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

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]

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.

optional arguments:
  -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).