Add a workflow that mocks up qsiprep outputs (#10)

Author: mattcieslak

pyproject.toml

@@ -21,9 +21,11 @@ dependencies = [
   "acres",
   "datalad",
   "nipype",
+  "nireports",
   "pandas",
   "pybids >= 0.15.6",
   "typer",
+  "toml",
   "pyyaml",
 ]
 dynamic = ["version"]
@@ -187,6 +189,7 @@ ignore = [
   "S113",
   "S202",
   "S602",
+  "T100",
 ]
 
 [tool.ruff.lint.flake8-quotes]

src/simbids/cli/parser.py

@@ -146,6 +146,12 @@ def _bids_filter(value, parser):
         ),
     )
 
+    parser.add_argument(
+        'bids_app',
+        choices=['qsiprep', 'qsirecon', 'xcp_d', 'fmriprep'],
+        help=('BIDS-App to be simulated'),
+    )
+
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument(
         '--skip_bids_validation',
@@ -336,3 +342,4 @@ def parse_args(args=None, namespace=None):
         )
 
     config.execution.participant_label = sorted(participant_label)
+    return opts

src/simbids/cli/raw_mri.py

@@ -31,7 +31,7 @@
 LGR = logging.getLogger(__name__)
 
 # Get all the yaml files using importlib
-with resources.path('simbids.data.bids-mri', '') as bids_mri_path:
+with resources.path('simbids.data.bids_mri', '') as bids_mri_path:
     yaml_files = [f.name for f in bids_mri_path.glob('*.yaml')]
 
 
@@ -83,12 +83,12 @@ def main():
         config_path = Path(args.config_file)
         if not config_path.exists():
             raise FileNotFoundError(f'Config file {args.config_file} not found')
+        # For custom config files, pass the string path
+        simulate_dataset(args.bids_dir, str(config_path), args.fill_files, args.datalad_init)
     else:
         LGR.info(f'Using bundled config file: {args.config_file}')
-        config_path = resources.path('simbids.data.bids-mri', args.config_file)
-
-    # Create the raw MRI BIDS dataset
-    simulate_dataset(args.bids_dir, config_path, args.fill_files, args.datalad_init)
+        # For bundled config files, pass the filename directly
+        simulate_dataset(args.bids_dir, args.config_file, args.fill_files, args.datalad_init)
 
 
 if __name__ == '__main__':

src/simbids/cli/run.py

@@ -30,13 +30,12 @@
 def main():
     """Entry point."""
     import gc
-    from multiprocessing import Manager, Process
 
+    from simbids.cli.parser import parse_args
     from simbids.cli.workflow import build_workflow
 
-    # Code Carbon
-    if config.execution.track_carbon:
-        pass
+    # Parse arguments
+    parse_args()
 
     if 'pdb' in config.execution.debug:
         from simbids.utils.debug import setup_exceptionhook
@@ -51,22 +50,7 @@ def main():
     config_file.parent.mkdir(exist_ok=True, parents=True)
     config.to_filename(config_file)
 
-    # CRITICAL Call build_workflow(config_file, retval) in a subprocess.
-    # Because Python on Linux does not ever free virtual memory (VM), running the
-    # workflow construction jailed within a process preempts excessive VM buildup.
-    if 'pdb' not in config.execution.debug:
-        with Manager() as mgr:
-            retval = mgr.dict()
-            p = Process(target=build_workflow, args=(str(config_file), retval))
-            p.start()
-            p.join()
-            retval = dict(retval.items())  # Convert to base dictionary
-
-            if p.exitcode:
-                retval['return_code'] = p.exitcode
-
-    else:
-        retval = build_workflow(str(config_file), {})
+    retval = build_workflow(str(config_file), {})
 
     global EXITCODE
     EXITCODE = retval.get('return_code', 0)

src/simbids/cli/workflow.py

@@ -36,8 +36,6 @@ def build_workflow(config_file, retval):
     """Create the Nipype Workflow that supports the whole execution graph."""
     from pathlib import Path
 
-    from fmriprep.utils.bids import check_pipeline_version
-    from fmriprep.utils.misc import check_deps
     from niworkflows.utils.bids import collect_participants
     from pkg_resources import resource_filename as pkgrf
 
@@ -48,7 +46,6 @@ def build_workflow(config_file, retval):
     config.load(config_file)
     build_log = config.loggers.workflow
 
-    output_dir = config.execution.output_dir
     version = config.environment.version
 
     retval['return_code'] = 1
@@ -64,15 +61,6 @@ def build_workflow(config_file, retval):
         banner += ['#' * len(banner[1])]
     build_log.log(25, f'\n{" " * 9}'.join(banner))
 
-    # warn if older results exist: check for dataset_description.json in output folder
-    msg = check_pipeline_version(
-        'SimBIDS',
-        version,
-        output_dir / 'dataset_description.json',
-    )
-    if msg is not None:
-        build_log.warning(msg)
-
     # Please note this is the input folder's dataset_description.json
     dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
     if dset_desc_path.exists():
@@ -103,6 +91,7 @@ def build_workflow(config_file, retval):
         "Building SimBIDS's workflow:",
         f'BIDS dataset path: {config.execution.bids_dir}.',
         f'Participant list: {subject_list}.',
+        f'BIDS-App: {config.workflow.bids_app}.',
         f'Run identifier: {config.execution.run_uuid}.',
         f'Output spaces: {config.execution.output_spaces}.',
     ]
@@ -114,16 +103,6 @@ def build_workflow(config_file, retval):
 
     retval['workflow'] = init_simbids_wf()
 
-    # Check workflow for missing commands
-    missing = check_deps(retval['workflow'])
-    if missing:
-        build_log.critical(
-            'Cannot run SimBIDS. Missing dependencies:%s',
-            '\n\t* '.join([''] + [f'{cmd} (Interface: {iface})' for iface, cmd in missing]),
-        )
-        retval['return_code'] = 127  # 127 == command not found.
-        return retval
-
     config.to_filename(config_file)
     build_log.info(
         'SimBIDS workflow graph with %d nodes built successfully.',

src/simbids/config.py

@@ -206,7 +206,7 @@
 
 # Debug modes are names that influence the exposure of internal details to
 # the user, either through additional derivatives or increased verbosity
-DEBUG_MODES = ('compcor', 'fieldmaps', 'pdb')
+DEBUG_MODES = ('pdb',)
 
 
 class _Config:
@@ -481,9 +481,7 @@ def init(cls):
                     'sourcedata',
                     'models',
                     re.compile(r'^\.'),
-                    re.compile(
-                        r'sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|dwi|eeg|ieeg|meg|perf)'
-                    ),
+                    re.compile(r'sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|eeg|ieeg|meg|perf)'),
                 ),
             )
             cls._layout = BIDSLayout(
@@ -541,15 +539,8 @@ class workflow(_Config):
 
     ignore = None
     """Ignore particular steps for *SimBIDS*."""
-    cifti_output = None
-    """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
-    dummy_scans = None
-    """Set a number of initial scans to be considered nonsteady states."""
-    slice_time_ref = 0.5
-    """The time of the reference slice to correct BOLD values to, as a fraction
-    acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end
-    of acquisition. The alias `start` corresponds to 0, and `middle` to 0.5.
-    The default value is 0.5."""
+    bids_app = 'qsiprep'
+    """The BIDS App to simulate."""
 
 
 class loggers:
@@ -738,14 +729,5 @@ def init_spaces(checkpoint=True):
     if 'MNI152NLin6Asym' not in spaces.get_spaces(nonstandard=False, dim=(3,)):
         spaces.add(Reference('MNI152NLin6Asym', {}))
 
-    # Ensure user-defined spatial references for outputs are correctly parsed.
-    # Certain options require normalization to a space not explicitly defined by users.
-    # These spaces will not be included in the final outputs.
-    cifti_output = workflow.cifti_output
-    if cifti_output:
-        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = '2' if cifti_output == '91k' else '1'
-        spaces.add(Reference('MNI152NLin6Asym', {'res': vol_res}))
-
     # Make the SpatialReferences object available
     workflow.spaces = spaces