feat: Save fieldmap mask to output directory

Author: effigies

sdcflows/workflows/base.py

@@ -137,6 +137,7 @@ def init_fmap_preproc_wf(
         fmap_derivatives_wf = init_fmap_derivatives_wf(
             output_dir=str(output_dir),
             write_coeff=True,
+            write_mask=True,
             bids_fmap_id=estimator.bids_id,
             name=f'fmap_derivatives_wf_{estimator.sanitized_id}',
         )
@@ -166,20 +167,21 @@ def init_fmap_preproc_wf(
                 ("outputnode.fmap", "inputnode.fieldmap"),
                 ("outputnode.fmap_ref", "inputnode.fmap_ref"),
                 ("outputnode.fmap_coeff", "inputnode.fmap_coeff"),
+                ("outputnode.fmap_mask", "inputnode.fmap_mask"),
             ]),
             (est_wf, fmap_reports_wf, [
                 ("outputnode.fmap", "inputnode.fieldmap"),
                 ("outputnode.fmap_ref", "inputnode.fmap_ref"),
                 ("outputnode.fmap_mask", "inputnode.fmap_mask"),
             ]),
+            (est_wf, out_map, [
+                ("outputnode.method", "method")
+            ]),
             (fmap_derivatives_wf, out_map, [
                 ("outputnode.fieldmap", "fmap"),
                 ("outputnode.fmap_ref", "fmap_ref"),
                 ("outputnode.fmap_coeff", "fmap_coeff"),
-            ]),
-            (est_wf, out_map, [
                 ("outputnode.fmap_mask", "fmap_mask"),
-                ("outputnode.method", "method")
             ]),
         ])  # fmt:skip
 

sdcflows/workflows/outputs.py

@@ -123,6 +123,7 @@ def init_fmap_derivatives_wf(
     custom_entities=None,
     name='fmap_derivatives_wf',
     write_coeff=False,
+    write_mask=False,
 ):
     """
     Set up datasinks to store derivatives in the right location.
@@ -159,12 +160,12 @@ def init_fmap_derivatives_wf(
     workflow = pe.Workflow(name=name)
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=['source_files', 'fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_meta']
+            fields=['source_files', 'fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_mask', 'fmap_meta']
         ),
         name='inputnode',
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=['fieldmap', 'fmap_coeff', 'fmap_ref']),
+        niu.IdentityInterface(fields=['fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_mask']),
         name='outputnode',
     )
 
@@ -216,6 +217,28 @@ def init_fmap_derivatives_wf(
         (ds_reference, outputnode, [("out_file", "fmap_ref")]),
     ])  # fmt:skip
 
+    if write_mask:
+        ds_mask = pe.Node(
+            DerivativesDataSink(
+                base_directory=output_dir,
+                compress=True,
+                desc='brain',
+                suffix='mask',
+                datatype='fmap',
+                dismiss_entities=('fmap',),
+                allowed_entities=tuple(custom_entities),
+            ),
+            name='ds_mask',
+        )
+
+        ds_mask.inputs.trait_set(**custom_entities)
+
+        workflow.connect([
+            (inputnode, ds_mask, [("source_files", "source_file"),
+                                  ("fmap_mask", "in_file")]),
+            (ds_mask, outputnode, [("out_file", "fmap_mask")]),
+        ])  # fmt:skip
+
     if not write_coeff:
         return workflow