Merge pull request #545 from bpinsard/fix/nipy

allow similarity computation without mask

Author: satra

nipype/interfaces/nipy/utils.py

@@ -28,8 +28,8 @@ class SimilarityInputSpec(BaseInterfaceInputSpec):
 
     volume1 = File(exists=True, desc="3D volume", mandatory=True)
     volume2 = File(exists=True, desc="3D volume", mandatory=True)
-    mask1 = File(exists=True, desc="3D volume", mandatory=True)
-    mask2 = File(exists=True, desc="3D volume", mandatory=True)
+    mask1 = File(exists=True, desc="3D volume")
+    mask2 = File(exists=True, desc="3D volume")
     metric = traits.Either(traits.Enum('cc', 'cr', 'crl1', 'mi', 'nmi', 'slr'),
                           traits.Callable(),
                          desc="""str or callable
@@ -73,29 +73,25 @@ def _run_interface(self, runtime):
         vol2_nii = nb.load(self.inputs.volume2)
 
         if isdefined(self.inputs.mask1):
-            mask1_nii = nb.load(self.inputs.mask1)
-            mask1_nii = nb.Nifti1Image(nb.load(self.inputs.mask1).get_data() == 1, mask1_nii.get_affine(),
-                                       mask1_nii.get_header())
+            mask1 = nb.load(self.inputs.mask1).get_data() == 1
         else:
-            mask1_nii = None
+            mask1 = None
 
         if isdefined(self.inputs.mask2):
-            mask2_nii = nb.load(self.inputs.mask2)
-            mask2_nii = nb.Nifti1Image(nb.load(self.inputs.mask2).get_data() == 1, mask2_nii.get_affine(),
-                                       mask2_nii.get_header())
+            mask2 = nb.load(self.inputs.mask2).get_data() == 1
         else:
-            mask2_nii = None
+            mask2 = None
 
         histreg = HistogramRegistration(from_img = vol1_nii,
                                         to_img = vol2_nii,
                                         similarity=self.inputs.metric,
-                                        from_mask = mask1_nii,
-                                        to_mask = mask2_nii)
+                                        from_mask = mask1,
+                                        to_mask = mask2)
         self._similarity = histreg.eval(Affine())
 
         return runtime
 
     def _list_outputs(self):
         outputs = self._outputs().get()
         outputs['similarity'] = self._similarity
-        return outputs
+        return outputs