SimBA UI pop-ups
simba.ui.pop_ups.about_simba_pop_up module
simba.ui.pop_ups.append_roi_features_animals_pop_up module
- class simba.ui.pop_ups.append_roi_features_animals_pop_up.AppendROIFeaturesByAnimalPopUp(config_path)[source]
Bases:
simba.mixins.config_reader.ConfigReader,simba.mixins.pop_up_mixin.PopUpMixin
simba.ui.pop_ups.append_roi_features_bodypart_pop_up module
- class simba.ui.pop_ups.append_roi_features_bodypart_pop_up.AppendROIFeaturesByBodyPartPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.archive_files_pop_up module
- class simba.ui.pop_ups.archive_files_pop_up.ArchiveProcessedFilesPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.batch_preprocess_pop_up module
- class simba.ui.pop_ups.batch_preprocess_pop_up.BatchPreProcessPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> BatchPreProcessPopUp()
simba.ui.pop_ups.clf_add_remove_print_pop_up module
- class simba.ui.pop_ups.clf_add_remove_print_pop_up.AddClfPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
- class simba.ui.pop_ups.clf_add_remove_print_pop_up.RemoveAClassifierPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.clf_by_roi_pop_up module
- class simba.ui.pop_ups.clf_by_roi_pop_up.ClfByROIPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = ClfByROIPopUp(config_path=r"C: roubleshooting\open_field_below\project_folder\project_config.ini")
simba.ui.pop_ups.clf_by_timebins_pop_up module
- class simba.ui.pop_ups.clf_by_timebins_pop_up.TimeBinsClfPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.clf_descriptive_statistics_pop_up module
- class simba.ui.pop_ups.clf_descriptive_statistics_pop_up.ClfDescriptiveStatsPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.clf_plot_pop_up module
- class simba.ui.pop_ups.clf_plot_pop_up.SklearnVisualizationPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = SklearnVisualizationPopUp(config_path=r"C: roubleshooting\RAT_NOR\project_folder\project_config.ini")
simba.ui.pop_ups.clf_probability_plot_pop_up module
- class simba.ui.pop_ups.clf_probability_plot_pop_up.VisualizeClassificationProbabilityPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = VisualizeClassificationProbabilityPopUp(config_path=r'C: roubleshooting\RAT_NOR\project_folder\project_config.ini')
simba.ui.pop_ups.clf_validation_plot_pop_up module
- class simba.ui.pop_ups.clf_validation_plot_pop_up.ClassifierValidationPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = ClassifierValidationPopUp(config_path=r'C: roubleshooting\RAT_NOR\project_folder\project_config.ini')
simba.ui.pop_ups.create_user_defined_pose_configuration_pop_up module
simba.ui.pop_ups.csv_2_parquet_pop_up module
simba.ui.pop_ups.data_plot_pop_up module
- class simba.ui.pop_ups.data_plot_pop_up.DataPlotterPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = DataPlotterPopUp(config_path=r'C: roubleshooting\RAT_NOR\project_folder\project_config.ini')
simba.ui.pop_ups.directing_other_animals_plot_pop_up module
- class simba.ui.pop_ups.directing_other_animals_plot_pop_up.DirectingOtherAnimalsVisualizerPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.distance_plot_pop_up module
- class simba.ui.pop_ups.distance_plot_pop_up.DistancePlotterPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = DistancePlotterPopUp(config_path=r'C: roubleshooting\RAT_NOR\project_folder\project_config.ini')
simba.ui.pop_ups.fsttc_pop_up module
- class simba.ui.pop_ups.fsttc_pop_up.FSTTCPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.gantt_pop_up module
- class simba.ui.pop_ups.gantt_pop_up.GanttPlotPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = GanttPlotPopUp(config_path=r"C: roubleshooting\RAT_NOR\project_folder\project_config.ini")
simba.ui.pop_ups.heatmap_clf_pop_up module
- class simba.ui.pop_ups.heatmap_clf_pop_up.HeatmapClfPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = HeatmapClfPopUp(config_path=r"C: roubleshooting\RAT_NOR\project_folder\project_config.ini")
simba.ui.pop_ups.heatmap_location_pop_up module
- class simba.ui.pop_ups.heatmap_location_pop_up.HeatmapLocationPopup(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> _ = HeatmapLocationPopup(config_path=r"C: roubleshooting\RAT_NOR\project_folder\project_config.ini") >>> _ = HeatmapLocationPopup(config_path=r"C: roubleshooting\mitra\project_folder\project_config.ini")
simba.ui.pop_ups.kleinberg_pop_up module
- class simba.ui.pop_ups.kleinberg_pop_up.KleinbergPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.make_path_plot_pop_up module
- class simba.ui.pop_ups.make_path_plot_pop_up.MakePathPlotPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixinTkinter pop-up window for creating simple path plots from pose estimation data.
This pop-up provides a simplified interface to visualize animal movement paths from pose estimation data files (H5 or CSV format). It creates a path plot showing where a selected body-part traveled over time, displayed as a line connecting sequential positions.
The path plot can be created as either: - A video showing the path growing frame-by-frame - A single image showing the complete cumulative path
This tool works independently of SimBA projects and can be used with any pose estimation data file. For more advanced path plots with multiple animals, ROI overlays, classification markers, and other features, use the full “CREATE PATH PLOTS” tool available in the SimBA project interface.
- Example
>>> popup = MakePathPlotPopUp() >>> # User selects video, data file, body-part, and styling options >>> # Then clicks RUN to generate the path plot
simba.ui.pop_ups.movement_analysis_pop_up module
- class simba.ui.pop_ups.movement_analysis_pop_up.MovementAnalysisPopUp(config_path)[source]
Bases:
simba.mixins.config_reader.ConfigReader,simba.mixins.pop_up_mixin.PopUpMixinANALYZE MOVEMENT / VELOCITY: AGGREGATES UI. SETTINGS can add VIDEO FRAME COUNT and VIDEO LENGTH (HH:MM:SS) rows to
Movement_log_*.csv(see Scenario 2 andROI_tutorial— Distances / velocity).
simba.ui.pop_ups.movement_analysis_time_bins_pop_up module
- class simba.ui.pop_ups.movement_analysis_time_bins_pop_up.MovementAnalysisTimeBinsPopUp(config_path)[source]
Bases:
simba.mixins.config_reader.ConfigReader,simba.mixins.pop_up_mixin.PopUpMixinTkinter pop-up for defining parameters when computing movements in time-bins.
- Example
>>> _ = MovementAnalysisTimeBinsPopUp(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini') >>> _ = MovementAnalysisTimeBinsPopUp(config_path=r"C: roubleshooting wo_black_animals_14bp\project_folder\project_config.ini")
simba.ui.pop_ups.outlier_settings_pop_up module
- class simba.ui.pop_ups.outlier_settings_pop_up.OutlierSettingsPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.path_plot_pop_up module
- class simba.ui.pop_ups.path_plot_pop_up.PathPlotPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.pose_bp_drop_pop_up module
simba.ui.pop_ups.pose_reorganizer_pop_up module
simba.ui.pop_ups.pup_retrieval_pop_up module
simba.ui.pop_ups.quick_path_plot_pop_up module
- class simba.ui.pop_ups.quick_path_plot_pop_up.QuickLineplotPopup(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.roi_analysis_pop_up module
- class simba.ui.pop_ups.roi_analysis_pop_up.ROIAnalysisPopUp(config_path)[source]
Bases:
simba.mixins.config_reader.ConfigReader,simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> _ = ROIAnalysisPopUp(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini')
simba.ui.pop_ups.roi_analysis_time_bins_pop_up module
- class simba.ui.pop_ups.roi_analysis_time_bins_pop_up.ROIAnalysisTimeBinsPopUp(config_path)[source]
Bases:
simba.mixins.config_reader.ConfigReader,simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> _ = ROIAnalysisTimeBinsPopUp(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini')
simba.ui.pop_ups.roi_features_plot_pop_up module
- class simba.ui.pop_ups.roi_features_plot_pop_up.VisualizeROIFeaturesPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader,simba.mixins.feature_extraction_mixin.FeatureExtractionMixin- Example
>>> _ = VisualizeROIFeaturesPopUp(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/project_config.ini')
simba.ui.pop_ups.roi_tracking_plot_pop_up module
- class simba.ui.pop_ups.roi_tracking_plot_pop_up.VisualizeROITrackingPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReaderPop-up UI for visualizing ROI tracking overlays on videos.
The interface lets users configure how tracked body-parts, animal names, bounding boxes, and behavior timers are rendered before creating ROI visualization videos using either single-core or multi-core plotting backends.
- Parameters
config_path (Union[str, os.PathLike]) – Path to the SimBA project configuration file.
- Example
>>> VisualizeROITrackingPopUp(config_path=r"C: roubleshooting wo_black_animals_14bp\project_folder\project_config.ini")
simba.ui.pop_ups.set_machine_model_parameters_pop_up module
simba.ui.pop_ups.severity_analysis_pop_up module
- class simba.ui.pop_ups.severity_analysis_pop_up.AnalyzeSeverityPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.smoothing_interpolation_pop_up module
simba.ui.pop_ups.subset_feature_extractor_pop_up module
- class simba.ui.pop_ups.subset_feature_extractor_pop_up.FeatureSubsetExtractorPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> FeatureSubsetExtractorPopUp(config_path=r"C: roubleshooting\mitra\project_folder\project_config.ini")
simba.ui.pop_ups.third_party_annotator_appender_pop_up module
- class simba.ui.pop_ups.third_party_annotator_appender_pop_up.ThirdPartyAnnotatorAppenderPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.validation_plot_pop_up module
- class simba.ui.pop_ups.validation_plot_pop_up.ValidationVideoPopUp(config_path, feature_path, model_path, discrimination_threshold, shortest_bout)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
simba.ui.pop_ups.video_processing_pop_up module
- class simba.ui.pop_ups.video_processing_pop_up.ClipMultipleVideosByFrameNumbersPopUp(data_dir, save_dir)[source]
- class simba.ui.pop_ups.video_processing_pop_up.ClipMultipleVideosByTimestamps(data_dir, save_dir)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- example
>>> ClipMultipleVideosByTimestamps(data_dir=r"C: roubleshooting\RAT_NOR\project_folder
ideos est”, save_dir=r”C: roubleshootingRAT_NORproject_folder ideos estout”)
>>> ClipMultipleVideosByTimestamps(data_dir=r"C: roubleshooting\mitra\project_folder
ideos”, save_dir=r”C: roubleshootingmitraproject_folder ideos emp_3”)
- class simba.ui.pop_ups.video_processing_pop_up.ConcatenatorPopUp(config_path=None)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
- class simba.ui.pop_ups.video_processing_pop_up.Convert2AVIPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> Convert2AVIPopUp()
- class simba.ui.pop_ups.video_processing_pop_up.Convert2MOVPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> Convert2MOVPopUp()
- class simba.ui.pop_ups.video_processing_pop_up.Convert2MP4PopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> Convert2MP4PopUp()
- class simba.ui.pop_ups.video_processing_pop_up.Convert2WEBMPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin- Example
>>> Convert2WEBMPopUp()
- class simba.ui.pop_ups.video_processing_pop_up.ExtractAnnotationFramesPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader- Example
>>> ExtractAnnotationFramesPopUp(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini')
- class simba.ui.pop_ups.video_processing_pop_up.ImportFrameDirectoryPopUp(config_path)[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin,simba.mixins.config_reader.ConfigReader
- class simba.ui.pop_ups.video_processing_pop_up.InitiateClipMultipleVideosByFrameNumbersPopUp[source]
simba.ui.pop_ups.visualize_pose_in_dir_pop_up module
- class simba.ui.pop_ups.visualize_pose_in_dir_pop_up.VisualizePoseInFolderPopUp[source]
Bases:
simba.mixins.pop_up_mixin.PopUpMixin
- Example
>>> VisualizePoseInFolderPopUp()