Merge pull request #166 from josephmje/enh/dwi-derivatives

ENH: Write out *b=0* reference(s)

Author: josephmje

.circleci/config.yml

@@ -242,11 +242,11 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - data-ds000206-v1-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
-            - data-ds000206-v1-{{ .Branch }}-{{ .Revision }}-
-            - data-ds000206-v1-{{ .Branch }}-
-            - data-ds000206-v1-master-
-            - data-ds000206-v1-
+            - data-ds000206-v2-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+            - data-ds000206-v2-{{ .Branch }}-{{ .Revision }}-
+            - data-ds000206-v2-{{ .Branch }}-
+            - data-ds000206-v2-master-
+            - data-ds000206-v2-
       - restore_cache:
           keys:
             - build-v1-{{ .Branch }}-{{ epoch }}

dmriprep/workflows/dwi/base.py

@@ -65,6 +65,7 @@ def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
     See Also
     --------
     * :py:func:`~dmriprep.workflows.dwi.util.init_dwi_reference_wf`
+    * :py:func:`~dmriprep.workflows.dwi.outputs.init_dwi_derivatives_wf`
     * :py:func:`~dmriprep.workflows.dwi.outputs.init_reportlets_wf`
 
     """
@@ -73,7 +74,7 @@ def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
     )
     from ...interfaces.vectors import CheckGradientTable
     from .util import init_dwi_reference_wf
-    from .outputs import init_reportlets_wf
+    from .outputs import init_dwi_derivatives_wf, init_reportlets_wf
     from .eddy import init_eddy_wf
 
     layout = config.execution.layout
@@ -146,15 +147,22 @@ def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
         mem_gb=config.DEFAULT_MEMORY_MIN_GB, omp_nthreads=config.nipype.omp_nthreads
     )
 
+    dwi_derivatives_wf = init_dwi_derivatives_wf(output_dir=str(config.execution.output_dir))
+
     # MAIN WORKFLOW STRUCTURE
     # fmt: off
     workflow.connect([
         (inputnode, gradient_table, [("dwi_file", "dwi_file"),
                                      ("in_bvec", "in_bvec"),
                                      ("in_bval", "in_bval")]),
         (inputnode, dwi_reference_wf, [("dwi_file", "inputnode.dwi_file")]),
+        (inputnode, dwi_derivatives_wf, [("dwi_file", "inputnode.source_file")]),
         (gradient_table, dwi_reference_wf, [("b0_ixs", "inputnode.b0_ixs")]),
         (gradient_table, outputnode, [("out_rasb", "gradients_rasb")]),
+        (outputnode, dwi_derivatives_wf, [
+            ("dwi_reference", "inputnode.dwi_ref"),
+            ("dwi_mask", "inputnode.dwi_mask"),
+        ]),
     ])
     # fmt: on
 

dmriprep/workflows/dwi/outputs.py

@@ -65,3 +65,63 @@ def init_reportlets_wf(output_dir, sdc_report=False, name="reportlets_wf"):
         ])
         # fmt:on
     return workflow
+
+
+def init_dwi_derivatives_wf(output_dir, name="dwi_derivatives_wf"):
+    """
+    Set up a battery of datasinks to store dwi derivatives in the right location.
+
+    Parameters
+    ----------
+    output_dir : :obj:`str`
+        Directory in which to save derivatives.
+    name : :obj:`str`
+        Workflow name (default: ``"dwi_derivatives_wf"``).
+
+    Inputs
+    ------
+    source_file
+        One dwi file that will serve as a file naming reference.
+    dwi_ref
+        The b0 reference.
+    dwi_mask
+        The brain mask for the dwi file.
+
+    """
+    workflow = pe.Workflow(name=name)
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=["source_file", "dwi_ref", "dwi_mask"]),
+        name="inputnode",
+    )
+
+    ds_reference = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            compress=True,
+            suffix="epiref",
+            datatype="dwi",
+        ),
+        name="ds_reference",
+    )
+
+    ds_mask = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            compress=True,
+            desc="brain",
+            suffix="mask",
+            datatype="dwi",
+        ),
+        name="ds_mask",
+    )
+
+    # fmt:off
+    workflow.connect([
+        (inputnode, ds_reference, [("source_file", "source_file"),
+                                   ("dwi_ref", "in_file")]),
+        (inputnode, ds_mask, [("source_file", "source_file"),
+                              ("dwi_mask", "in_file")]),
+    ])
+    # fmt:on
+
+    return workflow