LICENSE
MANIFEST.in
README.md
setup.py
Simba_UW_tf_dev.egg-info/PKG-INFO
Simba_UW_tf_dev.egg-info/SOURCES.txt
Simba_UW_tf_dev.egg-info/dependency_links.txt
Simba_UW_tf_dev.egg-info/entry_points.txt
Simba_UW_tf_dev.egg-info/requires.txt
Simba_UW_tf_dev.egg-info/top_level.txt
simba/.DS_Store
simba/SimBA.py
simba/SimBA_logo.ico
simba/__init__.py
simba/requirements.txt
simba/assets/.DS_Store
simba/assets/TheGoldenLab.PNG
simba/assets/UbuntuMono-Regular.ttf
simba/assets/__init__.py
simba/assets/dash_simba_base.css
simba/assets/icons/.DS_Store
simba/assets/icons/SimBA_logo.icns
simba/assets/icons/SimBA_logo.ico
simba/assets/icons/SimBA_logo.png
simba/assets/icons/__init__.py
simba/assets/icons/about.png
simba/assets/icons/add_on.png
simba/assets/icons/average.png
simba/assets/icons/blur.png
simba/assets/icons/boris.png
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simba/assets/icons/clahe.png
simba/assets/icons/clean.png
simba/assets/icons/clf.png
simba/assets/icons/clf_2.png
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simba/assets/icons/concat.png
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simba/assets/icons/dash_simba.css
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simba/assets/icons/readthedocs_logo.png
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simba/assets/icons/reorganize.png
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simba/assets/icons/roi.png
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simba/assets/icons/sample.png
simba/assets/icons/settings.png
simba/assets/icons/simba_logo_2.png
simba/assets/icons/stopwatch.png
simba/assets/icons/superimpose.png
simba/assets/icons/trash.png
simba/assets/icons/video.png
simba/assets/icons/visualize.png
simba/assets/icons/concat_icons/__init__.py
simba/assets/icons/concat_icons/horizontal.png
simba/assets/icons/concat_icons/mixed_mosaic.png
simba/assets/icons/concat_icons/mosaic.png
simba/assets/icons/concat_icons/vertical.png
simba/assets/img/__init__.py
simba/assets/img/about_me.png
simba/assets/img/bg.png
simba/assets/img/bg_2.png
simba/assets/img/bg_2024.png
simba/assets/img/splash.mp4
simba/assets/img/splash.pptx
simba/assets/img/splash_2024.mp4
simba/assets/img/~$splash.pptx
simba/assets/lookups/__init__.py
simba/assets/lookups/critical_values_05.pickle
simba/assets/lookups/feature_extraction_headers.csv
simba/assets/lookups/features.csv
simba/assets/lookups/model_names.parquet
simba/assets/lookups/unsupervised_example_x.csv
simba/assets/shap/UbuntuMono-Regular.ttf
simba/assets/shap/__init__.py
simba/assets/shap/animal_distances.jpg
simba/assets/shap/baseline_scale.jpg
simba/assets/shap/color_bar.jpg
simba/assets/shap/down_arrow.jpg
simba/assets/shap/intruder_movement.jpg
simba/assets/shap/intruder_shape.jpg
simba/assets/shap/resident_intruder_movement.jpg
simba/assets/shap/resident_intruder_shape.jpg
simba/assets/shap/resident_movement.jpg
simba/assets/shap/resident_shape.jpg
simba/assets/shap/side_scale.jpg
simba/assets/shap/side_scale_5.jpg
simba/assets/shap/ubuntu.regular.ttf
simba/assets/shap/feature_categories/__init__.py
simba/assets/shap/feature_categories/shap_feature_categories.csv
simba/assets/stl/__init__.py
simba/assets/stl/grid_floor.stl
simba/assets/stl/operant_lever.stl
simba/assets/stl/operant_tray.stl
simba/assets/stl/operant_walls.stl
simba/assets/unsupervised/__init__.py
simba/assets/unsupervised/features.csv
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simba/bounding_box_tools/__init__.py
simba/bounding_box_tools/agg_boundary_stats.py
simba/bounding_box_tools/boundary_menus.py
simba/bounding_box_tools/boundary_statistics.py
simba/bounding_box_tools/find_boundaries.py
simba/bounding_box_tools/visualize_boundaries.py
simba/cue_light_tools/__init__.py
simba/cue_light_tools/cue_light_analyzer.py
simba/cue_light_tools/cue_light_clf_statistics.py
simba/cue_light_tools/cue_light_menues.py
simba/cue_light_tools/cue_light_movement_statistics.py
simba/cue_light_tools/cue_light_tools.py
simba/cue_light_tools/cue_light_visualizer.py
simba/dash_app/SimBA_dash_app.py
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simba/dash_app/dash_app.py
simba/dash_app/run_dash_tkinter.py
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simba/data_processors/advanced_interpolator.py
simba/data_processors/advanced_smoothing.py
simba/data_processors/agg_clf_calculator.py
simba/data_processors/boolean_conditional_calculator.py
simba/data_processors/directing_animal_to_bodypart.py
simba/data_processors/directing_other_animals_calculator.py
simba/data_processors/fsttc_calculator.py
simba/data_processors/gibbs_sampler.py
simba/data_processors/interpolate.py
simba/data_processors/interpolate_pose.py
simba/data_processors/interpolation_smoothing.py
simba/data_processors/kleinberg_calculator.py
simba/data_processors/movement_calculator.py
simba/data_processors/mutual_exclusivity_corrector.py
simba/data_processors/pup_retrieval_calculator.py
simba/data_processors/pybursts_calculator.py
simba/data_processors/severity_bout_based_calculator.py
simba/data_processors/severity_calculator.py
simba/data_processors/severity_frame_based_calculator.py
simba/data_processors/smoothing.py
simba/data_processors/spontaneous_alternation_calculator.py
simba/data_processors/timebins_clf_calculator.py
simba/data_processors/timebins_movement_calculator.py
simba/feature_extractors/.DS_Store
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simba/feature_extractors/amber_feature_extractor.py
simba/feature_extractors/feature_extractor_14bp.py
simba/feature_extractors/feature_extractor_16bp.py
simba/feature_extractors/feature_extractor_4bp.py
simba/feature_extractors/feature_extractor_7bp.py
simba/feature_extractors/feature_extractor_8bp.py
simba/feature_extractors/feature_extractor_8bps_2_animals.py
simba/feature_extractors/feature_extractor_9bp.py
simba/feature_extractors/feature_extractor_user_defined.py
simba/feature_extractors/feature_subsets.py
simba/feature_extractors/perimeter_jit.py
simba/feature_extractors/misc/add_probability_cnt_features.py
simba/feature_extractors/misc/convex_hull_3_scratch_3.py
simba/feature_extractors/misc/convex_hull_scratch_1.py
simba/feature_extractors/misc/convex_hull_scratch_2.py
simba/feature_extractors/misc/count_values_in_range.py
simba/feature_extractors/misc/doctests.py
simba/feature_extractors/misc/egocentrical_aligner.py
simba/feature_extractors/misc/fish_feature_extractor_2022.py
simba/feature_extractors/misc/fish_feature_extractor_2023_version_2.py
simba/feature_extractors/misc/fish_feature_extractor_2023_version_3.py
simba/feature_extractors/misc/fish_feature_extractor_2023_version_4.py
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simba/feature_extractors/misc/mutual_exclusive.py
simba/feature_extractors/misc/peaks.py
simba/feature_extractors/misc/read_in_mp.py
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simba/feature_extractors/misc/video_color.py
simba/feature_extractors/misc/video_rotator.py
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simba/labelling/extract_labelled_frames.py
simba/labelling/extract_labelling_meta.py
simba/labelling/labelling_advanced_interface.py
simba/labelling/labelling_interface.py
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simba/mixins/feature_extraction_supplement_mixin.py
simba/mixins/geometry_mixin.py
simba/mixins/image_mixin.py
simba/mixins/network_mixin.py
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simba/mixins/pop_up_mixin.py
simba/mixins/pose_importer_mixin.py
simba/mixins/statistics_mixin.py
simba/mixins/timeseries_features_mixin.py
simba/mixins/train_model_mixin.py
simba/mixins/unsupervised_mixin.py
simba/mixins/video_processing_mixin.py
simba/model/__init__.py
simba/model/grid_search_multiclass_rf.py
simba/model/grid_search_rf.py
simba/model/inference_batch.py
simba/model/inference_multiclass_batch.py
simba/model/inference_validation.py
simba/model/train_multiclass_rf.py
simba/model/train_multilabel_rf.py
simba/model/train_rf.py
simba/outlier_tools/__init__.py
simba/outlier_tools/outlier_corrector_location.py
simba/outlier_tools/outlier_corrector_location_advanced.py
simba/outlier_tools/outlier_corrector_movement.py
simba/outlier_tools/outlier_corrector_movement_advanced.py
simba/outlier_tools/skip_outlier_correction.py
simba/plotting/.DS_Store
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simba/plotting/ROI_feature_visualizer_mp.py
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simba/plotting/ROI_plotter_mp.py
simba/plotting/__init__.py
simba/plotting/circular_feature_overlay_plotter.py
simba/plotting/circular_plotting.py
simba/plotting/clf_validator.py
simba/plotting/clf_validator_mp.py
simba/plotting/data_plotter.py
simba/plotting/directing_animals_to_bodypart_visualizer.py
simba/plotting/directing_animals_visualizer.py
simba/plotting/directing_animals_visualizer_mp.py
simba/plotting/distance_plotter.py
simba/plotting/distance_plotter_mp.py
simba/plotting/ez_path_plot.py
simba/plotting/frame_mergerer_ffmpeg.py
simba/plotting/gantt_creator.py
simba/plotting/gantt_creator_mp.py
simba/plotting/geometry_plotter.py
simba/plotting/heat_mapper_clf.py
simba/plotting/heat_mapper_clf_mp.py
simba/plotting/heat_mapper_location.py
simba/plotting/heat_mapper_location_mp.py
simba/plotting/interactive_probability_grapher.py
simba/plotting/path_plotter.py
simba/plotting/path_plotter_mp.py
simba/plotting/plot_clf_results.py
simba/plotting/plot_clf_results_mp.py
simba/plotting/plot_pose_in_dir.py
simba/plotting/pose_plotter_mp.py
simba/plotting/probability_plot_creator.py
simba/plotting/probability_plot_creator_mp.py
simba/plotting/shap_agg_stats_visualizer.py
simba/plotting/single_run_model_validation_video.py
simba/plotting/single_run_model_validation_video_mp.py
simba/plotting/spontaneous_alternation_plotter.py
simba/plotting/tools/__init__.py
simba/plotting/tools/tkinter_tools.py
simba/pose_configurations/.DS_Store
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simba/pose_configurations/bp_names/__init__.py
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simba/pose_configurations/no_animals/no_animals.csv
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simba/pose_configurations/schematics/10.png
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simba/pose_importers/.DS_Store
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simba/pose_importers/read_DANNCE_mat.py
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simba/roi_tools/.DS_Store
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simba/roi_tools/ROI_menus.py
simba/roi_tools/ROI_move_shape.py
simba/roi_tools/ROI_multiply.py
simba/roi_tools/ROI_reset.py
simba/roi_tools/ROI_size_calculations.py
simba/roi_tools/ROI_size_standardizer.py
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simba/sandbox/.DS_Store
simba/sandbox/AmberFeatureExtractor.py.zip
simba/sandbox/CLAHE.py
simba/sandbox/Geometry_7.py
simba/sandbox/MitraFeatureExtractor.py
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simba/sandbox/ROI_plotter_mp.py
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simba/sandbox/add_body_part.py.zip
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simba/sandbox/amber_tests.py
simba/sandbox/annotations_mitra.py
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simba/sandbox/bg_remover_popup.py
simba/sandbox/bg_substraction.py
simba/sandbox/biweight_midcorrelation.py
simba/sandbox/blank_img.py
simba/sandbox/blurbox.py
simba/sandbox/bouts_df
simba/sandbox/brillouins_index.py
simba/sandbox/calc_N_degree_direction_switches.py
simba/sandbox/calinski_harabasz.py
simba/sandbox/cb_frame.py
simba/sandbox/change_img_file_format.py
simba/sandbox/change_n_jobs_scikit.py
simba/sandbox/clean_sleap_filename.py
simba/sandbox/clip_multiple_videos_by_frame_numbers.py
simba/sandbox/clip_videos_by_frm.py
simba/sandbox/cochran_q.py
simba/sandbox/cohens_kappa.py
simba/sandbox/colinear_features.py
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simba/sandbox/cronbach_alpha.py
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simba/sandbox/crossfade.py
simba/sandbox/cuda_jit.ipynb
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simba/sandbox/data.npy
simba/sandbox/davis_bouldin.py
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simba/sandbox/directed_hausdorff.py
simba/sandbox/distance_velocity.py
simba/sandbox/distances.py
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simba/sandbox/downsample_multiple_videos_popup.py
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simba/sandbox/graph_flow.html
simba/sandbox/graph_katz.html
simba/sandbox/graph_pagerank.html
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simba/sandbox/hartley_fmax.py
simba/sandbox/hausdorff.py
simba/sandbox/heading.py
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simba/sandbox/path_geometry.py
simba/sandbox/path_geometry_2.py
simba/sandbox/path_plots.py
simba/sandbox/paths.py
simba/sandbox/pct_counts_in_top_N.py
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simba/sandbox/seekable.py
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simba/sandbox/sorensen_dice_coefficient.py
simba/sandbox/spontaneous_alternation_calculator.py
simba/sandbox/spontaneuous_alternation_plotter.py
simba/sandbox/spontanous_alternations.py
simba/sandbox/statistics_ex.py
simba/sandbox/structural_similarity_index.py
simba/sandbox/superimpose_elapsed_time.py
simba/sandbox/superimpose_frame_count.py
simba/sandbox/superimpose_frm_cnt.py
simba/sandbox/superimpose_popups.py
simba/sandbox/superimpose_text.py
simba/sandbox/superpixels.py
simba/sandbox/termite_rois.csv
simba/sandbox/time_stamp_calculator.py
simba/sandbox/total_variation_distance.py
simba/sandbox/train_model.py
simba/sandbox/two_fish_feature_extractor_040924.py
simba/sandbox/two_fish_feature_extractor_040924.py.zip
simba/sandbox/unsupervised_lof.py
simba/sandbox/unsupervised_outliers.py
simba/sandbox/velocity_aggregator.py
simba/sandbox/vertical_video_concatenator.py
simba/sandbox/video_color.py
simba/sandbox/video_rotator.py
simba/sandbox/video_rotator_mp.py
simba/sandbox/violin.py
simba/sandbox/visualize_networks.py
simba/sandbox/wald_wolfowitz.py
simba/sandbox/watermark.py
simba/sandbox/wilcoxon.py
simba/sandbox/youden_j.py
simba/third_party_label_appenders/.DS_Store
simba/third_party_label_appenders/BENTO_appender.py
simba/third_party_label_appenders/BORIS_appender.py
simba/third_party_label_appenders/__init__.py
simba/third_party_label_appenders/boris_source_cleaner.py
simba/third_party_label_appenders/deepethogram_importer.py
simba/third_party_label_appenders/ethovision_import.py
simba/third_party_label_appenders/observer_importer.py
simba/third_party_label_appenders/solomon_importer.py
simba/third_party_label_appenders/third_party_appender.py
simba/third_party_label_appenders/tools.py
simba/ui/.DS_Store
simba/ui/__init__.py
simba/ui/create_project_ui.py
simba/ui/import_pose_frame.py
simba/ui/import_videos_frame.py
simba/ui/machine_model_settings_ui.py
simba/ui/tkinter_functions.py
simba/ui/user_defined_pose_creator.py
simba/ui/video_info_ui.py
simba/ui/pop_ups/.DS_Store
simba/ui/pop_ups/__init__.py
simba/ui/pop_ups/about_simba_pop_up.py
simba/ui/pop_ups/animal_directing_other_animals_pop_up.py
simba/ui/pop_ups/append_roi_features_animals_pop_up.py
simba/ui/pop_ups/append_roi_features_bodypart_pop_up.py
simba/ui/pop_ups/archive_files_pop_up.py
simba/ui/pop_ups/batch_preprocess_pop_up.py
simba/ui/pop_ups/boolean_conditional_slicer_pup_up.py
simba/ui/pop_ups/clf_add_remove_print_pop_up.py
simba/ui/pop_ups/clf_annotation_counts_pop_up.py
simba/ui/pop_ups/clf_by_roi_pop_up.py
simba/ui/pop_ups/clf_by_timebins_pop_up.py
simba/ui/pop_ups/clf_descriptive_statistics_pop_up.py
simba/ui/pop_ups/clf_plot_pop_up.py
simba/ui/pop_ups/clf_probability_plot_pop_up.py
simba/ui/pop_ups/clf_validation_plot_pop_up.py
simba/ui/pop_ups/create_user_defined_pose_configuration_pop_up.py
simba/ui/pop_ups/csv_2_parquet_pop_up.py
simba/ui/pop_ups/data_plot_pop_up.py
simba/ui/pop_ups/directing_animal_to_bodypart_plot_pop_up.py
simba/ui/pop_ups/directing_other_animals_plot_pop_up.py
simba/ui/pop_ups/direction_animal_to_bodypart_settings_pop_up.py
simba/ui/pop_ups/distance_plot_pop_up.py
simba/ui/pop_ups/fsttc_pop_up.py
simba/ui/pop_ups/gantt_pop_up.py
simba/ui/pop_ups/heatmap_clf_pop_up.py
simba/ui/pop_ups/heatmap_location_pop_up.py
simba/ui/pop_ups/interpolate_pop_up.py
simba/ui/pop_ups/kleinberg_pop_up.py
simba/ui/pop_ups/make_path_plot_pop_up.py
simba/ui/pop_ups/movement_analysis_pop_up.py
simba/ui/pop_ups/movement_analysis_time_bins_pop_up.py
simba/ui/pop_ups/mutual_exclusivity_pop_up.py
simba/ui/pop_ups/outlier_settings_pop_up.py
simba/ui/pop_ups/path_plot_pop_up.py
simba/ui/pop_ups/pose_bp_drop_pop_up.py
simba/ui/pop_ups/pose_reorganizer_pop_up.py
simba/ui/pop_ups/pup_retrieval_pop_up.py
simba/ui/pop_ups/quick_path_plot_pop_up.py
simba/ui/pop_ups/remove_roi_features_pop_up.py
simba/ui/pop_ups/roi_analysis_pop_up.py
simba/ui/pop_ups/roi_analysis_time_bins_pop_up.py
simba/ui/pop_ups/roi_features_plot_pop_up.py
simba/ui/pop_ups/roi_size_standardizer_popup.py
simba/ui/pop_ups/roi_tracking_plot_pop_up.py
simba/ui/pop_ups/set_machine_model_parameters_pop_up.py
simba/ui/pop_ups/severity_analysis_pop_up.py
simba/ui/pop_ups/smoothing_popup.py
simba/ui/pop_ups/spontaneous_alternation_pop_up.py
simba/ui/pop_ups/subset_feature_extractor_pop_up.py
simba/ui/pop_ups/targeted_annotation_clips_pop_up.py
simba/ui/pop_ups/third_party_annotator_appender_pop_up.py
simba/ui/pop_ups/validation_plot_pop_up.py
simba/ui/pop_ups/video_processing_pop_up.py
simba/ui/pop_ups/visualize_pose_in_dir_pop_up.py
simba/unsupervised/.DS_Store
simba/unsupervised/__init__.py
simba/unsupervised/bout_aggregator.py
simba/unsupervised/cluster_frequentist_calculator.py
simba/unsupervised/cluster_validation_calculator.py
simba/unsupervised/cluster_video_visualizer.py
simba/unsupervised/cluster_xai_calculator.py
simba/unsupervised/clusterer_comparison_calculator.py
simba/unsupervised/data_extractor.py
simba/unsupervised/data_map.yaml
simba/unsupervised/dataset_creator.py
simba/unsupervised/dbcv_calculator.py
simba/unsupervised/embedding_correlation_calculator.py
simba/unsupervised/enums.py
simba/unsupervised/grid_search_visualizers.py
simba/unsupervised/hdbscan_clusterer.py
simba/unsupervised/outlier_detector.py
simba/unsupervised/tsne.py
simba/unsupervised/umap_embedder.py
simba/unsupervised/unsupervised_main.py
simba/unsupervised/pop_ups/.DS_Store
simba/unsupervised/pop_ups/cluster_frequentist_stats_popup.py
simba/unsupervised/pop_ups/cluster_validation_pop_up.py
simba/unsupervised/pop_ups/cluster_videos_popup.py
simba/unsupervised/pop_ups/cluster_xai_popup.py
simba/unsupervised/pop_ups/clusterer_comparison_popup.py
simba/unsupervised/pop_ups/data_extractor_popup.py
simba/unsupervised/pop_ups/embedding_correlations_popup.py
simba/unsupervised/pop_ups/fit_cluster_popup.py
simba/unsupervised/pop_ups/fit_dim_reduction_popup.py
simba/unsupervised/pop_ups/grid_search_visualizer_popup.py
simba/unsupervised/pop_ups/print_embedding_info_popup.py
simba/unsupervised/pop_ups/transform_cluster_popup.py
simba/unsupervised/pop_ups/transform_dim_reduction_popup.py
simba/utils/.DS_Store
simba/utils/__init__.py
simba/utils/checks.py
simba/utils/config_creator.py
simba/utils/custom_feature_extractor.py
simba/utils/data.py
simba/utils/enums.py
simba/utils/errors.py
simba/utils/lookups.py
simba/utils/printing.py
simba/utils/read_write.py
simba/utils/warnings.py
simba/utils/cli/__init__.py
simba/utils/cli/cli_tools.py
simba/video_processors/.DS_Store
simba/video_processors/__init__.py
simba/video_processors/batch_process_create_ffmpeg_commands.py
simba/video_processors/batch_process_menus.py
simba/video_processors/brightness_contrast_ui.py
simba/video_processors/calculate_px_dist.py
simba/video_processors/clahe_ui.py
simba/video_processors/extract_frames.py
simba/video_processors/extract_seqframes.py
simba/video_processors/multi_cropper.py
simba/video_processors/px_to_mm.py
simba/video_processors/roi_selector.py
simba/video_processors/roi_selector_circle.py
simba/video_processors/roi_selector_polygon.py
simba/video_processors/video_processing.py