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| Original file line number | Diff line number | Diff line change |
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| # 0.2.0 (Thu Feb 25 2021) | ||
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| #### 💥 Breaking Change during development | ||
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| - Add initial set of metrics [#19](https://github.com/physiopy/phys2denoise/pull/19) ([@CesarCaballeroGaudes](https://github.com/CesarCaballeroGaudes) [@tsalo](https://github.com/tsalo) [@smoia](https://github.com/smoia)) | ||
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| #### Authors: 3 | ||
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| - Cesar Caballero Gaudes ([@CesarCaballeroGaudes](https://github.com/CesarCaballeroGaudes)) | ||
| - Stefano Moia ([@smoia](https://github.com/smoia)) | ||
| - Taylor Salo ([@tsalo](https://github.com/tsalo)) | ||
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| --- | ||
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| # 0.1.0 (Thu Feb 25 2021) | ||
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| :tada: This release contains work from new contributors! :tada: | ||
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| Thanks for all your work! | ||
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| :heart: Stefano Moia ([@smoia](https://github.com/smoia)) | ||
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| :heart: Inés Chavarría ([@ineschh](https://github.com/ineschh)) | ||
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| #### 💥 Breaking Change during development | ||
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| - Add main workflow of phys2denoise [#17](https://github.com/physiopy/phys2denoise/pull/17) ([@smoia](https://github.com/smoia) [@ineschh](https://github.com/ineschh)) | ||
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| #### ⚠️ Pushed to `master` | ||
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| - update all-contributors ([@smoia](https://github.com/smoia)) | ||
| - Correct attributes ([@smoia](https://github.com/smoia)) | ||
| - Add duecredit to setup ([@smoia](https://github.com/smoia)) | ||
| - General configuration of the infrastructure ([@smoia](https://github.com/smoia)) | ||
| - Correct development status ([@smoia](https://github.com/smoia)) | ||
| - Add infra files ([@smoia](https://github.com/smoia)) | ||
| - Initial commit ([@smoia](https://github.com/smoia)) | ||
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| #### 🏠 Internal | ||
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| - Update PR template to match `phys2bids` [#20](https://github.com/physiopy/phys2denoise/pull/20) ([@smoia](https://github.com/smoia)) | ||
| - Add initial infrastructure [#12](https://github.com/physiopy/phys2denoise/pull/12) ([@smoia](https://github.com/smoia)) | ||
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| #### Authors: 2 | ||
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| - Inés Chavarría ([@ineschh](https://github.com/ineschh)) | ||
| - Stefano Moia ([@smoia](https://github.com/smoia)) |
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| Original file line number | Diff line number | Diff line change |
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| # -*- coding: utf-8 -*- | ||
| """Parser for phys2denoise.""" | ||
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| import argparse | ||
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| from phys2denoise import __version__ | ||
| from phys2denoise.metrics.cardiac import crf | ||
| from phys2denoise.metrics.chest_belt import rpv, rv, rvt, rrf, env | ||
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| 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 | ||
| """ | ||
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| 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) | ||
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| # 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__)) | ||
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| parser._action_groups.append(optional) | ||
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| return parser | ||
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| if __name__ == "__main__": | ||
| raise RuntimeError("phys2denoise/cli/run.py should not be run directly;\n" | ||
| "Please `pip install` phys2denoise and use the " | ||
| "`phys2denoise` command") |
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| # emacs: at the end of the file | ||
| # ex: set sts=4 ts=4 sw=4 et: | ||
| # ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### # | ||
| """Stub file for a guaranteed safe import of duecredit constructs if duecredit is not available. | ||
| To use it, place it into your project codebase to be imported, e.g. copy as | ||
| cp stub.py /path/tomodule/module/due.py | ||
| Note that it might be better to avoid naming it duecredit.py to avoid shadowing | ||
| installed duecredit. | ||
| Then use in your code as | ||
| from .due import due, Doi, BibTeX, Text | ||
| See https://github.com/duecredit/duecredit/blob/master/README.md for examples. | ||
| Origin: Originally a part of the duecredit | ||
| Copyright: 2015-2019 DueCredit developers | ||
| License: BSD-2 | ||
| """ | ||
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| __version__ = "0.0.8" | ||
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|
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| class InactiveDueCreditCollector(object): | ||
| """Just a stub at the Collector which would not do anything.""" | ||
|
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| def _donothing(self, *args, **kwargs): | ||
| """Perform no good and no bad.""" | ||
| pass | ||
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| def dcite(self, *args, **kwargs): | ||
| """If I could cite I would.""" | ||
|
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| def nondecorating_decorator(func): | ||
| return func | ||
|
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| return nondecorating_decorator | ||
|
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| active = False | ||
| activate = add = cite = dump = load = _donothing | ||
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| def __repr__(self): | ||
| """Perform magic.""" | ||
| return self.__class__.__name__ + "()" | ||
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| def _donothing_func(*args, **kwargs): | ||
| """Perform no good and no bad.""" | ||
| pass | ||
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| try: | ||
| from duecredit import BibTeX, Doi, Text, Url, due | ||
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| if "due" in locals() and not hasattr(due, "cite"): | ||
| raise RuntimeError("Imported due lacks .cite. DueCredit is now disabled") | ||
| except Exception as e: | ||
| if not isinstance(e, ImportError): | ||
| import logging | ||
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| logging.getLogger("duecredit").error( | ||
| "Failed to import duecredit due to %s" % str(e) | ||
| ) | ||
| # Initiate due stub | ||
| due = InactiveDueCreditCollector() | ||
| BibTeX = Doi = Url = Text = _donothing_func | ||
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| # Emacs mode definitions | ||
| # Local Variables: | ||
| # mode: python | ||
| # py-indent-offset: 4 | ||
| # tab-width: 4 | ||
| # indent-tabs-mode: nil | ||
| # End: |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| """Metrics derived from physiological signals.""" | ||
| from .cardiac import crf, cardiac_phase | ||
| from .chest_belt import rpv, env, rv, rrf, respiratory_phase | ||
| from .multimodal import retroicor | ||
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| __all__ = [ | ||
| "crf", | ||
| "cardiac_phase", | ||
| "rpv", | ||
| "env", | ||
| "rv", | ||
| "rrf", | ||
| "respiratory_phase", | ||
| "retroicor", | ||
| ] |
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