Command Line API

This page describes usage of the heteromotility command line interface (CLI).

The heteromotility command is installed by default when heteromotility was installed using pip or setup.py.

The help information can be rendered in your terminal by executing

heteromotility -h

usage: heteromotility [-h] [--output_suffix OUTPUT_SUFFIX]
                      [--exttrack EXTTRACK] [--tracksX TRACKSX]
                      [--tracksY TRACKSY] [--move_thresh MOVE_THRESH]
                      [--detailedbalance DETAILEDBALANCE] [--dbmax DBMAX]
                      [--sliding_window SLIDING_WINDOW]
                      [--max_windows MAX_WINDOWS] [--sanity SANITY]
                      [--interp_lim INTERP_LIM]
                      output_dir

Positional Arguments

output_dir

directory for CSV export Default: [‘./’]

Named Arguments

--output_suffix
	Optional suffix to place on output csv name Default: [False]
--exttrack	specifies external tracking algo, provide location of cell_ids.pickle Default: [False]
--tracksX	path to input CSV containing N x T matrix of X locations Default: [False]
--tracksY	path to input CSV containing N x T matrix of Y locations Default: [False]
--move_thresh	highest speed to check as a threshold for movement [px/frame]. Default = 10 Default: 10
--detailedbalance
	Split cell paths for detailed balance calculation, with a provided minimum path size Default: -1
--dbmax	Maximum tau for detailed balance splitting
--sliding_window
	Specify a stride length for subpath feature extraction using a sliding window of length supplied in detailedbalance Default: -1
--max_windows	Maximum number of sliding windows to extract. Defaults to extracting all possible windows. Default: -1
--sanity	integer [px] determining the maximum sane movement of an object. Default = 10000 px Default: 10000
--interp_lim	Number of frames allowed for interpolation if an object is not detected temporarily. Default = 3 Default: 3