diplomat sleap analyze_frames

Summary

Run DIPLOMAT tracking on a set of frame store files or a single frame store using metadata from a SLEAP model, generating results in “.slp” files.

Usage

diplomat sleap analyze_frames [-h] --config
                                     [FILE, ...]|FILE --frame_stores [FILE, ...]|FILE [--batch_size INT]
                                     [--num_outputs INT] [--predictor STR]
                                     [--predictor_settings {STR: VAL, ...}]
                                     [--output_suffix STR]
                                     [--refinement_kernel_size INT]
                                     [--pcutoff FLOAT] [--dotsize INT]
                                     [--alphavalue FLOAT]
                                     [--colormap TO_COLORMAP]
                                     [--shape_list [STR, ...]]
                                     [--line_thickness INT]
                                     [--skeleton [[STR, STR], ...]|{STR: [STR, ...], ...}|[STR, ...]|NONE|BOOL]

Options

-h, --help            show this help message and exit
--config [FILE, ...]|FILE, -c [FILE, ...]|FILE
                      The path (or list of paths) to the sleap model(s) used
                      for inference, each as either as a folder or zip file.
--frame_stores [FILE, ...]|FILE, -fs [FILE, ...]|FILE
                      A path or list of paths to frame store ('.dlfs') files
                      to run DIPLOMAT on.
--batch_size INT, -bs INT
                      An integer, the number of frames to read in from the
                      frame store at a time.
--num_outputs INT, -no INT
                      An integer, the number of individuals in the video
                      defaults to 1.
--predictor STR, -p STR
                      A string, the name of the predictor to use to perform
                      the task of tracking.
--predictor_settings {STR: VAL, ...}, -ps {STR: VAL, ...}
                      A dictionary of strings to any values, the settings to
                      use for the predictor. Each predictor offers different
                      settings, see
--output_suffix STR, -os STR
                      A string, the suffix to append onto the output .slp
                      file. Defaults to an empty string.
--refinement_kernel_size INT, -rks INT
                      An integer, the kernel size to use for creating offset
                      maps if they don't exist (via integral refinement).
                      defaults to False, if set to 0 or a negative integer
                      disables integral refinement.
--pcutoff FLOAT       The probability to cutoff results below.
--dotsize INT         The size of the dots.
--alphavalue FLOAT    The alpha value of the dots.
--colormap TO_COLORMAP
                      The colormap to use for tracked points in the video.
                      Can be a matplotlib colormap or a list of matplotlib
                      colors.
--shape_list [STR, ...]
                      A list of shape names, shapes to use for drawing each
                      individual's dots.
--line_thickness INT  Thickness of lines drawn.
--skeleton [[STR, STR], ...]|{STR: [STR, ...], ...}|[STR, ...]|NONE|BOOL
                      The skeleton to use for this this run of DIPLOMAT.
                      Defaults to None, which uses the skeleton associated
                      with the sleap project. Can be a list of strings, a
                      list of tuples of strings, a dictionary of strings to
                      strings or lists of strings, or True/False (True
                      connects all parts, False connects no parts, disabling
                      the skeleton).