Add main workflow of phys2denoise

phys2denoise/cli/run.py

@@ -0,0 +1,195 @@
+# -*- coding: utf-8 -*-
+"""Parser for phys2denoise."""
+
+
+import argparse
+
+from phys2denoise import __version__
+from phys2denoise.metrics.cardiac import crf
+from phys2denoise.metrics.chest_belt import rpv, rv, rvt, rrf, env
+
+
+def _get_parser():
+    """
+    Parse command line inputs for this function.
+
+    Returns
+    -------
+    parser.parse_args() : argparse dict
+
+    Notes
+    -----
+    Default values must be updated in __call__ method from MetricsArgDict class.
+    # Argument parser follow template provided by RalphyZ.
+    # https://stackoverflow.com/a/43456577
+    """
+
+    parser = argparse.ArgumentParser()
+    optional = parser._action_groups.pop()
+    required = parser.add_argument_group("Required Argument")
+    metrics = parser.add_argument_group("Metrics")
+    metric_arg = parser.add_argument_group("Metrics Arguments")
+    # Required arguments
+    required.add_argument("-in", "--input-file",
+                          dest="filename",
+                          type=str,
+                          help="Full path and name of the file containing "
+                               "physiological data, with or without extension.",
+                          required=True)
+    # Important optional arguments
+    optional.add_argument("-outdir", "--output-dir",
+                          dest="outdir",
+                          type=str,
+                          help="Folder where output should be placed. "
+                               "Default is current folder.",
+                          default=".")
+    # Metric selection
+    metrics.add_argument("-crf", "--cardiac-response-function",
+                         dest="metrics",
+                         action="append_const",
+                         const=crf,
+                         help="Cardiac response function. Requires the following "
+                              "inputs:sample-rate, oversampling, time-length, "
+                              "onset and tr.",
+                         default=[])
+    metrics.add_argument("-rpv", "--respiratory-pattern-variability",
+                         dest="metrics",
+                         action="append_const",
+                         const=rpv,
+                         help="Respiratory pattern variability. Requires the following "
+                              "input: window.",
+                         default=[])
+    metrics.add_argument("-env", "--envelope",
+                         dest="metrics",
+                         action="append_const",
+                         const=env,
+                         help="Respiratory pattern variability calculated across a sliding "
+                              "window. Requires the following inputs: sample-rate, window and lags.",
+                         default=[])
+    metrics.add_argument("-rv", "--respiratory-variance",
+                         dest="metrics",
+                         action="append_const",
+                         const=rv,
+                         help="Respiratory variance. Requires the following inputs: "
+                              "sample-rate, window and lags. If the input file "
+                              "not a .phys file, it also requires peaks and troughs",
+                         default=[])
+    """
+    metrics.add_argument("-rvt", "--respiratory-volume-per-time",
+                         dest="metrics",
+                         action="append_const",
+                         const="rvt",
+                         help="Respiratory volume-per-time. Requires the following inputs: "
+                              "sample-rate, window, lags, peaks and troughs.",
+                         default=[])
+     """
+    metrics.add_argument("-rrf", "--respiratory-response-function",
+                         dest="metrics",
+                         action="append_const",
+                         const=rrf,
+                         help="Respiratory response function. Requires the following inputs: "
+                              "sample-rate, oversampling, time-length, onset and tr.",
+                         default=[])
+    metrics.add_argument("-rcard", "--retroicor-card",
+                         dest="metrics",
+                         action="append_const",
+                         const="r_card",
+                         help="Computes regressors for cardiac signal. Requires the following "
+                              "inputs: tr, nscans and n_harm.",
+                         default=[])
+    metrics.add_argument("-rresp", "--retroicor-resp",
+                         dest="metrics",
+                         action="append_const",
+                         const="r_resp",
+                         help="Computes regressors for respiratory signal. Requires the following  "
+                              "inputs: tr, nscans and n_harm.",
+                         default=[])
+    # Metric arguments
+    metric_arg.add_argument("-sr", "--sample-rate",
+                            dest="sample_rate",
+                            type=float,
+                            help="Sampling rate of the physiological data in Hz.",
+                            default=None)
+    metric_arg.add_argument("-pk", "--peaks",
+                            dest="peaks",
+                            type=str,
+                            help="Full path and filename of the list with the indexed peaks' "
+                                 "positions of the physiological data.",
+                            default=None)
+    metric_arg.add_argument("-tg", "--troughs",
+                            dest="troughs",
+                            type=str,
+                            help="Full path and filename of the list with the indexed troughs' "
+                                 "positions of the physiological data.",
+                            default=None)
+    metric_arg.add_argument("-os", "--oversampling",
+                            dest="oversampling",
+                            type=int,
+                            help="Temporal oversampling factor. "
+                                 "Default is 50.",
+                            default=50)
+    metric_arg.add_argument("-tl", "--time-length",
+                            dest="time_length",
+                            type=int,
+                            help="RRF or CRF Kernel length in seconds.",
+                            default=None)
+    metric_arg.add_argument("-onset", "--onset",
+                            dest="onset",
+                            type=float,
+                            help="Onset of the response in seconds. "
+                                 "Default is 0.",
+                            default=0)
+    metric_arg.add_argument("-tr", "--tr",
+                            dest="tr",
+                            type=float,
+                            help="TR of sequence in seconds.",
+                            default=None)
+    metric_arg.add_argument("-win", "--window",
+                            dest="window",
+                            type=int,
+                            help="Size of the sliding window in seconds. "
+                                 "Default is 6 seconds.",
+                            default=6)
+    metric_arg.add_argument("-lags", "--lags",
+                            dest="lags",
+                            nargs="*",
+                            type=int,
+                            help="List of lags to apply to the RV estimate "
+                                 "in seconds.",
+                            default=None)
+    metric_arg.add_argument("-nscans", "--number-scans",
+                            dest="nscans",
+                            type=int,
+                            help="Number of timepoints in the imaging data. "
+                                 "Also called sub-bricks, TRs, scans, volumes."
+                                 "Default is 1.",
+                            default=1)
+    metric_arg.add_argument("-nharm", "--number-harmonics",
+                            dest="n_harm",
+                            type=int,
+                            help="Number of harmonics.",
+                            default=None)
+
+    # Other optional arguments
+    optional.add_argument("-debug", "--debug",
+                          dest="debug",
+                          action="store_true",
+                          help="Only print debugging info to log file. Default is False.",
+                          default=False)
+    optional.add_argument("-quiet", "--quiet",
+                          dest="quiet",
+                          action="store_true",
+                          help="Only print warnings to log file. Default is False.",
+                          default=False)
+    optional.add_argument("-v", "--version", action="version",
+                          version=("%(prog)s " + __version__))
+
+    parser._action_groups.append(optional)
+
+    return parser
+
+
+if __name__ == "__main__":
+    raise RuntimeError("phys2denoise/cli/run.py should not be run directly;\n"
+                       "Please `pip install` phys2denoise and use the "
+                       "`phys2denoise` command")