Module Expr Str Import alias Import alias Import alias identifier Import alias identifier Import alias identifier Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Import alias identifier FunctionDef arguments args NameParam defaults Num body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Num Num AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad NameLoad attr Num Num AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr ListLoad NameLoad NameLoad keyword Num keyword Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num Num NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num Num NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr ListLoad NameLoad NameLoad keyword Num keyword Num Return NameLoad decorator_list FunctionDef arguments args defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Str Assign NameStore ListLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad SubscriptLoad NameLoad Index Num attr keyword NameLoad keyword NameLoad Print BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad For TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq SubscriptLoad NameLoad Slice Num Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Pass decorator_list Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str Lambda arguments args NameParam defaults BinOpMod Str NameLoad If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call NameLoad Print BinOpMod Str BinOpSub Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad
N/A N/A 
An example showing how to use the open-worm-analysis-toolbox package to go from a
raw video .avi file to a fitness function result.

 N/A sys N/A os N/A numpy np N/A pandas pd N/A matplotlib.pyplot plt N/A N/A N/A N/A sys path append .. N/A open_worm_analysis_toolbox mv example_worms N/A N/A num_frames N/A 1000 N/A N/A 
    Construct a simple set of worm positions over time, for testing purposes.

    Returns
    ------------
    Tuple of BasicWorm objects
        One moving, one not

     N/A skeleton_x N/A N/A np linspace 10000 11000 N/A N/A mv config N_POINTS_NORMALIZED N/A skeleton_y N/A N/A np linspace 5000 5000 N/A N/A mv config N_POINTS_NORMALIZED N/A skeleton_frame1 N/A N/A np rollaxis N/A N/A np dstack N/A skeleton_x skeleton_y axis 0 start 3 N/A skeleton N/A N/A np repeat skeleton_frame1 num_frames axis 2 N/A bw N/A N/A N/A mv BasicWorm from_skeleton_factory skeleton N/A motion_overlay_x N/A N/A np linspace 0 100 num_frames N/A motion_overlay_y N/A N/A np linspace 0 0 num_frames N/A motion_overlay N/A N/A np rollaxis N/A N/A np dstack N/A motion_overlay_x motion_overlay_y axis 0 start 3 N/A bw N/A main N/A N/A N/A N/A N/A base_path N/A N/A N/A os path abspath N/A N/A mv user_config EXAMPLE_DATA_PATH N/A schafer_bw_file_path N/A N/A N/A os path join base_path example_contour_and_skeleton_info.mat N/A bw N/A N/A N/A mv BasicWorm from_schafer_file_factory schafer_bw_file_path N/A nw N/A N/A N/A mv NormalizedWorm from_BasicWorm_factory bw N/A wf N/A N/A mv WormFeaturesDos nw N/A base_path N/A N/A N/A os path abspath N/A N/A mv user_config EXAMPLE_DATA_PATH N/A control_path N/A N/A N/A os path join base_path 30m_wait R N/A experiment_files N/A wf wf N/A control_files N/A get_matlab_filepaths control_path N/A experiment_histograms N/A N/A mv HistogramManager experiment_files N/A control_histograms N/A N/A mv HistogramManager control_files N/A N/A N/A experiment_histograms plot_information N/A stat N/A N/A mv StatisticsManager experiment_histograms control_histograms N/A N/A N/A N/A stat N/A 0 plot ax None use_alternate_plot True N/A N/A Nonparametric p and q values are %.2f and %.2f, respectively. N/A N/A stat min_p_wilcoxon N/A stat min_q_wilcoxon N/A get_matlab_filepaths N/A N/A root_path N/A N/A N/A 
    Recursively traverses from root_path to find all .mat files
    Returns a list of .mat files, with full path

    Parameters
    -----------------------
    root_path: string
        The absolute path to start searching from

     N/A matlab_filepaths N/A N/A N/A root dirs files N/A N/A os walk root_path N/A N/A mat_files N/A f N/A f files N/A N/A f N/A -4 .mat N/A f mat_files N/A N/A N/A N/A matlab_filepaths append N/A N/A N/A os path join root f N/A matlab_filepaths N/A geppetto_to_features N/A N/A minimal_worm_spec_path N/A N/A N/A N/A N/A N/A N/A pd set_option expand_frame_repr False N/A N/A N/A pd set_option display.float_format N/A N/A N/A x N/A N/A %.4f x N/A N/A __name__ __main__ N/A N/A start_time N/A N/A N/A mv utils timing_function N/A N/A main N/A N/A Time elapsed: %.2fs N/A N/A N/A N/A mv utils timing_function start_time