Skip to content

Add Parser #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
ineschh wants to merge 7 commits into from
Closed

Add Parser #14

Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
5f685eb
add parser
ineschh Nov 12, 2020
2fa576f
Update phys2denoise/cli/run.py
ineschh Nov 12, 2020
6142d30
Update
ineschh Nov 12, 2020
ae489ad
Merge branch 'master' of https://github.com/ineschh/phys2denoise
ineschh Nov 12, 2020
4c265e3
More updates
ineschh Nov 13, 2020
8bd4b8f
Suggested changes
ineschh Nov 13, 2020
1541149
metric_args into dict
ineschh Nov 26, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
213 changes: 213 additions & 0 deletions phys2denoise/cli/run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,213 @@
# -*- 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


class MetricsArgDict(argparse.Action):
"""
Custom Argparse Action to create a dictionary with the metrics' arguments in parser's output.

"""
def __call__(self, parser, namespace, values, option_strings):
if not hasattr(namespace, "metrics_arg"):
setattr(namespace, "metrics_arg", dict())
Keys = ["sample_rate", "peaks", "throughs", "oversampling", "time_length", "onset",
"tr", "window", "lags", "nscans", "nharm"]
Vals = ["None", "None", "None", "50", "None", "0", "None", "6", "None", "1", "None"]
for k, v in zip(Keys, Vals):
getattr(namespace, "metrics_arg")[k] = v
getattr(namespace, "metrics_arg")[self.dest] = values


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")
metric = parser.add_argument_group("Metrics")
metric_arg = parser.add_argument_group("Metrics 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)
metric.add_argument("-crf", "--cardiac-response-function",
dest="metrics",
action="append_const",
const=crf,
help="Cardiac response function. Needs the following "
"inputs:sample-rate, oversampling, time-length, "
"onset and tr.",
default=[])
metric.add_argument("-rpv", "--respiratory-pattern-variability",
dest="metrics",
action="append_const",
const=rpv,
help="Respiratory pattern variability. Needs the following "
"input: window.",
default=[])
metric.add_argument("-env", "--envelope",
dest="metrics",
action="append_const",
const=env,
help="Respiratory pattern variability calculated across a sliding "
"window. Needs the following inputs: sample-rate, window and lags.",
default=[])
metric.add_argument("-rv", "--respiratory-variance",
dest="metrics",
action="append_const",
const=rv,
help="Respiratory variance. Needs the following inputs: "
"sample-rate, window and lags.",
default=[])
"""
metric.add_argument("-rvt", "--respiratory-volume-per-time",
dest="metrics",
action="append_const",
const="rvt",
help="Respiratory volume-per-time. Needs the following inputs: "
"sample-rate, window, lags, peaks and troughs.",
default=[])
"""
metric.add_argument("-rrf", "--respiratory-response-function",
dest="metrics",
action="append_const",
const=rrf,
help="Respiratory response function. Needs the following inputs: "
"sample-rate, oversampling, time-length, onset and tr.",
default=[])
metric.add_argument("-rcard", "--retroicor-card",
dest="metrics",
action="append_const",
const="r_card",
help="Computes regressors for cardiac signal. Needs the following "
"inputs: tr, nscans and n_harm.",
default=[])
metric.add_argument("-rresp", "--retroicor-resp",
dest="metrics",
action="append_const",
const="r_resp",
help="Computes regressors for respiratory signal. Needs the following "
"inputs: tr, nscans and n_harm.",
default=[])
optional.add_argument("-outdir", "--output-dir",
dest="outdir",
type=str,
help="Folder where output should be placed. "
"Default is current folder.",
default=".")
metric_arg.add_argument("-sr", "--sample-rate",
dest="sample_rate",
type=float,
action=MetricsArgDict,
help="Sampling rate of the physiological data in Hz.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-pk", "--peaks",
dest="peaks",
type=str,
action=MetricsArgDict,
help="Full path and filename of the list with the indexed peaks' "
"positions of the physiological data.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-tg", "--troughs",
dest="troughs",
type=str,
action=MetricsArgDict,
help="Full path and filename of the list with the indexed troughs' "
"positions of the physiological data.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-os", "--oversampling",
dest="oversampling",
type=int,
action=MetricsArgDict,
help="Temporal oversampling factor. "
"Default is 50.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-tl", "--time-length",
dest="time_length",
type=int,
action=MetricsArgDict,
help="RRF or CRF Kernel length in seconds.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-onset", "--onset",
dest="onset",
type=float,
action=MetricsArgDict,
help="Onset of the response in seconds. "
"Default is 0.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-tr", "--tr",
dest="tr",
type=float,
action=MetricsArgDict,
help="TR of sequence in seconds.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-win", "--window",
dest="window",
type=int,
action=MetricsArgDict,
help="Size of the sliding window in seconds. "
"Default is 6 seconds.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-lags", "--lags",
dest="lags",
nargs="*",
type=int,
action=MetricsArgDict,
help="List of lags to apply to the RV estimate "
"in seconds.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-nscans", "--number-scans",
dest="nscans",
type=int,
action=MetricsArgDict,
help="Number of scans. Default is 1.",
default=argparse.SUPPRESS)
metric_arg.add_argument("-nharm", "--number-harmonics",
dest="n_harm",
type=int,
action=MetricsArgDict,
help="Number of harmonics.",
default=argparse.SUPPRESS)
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")