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Remove QSIPrep-specific parameters.
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@tsalo
tsalo committed Aug 9, 2024
1 parent d071473 commit 890ed8e
Showing 1 changed file with 1 addition and 322 deletions.
323 changes: 1 addition & 322 deletions qsirecon/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,52 +34,12 @@ def _build_parser(**kwargs):
``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging).
"""
from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
from functools import partial
from pathlib import Path

from packaging.version import Version

deprecations = {
# parser attribute name: (replacement flag, version slated to be removed in)
"dwi_only": ("--anat-modality none", "0.23.0"),
"prefer_dedicated_fmaps": (None, "0.23.0"),
"do_reconall": (None, "0.23.0"),
"dwi_no_biascorr": ("--b1-biascorrect-stage none", "0.23.0"),
"recon_only": (None, "0.23.0"),
"b0_motion_corr_to": (None, "0.23.0"),
"b0_to_t1w_transform": ("--b0-t0-anat-transform", "0.23.0"),
}

class DeprecatedAction(Action):
def __call__(self, parser, namespace, values, option_string=None):
new_opt, rem_vers = deprecations.get(self.dest, (None, None))
msg = (
f"{self.option_strings} has been deprecated and will be removed in "
f"{rem_vers or 'a later version'}."
)
if new_opt:
msg += f" Please use `{new_opt}` instead."
print(msg, file=sys.stderr)
delattr(namespace, self.dest)

class ToDict(Action):
def __call__(self, parser, namespace, values, option_string=None):
d = {}
for spec in values:
try:
name, loc = spec.split("=")
loc = Path(loc)
except ValueError:
loc = Path(spec)
name = loc.name

if name in d:
raise ValueError(f"Received duplicate derivative name: {name}")

d[name] = loc
setattr(namespace, self.dest, d)

def _path_exists(path, parser):
"""Ensure a given path exists."""
if path is None or not Path(path).exists():
Expand Down Expand Up @@ -177,13 +137,6 @@ def _bids_filter(value, parser):
)

g_bids = parser.add_argument_group("Options for filtering BIDS queries")
g_bids.add_argument(
"--skip_bids_validation",
"--skip-bids-validation",
action="store_true",
default=False,
help="Assume the input dataset is BIDS compliant and skip the validation",
)
g_bids.add_argument(
"--participant-label",
"--participant_label",
Expand Down Expand Up @@ -268,7 +221,6 @@ def _bids_filter(value, parser):
)

g_subset = parser.add_argument_group("Options for performing only a subset of the workflow")
g_subset.add_argument("--anat-only", action="store_true", help="Run anatomical workflows only")
g_subset.add_argument(
"--dwi-only",
action="store_true",
Expand Down Expand Up @@ -297,16 +249,6 @@ def _bids_filter(value, parser):
)

g_conf = parser.add_argument_group("Workflow configuration")
g_conf.add_argument(
"--ignore",
required=False,
action="store",
nargs="+",
default=[],
choices=["fieldmaps", "sbref", "t2w", "flair", "fmap-jacobian"],
help="Ignore selected aspects of the input dataset to disable corresponding "
"parts of the workflow (a space delimited list)",
)
g_conf.add_argument(
"--infant", action="store_true", help="configure pipelines to process infant brains"
)
Expand All @@ -315,157 +257,6 @@ def _bids_filter(value, parser):
action="store_true",
help="Treat dataset as longitudinal - may increase runtime",
)
g_conf.add_argument(
"--skip-anat-based-spatial-normalization",
action="store_true",
default=False,
help="skip running the anat-based normalization to template space. "
"Default is to run the normalization.",
)
g_conf.add_argument(
"--anat-modality",
"--anat_modality",
choices=["T1w", "T2w", "none"],
default="T1w",
help="Modality to use as the anatomical reference. Images of this "
"contrast will be skull stripped and segmented for use in the "
"visual reports and reconstruction. If --infant, T2w is forced.",
)
g_conf.add_argument(
"--b0-threshold",
"--b0_threshold",
action="store",
type=int,
default=100,
help="any value in the .bval file less than this will be considered "
"a b=0 image. Current default threshold = 100; this threshold can be "
"lowered or increased. Note, setting this too high can result in inaccurate results.",
)
g_conf.add_argument(
"--dwi_denoise_window",
"--dwi-denoise-window",
action="store",
default="auto",
help='window size in voxels for image-based denoising, integer or "auto".'
'If "auto", 5 will be used for dwidenoise and auto-configured for '
"patch2self based on the number of b>0 images.",
)
g_conf.add_argument(
"--denoise-method",
"--denoise_method",
action="store",
choices=["dwidenoise", "patch2self", "none"],
default="dwidenoise",
help='Image-based denoising method. Either "dwidenoise" (MRtrix), '
'"patch2self" (DIPY) or none. (default: dwidenoise)',
)
g_conf.add_argument(
"--unringing-method",
"--unringing_method",
action="store",
choices=["none", "mrdegibbs", "rpg"],
help="Method for Gibbs-ringing removal.\n - none: no action\n - mrdegibbs: "
"use mrdegibbs from mrtrix3\n - rpg: Gibbs from TORTOISE, suggested for partial"
" Fourier acquisitions (default: none).",
)
g_conf.add_argument(
"--dwi-no-biascorr",
"--dwi_no_biascorr",
action="store_true",
help="DEPRECATED: see --b1-biascorrect-stage",
)
g_conf.add_argument(
"--b1-biascorrect-stage",
"--b1_biascorrect_stage",
action="store",
choices=["final", "none", "legacy"],
default="final",
help="Which stage to apply B1 bias correction. The default 'final' will "
"apply it after all the data has been resampled to its final space. "
"'none' will skip B1 bias correction and 'legacy' will behave consistent "
"with qsirecon < 0.17.",
)
g_conf.add_argument(
"--no-b0-harmonization",
"--no_b0_harmonization",
action="store_true",
help="skip re-scaling dwi scans to have matching b=0 intensities",
)
g_conf.add_argument(
"--denoise-after-combining",
"--denoise_after_combining",
action="store_true",
help="run ``dwidenoise`` after combining dwis, but before motion correction",
)
g_conf.add_argument(
"--separate_all_dwis",
"--separate-all-dwis",
action="store_true",
help="don't attempt to combine dwis from multiple runs. Each will be "
"processed separately.",
)
g_conf.add_argument(
"--distortion-group-merge",
"--distortion_group_merge",
action="store",
choices=["concat", "average", "none"],
default="none",
help="How to combine images across distorted groups.\n"
" - concatenate: append images in the 4th dimension\n "
" - average: if a whole sequence was duplicated in both PE\n"
" directions, average the corrected images of the same\n"
" q-space coordinate\n"
" - none: Default. Keep distorted groups separate",
)
g_conf.add_argument(
"--anatomical-template",
required=False,
action="store",
choices=["MNI152NLin2009cAsym"],
default="MNI152NLin2009cAsym",
help="volume template space (default: MNI152NLin2009cAsym)",
)
g_conf.add_argument(
"--output-resolution",
"--output_resolution",
action="store",
# required when not recon-only (which can be specified in sysargs 2 ways)
required=not any(rcn in sys.argv for rcn in ["--recon-only", "--recon_only"]),
type=float,
help="the isotropic voxel size in mm the data will be resampled to "
"after preprocessing. If set to a lower value than the original voxel "
"size, your data will be upsampled using BSpline interpolation.",
)

g_coreg = parser.add_argument_group("Options for dwi-to-Anatomical coregistration")
g_coreg.add_argument(
"--b0-to-t1w-transform",
"--b0_to_t1w_transform",
action="store",
default="Rigid",
choices=["Rigid", "Affine"],
help="Degrees of freedom when registering b0 to anatomical images. "
"6 degrees (rotation and translation) are used by default.",
)
g_coreg.add_argument(
"--intramodal-template-iters",
"--intramodal_template_iters",
action="store",
default=0,
type=int,
help="Number of iterations for finding the midpoint image "
"from the b0 templates from all groups. Has no effect if there "
"is only one group. If 0, all b0 templates are directly registered "
"to the t1w image.",
)
g_coreg.add_argument(
"--intramodal-template-transform",
"--intramodal_template_transform",
default="BSplineSyN",
choices=["Rigid", "Affine", "BSplineSyN", "SyN"],
action="store",
help="Transformation used for building the intramodal template.",
)

# FreeSurfer options
g_fs = parser.add_argument_group("Specific options for FreeSurfer preprocessing")
Expand All @@ -478,120 +269,15 @@ def _bids_filter(value, parser):
"at https://surfer.nmr.mgh.harvard.edu/registration.html",
)

g_moco = parser.add_argument_group("Specific options for motion correction and coregistration")
g_moco.add_argument(
"--b0-motion-corr-to",
"--bo_motion_corr_to",
action="store",
default="iterative",
choices=["iterative", "first"],
help='align to the "first" b0 volume or do an "iterative" registration'
" of all b0 images to their midpoint image (default: iterative)",
)
g_moco.add_argument(
"--hmc-transform",
"--hmc_transform",
action="store",
default="Affine",
choices=["Affine", "Rigid"],
help="transformation to be optimized during head motion correction " "(default: affine)",
)
g_moco.add_argument(
"--hmc_model",
"--hmc-model",
action="store",
default="eddy",
choices=["none", "3dSHORE", "eddy", "tensor"],
help='model used to generate target images for hmc. If "none" the '
"non-b0 images will be warped using the same transform as their "
'nearest b0 image. If "3dSHORE", SHORELine will be used. if "tensor", '
"SHORELine iterations with a tensor model will be used",
)
g_moco.add_argument(
"--eddy-config",
"--eddy_config",
action="store",
help="path to a json file with settings for the call to eddy. If no "
"json is specified, a default one will be used. The current default "
"json can be found here: "
"https://github.com/PennLINC/qsirecon/blob/main/qsirecon/data/eddy_params.json",
)
g_moco.add_argument(
"--shoreline_iters",
"--shoreline-iters",
action="store",
type=int,
default=2,
help="number of SHORELine iterations. (default: 2)",
)

# Fieldmap options
g_fmap = parser.add_argument_group("Specific options for handling fieldmaps")
g_fmap.add_argument(
"--pepolar-method",
"--pepolar_method",
action="store",
default="TOPUP",
choices=["TOPUP", "DRBUDDI", "TOPUP+DRBUDDI"],
help="select which SDC method to use for PEPOLAR fieldmaps (default: TOPUP)",
)
g_fmap.add_argument(
"--fmap-bspline",
action="store_true",
default=False,
help="Fit a B-Spline field using least-squares (experimental)",
)
g_fmap.add_argument(
"--fmap-no-demean",
action="store_false",
default=True,
help="Do not remove median (within mask) from fieldmap",
)

# SyN-unwarp options
g_syn = parser.add_argument_group("Specific options for SyN distortion correction")
g_syn.add_argument(
"--use-syn-sdc",
nargs="?",
choices=["warn", "error"],
action="store",
const="error",
default=False,
help="Use fieldmap-less distortion correction based on anatomical image; "
"if unable, error (default) or warn based on optional argument.",
)
g_syn.add_argument(
"--force-syn",
action="store_true",
default=False,
help="EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to "
"fieldmap correction, if available",
)

# arguments for reconstructing QSI data
g_recon = parser.add_argument_group("Options for reconstructing qsirecon outputs")
g_recon.add_argument(
"--recon-only",
"--recon_only",
action="store_true",
default=False,
help="run only reconstruction, assumes preprocessing has already completed.",
)
g_recon.add_argument(
"--recon-spec",
"--recon_spec",
action="store",
type=str,
help="json file specifying a reconstruction pipeline to be run after preprocessing",
)
g_recon.add_argument(
"--recon-input",
"--recon_input",
action="store",
metavar="PATH",
type=Path,
help="use this directory as inputs to qsirecon. This option skips qsirecon.",
)
g_recon.add_argument(
"--recon-input-pipeline",
"--recon_input_pipeline",
Expand All @@ -612,13 +298,6 @@ def _bids_filter(value, parser):
type=Path,
help="Directory containing freesurfer outputs to be integrated into recon.",
)
g_recon.add_argument(
"--skip-odf-reports",
"--skip_odf_reports",
action="store_true",
default=False,
help="run only reconstruction, assumes preprocessing has already completed.",
)

g_other = parser.add_argument_group("Other options")
g_other.add_argument("--version", action="version", version=verstr)
Expand Down

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