Merge pull request #150 from oesteban/fix/issue-146

ENH: Write ``fmapid-`` entity in Derivatives

Author: oesteban

sdcflows/workflows/base.py

@@ -71,17 +71,19 @@ def init_fmap_preproc_wf(
 
     workflow = Workflow(name=name)
 
-    out_fields = ("fmap", "fmap_ref", "fmap_coeff", "fmap_mask")
+    out_fields = ("fmap", "fmap_ref", "fmap_coeff", "fmap_mask", "fmap_id")
     out_merge = {
         f: pe.Node(niu.Merge(len(estimators)), name=f"out_merge_{f}")
         for f in out_fields
     }
     outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name="outputnode")
 
-    workflow.connect([
-        (mergenode, outputnode, [("out", field)])
-        for field, mergenode in out_merge.items()
-    ])
+    workflow.connect(
+        [
+            (mergenode, outputnode, [("out", field)])
+            for field, mergenode in out_merge.items()
+        ]
+    )
 
     for n, estimator in enumerate(estimators):
         est_wf = estimator.get_workflow(omp_nthreads=omp_nthreads, debug=debug)
@@ -90,11 +92,12 @@ def init_fmap_preproc_wf(
         out_map = pe.Node(
             niu.IdentityInterface(fields=out_fields), name=f"out_{estimator.bids_id}"
         )
+        out_map.inputs.fmap_id = estimator.bids_id
 
         fmap_derivatives_wf = init_fmap_derivatives_wf(
             output_dir=str(output_dir),
             write_coeff=True,
-            bids_fmap_id=estimator.bids_id.replace("_", ""),
+            bids_fmap_id=estimator.bids_id,
             name=f"fmap_derivatives_wf_{estimator.bids_id}",
         )
         fmap_derivatives_wf.inputs.inputnode.source_files = source_files
@@ -105,6 +108,7 @@ def init_fmap_preproc_wf(
         fmap_reports_wf = init_fmap_reports_wf(
             output_dir=str(output_dir),
             fmap_type=str(estimator.method).rpartition(".")[-1].lower(),
+            bids_fmap_id=estimator.bids_id,
             name=f"fmap_reports_wf_{estimator.bids_id}",
         )
         fmap_reports_wf.inputs.inputnode.source_files = source_files

sdcflows/workflows/outputs.py

@@ -16,7 +16,12 @@ class DerivativesDataSink(_DDS):
 
 
 def init_fmap_reports_wf(
-    *, output_dir, fmap_type, custom_entities=None, name="fmap_reports_wf",
+    *,
+    output_dir,
+    fmap_type,
+    bids_fmap_id=None,
+    custom_entities=None,
+    name="fmap_reports_wf",
 ):
     """
     Set up a battery of datasinks to store reports in the right location.
@@ -25,10 +30,12 @@ def init_fmap_reports_wf(
     ----------
     fmap_type : :obj:`str`
         The fieldmap estimator type.
-    custom_entities : :obj:`dict`
-        Define extra entities that will be written out in filenames.
     output_dir : :obj:`str`
         Directory in which to save derivatives
+    bids_fmap_id : :obj:`str`
+        Sets the ``B0FieldIdentifier`` metadata into the outputs.
+    custom_entities : :obj:`dict`
+        Define extra entities that will be written out in filenames.
     name : :obj:`str`
         Workflow name (default: ``"fmap_reports_wf"``)
 
@@ -47,6 +54,8 @@ def init_fmap_reports_wf(
     from ..interfaces.reportlets import FieldmapReportlet
 
     custom_entities = custom_entities or {}
+    if bids_fmap_id:
+        custom_entities["fmapid"] = bids_fmap_id.replace("_", "")
 
     workflow = pe.Workflow(name=name)
     inputnode = pe.Node(
@@ -100,14 +109,16 @@ def init_fmap_derivatives_wf(
 
     Parameters
     ----------
+    output_dir : :obj:`str`
+        Directory in which to save derivatives
     bids_fmap_id : :obj:`str`
         Sets the ``B0FieldIdentifier`` metadata into the outputs.
     custom_entities : :obj:`dict`
         Define extra entities that will be written out in filenames.
-    output_dir : :obj:`str`
-        Directory in which to save derivatives
     name : :obj:`str`
         Workflow name (default: ``"fmap_derivatives_wf"``)
+    write_coeff : :obj:`bool`
+        Build the workflow path to map coefficients into target space.
 
     Inputs
     ------
@@ -122,6 +133,8 @@ def init_fmap_derivatives_wf(
 
     """
     custom_entities = custom_entities or {}
+    if bids_fmap_id:
+        custom_entities["fmapid"] = bids_fmap_id.replace("_", "")
 
     workflow = pe.Workflow(name=name)
     inputnode = pe.Node(