Index Symbols | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z Symbols --arms camap-define-zones command line option --config camap-analysis command line option --data camap-analysis command line option camap-define-zones command line option camap-detect-zones command line option --force-redetect camap-analysis command line option --interpolate camap-detect-zones command line option --output camap-analysis command line option camap-detect-zones command line option --playback-speed camap-detect-zones command line option --rooms camap-define-zones command line option --show camap-analysis command line option --subset-frames camap-analysis command line option --subset-units camap-analysis command line option --version camap command line option --workers camap-analysis command line option --yes camap-analysis command line option -c camap-analysis command line option -d camap-analysis command line option camap-define-zones command line option camap-detect-zones command line option -o camap-analysis command line option camap-detect-zones command line option -V camap command line option -w camap-analysis command line option -y camap-analysis command line option A AnalysisConfig (class in camap.config) analyze_units() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) apply_time_window() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) arena_bounds (camap.config.ArenaBehaviorDataConfig attribute) arena_size_mm (camap.config.ArenaBehaviorDataConfig attribute) ArenaBehaviorDataConfig (class in camap.config) ArenaDataset (class in camap.dataset) (class in camap.dataset.arena) arm_decay_power (camap.config.ZoneDetectionConfig attribute) arm_max_distance (camap.config.ZoneDetectionConfig attribute) arm_order (camap.config.MazeBehaviorDataConfig attribute) arm_position_column (camap.config.MazeBehaviorDataConfig attribute) assign_traversal_direction() (in module camap.maze_helper) B BaseBehaviorDataConfig (class in camap.config) BaseCaMAPDataset (class in camap.dataset) (class in camap.dataset.base) baseline (camap.config.OasisConfig attribute) BaseSpatialMapConfig (class in camap.config) behavior (camap.config.AnalysisConfig attribute) (camap.config.DataConfig attribute) behavior_graph (camap.config.MazeBehaviorDataConfig attribute) behavior_video_frame (camap.dataset.base.BaseCaMAPDataset attribute) BehaviorConfig (class in camap.config) bin_width_mm (camap.config.SpatialMap1DConfig attribute) bins (camap.config.SpatialMap2DConfig attribute) block_shift (camap.config.BaseSpatialMapConfig attribute) bodypart (camap.config.BaseBehaviorDataConfig attribute) C camap command line option --version -V camap-analysis command line option --config --data --force-redetect --output --show --subset-frames --subset-units --workers --yes -c -d -o -w -y camap-define-zones command line option --arms --data --rooms -d camap-detect-zones command line option --data --interpolate --output --playback-speed -d -o camap.analysis.spatial_1d module camap.analysis.spatial_2d module camap.behavior module camap.config module camap.dataset module camap.dataset.arena module camap.dataset.base module camap.dataset.maze module camap.loaders module camap.maze_helper module camap.neural module camap.visualization module camera_height_mm (camap.config.ArenaBehaviorDataConfig attribute) canonical (camap.dataset.base.BaseCaMAPDataset attribute) clip_to_arena() (in module camap.behavior) compute_arm_lengths() (in module camap.maze_helper) compute_coverage_curve() (in module camap.analysis.spatial_2d) compute_coverage_map() (in module camap.analysis.spatial_2d) compute_occupancy() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) compute_occupancy_map() (in module camap.analysis.spatial_2d) compute_occupancy_map_1d() (in module camap.analysis.spatial_1d) compute_overlap_time_range() (in module camap.loaders) compute_place_field_mask() (in module camap.analysis.spatial_2d) compute_rate_map() (in module camap.analysis.spatial_2d) compute_rate_map_1d() (in module camap.analysis.spatial_1d) compute_raw_rate_map() (in module camap.analysis.spatial_2d) compute_raw_rate_map_1d() (in module camap.analysis.spatial_1d) compute_shuffled_rate_percentile() (in module camap.analysis.spatial_2d) compute_spatial_information() (in module camap.analysis.spatial_2d) compute_spatial_information_1d() (in module camap.analysis.spatial_1d) compute_speed_1d() (in module camap.maze_helper) compute_stability_score() (in module camap.analysis.spatial_2d) compute_stability_score_1d() (in module camap.analysis.spatial_1d) compute_unit_analysis() (in module camap.analysis.spatial_2d) compute_unit_analysis_1d() (in module camap.analysis.spatial_1d) config_override (camap.config.DataConfig attribute) corr (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) correct_perspective() (in module camap.behavior) coverage() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) D DataConfig (class in camap.config) deconvolve() (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) E event_count_rate (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) event_index (camap.dataset.base.BaseCaMAPDataset attribute) event_place (camap.dataset.base.BaseCaMAPDataset attribute) event_threshold_sigma (camap.config.SpatialMap2DConfig attribute) F filter_complete_traversals() (in module camap.maze_helper) fisher_z (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) footprints (camap.dataset.base.BaseCaMAPDataset attribute) fps (camap.config.BaseBehaviorDataConfig attribute) (camap.config.NeuralConfig attribute) from_yaml() (camap.config.AnalysisConfig class method) (camap.config.DataConfig class method) (camap.dataset.base.BaseCaMAPDataset class method) (camap.dataset.BaseCaMAPDataset class method) G g (camap.config.OasisConfig attribute) gaussian_filter_normalized() (in module camap.analysis.spatial_2d) gaussian_filter_normalized_1d() (in module camap.analysis.spatial_1d) good_unit_ids (camap.dataset.base.BaseCaMAPDataset attribute) H hampel_n_sigmas (camap.config.BehaviorConfig attribute) (camap.config.ZoneDetectionConfig attribute) hampel_window_frames (camap.config.BehaviorConfig attribute) (camap.config.ZoneDetectionConfig attribute) I interpolate (camap.config.ZoneDetectionConfig attribute) is_stable() (camap.dataset.base.UnitResult method) (camap.dataset.UnitResult method) L load() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) load_behavior_data() (in module camap.loaders) load_bundle() (camap.dataset.base.BaseCaMAPDataset class method) (camap.dataset.BaseCaMAPDataset class method) (camap.dataset.maze.MazeDataset class method) (camap.dataset.MazeDataset class method) load_calcium_traces() (in module camap.neural) load_graph_polylines() (in module camap.maze_helper) load_visualization_data() (in module camap.loaders) M match_events() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) max_proj (camap.dataset.base.BaseCaMAPDataset attribute) MazeBehaviorDataConfig (class in camap.config) MazeDataset (class in camap.dataset) (class in camap.dataset.maze) min_confidence (camap.config.ZoneDetectionConfig attribute) min_confidence_forbidden (camap.config.ZoneDetectionConfig attribute) min_events (camap.config.BaseSpatialMapConfig attribute) min_occupancy (camap.config.BaseSpatialMapConfig attribute) min_seconds_forbidden (camap.config.ZoneDetectionConfig attribute) min_seconds_same (camap.config.ZoneDetectionConfig attribute) min_shift_seconds (camap.config.BaseSpatialMapConfig attribute) mm_per_pixel (camap.config.MazeBehaviorDataConfig attribute) mm_per_px (camap.dataset.arena.ArenaDataset property) (camap.dataset.ArenaDataset property) mm_per_px_xy (camap.dataset.arena.ArenaDataset property) (camap.dataset.ArenaDataset property) model_config (camap.config.AnalysisConfig attribute) (camap.config.ArenaBehaviorDataConfig attribute) (camap.config.BaseBehaviorDataConfig attribute) (camap.config.BaseSpatialMapConfig attribute) (camap.config.BehaviorConfig attribute) (camap.config.DataConfig attribute) (camap.config.MazeBehaviorDataConfig attribute) (camap.config.NeuralConfig attribute) (camap.config.NeuralDataConfig attribute) (camap.config.OasisConfig attribute) (camap.config.SpatialMap1DConfig attribute) (camap.config.SpatialMap2DConfig attribute) (camap.config.ZoneDetectionConfig attribute) module camap.analysis.spatial_1d camap.analysis.spatial_2d camap.behavior camap.config camap.dataset camap.dataset.arena camap.dataset.base camap.dataset.maze camap.loaders camap.maze_helper camap.neural camap.visualization N n_shuffles (camap.config.BaseSpatialMapConfig attribute) n_split_blocks (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) neural (camap.config.AnalysisConfig attribute) (camap.config.DataConfig attribute) neural_fps (camap.dataset.base.BaseCaMAPDataset property) (camap.dataset.BaseCaMAPDataset property) NeuralConfig (class in camap.config) NeuralDataConfig (class in camap.config) O oasis (camap.config.NeuralConfig attribute) OasisConfig (class in camap.config) occupancy_time (camap.dataset.base.BaseCaMAPDataset attribute) overall_rate (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) overlay_frame_index (camap.config.BaseBehaviorDataConfig attribute) P p_val (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.base.UnitResult attribute) (camap.dataset.StabilitySplitResult attribute) (camap.dataset.UnitResult attribute) p_value_threshold (camap.config.BaseSpatialMapConfig attribute) (camap.dataset.arena.ArenaDataset property) (camap.dataset.ArenaDataset property) (camap.dataset.base.BaseCaMAPDataset property) (camap.dataset.BaseCaMAPDataset property) (camap.dataset.maze.MazeDataset property) (camap.dataset.MazeDataset property) path (camap.config.NeuralDataConfig attribute) penalty (camap.config.OasisConfig attribute) place_cells() (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) place_field_min_bins (camap.config.SpatialMap2DConfig attribute) place_field_seed_percentile (camap.config.SpatialMap2DConfig attribute) place_field_threshold (camap.config.SpatialMap2DConfig attribute) playback_speed (camap.config.ZoneDetectionConfig attribute) plot_arena_calibration() (in module camap.visualization) plot_behavior_preview() (in module camap.visualization) plot_coverage() (in module camap.visualization) plot_diagnostics() (in module camap.visualization) plot_footprints() (in module camap.visualization) plot_footprints_filled() (in module camap.visualization) plot_graph_overlay() (in module camap.visualization) plot_occupancy_preview() (in module camap.visualization) plot_occupancy_preview_1d() (in module camap.visualization) plot_position_and_traces_1d() (in module camap.visualization) plot_position_and_traces_2d() (in module camap.visualization) plot_preprocess_steps() (in module camap.visualization) plot_rate_map_1d() (in module camap.visualization) plot_session_summary() (in module camap.visualization) plot_shuffle_test_1d() (in module camap.visualization) plot_speed_histogram() (in module camap.visualization) plot_stability_splits_summary() (in module camap.visualization) plot_summary_scatter() (in module camap.visualization) plot_timestamp_diagnostics() (in module camap.visualization) position (camap.config.BaseBehaviorDataConfig attribute) preprocess_behavior() (camap.dataset.arena.ArenaDataset method) (camap.dataset.ArenaDataset method) (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) R random_seed (camap.config.BaseSpatialMapConfig attribute) rate_map_first (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) rate_map_peak_normalized (camap.dataset.base.UnitResult property) (camap.dataset.UnitResult property) rate_map_raw (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) rate_map_second (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) rate_map_smoothed (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) remove_position_jumps() (in module camap.behavior) require_complete_traversal (camap.config.SpatialMap1DConfig attribute) room_decay_power (camap.config.ZoneDetectionConfig attribute) run_deconvolution() (in module camap.neural) S S_list (camap.dataset.base.BaseCaMAPDataset attribute) s_min (camap.config.OasisConfig attribute) save_bundle() (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) (camap.dataset.maze.MazeDataset method) (camap.dataset.MazeDataset method) serialize_arm_position() (in module camap.maze_helper) shuffled_corrs (camap.dataset.base.StabilitySplitResult attribute) (camap.dataset.StabilitySplitResult attribute) shuffled_rate_p95 (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) shuffled_sis (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) si (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) si_weight_mode (camap.config.BaseSpatialMapConfig attribute) soft_boundary (camap.config.ZoneDetectionConfig attribute) spatial (camap.dataset.arena.ArenaDataset property) (camap.dataset.ArenaDataset property) spatial_1d (camap.dataset.maze.MazeDataset property) (camap.dataset.MazeDataset property) spatial_map_1d (camap.config.BehaviorConfig attribute) spatial_map_2d (camap.config.BehaviorConfig attribute) spatial_sigma (camap.config.BaseSpatialMapConfig attribute) SpatialMap1DConfig (class in camap.config) SpatialMap2DConfig (class in camap.config) speed_threshold (camap.config.BehaviorConfig attribute) speed_window_seconds (camap.config.BehaviorConfig attribute) split_by_direction (camap.config.SpatialMap1DConfig attribute) stability_splits (camap.config.BaseSpatialMapConfig attribute) (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) StabilitySplitResult (class in camap.dataset) (class in camap.dataset.base) subset() (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) summary() (camap.dataset.base.BaseCaMAPDataset method) (camap.dataset.BaseCaMAPDataset method) T timestamp (camap.config.BaseBehaviorDataConfig attribute) (camap.config.NeuralDataConfig attribute) to_yaml() (camap.config.AnalysisConfig method) trace_data (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) trace_name (camap.config.NeuralConfig attribute) trace_times (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) traces (camap.dataset.base.BaseCaMAPDataset attribute) tracking_height_mm (camap.config.ArenaBehaviorDataConfig attribute) trajectory (camap.dataset.base.BaseCaMAPDataset attribute) trajectory_filtered (camap.dataset.base.BaseCaMAPDataset attribute) trajectory_raw (camap.dataset.base.BaseCaMAPDataset attribute) type (camap.config.ArenaBehaviorDataConfig attribute) (camap.config.BehaviorConfig attribute) (camap.config.MazeBehaviorDataConfig attribute) U unique_bundle_path() (in module camap.dataset) (in module camap.dataset.base) unit_data (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) unit_results (camap.dataset.base.BaseCaMAPDataset attribute) UnitResult (class in camap.dataset) (class in camap.dataset.base) V valid_mask (camap.dataset.base.BaseCaMAPDataset attribute) video (camap.config.BaseBehaviorDataConfig attribute) vis_data_above (camap.dataset.base.UnitResult attribute) (camap.dataset.UnitResult attribute) W with_data_overrides() (camap.config.AnalysisConfig method) X x_col (camap.config.BaseBehaviorDataConfig attribute) x_edges (camap.dataset.base.BaseCaMAPDataset attribute) Y y_col (camap.config.BaseBehaviorDataConfig attribute) y_edges (camap.dataset.base.BaseCaMAPDataset attribute) Z zone_column (camap.config.MazeBehaviorDataConfig attribute) zone_connections (camap.config.MazeBehaviorDataConfig attribute) zone_detection (camap.config.MazeBehaviorDataConfig attribute) zone_tracking (camap.config.MazeBehaviorDataConfig attribute) ZoneDetectionConfig (class in camap.config)