApp.apply_brush_release()
      • ModifyMaskApp.apply_dividing_line()
      • ModifyMaskApp.apply_magic_wand()
      • ModifyMaskApp.apply_normalization()
      • ModifyMaskApp.apply_zoom_on_enter()
      • ModifyMaskApp.canvas_to_image()
      • ModifyMaskApp.clear_objects()
      • ModifyMaskApp.display_image()
      • ModifyMaskApp.display_zoomed_image()
      • ModifyMaskApp.draw()
      • ModifyMaskApp.draw_on_zoomed_mask()
      • ModifyMaskApp.erase_brush()
      • ModifyMaskApp.erase_brush_release()
      • ModifyMaskApp.erase_object()
      • ModifyMaskApp.fill_objects()
      • ModifyMaskApp.finish_dividing_line()
      • ModifyMaskApp.finish_drawing()
      • ModifyMaskApp.finish_drawing_if_active()
      • ModifyMaskApp.get_scaling_factors()
      • ModifyMaskApp.image_to_canvas()
      • ModifyMaskApp.initialize_flags()
      • ModifyMaskApp.invert_mask()
      • ModifyMaskApp.load_first_image()
      • ModifyMaskApp.load_image_and_mask()
      • ModifyMaskApp.magic_wand_normal()
      • ModifyMaskApp.magic_wand_zoomed()
      • ModifyMaskApp.next_image()
      • ModifyMaskApp.normalize_image()
      • ModifyMaskApp.overlay_mask_on_image()
      • ModifyMaskApp.previous_image()
      • ModifyMaskApp.relabel_objects()
      • ModifyMaskApp.remove_small_objects()
      • ModifyMaskApp.resize_arrays()
      • ModifyMaskApp.save_mask()
      • ModifyMaskApp.set_zoom_rectangle_end()
      • ModifyMaskApp.set_zoom_rectangle_start()
      • ModifyMaskApp.setup_canvas()
      • ModifyMaskApp.setup_function_toolbar()
      • ModifyMaskApp.setup_mode_toolbar()
      • ModifyMaskApp.setup_navigation_toolbar()
      • ModifyMaskApp.setup_zoom_toolbar()
      • ModifyMaskApp.start_dividing_line()
      • ModifyMaskApp.toggle_brush_mode()
      • ModifyMaskApp.toggle_dividing_line_mode()
      • ModifyMaskApp.toggle_draw_mode()
      • ModifyMaskApp.toggle_erase_mode()
      • ModifyMaskApp.toggle_magic_wand_mode()
      • ModifyMaskApp.toggle_zoom_mode()
      • ModifyMaskApp.update_display()
      • ModifyMaskApp.update_dividing_line_preview()
      • ModifyMaskApp.update_mouse_info()
      • ModifyMaskApp.update_original_mask()
      • ModifyMaskApp.update_original_mask_from_zoom()
      • ModifyMaskApp.update_zoom_box()
      • ModifyMaskApp.use_magic_wand()
    • create_menu_bar()
    • modify_figure()
    • modify_figure_properties()
    • save_figure_as_format()
    • set_dark_style()
    • set_element_size()
    • spacrButton
      • spacrButton.animate_zoom()
      • spacrButton.clear_description()
      • spacrButton.create_rounded_rectangle()
      • spacrButton.get_icon_path()
      • spacrButton.load_icon()
      • spacrButton.on_click()
      • spacrButton.on_enter()
      • spacrButton.on_leave()
      • spacrButton.update_description()
      • spacrButton.zoom_icon()
    • spacrCheck
      • spacrCheck.draw_rounded_square()
      • spacrCheck.toggle_variable()
      • spacrCheck.update_check()
    • spacrCheckbutton
    • spacrCombo
      • spacrCombo.close_dropdown()
      • spacrCombo.draw_rounded_rectangle()
      • spacrCombo.on_click()
      • spacrCombo.on_select()
      • spacrCombo.open_dropdown()
      • spacrCombo.set()
    • spacrContainer
      • spacrContainer.add()
      • spacrContainer.create_sash()
      • spacrContainer.on_configure()
      • spacrContainer.on_enter_sash()
      • spacrContainer.on_leave_sash()
      • spacrContainer.perform_resize()
      • spacrContainer.reposition_panes()
      • spacrContainer.start_resize()
    • spacrDropdownMenu
      • spacrDropdownMenu.create_rounded_rectangle()
      • spacrDropdownMenu.on_click()
      • spacrDropdownMenu.on_enter()
      • spacrDropdownMenu.on_leave()
      • spacrDropdownMenu.on_select()
      • spacrDropdownMenu.post_menu()
      • spacrDropdownMenu.update_styles()
    • spacrEntry
      • spacrEntry.draw_rounded_rectangle()
      • spacrEntry.on_focus_in()
      • spacrEntry.on_focus_out()
    • spacrFont
      • spacrFont.get_font()
      • spacrFont.get_font_path()
      • spacrFont.load_font()
    • spacrFrame
      • spacrFrame.rounded_rectangle()
    • spacrLabel
      • spacrLabel.set_text()
    • spacrProgressBar
      • spacrProgressBar.set_label_position()
      • spacrProgressBar.update_label()
    • spacrScrollbarStyle()
    • spacrSwitch
      • spacrSwitch.animate_movement()
      • spacrSwitch.animate_switch()
      • spacrSwitch.create_rounded_rectangle()
      • spacrSwitch.get()
      • spacrSwitch.set()
      • spacrSwitch.toggle()
      • spacrSwitch.update_switch()
    • spacrToolTip
      • spacrToolTip.hide_tooltip()
      • spacrToolTip.show_tooltip()
    • standardize_figure()
  • spacr.gui_utils module
    • WriteToQueue
      • WriteToQueue.flush()
      • WriteToQueue.write()
    • annotate()
    • annotate_app()
    • annotate_with_image_refs()
    • cancel_after_tasks()
    • convert_settings_dict_for_gui()
    • create_input_field()
    • download_dataset()
    • download_hug_dataset()
    • ensure_after_tasks()
    • function_gui_wrapper()
    • generate_annotate_fields()
    • hide_all_settings()
    • initialize_cuda()
    • load_app()
    • load_next_app()
    • parse_list()
    • proceed_with_app()
    • process_stdout_stderr()
    • run_annotate_app()
    • run_function_gui()
    • set_cpu_affinity()
    • set_high_priority()
    • setup_frame()
    • spacrFigShow()
  • spacr.io module
    • CombineLoaders
      • CombineLoaders.train_loaders
      • CombineLoaders.loader_iters
      • CombineLoaders.__iter__()
      • CombineLoaders.__next__()
    • CombinedDataset
    • NoClassDataset
      • NoClassDataset.load_image()
      • NoClassDataset.shuffle_dataset()
    • TarImageDataset
    • concatenate_and_normalize()
    • convert_numpy_to_tiff()
    • delete_empty_subdirectories()
    • generate_cellpose_train_test()
    • preprocess_img_data()
    • read_plot_model_stats()
    • spacrDataLoader
      • spacrDataLoader.cleanup()
    • spacrDataset
      • spacrDataset.get_plate()
      • spacrDataset.load_image()
      • spacrDataset.shuffle_dataset()
  • spacr.logger module
    • log_function_call()
  • spacr.measure module
    • filepaths_to_database()
    • generate_cellpose_train_set()
    • get_components()
    • get_object_counts()
    • img_list_to_grid()
    • measure_crop()
    • process_meassure_crop_results()
    • save_and_add_image_to_grid()
  • spacr.plot module
    • generate_mask_random_cmap()
    • generate_plate_heatmap()
    • normalize_and_visualize()
    • plot_arrays()
    • plot_comparison_results()
    • plot_feature_importance()
    • plot_histogram()
    • plot_image_mask_overlay()
    • plot_images_and_arrays()
    • plot_lorenz_curves()
    • plot_masks()
    • plot_merged()
    • plot_object_outlines()
    • plot_permutation()
    • plot_plates()
    • plot_resize()
    • print_mask_and_flows()
    • random_cmap()
    • read_and_plot__vision_results()
    • visualize_cellpose_masks()
    • visualize_masks()
    • volcano_plot()
  • spacr.sequencing module
    • apply_transformation()
    • calculate_p_values()
    • check_normality()
    • clean_controls()
    • complement()
    • consensus_sequence()
    • consensus_sequence_v1()
    • count_mismatches()
    • equalize_lengths()
    • extract_barcodes_from_fastq()
    • extract_barcodes_from_fastq_v1()
    • extract_barecodes()
    • file_len()
    • find_grna()
    • generate_barecode_mapping()
    • generate_fraction_map()
    • generate_plate_heatmap()
    • get_read_data()
    • get_sequence_data()
    • get_top_two_matches()
    • grna_plate_heatmap()
    • map_unmapped_grnas()
    • parse_gz_files()
    • perform_mixed_model()
    • perform_regression()
    • plot_data()
    • plot_plates()
    • pos_dict()
    • precess_reads()
    • process_barecodes()
    • process_chunk_for_consensus()
    • process_chunk_for_mapping()
    • process_scores()
    • regression()
    • regression_model()
    • remove_outliers()
    • reverse_complement()
    • save_to_hdf()
    • split_fastq()
    • test_error()
    • translate_barecodes()
    • truncate_read()
    • vert_horiz()
  • spacr.settings module
    • check_settings()
    • deep_spacr_defaults()
    • generate_fields()
    • get_analyze_reads_default_settings()
    • get_analyze_recruitment_default_settings()
    • get_check_cellpose_models_default_settings()
    • get_identify_masks_finetune_default_settings()
    • get_map_barcodes_default_settings()
    • get_measure_crop_settings()
    • get_perform_regression_default_settings()
    • get_train_cellpose_default_settings()
    • set_annotate_default_settings()
    • set_default_analyze_screen()
    • set_default_generate_barecode_mapping()
    • set_default_plot_merge_settings()
    • set_default_settings_preprocess_generate_masks()
    • set_default_settings_preprocess_img_data()
    • set_default_train_test_model()
    • set_default_umap_image_settings()
    • set_generate_training_dataset_defaults()
  • spacr.sim module
    • append_database()
    • calculate_permutation_importance()
    • cell_level_roc_auc()
    • classifier()
    • classifier_v2()
    • compute_precision_recall()
    • compute_roc_auc()
    • create_database()
    • dist_gen()
    • generate_floats()
    • generate_gene_list()
    • generate_gene_weights()
    • generate_integers()
    • generate_paramiters()
    • generate_plate_map()
    • generate_power_law_distribution()
    • generate_shap_summary_plot()
    • generate_well_score()
    • get_optimum_threshold()
    • gini()
    • gini_coefficient()
    • gini_gene_well()
    • normalize_array()
    • plot_confusion_matrix()
    • plot_correlation_matrix()
    • plot_feature_importance()
    • plot_histogram()
    • plot_partial_dependences()
    • plot_roc_pr()
    • plot_simulations()
    • power_law_dist_gen()
    • read_simulations_table()
    • regression_roc_auc()
    • remove_columns_with_single_value()
    • remove_constant_columns()
    • run_and_save()
    • run_experiment()
    • run_multiple_simulations()
    • run_simulation()
    • save_data()
    • save_plot()
    • save_shap_plot()
    • sequence_plates()
    • update_scores_and_get_cm()
    • validate_and_adjust_beta_params()
    • vis_dists()
    • visualize_all()
  • spacr.sim_app module
  • spacr.timelapse module
    • analyze_calcium_oscillations()
    • exponential_decay()
    • infected_vs_noninfected()
    • plot_data()
    • preprocess_pathogen_data()
    • save_figure()
    • save_results_dataframe()
    • summarize_per_well()
    • summarize_per_well_inf_non_inf()
  • spacr.utils module
    • Cache
      • Cache.max_size
      • Cache.cache
      • Cache.get()
      • Cache.put()
    • CustomCellClassifier
      • CustomCellClassifier.custom_forward()
      • CustomCellClassifier.forward()
    • EarlyFusion
      • EarlyFusion.forward()
    • FocalLossWithLogits
      • FocalLossWithLogits.forward()
    • GradCAM
      • GradCAM.forward()
    • IntegratedGradients
      • IntegratedGradients.generate_integrated_gradients()
    • MLR()
    • MultiScaleBlockWithAttention
      • MultiScaleBlockWithAttention.custom_forward()
      • MultiScaleBlockWithAttention.forward()
    • ResNet
      • ResNet.forward()
      • ResNet.initialize_base()
    • SaliencyMapGenerator
      • SaliencyMapGenerator.compute_saliency_maps()
      • SaliencyMapGenerator.plot_saliency_maps()
    • ScaledDotProductAttention
      • ScaledDotProductAttention.forward()
    • SelectChannels
    • SelfAttention
      • SelfAttention.forward()
    • SpatialAttention
      • SpatialAttention.forward()
    • TorchModel
      • TorchModel.apply_dropout_rate()
      • TorchModel.forward()
      • TorchModel.get_num_ftrs()
      • TorchModel.get_weight_choice()
      • TorchModel.init_base_model()
      • TorchModel.init_spacr_classifier()
    • add_images_to_tar()
    • adjust_cell_masks()
    • annotate_conditions()
    • annotate_predictions()
    • apply_mask()
    • assign_colors()
    • augment_classes()
    • augment_dataset()
    • augment_image()
    • augment_images()
    • augment_single_image()
    • boundary_f1_score()
    • calculate_iou()
    • calculate_loss()
    • check_mask_folder()
    • check_multicollinearity()
    • check_normality()
    • check_overlap()
    • choose_model()
    • class_visualization()
    • classification_metrics()
    • close_file_descriptors()
    • close_multiprocessing_processes()
    • cluster_feature_analysis()
    • combine_results()
    • compute_ap_over_iou_thresholds()
    • compute_average_precision()
    • compute_irm_penalty()
    • compute_segmentation_ap()
    • convert_and_relabel_masks()
    • correct_masks()
    • correct_paths()
    • count_reads_in_fastq()
    • create_circular_mask()
    • delete_folder()
    • dice_coefficient()
    • extract_boundaries()
    • extract_features()
    • filter_columns()
    • filter_dataframe_features()
    • find_non_overlapping_position()
    • fishers_odds()
    • generate_colors()
    • generate_dependent_variable()
    • generate_fraction_map()
    • get_db_paths()
    • get_files_from_dir()
    • get_ml_results_paths()
    • get_paths_from_db()
    • get_sequencing_paths()
    • get_submodules()
    • initiate_counter()
    • invert_image()
    • is_list_of_lists()
    • is_multiprocessing_process()
    • jaccard_index()
    • lasso_reg()
    • load_image()
    • load_image_paths()
    • mask_object_count()
    • match_masks()
    • measure_test_mode()
    • merge_dataframes()
    • merge_regression_res_with_metadata()
    • merge_touching_objects()
    • model_metrics()
    • normalize_to_dtype()
    • pad_to_same_shape()
    • perform_statistical_tests()
    • pick_best_model()
    • plot_clusters()
    • plot_clusters_grid()
    • plot_embedding()
    • plot_grid()
    • plot_image()
    • plot_images_by_cluster()
    • plot_umap_images()
    • preprocess_data()
    • preprocess_image()
    • print_progress()
    • process_masks()
    • process_vision_results()
    • random_forest_feature_importance()
    • recommend_target_layers()
    • reduction_and_clustering()
    • remove_canvas()
    • remove_highly_correlated_columns()
    • remove_intensity_objects()
    • remove_low_variance_columns()
    • remove_noise()
    • reset_mp()
    • resize_images_and_labels()
    • resize_labels_back()
    • save_file_lists()
    • save_settings()
    • search_reduction_and_clustering()
    • setup_plot()
    • show_cam_on_image()
    • smooth_hull_lines()
    • split_my_dataset()
  • spacr.version module
  • Module contents