fix fieldmap querying for pybids 0.7

Author: oesteban

fmriprep/workflows/bold/base.py

@@ -254,7 +254,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             'PhaseEncodingDirection': 'j',
         }
         fmaps = [{
-            'type': 'phasediff',
+            'suffix': 'phasediff',
             'phasediff': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_phasediff.nii.gz',
             'magnitude1': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude1.nii.gz',
             'magnitude2': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude2.nii.gz',
@@ -291,11 +291,11 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         if 'fieldmaps' not in ignore:
             fmaps = layout.get_fieldmap(ref_file, return_list=True)
             for fmap in fmaps:
-                fmap['metadata'] = layout.get_metadata(fmap[fmap['type']])
+                fmap['metadata'] = layout.get_metadata(fmap[fmap['suffix']])
 
         # Run SyN if forced or in the absence of fieldmap correction
         if force_syn or (use_syn and not fmaps):
-            fmaps.append({'type': 'syn'})
+            fmaps.append({'suffix': 'syn'})
 
         # Short circuits: (True and True and (False or 'TooShort')) == 'TooShort'
         run_stc = ("SliceTiming" in metadata and
@@ -476,14 +476,14 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
     if not fmaps:
         LOGGER.warning('SDC: no fieldmaps found or they were ignored (%s).',
                        ref_file)
-    elif fmaps[0]['type'] == 'syn':
+    elif fmaps[0]['suffix'] == 'syn':
         LOGGER.warning(
             'SDC: no fieldmaps found or they were ignored. '
             'Using EXPERIMENTAL "fieldmap-less SyN" correction '
             'for dataset %s.', ref_file)
     else:
         LOGGER.log(25, 'SDC: fieldmap estimation of type "%s" intended for %s found.',
-                   fmaps[0]['type'], ref_file)
+                   fmaps[0]['suffix'], ref_file)
 
     # MULTI-ECHO EPI DATA #############################################
     if multiecho:
@@ -613,7 +613,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
     if fmaps:
         from ..fieldmap.unwarp import init_fmap_unwarp_report_wf
-        sdc_type = fmaps[0]['type']
+        sdc_type = fmaps[0]['suffix']
 
         # Report on BOLD correction
         fmap_unwarp_report_wf = init_fmap_unwarp_report_wf(

fmriprep/workflows/fieldmap/base.py

@@ -79,7 +79,7 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
         from fmriprep.workflows.fieldmap import init_sdc_wf
         wf = init_sdc_wf(
             fmaps=[{
-                'type': 'phasediff',
+                'suffix': 'phasediff',
                 'phasediff': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_phasediff.nii.gz',
                 'magnitude1': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude1.nii.gz',
                 'magnitude2': 'sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude2.nii.gz',
@@ -140,7 +140,7 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
     """
 
     # TODO: To be removed (filter out unsupported fieldmaps):
-    fmaps = [fmap for fmap in fmaps if fmap['type'] in FMAP_PRIORITY]
+    fmaps = [fmap for fmap in fmaps if fmap['suffix'] in FMAP_PRIORITY]
 
     workflow = Workflow(name='sdc_wf' if fmaps else 'sdc_bypass_wf')
     inputnode = pe.Node(niu.IdentityInterface(
@@ -170,15 +170,15 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
 """
 
     # In case there are multiple fieldmaps prefer EPI
-    fmaps.sort(key=lambda fmap: FMAP_PRIORITY[fmap['type']])
+    fmaps.sort(key=lambda fmap: FMAP_PRIORITY[fmap['suffix']])
     fmap = fmaps[0]
 
     # PEPOLAR path
-    if fmap['type'] == 'epi':
+    if fmap['suffix'] == 'epi':
         outputnode.inputs.method = 'PEB/PEPOLAR (phase-encoding based / PE-POLARity)'
         # Get EPI polarities and their metadata
         epi_fmaps = [(fmap_['epi'], fmap_['metadata']["PhaseEncodingDirection"])
-                     for fmap_ in fmaps if fmap_['type'] == 'epi']
+                     for fmap_ in fmaps if fmap_['suffix'] == 'epi']
         sdc_unwarp_wf = init_pepolar_unwarp_wf(
             bold_meta=bold_meta,
             epi_fmaps=epi_fmaps,
@@ -193,11 +193,11 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
         ])
 
     # FIELDMAP path
-    if fmap['type'] in ['fieldmap', 'phasediff']:
-        outputnode.inputs.method = 'FMB (%s-based)' % fmap['type']
+    if fmap['suffix'] in ['fieldmap', 'phasediff']:
+        outputnode.inputs.method = 'FMB (%s-based)' % fmap['suffix']
         # Import specific workflows here, so we don't break everything with one
         # unused workflow.
-        if fmap['type'] == 'fieldmap':
+        if fmap['suffix'] == 'fieldmap':
             from .fmap import init_fmap_wf
             fmap_estimator_wf = init_fmap_wf(
                 omp_nthreads=omp_nthreads,
@@ -206,7 +206,7 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
             fmap_estimator_wf.inputs.inputnode.fieldmap = fmap['fieldmap']
             fmap_estimator_wf.inputs.inputnode.magnitude = fmap['magnitude']
 
-        if fmap['type'] == 'phasediff':
+        if fmap['suffix'] == 'phasediff':
             from .phdiff import init_phdiff_wf
             fmap_estimator_wf = init_phdiff_wf(omp_nthreads=omp_nthreads)
             # set inputs
@@ -235,7 +235,7 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
         ])
 
     # FIELDMAP-less path
-    if any(fm['type'] == 'syn' for fm in fmaps):
+    if any(fm['suffix'] == 'syn' for fm in fmaps):
         syn_sdc_wf = init_syn_sdc_wf(
             bold_pe=bold_meta.get('PhaseEncodingDirection', None),
             omp_nthreads=omp_nthreads)
@@ -250,7 +250,7 @@ def init_sdc_wf(fmaps, bold_meta, omp_nthreads=1,
         ])
 
         # XXX Eliminate branch when forcing isn't an option
-        if fmap['type'] == 'syn':  # No fieldmaps, but --use-syn
+        if fmap['suffix'] == 'syn':  # No fieldmaps, but --use-syn
             outputnode.inputs.method = 'FLB ("fieldmap-less", SyN-based)'
             sdc_unwarp_wf = syn_sdc_wf
         else:  # --force-syn was called when other fieldmap was present