cogrecon.core.visualization package

Submodules

cogrecon.core.visualization.vis_iposition module

cogrecon.core.visualization.vis_iposition.visualization(trial_data, analysis_configuration, min_points, transformed_points, output_list, start_threshold, end_threshold, start_accuracy_map, end_accuracy_map, animation_duration=2, animation_ticks=20, print_output=True, extent=None, fig_size=None, legend_args=None)

This function visualizes TrialData, showing all the steps in the pipeline.

Parameters:

• end_accuracy_map – the accuracy map at the end of processing
• start_accuracy_map – the accuracy map at the beginning of processing
• end_threshold – the accuracy threshold at the end of processing
• start_threshold – the accuracy threshold at the beginning of processing
• trial_data – the TrialData to be visualized
• analysis_configuration – the AnalysisConfiguration to use to visualize (for accuracy visualization mainly)
• min_points – the points output from the deanonymization task
• transformed_points – the points output from the transformation task
• output_list – the final outputs produced by full_pipeline
• animation_duration – a time in seconds specifying the duration of the transform animation
• animation_ticks – the number of ticks (frame updates) which should occur throughout the animation
• print_output – if True, the output_list values will be printed in a user friendly form
• extent – the extents to plot in the data space
• fig_size – a tuple containing the size of the figure in inches
• legend_args – a list of arguments to be passed to the legend (default is None)

cogrecon.core.visualization.vis_spatial_navigation_2room module

cogrecon.core.visualization.vis_spatial_navigation_2room.get_direction_patch_location(center, radius, angle)

Returns a point whose location is determined by a location, radius and angle.

Parameters:

• center – the center/anchor point from which the new point is determined
• radius – the distance from the center at which the new point is located
• angle – the angle at which the new point is located

Returns:

a new point

cogrecon.core.visualization.vis_spatial_navigation_2room.update_line(num, avatar, avatar_direction_marker, fig, pos, orient, line, r)

This helper function animates the visualization.

Parameters:

• avatar – the character marker
• avatar_direction_marker – the character direction marker
• fig – the figure to which plotting is performed
• num – the iteration number
• pos – the position data
• orient – the orientation data
• line – the path line to be updated
• r – the radius for the direction marker

Returns:

the updated line information associated with ‘line’ input

cogrecon.core.visualization.vis_spatial_navigation_2room.visualize(raw_file, summary_file, background_img_path='./media/spatial_navigation/background.png', frame_interval_ms=1)

This function provides basic visualization for the 2-Room Spatial Navigation task given a raw and summary input file.

Parameters:

• frame_interval_ms – the updated interval of the animation in ms
• background_img_path – the path to the image to be displayed in the background
• raw_file – the full path to the raw data file
• summary_file – the full path to the summary data file

cogrecon.core.visualization.vis_spatial_navigation_4room module

cogrecon.core.visualization.vis_spatial_navigation_4room.generate_buffered_points(data_dict, subject_id, trial_num)

cogrecon.core.visualization.vis_spatial_navigation_4room.update()

cogrecon.core.visualization.vis_spatial_navigation_4room.visualize(input_path, point_speed=100, colors='rg')

cogrecon.core.visualization.vis_time_travel_task module

cogrecon.core.visualization.vis_time_travel_task.generate_normed_segments(path, __meta=None, normalize_translation=True, normalize_length=True, normalize_rotation=True)

This function generates normalized line segments given a path, meta-data, and normalization flags.

Parameters:

• path – the path to the data to process.
• __meta – the meta information from the data filename (automatically detected if None)
• normalize_translation – if True, translation will be normalized
• normalize_length – if True, scaling will be normalized
• normalize_rotation – if True, rotation will be normalized

Returns:

cogrecon.core.visualization.vis_time_travel_task.get_rotation_matrix(i_v, unit=None)

This function gets a rotation matrix given a vector from a unit vector.

Parameters:

• i_v – the vector whose rotation should be calculated
• unit – the unit vector for reference

Returns:

a rotation matrix

cogrecon.core.visualization.vis_time_travel_task.item_path_visualization(search_directory=None, file_regex='\\d\\d\\d_\\d_1_\\d_\\d\\d\\d\\d-\\d\\d-\\d\\d_\\d\\d-\\d\\d-\\d\\d.dat')

This function visualizes item-to-item paths given some input files.

Parameters:

• search_directory – a directory to search recursively for input files
• file_regex – a regular expression to search for in the files in search_directory

Return type:

bool

Returns:

True if files were successfully processed, False otherwise.

cogrecon.core.visualization.vis_time_travel_task.subsetter(path)

This function is used as a helper to subset data via a particular criteria.

Parameters:path – the path to the data Returns:a bool which, if True, suggests keeping the data, otherwise it suggests removing the data from the visualization

cogrecon.core.visualization.vis_time_travel_task.update()

This function is the animation update function used internally in visualize_time_travel_data.

cogrecon.core.visualization.vis_time_travel_task.visualize_time_travel_data(path=None, automatically_rotate=True)

This function visualizes data from the Time Travel Task in 3D.

Parameters:

• path – the path to a data file to visualize
• automatically_rotate – If True, the figure will automatically rotate in an Abs(Sin(x)) function shape, otherwise the user can interact with the figure.

Returns:

Nothing

cogrecon.core.visualization.vis_virtual_morris_water_maze module

cogrecon.core.visualization.vis_virtual_morris_water_maze.update()

This function is the animation update function used internally in visualize.

cogrecon.core.visualization.vis_virtual_morris_water_maze.visualize(path=None)

This function visualizes data for the virtual morris water maze task.

Parameters:path – a path to a log file from the virtual morris water maze task Returns:Nothing

Module contents