Collect and apply field maps

src/fmripost_aroma/data/io_spec.json

@@ -1,4 +1,5 @@
 {
+    "name": "aroma",
     "queries": {
         "raw": {
             "bold_raw": {
@@ -152,8 +153,8 @@
     },
     "entities": [
         {
-            "name": "datatype",
-            "pattern": "[/\\\\]+(anat|func)[/\\\\]+"
+            "name": "fmapid",
+            "pattern": "fmapid-([a-zA-Z0-9]+)"
         },
         {
             "name": "cohort",
@@ -173,7 +174,7 @@
             "pattern": "(?:^|_)thresh-([a-zA-Z0-9]+)"
         }
       ],
-    "patterns": [
+    "default_path_patterns": [
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",

src/fmripost_aroma/interfaces/bids.py

@@ -31,4 +31,4 @@ class DerivativesDataSink(BaseDerivativesDataSink):
     _allowed_entities = set(config_entities)
     _config_entities = config_entities
     _config_entities_dict = merged_entities
-    _file_patterns = fmripost_aroma_spec['patterns']
+    _file_patterns = fmripost_aroma_spec['default_path_patterns']

src/fmripost_aroma/utils/bids.py

@@ -98,14 +98,21 @@ def collect_derivatives(
     if not entities:
         entities = {}
 
+    _spec = None
     if spec is None or patterns is None:
         _spec = json.loads(load_data.readable('io_spec.json').read_text())
 
         if spec is None:
             spec = _spec['queries']
 
         if patterns is None:
-            patterns = _spec['patterns']
+            patterns = _spec['default_path_patterns']
+
+        _spec.pop('queries')
+
+    config = ['bids', 'derivatives']
+    if _spec:
+        config = ['bids', 'derivatives', _spec]
 
     # Search for derivatives data
     derivs_cache = defaultdict(list, {})
@@ -114,7 +121,7 @@ def collect_derivatives(
         if isinstance(layout, Path):
             layout = BIDSLayout(
                 layout,
-                config=['bids', 'derivatives'],
+                config=config,
                 validate=False,
             )
 

src/fmripost_aroma/workflows/base.py

@@ -179,6 +179,7 @@
     if config.execution.derivatives:
         # Raw dataset + derivatives dataset
         config.loggers.workflow.info('Raw+derivatives workflow mode enabled')
+        # Just build a list of BOLD files right now
         subject_data = collect_derivatives(
             raw_dataset=config.execution.layout,
             derivatives_dataset=None,
@@ -191,6 +192,7 @@
     else:
         # Derivatives dataset only
         config.loggers.workflow.info('Derivatives-only workflow mode enabled')
+        # Just build a list of BOLD files right now
         subject_data = collect_derivatives(
             raw_dataset=None,
             derivatives_dataset=config.execution.layout,
@@ -304,14 +306,31 @@
 
     entities = extract_entities(bold_file)
 
+    # Attempt to extract the associated fmap ID
+    fmapid = None
+    all_fmapids = config.execution.layout.get_fmapids(
+        subject=entities['subject'],
+        session=entities.get('session', None),
+    )
+    if all_fmapids:
+        fmap_file = config.execution.layout.get_nearest(
+            bold_file,
+            to=all_fmapids,
+            suffix='xfm',
+            extension='.txt',
+            strict=False,
+            **{'from': 'boldref'},
+        )
+        fmapid = config.execution.layout.get_file(fmap_file).entities['to']
+
     functional_cache = defaultdict(list, {})
     if config.execution.derivatives:
         # Collect native-space derivatives and transforms
         functional_cache = collect_derivatives(
             raw_dataset=config.execution.layout,
             derivatives_dataset=None,
             entities=entities,
-            fieldmap_id=None,
+            fieldmap_id=fmapid,
             allow_multiple=False,
             spaces=None,
         )
@@ -322,7 +341,7 @@
                     raw_dataset=None,
                     derivatives_dataset=deriv_dir,
                     entities=entities,
-                    fieldmap_id=None,
+                    fieldmap_id=fmapid,
                     allow_multiple=False,
                     spaces=spaces,
                 ),
@@ -347,7 +366,7 @@
                 raw_dataset=None,
                 derivatives_dataset=config.execution.layout,
                 entities=entities,
-                fieldmap_id=None,
+                fieldmap_id=fmapid,
                 allow_multiple=False,
                 spaces=spaces,
             ),