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Stefano Moia
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Merge pull request #17 from smoia/enh/skeleton
Add main workflow of phys2denoise Merging by agreement.
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‎phys2denoise/cli/run.py‎

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# -*- coding: utf-8 -*-
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"""Parser for phys2denoise."""
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import argparse
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from phys2denoise import __version__
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from phys2denoise.metrics.cardiac import crf
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from phys2denoise.metrics.chest_belt import rpv, rv, rvt, rrf, env
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def _get_parser():
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"""
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Parse command line inputs for this function.
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Returns
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-------
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parser.parse_args() : argparse dict
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Notes
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-----
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Default values must be updated in __call__ method from MetricsArgDict class.
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# Argument parser follow template provided by RalphyZ.
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# https://stackoverflow.com/a/43456577
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"""
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parser = argparse.ArgumentParser()
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optional = parser._action_groups.pop()
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required = parser.add_argument_group("Required Argument")
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metrics = parser.add_argument_group("Metrics")
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metric_arg = parser.add_argument_group("Metrics Arguments")
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# Required arguments
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required.add_argument("-in", "--input-file",
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dest="filename",
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type=str,
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help="Full path and name of the file containing "
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"physiological data, with or without extension.",
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required=True)
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# Important optional arguments
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optional.add_argument("-outdir", "--output-dir",
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dest="outdir",
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type=str,
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help="Folder where output should be placed. "
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"Default is current folder.",
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default=".")
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# Metric selection
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metrics.add_argument("-crf", "--cardiac-response-function",
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dest="metrics",
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action="append_const",
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const=crf,
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help="Cardiac response function. Requires the following "
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"inputs:sample-rate, oversampling, time-length, "
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"onset and tr.",
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default=[])
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metrics.add_argument("-rpv", "--respiratory-pattern-variability",
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dest="metrics",
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action="append_const",
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const=rpv,
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help="Respiratory pattern variability. Requires the following "
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"input: window.",
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default=[])
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metrics.add_argument("-env", "--envelope",
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dest="metrics",
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action="append_const",
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const=env,
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help="Respiratory pattern variability calculated across a sliding "
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"window. Requires the following inputs: sample-rate, window and lags.",
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default=[])
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metrics.add_argument("-rv", "--respiratory-variance",
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dest="metrics",
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action="append_const",
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const=rv,
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help="Respiratory variance. Requires the following inputs: "
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"sample-rate, window and lags. If the input file "
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"not a .phys file, it also requires peaks and troughs",
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default=[])
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"""
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metrics.add_argument("-rvt", "--respiratory-volume-per-time",
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dest="metrics",
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action="append_const",
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const="rvt",
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help="Respiratory volume-per-time. Requires the following inputs: "
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"sample-rate, window, lags, peaks and troughs.",
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default=[])
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"""
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metrics.add_argument("-rrf", "--respiratory-response-function",
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dest="metrics",
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action="append_const",
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const=rrf,
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help="Respiratory response function. Requires the following inputs: "
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"sample-rate, oversampling, time-length, onset and tr.",
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default=[])
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metrics.add_argument("-rcard", "--retroicor-card",
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dest="metrics",
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action="append_const",
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const="r_card",
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help="Computes regressors for cardiac signal. Requires the following "
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"inputs: tr, nscans and n_harm.",
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default=[])
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metrics.add_argument("-rresp", "--retroicor-resp",
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dest="metrics",
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action="append_const",
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const="r_resp",
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help="Computes regressors for respiratory signal. Requires the following "
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"inputs: tr, nscans and n_harm.",
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default=[])
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# Metric arguments
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metric_arg.add_argument("-sr", "--sample-rate",
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dest="sample_rate",
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type=float,
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help="Sampling rate of the physiological data in Hz.",
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default=None)
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metric_arg.add_argument("-pk", "--peaks",
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dest="peaks",
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type=str,
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help="Full path and filename of the list with the indexed peaks' "
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"positions of the physiological data.",
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default=None)
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metric_arg.add_argument("-tg", "--troughs",
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dest="troughs",
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type=str,
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help="Full path and filename of the list with the indexed troughs' "
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"positions of the physiological data.",
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default=None)
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metric_arg.add_argument("-os", "--oversampling",
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dest="oversampling",
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type=int,
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help="Temporal oversampling factor. "
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"Default is 50.",
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default=50)
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metric_arg.add_argument("-tl", "--time-length",
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dest="time_length",
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type=int,
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help="RRF or CRF Kernel length in seconds.",
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default=None)
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metric_arg.add_argument("-onset", "--onset",
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dest="onset",
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type=float,
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help="Onset of the response in seconds. "
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"Default is 0.",
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default=0)
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metric_arg.add_argument("-tr", "--tr",
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dest="tr",
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type=float,
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help="TR of sequence in seconds.",
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default=None)
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metric_arg.add_argument("-win", "--window",
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dest="window",
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type=int,
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help="Size of the sliding window in seconds. "
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"Default is 6 seconds.",
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default=6)
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metric_arg.add_argument("-lags", "--lags",
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dest="lags",
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nargs="*",
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type=int,
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help="List of lags to apply to the RV estimate "
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"in seconds.",
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default=None)
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metric_arg.add_argument("-nscans", "--number-scans",
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dest="nscans",
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type=int,
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help="Number of timepoints in the imaging data. "
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"Also called sub-bricks, TRs, scans, volumes."
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"Default is 1.",
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default=1)
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metric_arg.add_argument("-nharm", "--number-harmonics",
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dest="n_harm",
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type=int,
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help="Number of harmonics.",
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default=None)
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# Other optional arguments
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optional.add_argument("-debug", "--debug",
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dest="debug",
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action="store_true",
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help="Only print debugging info to log file. Default is False.",
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default=False)
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optional.add_argument("-quiet", "--quiet",
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dest="quiet",
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action="store_true",
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help="Only print warnings to log file. Default is False.",
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default=False)
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optional.add_argument("-v", "--version", action="version",
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version=("%(prog)s " + __version__))
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parser._action_groups.append(optional)
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return parser
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if __name__ == "__main__":
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raise RuntimeError("phys2denoise/cli/run.py should not be run directly;\n"
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"Please `pip install` phys2denoise and use the "
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"`phys2denoise` command")

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