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Merged
merged 4 commits into from
Apr 1, 2025
Merged

Add a CLI for creating raw bids mri data #9

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f060063
passing tests
mattcieslak Apr 1, 2025
db375c6
ruff
mattcieslak Apr 1, 2025
c819468
add cli
mattcieslak Apr 1, 2025
37451cb
add yamls
mattcieslak Apr 1, 2025
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8 changes: 7 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ dependencies = [
"pandas",
"pybids >= 0.15.6",
"typer",
"yaml",
"pyyaml",
]
dynamic = ["version"]

Expand Down Expand Up @@ -63,6 +63,7 @@ Source = "https://github.com/nipreps/simbids"

[project.scripts]
simbids = "simbids.cli.run:main"
simbids-raw-mri = "simbids.cli.raw_mri:main"

[tool.hatch.metadata]
allow-direct-references = true
Expand All @@ -83,6 +84,11 @@ exclude = [
"tests/data", # Large test data directory
]

[tool.hatch.build]
artifacts = [
"src/simbids/data/bids_mri/*.yaml",
]

[tool.hatch.envs.default]
dependencies = [
"pytest",
Expand Down
2 changes: 2 additions & 0 deletions src/simbids/cli/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,15 @@

from . import (
parser,
raw_mri,
run,
version,
workflow,
)

__all__ = [
'parser',
'raw_mri',
'run',
'version',
'workflow',
Expand Down
244 changes: 5 additions & 239 deletions src/simbids/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,6 @@
#
"""Parser."""

import sys

from simbids import config


Expand All @@ -39,8 +37,6 @@ def _build_parser(**kwargs):

from packaging.version import Version

from simbids.cli.version import check_latest, is_flagged

# from niworkflows.utils.spaces import OutputReferencesAction

class ToDict(Action):
Expand Down Expand Up @@ -114,14 +110,12 @@ def _bids_filter(value, parser):
is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))

parser = ArgumentParser(
description=(
f'SimBIDS: fMRI POSTprocessing template workflow v{config.environment.version}'
),
description=(f'SimBIDS: Simulated BIDS data and workflows v{config.environment.version}'),
formatter_class=ArgumentDefaultsHelpFormatter,
**kwargs,
)
PathExists = partial(_path_exists, parser=parser)
IsFile = partial(_is_file, parser=parser)
# IsFile = partial(_is_file, parser=parser)
PositiveInt = partial(_min_one, parser=parser)
BIDSFilter = partial(_bids_filter, parser=parser)

Expand Down Expand Up @@ -171,12 +165,6 @@ def _bids_filter(value, parser):
'identifier (the sub- prefix can be removed)'
),
)
g_bids.add_argument(
'-t',
'--task-id',
action='store',
help='Select a specific task to be processed',
)
g_bids.add_argument(
'--bids-filter-file',
dest='bids_filters',
Expand All @@ -203,16 +191,6 @@ def _bids_filter(value, parser):
'(e.g., `--derivatives smriprep=/path/to/smriprep`).'
),
)
g_bids.add_argument(
'--bids-database-dir',
metavar='PATH',
type=Path,
help=(
'Path to a PyBIDS database folder, for faster indexing '
'(especially useful for large datasets). '
'Will be created if not present.'
),
)

g_perfm = parser.add_argument_group('Options to handle performance')
g_perfm.add_argument(
Expand Down Expand Up @@ -241,122 +219,12 @@ def _bids_filter(value, parser):
metavar='MEMORY_MB',
help='Upper bound memory limit for SimBIDS processes',
)
g_perfm.add_argument(
'--low-mem',
action='store_true',
help='Attempt to reduce memory usage (will increase disk usage in working directory)',
)
g_perfm.add_argument(
'--use-plugin',
'--nipype-plugin-file',
action='store',
metavar='FILE',
type=IsFile,
help='Nipype plugin configuration file',
)
g_perfm.add_argument(
'--sloppy',
action='store_true',
default=False,
help='Use low-quality tools for speed - TESTING ONLY',
)

g_subset = parser.add_argument_group('Options for performing only a subset of the workflow')
g_subset.add_argument(
'--boilerplate-only',
'--boilerplate_only',
action='store_true',
default=False,
help='Generate boilerplate only',
)
g_subset.add_argument(
'--reports-only',
action='store_true',
default=False,
help=(
"Only generate reports, don't run workflows. "
'This will only rerun report aggregation, not reportlet generation for specific '
'nodes.'
),
)

g_conf = parser.add_argument_group('Workflow configuration')
g_conf.add_argument(
'--ignore',
required=False,
action='store',
nargs='+',
default=['fieldmaps'],
choices=['fieldmaps', 'slicetiming', 'fmap-jacobian'],
help=(
'Ignore selected aspects of the input dataset to disable corresponding '
'parts of the resampling workflow (a space delimited list)'
),
)
# Disable output spaces until warping works
# g_conf.add_argument(
# '--output-spaces',
# nargs='*',
# action=OutputReferencesAction,
# help="""\
# Standard and non-standard spaces to resample denoised functional images to. \
# Standard spaces may be specified by the form \
# ``<SPACE>[:cohort-<label>][:res-<resolution>][...]``, where ``<SPACE>`` is \
# a keyword designating a spatial reference, and may be followed by optional, \
# colon-separated parameters. \
# Non-standard spaces imply specific orientations and sampling grids. \
# For further details, please check out \
# https://fmriprep.readthedocs.io/en/%s/spaces.html"""
# % (currentv.base_version if is_release else 'latest'),
# )
g_conf.add_argument(
'--dummy-scans',
required=False,
action='store',
default=None,
type=int,
help='Number of nonsteady-state volumes. Overrides automatic detection.',
)
g_conf.add_argument(
'--random-seed',
dest='_random_seed',
action='store',
type=int,
default=None,
help='Initialize the random seed for the workflow',
)

g_outputs = parser.add_argument_group('Options for modulating outputs')
g_outputs.add_argument(
'--md-only-boilerplate',
action='store_true',
default=False,
help='Skip generation of HTML and LaTeX formatted citation with pandoc',
)
g_outputs.add_argument(
'--aggregate-session-reports',
dest='aggr_ses_reports',
action='store',
type=PositiveInt,
default=4,
help=(
"Maximum number of sessions aggregated in one subject's visual report. "
'If exceeded, visual reports are split by session.'
),
)

g_carbon = parser.add_argument_group('Options for carbon usage tracking')
g_carbon.add_argument(
'--track-carbon',
action='store_true',
help='Tracks power draws using CodeCarbon package',
)
g_carbon.add_argument(
'--country-code',
action='store',
default='CAN',
type=str,
help='Country ISO code used by carbon trackers',
'--processing-level',
choices=['participant', 'session'],
help='Processing level to be run, only "participant" or "session" in the case of SimBIDS',
)

g_other = parser.add_argument_group('Other options')
Expand All @@ -369,55 +237,19 @@ def _bids_filter(value, parser):
default=0,
help='Increases log verbosity for each occurrence, debug level is -vvv',
)
g_other.add_argument(
'-w',
'--work-dir',
action='store',
type=Path,
default=Path('work').absolute(),
help='Path where intermediate results should be stored',
)
g_other.add_argument(
'--clean-workdir',
action='store_true',
default=False,
help='Clears working directory of contents. Use of this flag is not '
'recommended when running concurrent processes of SimBIDS.',
)
g_other.add_argument(
'--resource-monitor',
action='store_true',
default=False,
help="Enable Nipype's resource monitoring to keep track of memory and CPU usage",
)
g_other.add_argument(
'--config-file',
action='store',
metavar='FILE',
help='Use pre-generated configuration file. Values in file will be overridden '
'by command-line arguments.',
)
g_other.add_argument(
'--write-graph',
action='store_true',
default=False,
help='Write workflow graph.',
)
g_other.add_argument(
'--stop-on-first-crash',
action='store_true',
default=False,
help='Force stopping on first crash, even if a work directory was specified.',
)
g_other.add_argument(
'--notrack',
action='store_true',
default=False,
help='Opt out of sending tracking information of this run to '
'the NiPreps developers. This information helps to '
'improve NiPreps and provides an indicator of real '
'world usage crucial for obtaining funding.',
)
g_other.add_argument(
'--debug',
action='store',
Expand All @@ -426,29 +258,6 @@ def _bids_filter(value, parser):
help="Debug mode(s) to enable. 'all' is alias for all available modes.",
)

latest = check_latest()
if latest is not None and currentv < latest:
print(
f"""\
You are using SimBIDS-{currentv},
and a newer version of SimBIDS is available: {latest}.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""",
file=sys.stderr,
)

_blist = is_flagged()
if _blist[0]:
_reason = _blist[1] or 'unknown'
print(
f"""\
WARNING: Version {config.environment.version} of SimBIDS (current) has been FLAGGED
(reason: {_reason}).
That means some severe flaw was found in it and we strongly
discourage its usage.""",
file=sys.stderr,
)

return parser


Expand All @@ -468,58 +277,15 @@ def parse_args(args=None, namespace=None):
config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
config.from_dict(vars(opts), init=['nipype'])

if not config.execution.notrack:
import importlib.util

if importlib.util.find_spec('sentry_sdk') is None:
config.execution.notrack = True
config.loggers.cli.warning('Telemetry disabled because sentry_sdk is not installed.')
else:
config.loggers.cli.info(
'Telemetry system to collect crashes and errors is enabled '
'- thanks for your feedback!. Use option ``--notrack`` to opt out.'
)

# Retrieve logging level
build_log = config.loggers.cli

# Load base plugin_settings from file if --use-plugin
if opts.use_plugin is not None:
import yaml

with open(opts.use_plugin) as f:
plugin_settings = yaml.safe_load(f)
_plugin = plugin_settings.get('plugin')
if _plugin:
config.nipype.plugin = _plugin
config.nipype.plugin_args = plugin_settings.get('plugin_args', {})
config.nipype.nprocs = opts.nprocs or config.nipype.plugin_args.get(
'n_procs', config.nipype.nprocs
)

# Resource management options
# Note that we're making strong assumptions about valid plugin args
# This may need to be revisited if people try to use batch plugins
if 1 < config.nipype.nprocs < config.nipype.omp_nthreads:
build_log.warning(
f'Per-process threads (--omp-nthreads={config.nipype.omp_nthreads}) exceed '
f'total threads (--nthreads/--n_cpus={config.nipype.nprocs})'
)

bids_dir = config.execution.bids_dir
output_dir = config.execution.output_dir
derivatives = config.execution.derivatives
work_dir = config.execution.work_dir
version = config.environment.version

# Wipe out existing work_dir
if opts.clean_workdir and work_dir.exists():
from niworkflows.utils.misc import clean_directory

build_log.info(f'Clearing previous SimBIDS working directory: {work_dir}')
if not clean_directory(work_dir):
build_log.warning(f'Could not clear all contents of working directory: {work_dir}')

# Update the config with an empty dict to trigger initialization of all config
# sections (we used `init=False` above).
# This must be done after cleaning the work directory, or we could delete an
Expand Down
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