Merge pull request #190 from nipreps/add_trc_label

ENH: add tracer-label functionality for filtering

Author: mnoergaard

petprep/cli/parser.py

@@ -195,6 +195,13 @@ def _bids_filter(value, parser):
         help='A space delimited list of session identifiers or a single '
         'identifier (the ses- prefix can be removed)',
     )
+    g_bids.add_argument(
+        '--tracer-label',
+        nargs='+',
+        type=lambda label: label.removeprefix('trc-'),
+        help='A space delimited list of tracer identifiers or a single '
+        'identifier (the trc- prefix can be removed)',
+    )
     # Re-enable when option is actually implemented
     # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
     #                     help='Select a specific run to be processed')
@@ -776,6 +783,13 @@ def parse_args(args=None, namespace=None):
             'session': config.execution.session_label,
         }
 
+    if config.execution.tracer_label:
+        config.execution.bids_filters = config.execution.bids_filters or {}
+        config.execution.bids_filters['pet'] = {
+            **config.execution.bids_filters.get('pet', {}),
+            'tracer': config.execution.tracer_label,
+        }
+
     pvc_vals = (opts.pvc_tool, opts.pvc_method, opts.pvc_psf)
     if any(val is not None for val in pvc_vals) and not all(val is not None for val in pvc_vals):
         parser.error('Options --pvc-tool, --pvc-method and --pvc-psf must be used together.')
@@ -946,5 +960,25 @@ def parse_args(args=None, namespace=None):
                 f'{", ".join(sorted(missing_sessions))}.'
             )
 
+    if config.execution.tracer_label:
+        tracer_filters = (
+            config.execution.bids_filters.get('pet', {}) if config.execution.bids_filters else {}
+        )
+        tracer_filters = {key: value for key, value in tracer_filters.items() if key != 'tracer'}
+        available_tracers = set(
+            config.execution.layout.get(
+                target='tracer',
+                return_type='id',
+                subject=list(participant_label) or None,
+                **tracer_filters,
+            )
+        )
+        missing_tracers = set(config.execution.tracer_label) - available_tracers
+        if missing_tracers:
+            parser.error(
+                'One or more tracer labels were not found in the BIDS directory: '
+                f'{", ".join(sorted(missing_tracers))}.'
+            )
+
     config.execution.participant_label = sorted(participant_label)
     config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]

petprep/cli/tests/test_parser.py

@@ -266,6 +266,76 @@ def test_session_label_only_filters_pet(tmp_path):
         _reset_config()
 
 
+def test_tracer_label_only_filters_pet(tmp_path):
+    bids = tmp_path / 'bids'
+    out_dir = tmp_path / 'out'
+    work_dir = tmp_path / 'work'
+    bids.mkdir()
+    (bids / 'dataset_description.json').write_text('{"Name": "Test", "BIDSVersion": "1.8.0"}')
+
+    anat_path = bids / 'sub-01' / 'anat' / 'sub-01_T1w.nii.gz'
+    anat_path.parent.mkdir(parents=True, exist_ok=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5)), np.eye(4)).to_filename(anat_path)
+
+    pet_path = bids / 'sub-01' / 'pet' / 'sub-01_trc-ucbj_pet.nii.gz'
+    pet_path.parent.mkdir(parents=True, exist_ok=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5, 1)), np.eye(4)).to_filename(pet_path)
+    (pet_path.with_suffix('').with_suffix('.json')).write_text(
+        '{"FrameTimesStart": [0], "FrameDuration": [1]}'
+    )
+
+    try:
+        parse_args(
+            args=[
+                str(bids),
+                str(out_dir),
+                'participant',
+                '--tracer-label',
+                'ucbj',
+                '--skip-bids-validation',
+                '-w',
+                str(work_dir),
+            ]
+        )
+
+        filters = config.execution.bids_filters
+        assert filters.get('pet', {}).get('tracer') == ['ucbj']
+        assert 'tracer' not in filters.get('anat', {})
+    finally:
+        _reset_config()
+
+
+def test_tracer_label_validation(tmp_path):
+    bids = tmp_path / 'bids'
+    out_dir = tmp_path / 'out'
+    work_dir = tmp_path / 'work'
+    bids.mkdir()
+    (bids / 'dataset_description.json').write_text('{"Name": "Test", "BIDSVersion": "1.8.0"}')
+
+    pet_path = bids / 'sub-01' / 'pet' / 'sub-01_trc-ucbj_pet.nii.gz'
+    pet_path.parent.mkdir(parents=True, exist_ok=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5, 1)), np.eye(4)).to_filename(pet_path)
+    (pet_path.with_suffix('').with_suffix('.json')).write_text(
+        '{"FrameTimesStart": [0], "FrameDuration": [1]}'
+    )
+
+    with pytest.raises(SystemExit):
+        parse_args(
+            args=[
+                str(bids),
+                str(out_dir),
+                'participant',
+                '--tracer-label',
+                'dasb',
+                '--skip-bids-validation',
+                '-w',
+                str(work_dir),
+            ]
+        )
+
+    _reset_config()
+
+
 def test_pvc_argument_handling(tmp_path, minimal_bids):
     out_dir = tmp_path / 'out'
     work_dir = tmp_path / 'work'

petprep/config.py

@@ -434,6 +434,8 @@ class execution(_Config):
     """List of participant identifiers that are to be preprocessed."""
     session_label = None
     """List of session identifiers that are to be preprocessed."""
+    tracer_label = None
+    """List of tracer identifiers that are to be preprocessed."""
     task_id = None
     """Select a particular task from all available in the dataset."""
     templateflow_home = _templateflow_home