Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W A algorithm_time (encore.validators.algorithm_results.AnalysisOutput attribute) AlgorithmConfig (class in encore.validators.runners_config) analysis_function (encore.validators.runners_config.AlgorithmConfig attribute) AnalysisOutput (class in encore.validators.algorithm_results) answer (encore.validators.algorithm_results.AnalysisOutput attribute) assign_data_from_file() (in module encore.data.assign_data) B bin_matrix() (encore.main.MainWindow method) browse_files() (encore.main.MainWindow method) build_parameters_model() (in module encore.validators.algorithm_parameters) C calculate_neuron_overlap_ratio() (in module encore.utils.metrics) calculate_neuron_overlap_shared() (in module encore.utils.metrics) child() (encore.data.load_data.FileTreeItem method) child_count() (encore.data.load_data.FileTreeItem method) clear_behavior() (encore.main.MainWindow method) clear_cells() (encore.main.MainWindow method) clear_coordinates() (encore.main.MainWindow method) clear_dFFo() (encore.main.MainWindow method) clear_neuronal_activity() (encore.main.MainWindow method) clear_stims() (encore.main.MainWindow method) collect_algorithm_data() (encore.main.MainWindow method) collect_algorithm_parameters() (encore.main.MainWindow method) collect_parameters() (in module encore.validators.algorithm_parameters) column_count() (encore.data.load_data.FileTreeItem method) columnCount() (encore.data.load_data.FileTreeModel method) compute_auc_roc_ensemble_stimuli() (in module encore.utils.metrics) compute_correlation_between_ensembles() (in module encore.utils.metrics) compute_correlation_inside_ensemble() (in module encore.utils.metrics) compute_correlation_with_stimuli() (in module encore.utils.metrics) compute_cross_correlations() (in module encore.utils.metrics) CustomNavigationToolbar (class in encore.plotters.MatplotlibWidget) D data() (encore.data.load_data.FileTreeItem method) (encore.data.load_data.FileTreeModel method) data_name() (encore.data.load_data.FileTreeModel method) data_size() (encore.data.load_data.FileTreeModel method) data_type() (encore.data.load_data.FileTreeModel method) default_value (encore.validators.runners_config.ParameterConfig attribute) description (encore.validators.runners_config.ParameterConfig attribute) (encore.validators.runners_config.ParameterOption attribute) dict_to_matlab_struct() (in module encore.utils.data_converters) display_name (encore.validators.runners_config.FigureConfig attribute) (encore.validators.runners_config.ParameterConfig attribute) E edit_bin() (encore.main.MainWindow method) edit_transpose() (encore.main.MainWindow method) edit_trimmatrix() (encore.main.MainWindow method) enabled (encore.validators.algorithm_results.AnalysisOutput attribute) (encore.validators.runners_config.AlgorithmConfig attribute) encore.data.assign_data module encore.data.load_data module encore.main module encore.plotters.encore module encore.plotters.encore_plots module encore.plotters.MatplotlibWidget module encore.runners.encore module encore.utils.data_converters module encore.utils.metrics module encore.utils.parameters_validators module encore.utils.text_formatting module encore.validators.algorithm_inputs module encore.validators.algorithm_parameters module encore.validators.algorithm_results module encore.validators.runners_config module encore_runners (encore.validators.runners_config.EncoreConfigFile attribute) EncoreConfig (class in encore.validators.runners_config) EncoreConfigFile (class in encore.validators.runners_config) engine_time (encore.validators.algorithm_results.AnalysisOutput attribute) enscomp_get_color() (encore.main.MainWindow method) enscomp_get_color_behavior() (encore.main.MainWindow method) enscomp_get_color_stims() (encore.main.MainWindow method) enscomp_plot_similarity() (in module encore.plotters.encore_plots) enscomp_update_map() (in module encore.plotters.encore_plots) enscomp_update_timelines() (in module encore.plotters.encore_plots) ensemble_color (encore.validators.runners_config.AlgorithmConfig attribute) ensembles_cant (encore.validators.algorithm_results.ResultsBlock attribute) ensembles_compare_get_elements_labels() (encore.main.MainWindow method) ensembles_compare_get_simmatrix() (encore.main.MainWindow method) ensembles_compare_similarity() (encore.main.MainWindow method) ensembles_compare_similarity_update_combbox() (encore.main.MainWindow method) ensembles_compare_tabchange() (encore.main.MainWindow method) ensembles_compare_update_combo_results() (encore.main.MainWindow method) ensembles_compare_update_ensembles() (encore.main.MainWindow method) ensembles_compare_update_map() (encore.main.MainWindow method) ensembles_compare_update_opts() (encore.main.MainWindow method) ensembles_compare_update_timecourses() (encore.main.MainWindow method) ensvis_tabchange() (encore.main.MainWindow method) F FigureConfig (class in encore.validators.runners_config) figures (encore.validators.runners_config.AlgorithmConfig attribute) FileTreeItem (class in encore.data.load_data) FileTreeModel (class in encore.data.load_data) flags() (encore.data.load_data.FileTreeModel method) flatten_dict() (encore.main.MainWindow method) format_nums_to_string() (in module encore.utils.text_formatting) full_name (encore.validators.runners_config.AlgorithmConfig attribute) G get_algorithm_config() (in module encore.validators.algorithm_inputs) get_data_to_save() (encore.main.MainWindow method) H headerData() (encore.data.load_data.FileTreeModel method) I index() (encore.data.load_data.FileTreeModel method) initialize_ensemble_view() (encore.main.MainWindow method) initialize_user_algorithms() (encore.main.MainWindow method) item_clicked() (encore.main.MainWindow method) item_path() (encore.data.load_data.FileTreeItem method) item_size() (encore.data.load_data.FileTreeItem method) item_type() (encore.data.load_data.FileTreeItem method) L label (encore.validators.runners_config.ParameterOption attribute) language (encore.validators.runners_config.AlgorithmConfig attribute) load_algorithm_defaults() (encore.main.MainWindow method) load_project_metadata() (encore.main.MainWindow method) log (encore.main.WorkerSignals attribute) M main() (in module encore.main) main_tabs_change() (encore.main.MainWindow method) MainWindow (class in encore.main) MatplotlibWidget (class in encore.plotters.MatplotlibWidget) max_value (encore.validators.runners_config.ParameterConfig attribute) min_value (encore.validators.runners_config.ParameterConfig attribute) model_config (encore.validators.algorithm_results.AnalysisOutput attribute) (encore.validators.algorithm_results.ResultsBlock attribute) (encore.validators.runners_config.AlgorithmConfig attribute) (encore.validators.runners_config.EncoreConfig attribute) (encore.validators.runners_config.EncoreConfigFile attribute) (encore.validators.runners_config.FigureConfig attribute) (encore.validators.runners_config.ParameterConfig attribute) (encore.validators.runners_config.ParameterOption attribute) module encore.data.assign_data encore.data.load_data encore.main encore.plotters.encore encore.plotters.encore_plots encore.plotters.MatplotlibWidget encore.runners.encore encore.utils.data_converters encore.utils.metrics encore.utils.parameters_validators encore.utils.text_formatting encore.validators.algorithm_inputs encore.validators.algorithm_parameters encore.validators.algorithm_results encore.validators.runners_config N name (encore.validators.runners_config.FigureConfig attribute) needed_data (encore.validators.runners_config.AlgorithmConfig attribute) neus_in_ens (encore.validators.algorithm_results.ResultsBlock attribute) O object_name (encore.validators.runners_config.ParameterConfig attribute) options (encore.validators.runners_config.ParameterConfig attribute) P ParameterConfig (class in encore.validators.runners_config) ParameterOption (class in encore.validators.runners_config) parameters (encore.validators.runners_config.AlgorithmConfig attribute) parent() (encore.data.load_data.FileTreeItem method) (encore.data.load_data.FileTreeModel method) parse_project_urls() (encore.main.MainWindow method) performance_check_change() (encore.main.MainWindow method) performance_compare() (encore.main.MainWindow method) performance_tabchange() (encore.main.MainWindow method) plot_algorithm_plots() (encore.main.MainWindow method) plot_all_binary() (in module encore.plotters.encore_plots) plot_all_coords() (in module encore.plotters.encore_plots) plot_all_dFFo() (in module encore.plotters.encore_plots) plot_assembly_patterns() (in module encore.plotters.encore_plots) plot_cell_assemblies_activity() (in module encore.plotters.encore_plots) plot_coordinates2D_highlight() (in module encore.plotters.encore_plots) plot_core_cells() (in module encore.plotters.encore_plots) plot_delta_rho() (in module encore.plotters.encore_plots) plot_eigs() (in module encore.plotters.encore_plots) plot_ens_corr() (in module encore.plotters.encore_plots) plot_ens_seq() (in module encore.plotters.encore_plots) plot_ensemble_dFFo() (in module encore.plotters.encore_plots) plot_ensembles_timecourse() (in module encore.plotters.encore_plots) plot_example() (in module encore.plotters.encore) plot_for_example_simple_line() (in module encore.plotters.encore_plots) plot_function (encore.validators.runners_config.AlgorithmConfig attribute) plot_ica() (in module encore.plotters.encore) plot_pca() (in module encore.plotters.encore) (in module encore.plotters.encore_plots) plot_perf_correlations_cells() (in module encore.plotters.encore_plots) plot_perf_correlations_ens_group() (in module encore.plotters.encore_plots) plot_perf_cross_ens_stims() (in module encore.plotters.encore_plots) plot_sgc() (in module encore.plotters.encore) plot_singular_values() (in module encore.plotters.encore_plots) plot_states_from_svd() (in module encore.plotters.encore_plots) plot_svd() (in module encore.plotters.encore) plot_x2p() (in module encore.plotters.encore) preview_coordinates2D() (in module encore.plotters.encore_plots) preview_dataset() (in module encore.plotters.encore_plots) Q QtLoggerAdapter (class in encore.main) R raster_plot() (in module encore.plotters.encore_plots) reset() (encore.plotters.MatplotlibWidget.MatplotlibWidget method) reset_gui() (encore.main.MainWindow method) result_ready (encore.main.WorkerSignals attribute) results (encore.validators.algorithm_results.AnalysisOutput attribute) ResultsBlock (class in encore.validators.algorithm_results) root (encore.validators.runners_config.EncoreConfig attribute) row() (encore.data.load_data.FileTreeItem method) rowCount() (encore.data.load_data.FileTreeModel method) run() (encore.main.WorkerRunnable method) run_algorithm() (encore.main.MainWindow method) run_algorithm_end() (encore.main.MainWindow method) run_analysis_function() (encore.main.MainWindow method) run_example() (in module encore.runners.encore) run_ica() (in module encore.runners.encore) run_pca() (in module encore.runners.encore) run_sgc() (in module encore.runners.encore) run_svd() (in module encore.runners.encore) run_x2p() (in module encore.runners.encore) S save_data_to_hdf5() (encore.main.MainWindow method) save_figure() (encore.plotters.MatplotlibWidget.CustomNavigationToolbar method) save_results_hdf5() (encore.main.MainWindow method) save_results_mat() (encore.main.MainWindow method) save_results_npz() (encore.main.MainWindow method) save_results_pkl() (encore.main.MainWindow method) set_able_edit_options() (encore.main.MainWindow method) set_behavior() (encore.main.MainWindow method) set_cells() (encore.main.MainWindow method) set_coordinates() (encore.main.MainWindow method) set_dFFo() (encore.main.MainWindow method) set_neuronal_activity() (encore.main.MainWindow method) set_stims() (encore.main.MainWindow method) set_subplots() (encore.plotters.MatplotlibWidget.MatplotlibWidget method) set_theme() (encore.main.MainWindow method) setup_about_tab() (encore.main.MainWindow method) simple_validate() (in module encore.validators.algorithm_inputs) source (encore.validators.runners_config.AlgorithmConfig attribute) success (encore.validators.algorithm_results.AnalysisOutput attribute) T timecourse (encore.validators.algorithm_results.ResultsBlock attribute) type (encore.validators.runners_config.ParameterConfig attribute) U update_analysis_results() (encore.main.MainWindow method) update_console_log() (encore.main.MainWindow method) update_corr_behavior() (encore.main.MainWindow method) update_corr_behavior_parallel() (encore.main.MainWindow method) update_corr_stim() (encore.main.MainWindow method) update_corr_stim_parallel() (encore.main.MainWindow method) update_correlation_cells() (encore.main.MainWindow method) update_correlation_cells_parallel() (encore.main.MainWindow method) update_cross_behavior() (encore.main.MainWindow method) update_cross_behavior_parallel() (encore.main.MainWindow method) update_cross_ens_stim() (encore.main.MainWindow method) update_cross_ens_stim_parallel() (encore.main.MainWindow method) update_datetime() (encore.main.MainWindow method) update_edit_validators() (encore.main.MainWindow method) update_ens_vis_coords() (encore.main.MainWindow method) update_enscomp_options() (encore.main.MainWindow method) update_ensemble_visualization() (encore.main.MainWindow method) update_ensvis_allbinary() (encore.main.MainWindow method) update_ensvis_allcoords() (encore.main.MainWindow method) update_ensvis_alldFFo() (encore.main.MainWindow method) update_ensvis_allens() (encore.main.MainWindow method) update_params (encore.validators.algorithm_results.AnalysisOutput attribute) update_user_analysis_requirements() (encore.main.MainWindow method) V validate() (in module encore.validators.algorithm_parameters) validate_algorithm_keys() (encore.validators.runners_config.EncoreConfig class method) validate_algorithm_short_name() (in module encore.validators.runners_config) validate_analysis_output() (in module encore.validators.algorithm_results) validate_binary_matrix() (encore.validators.algorithm_results.ResultsBlock class method) (in module encore.utils.parameters_validators) validate_color() (encore.validators.runners_config.AlgorithmConfig class method) validate_encore_algorithm_config() (in module encore.validators.runners_config) validate_encore_config() (in module encore.validators.runners_config) validate_loaded_data() (encore.main.MainWindow method) validate_needed_data() (encore.validators.runners_config.AlgorithmConfig class method) validate_parameter_config() (encore.validators.runners_config.ParameterConfig method) validate_parameter_keys() (encore.validators.runners_config.AlgorithmConfig class method) validate_params() (in module encore.utils.parameters_validators) validate_shapes_with_context() (encore.validators.algorithm_results.AnalysisOutput method) validate_user_parameters() (in module encore.validators.algorithm_parameters) value (encore.validators.runners_config.ParameterOption attribute) varlabels_clear() (encore.main.MainWindow method) varlabels_save() (encore.main.MainWindow method) varlabels_setup_tab() (encore.main.MainWindow method) view_behavior() (encore.main.MainWindow method) view_cells() (encore.main.MainWindow method) view_coordinates() (encore.main.MainWindow method) view_dFFo() (encore.main.MainWindow method) view_neuronal_activity() (encore.main.MainWindow method) view_stims() (encore.main.MainWindow method) visualize_ensembles() (encore.main.MainWindow method) W we_have_results() (encore.main.MainWindow method) WorkerRunnable (class in encore.main) WorkerSignals (class in encore.main)