ENH: Add interface to invert shape files

smriprep/interfaces/gifti.py

@@ -0,0 +1,71 @@
+"""Interfaces for manipulating GIFTI files."""
+import os
+
+import nibabel as nb
+from nipype.interfaces.base import File, SimpleInterface, TraitedSpec, isdefined, traits
+
+
+class InvertShapeInputSpec(TraitedSpec):
+    subject_id = traits.Str(desc='subject ID')
+    hemisphere = traits.Enum(
+        "L",
+        "R",
+        mandatory=True,
+        desc='hemisphere',
+    )
+    shape = traits.Str(desc='name of shape to invert')
+    shape_file = File(exists=True, mandatory=True, desc='input GIFTI file')
+
+
+class InvertShapeOutputSpec(TraitedSpec):
+    shape_file = File(desc='output GIFTI file')
+
+
+class InvertShape(SimpleInterface):
+    """Prepare GIFTI shape file for use in MSMSulc
+
+    This interface mirrors the action of the following portion
+    of FreeSurfer2CaretConvertAndRegisterNonlinear.sh::
+
+        wb_command -set-structure ${shape_file} CORTEX_[LEFT|RIGHT]
+        wb_command -metric-math "var * -1" ${shape_file} -var var ${shape_file}
+        wb_command -set-map-names ${shape_file} -map 1 ${subject}_[L|R]_${shape}
+
+    We do not add palette information to the output file.
+    """
+
+    input_spec = InvertShapeInputSpec
+    output_spec = InvertShapeOutputSpec
+
+    def _run_interface(self, runtime):
+        subject, hemi, shape = self.inputs.subject_id, self.inputs.hemisphere, self.inputs.shape
+        if not isdefined(subject):
+            subject = 'sub-XYZ'
+
+        img = nb.GiftiImage.from_filename(self.inputs.shape_file)
+        # wb_command -set-structure
+        img.meta["AnatomicalStructurePrimary"] = {'L': 'CortexLeft', 'R': 'CortexRight'}[hemi]
+        darray = img.darrays[0]
+        # wb_command -set-map-names
+        meta = darray.meta
+        meta['Name'] = f"{subject}_{hemi}_{shape}"
+
+        # wb_command -metric-math "var * -1"
+        inv = -darray.data
+
+        darray = nb.gifti.GiftiDataArray(
+            inv,
+            intent=darray.intent,
+            datatype=darray.datatype,
+            encoding=darray.encoding,
+            endian=darray.endian,
+            coordsys=darray.coordsys,
+            ordering=darray.ind_ord,
+            meta=meta,
+        )
+        img.darrays[0] = darray
+
+        out_filename = os.path.join(runtime.cwd, f"{subject}.{hemi}.{shape}.native.shape.gii")
+        img.to_filename(out_filename)
+        self._results["shape_file"] = out_filename
+        return runtime