REF: extract_entities to base wf

fprodents/patch/utils/__init__.py

@@ -61,3 +61,40 @@ def get_template_specs(in_template, template_spec=None, default_resolution=None)
         )
 
     return str(tpl_target_path), common_spec
+
+
+def extract_entities(file_list):
+    """
+    Return a dictionary of common entities given a list of files.
+
+    Examples
+    --------
+    >>> extract_entities('sub-01/anat/sub-01_T1w.nii.gz')
+    {'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': 'nii.gz'}
+    >>> extract_entities(['sub-01/anat/sub-01_T1w.nii.gz'] * 2)
+    {'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': 'nii.gz'}
+    >>> extract_entities(['sub-01/anat/sub-01_run-1_T1w.nii.gz',
+    ...                   'sub-01/anat/sub-01_run-2_T1w.nii.gz'])
+    {'subject': '01', 'run': [1, 2], 'suffix': 'T1w', 'datatype': 'anat',
+     'extension': 'nii.gz'}
+
+    """
+    from collections import defaultdict
+    from bids.layout import parse_file_entities
+    from niworkflows.utils.connections import listify
+
+    entities = defaultdict(list)
+    for e, v in [
+        ev_pair
+        for f in listify(file_list)
+        for ev_pair in parse_file_entities(f).items()
+    ]:
+        entities[e].append(v)
+
+    def _unique(inlist):
+        inlist = sorted(set(inlist))
+        if len(inlist) == 1:
+            return inlist[0]
+        return inlist
+
+    return {k: _unique(v) for k, v in entities.items()}

fprodents/workflows/base.py

@@ -105,11 +105,12 @@ def init_single_subject_wf(subject_id):
     from niworkflows.interfaces.bids import BIDSInfo
     from niworkflows.interfaces.nilearn import NILEARN_VERSION
     from niworkflows.utils.bids import collect_data
+    from niworkflows.utils.connections import listify
     from niworkflows.utils.spaces import Reference
     from niworkflows.workflows.epi.refmap import init_epi_reference_wf
     from nirodents.workflows.brainextraction import init_rodent_brain_extraction_wf
     from ..patch.interfaces import BIDSDataGrabber
-    from ..patch.utils import fix_multi_source_name
+    from ..patch.utils import extract_entities, fix_multi_source_name
     from ..patch.workflows.anatomical import init_anat_preproc_wf
 
     subject_data = collect_data(
@@ -299,6 +300,10 @@ def init_single_subject_wf(subject_id):
     )
 
     for bold_file in subject_data["bold"]:
+        echoes = extract_entities(bold_file).get("echo", [])
+        echo_idxs = listify(echoes)
+        multiecho = len(echo_idxs) > 2
+
         bold_ref_wf = init_epi_reference_wf(
             auto_bold_nss=True,
             omp_nthreads=config.nipype.omp_nthreads

fprodents/workflows/bold/base.py

@@ -125,6 +125,8 @@ def init_func_preproc_wf(bold_file):
     from niworkflows.interfaces.utility import KeySelect, DictMerge
     from nipype.interfaces.freesurfer.utils import LTAConvert
 
+    from ...patch.utils import extract_entities
+
     mem_gb = {"filesize": 1, "resampled": 1, "largemem": 1}
     bold_tlen = 10
 
@@ -769,39 +771,3 @@ def _to_join(in_file, join_file):
         return in_file
     res = JoinTSVColumns(in_file=in_file, join_file=join_file).run()
     return res.outputs.out_file
-
-
-def extract_entities(file_list):
-    """
-    Return a dictionary of common entities given a list of files.
-
-    Examples
-    --------
-    >>> extract_entities('sub-01/anat/sub-01_T1w.nii.gz')
-    {'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': 'nii.gz'}
-    >>> extract_entities(['sub-01/anat/sub-01_T1w.nii.gz'] * 2)
-    {'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': 'nii.gz'}
-    >>> extract_entities(['sub-01/anat/sub-01_run-1_T1w.nii.gz',
-    ...                   'sub-01/anat/sub-01_run-2_T1w.nii.gz'])
-    {'subject': '01', 'run': [1, 2], 'suffix': 'T1w', 'datatype': 'anat',
-     'extension': 'nii.gz'}
-
-    """
-    from collections import defaultdict
-    from bids.layout import parse_file_entities
-
-    entities = defaultdict(list)
-    for e, v in [
-        ev_pair
-        for f in listify(file_list)
-        for ev_pair in parse_file_entities(f).items()
-    ]:
-        entities[e].append(v)
-
-    def _unique(inlist):
-        inlist = sorted(set(inlist))
-        if len(inlist) == 1:
-            return inlist[0]
-        return inlist
-
-    return {k: _unique(v) for k, v in entities.items()}