Index

A

accuracy() (in module cogrecon.core.full_pipeline) actual_labels (cogrecon.core.data_structures.TrialData attribute) actual_points (cogrecon.core.data_structures.TrialData attribute)

All (cogrecon.core.data_structures.PipelineFlags attribute) all_trial_dates_match() (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.Trial method) AnalysisConfiguration (class in cogrecon.core.data_structures)

B

batch_pipeline() (in module cogrecon.core.batch_pipeline)

brute_force_find_minimal_mapping() (in module cogrecon.core.tools)

C

calculate_euler_vector_from_quaternion() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) calculate_fd_and_lacunarity() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics) catalog_files() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) category_labels (cogrecon.core.data_structures.TrialData attribute) category_split_participant() (cogrecon.core.data_structures.ParticipantData static method) close_writer() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) cogrecon (module) cogrecon.core (module) cogrecon.core.batch_pipeline (module) cogrecon.core.cogrecon_globals (module) cogrecon.core.data_flexing (module) cogrecon.core.data_flexing.category_data_flexor (module) cogrecon.core.data_flexing.descrambler (module) cogrecon.core.data_flexing.dimension_removal (module) cogrecon.core.data_flexing.spatial_navigation (module) cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics (module) cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser (module) cogrecon.core.data_flexing.time_travel_task (module) cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics (module) cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader (module) cogrecon.core.data_flexing.time_travel_task.time_travel_task_to_iposition (module) cogrecon.core.data_flexing.virtual_morris_water_maze (module) cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_analytics (module)

cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser (module) cogrecon.core.data_structures (module) cogrecon.core.file_io (module) cogrecon.core.full_pipeline (module) cogrecon.core.similarity_transform (module) cogrecon.core.tools (module) cogrecon.core.visualization (module) cogrecon.core.visualization.vis_iposition (module) cogrecon.core.visualization.vis_spatial_navigation_2room (module) cogrecon.core.visualization.vis_spatial_navigation_4room (module) cogrecon.core.visualization.vis_time_travel_task (module) cogrecon.core.visualization.vis_virtual_morris_water_maze (module) cogrecon.misc (module) cogrecon.misc.draggable_points (module) cogrecon.misc.heatmap_transform (module) collapse_unique_components() (in module cogrecon.core.tools) compare_summary_and_raw_events() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) compress() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) compute_accuracy() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) connect() (cogrecon.misc.draggable_points.DraggablePoint method) context_item_indicies (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) convert_to_iposition() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) count_boundary_crossings() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics) count_boxes() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics)

D

data_labels (cogrecon.core.data_structures.TrialData attribute) data_order (cogrecon.core.data_structures.TrialData attribute) data_points (cogrecon.core.data_structures.TrialData attribute) datetime_from_dot_net_binary() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser) Deanonymize (cogrecon.core.data_structures.PipelineFlags attribute) deanonymize() (in module cogrecon.core.full_pipeline)

decode_7bit_int_length() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser) descrambler() (in module cogrecon.core.data_flexing.descrambler) detect_shape_from_file() (in module cogrecon.core.file_io) disconnect() (cogrecon.misc.draggable_points.DraggablePoint method) distance_accuracy_map (cogrecon.core.data_structures.TrialData attribute) distance_threshold (cogrecon.core.data_structures.TrialData attribute) DraggablePoint (class in cogrecon.misc.draggable_points)

E

enforce_single_file_contents() (in module cogrecon.core.file_io) extract_basic_order() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_to_iposition)

extract_date_time_from_filename_custom() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) extract_prefixes_from_file_list_via_suffix() (in module cogrecon.core.file_io)

F

file_list_contents_equal() (in module cogrecon.core.file_io) FileType (class in cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) find_data_files_in_directory() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser) (in module cogrecon.core.file_io)

find_last() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) find_minimal_mapping() (in module cogrecon.core.tools) full_pipeline() (in module cogrecon.core.full_pipeline)

G

generate_basic_exploration_metrics_from_intermediate_files() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_basic_exploration_metrics_from_intermediate_files_command_line() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_buffered_points() (in module cogrecon.core.visualization.vis_spatial_navigation_4room) generate_buffered_points_and_clicks() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_intermediate_files() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_intermediate_files_command_line() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_item_specific_efficiency() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_normed_segments() (in module cogrecon.core.visualization.vis_time_travel_task) generate_random_test_points() (in module cogrecon.core.tools) generate_segmentation_analysis() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_segmentation_analysis_command_line() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_study_path_efficiency() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_study_path_efficiency_command_line() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_analytics) generate_virtual_morris_water_maze_summary_file() (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_analytics) geometric_transform() (in module cogrecon.core.full_pipeline) get_aggregation_functions() (in module cogrecon.core.full_pipeline) get_all_from_trials() (cogrecon.core.data_structures.ParticipantData method) get_click_locations_and_indicies() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) get_coordinates_from_file() (in module cogrecon.core.file_io) get_direction_patch_location() (in module cogrecon.core.visualization.vis_spatial_navigation_2room) get_exploration_metrics() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser)

get_filename_meta_data() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser) get_final_state_from_summary_events() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_full_file_list() (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.Individual method) (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.Trial method) get_header_labels() (in module cogrecon.core.full_pipeline) get_id_from_file_prefix_via_suffix() (in module cogrecon.core.file_io) get_item_details() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) get_items_solutions() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) get_location_by_name() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_object_info_from_string() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_object_info_from_summary_string() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_regions_of_points() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics) get_rotation_matrix() (in module cogrecon.core.visualization.vis_time_travel_task) get_simple_orientation_path_from_raw_iterations() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_simple_path_from_raw_iterations() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) get_single_file_result() (in module cogrecon.core.batch_pipeline) GlobalTransformation (cogrecon.core.data_structures.PipelineFlags attribute) greedy_find_minimal_mapping() (in module cogrecon.core.tools)

I

Individual (class in cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) is_correct_color() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) is_path_exists_or_creatable_portable() (in module cogrecon.core.file_io)

is_path_sibling_creatable() (in module cogrecon.core.file_io) is_pathname_valid() (in module cogrecon.core.file_io) item_path_visualization() (in module cogrecon.core.visualization.vis_time_travel_task)

L

lerp() (in module cogrecon.core.tools) lexicographic_index() (in module cogrecon.core.tools) load_from_file() (cogrecon.core.data_structures.ParticipantData static method)

lock (cogrecon.misc.draggable_points.DraggablePoint attribute) LogParseError look_file (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.FileType attribute)

M

make_output_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) make_singular_filename_values_list() (in module cogrecon.core.file_io) mask_dimensions() (in module cogrecon.core.tools)

mask_points() (in module cogrecon.core.tools) match_file_prefixes() (in module cogrecon.core.file_io) meets_trial_number_requirement() (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.Individual method)

N

n_perms() (in module cogrecon.core.tools)

nav_get_room_by_location() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) nav_time_format_string (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser)

O

on_motion() (cogrecon.misc.draggable_points.DraggablePoint method) on_press() (cogrecon.misc.draggable_points.DraggablePoint method)

on_release() (cogrecon.misc.draggable_points.DraggablePoint method) output_results() (in module cogrecon.core.batch_pipeline)

P

parse_file_and_write() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_look_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_nav_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_path_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_summary_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_test_2d_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) parse_test_items() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader)

parse_test_vr_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) ParticipantData (class in cogrecon.core.data_structures) path_file (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.FileType attribute) permutation_from_index() (in module cogrecon.core.tools) phase_num_to_str() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) PipelineFlags (class in cogrecon.core.data_structures) point_is_in_rectangle() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) process_category_files() (in module cogrecon.core.data_flexing.category_data_flexor)

Q

quat2euler() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser)

R

read_binary_file() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_binary_reader) (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser)

read_raw_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) read_summary_file() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) remove_dimensions() (in module cogrecon.core.data_flexing.dimension_removal)

S

save_iposition_items_to_file() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_to_iposition) save_tsv() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_to_iposition) set_all_to_trials() (cogrecon.core.data_structures.ParticipantData method) similarity_transform() (in module cogrecon.core.similarity_transform) Simple (cogrecon.core.data_structures.PipelineFlags attribute) study_context_boundries (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser)

study_practice (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.SummaryType attribute) subsetter() (in module cogrecon.core.visualization.vis_time_travel_task) sum_of_distance() (in module cogrecon.core.tools) summarize_navigation_data() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics) summarize_test_data() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_analytics) SummaryType (class in cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) swaps() (in module cogrecon.core.full_pipeline)

T

test (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.SummaryType attribute) test2d_get_room_by_location() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) test2d_raw_regex_search_key (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) test_context_boundries (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) test_draggable_points() (in module cogrecon.misc.draggable_points) test_file_2d (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.FileType attribute) test_file_vr (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.FileType attribute) test_heatmap_transform() (in module cogrecon.misc.heatmap_transform) test_skip_lines (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser)

time_travel_task_to_iposition() (in module cogrecon.core.data_flexing.time_travel_task.time_travel_task_to_iposition) Trial (class in cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) trial_axis_swap() (in module cogrecon.core.full_pipeline) trial_edge_distortion() (in module cogrecon.core.full_pipeline) trial_edge_resizing() (in module cogrecon.core.full_pipeline) trial_geometric_transform() (in module cogrecon.core.full_pipeline) trial_num_to_str() (in module cogrecon.core.data_flexing.virtual_morris_water_maze.virtual_morris_water_maze_parser) trial_swaps() (in module cogrecon.core.full_pipeline) TrialData (class in cogrecon.core.data_structures)

U

unknown (cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser.SummaryType attribute) update() (in module cogrecon.core.visualization.vis_spatial_navigation_4room) (in module cogrecon.core.visualization.vis_time_travel_task) (in module cogrecon.core.visualization.vis_virtual_morris_water_maze)

update_line() (in module cogrecon.core.visualization.vis_spatial_navigation_2room)

V

validate_equal_list_shapes() (in module cogrecon.core.batch_pipeline) validate_list_format() (in module cogrecon.core.batch_pipeline) validate_summary_events_are_complete() (in module cogrecon.core.data_flexing.spatial_navigation.spatial_navigation_parser) validate_type() (in module cogrecon.core.tools)

visualization() (in module cogrecon.core.visualization.vis_iposition) visualize() (in module cogrecon.core.visualization.vis_spatial_navigation_2room) (in module cogrecon.core.visualization.vis_spatial_navigation_4room) (in module cogrecon.core.visualization.vis_virtual_morris_water_maze) visualize_time_travel_data() (in module cogrecon.core.visualization.vis_time_travel_task)