fix: sidestep Undefined issue

Author: mgxd

nipype/algorithms/confounds.py

@@ -308,10 +308,11 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
     mask_files = InputMultiPath(File(exists=True,
         desc='One or more mask files that determines ROI (3D)'))
     merge_method = traits.Enum('union', 'intersect', 'none', xor=['mask_index'],
+        requires=['mask_files'],
         desc='Merge method if multiple masks are present - `union` aggregates '
         'all masks, `intersect` computes the truth value of all masks, `none` '
         'performs CompCor on each mask individually')
-    mask_index = traits.Range(0, value=0, xor=['merge_method'], usedefault=True,
+    mask_index = traits.Range(0, xor=['merge_method'], requires=['mask_files'],
         desc='Position of mask in `mask_files` to use - first is the default')
     components_file = File('components_file.txt', exists=False, usedefault=True,
         desc='filename to store physiological components')
@@ -364,6 +365,11 @@ def _run_interface(self, runtime, tCompCor_mask=False):
                             mmap=NUMPY_MMAP).get_data()
         components = None
 
+        if isdefined(self.inputs.mask_files) or isdefined(self.inputs.mask_file):
+            if (not isdefined(self.inputs.mask_index) and
+              not isdefined(self.inputs.merge_method)):
+                self.inputs.mask_index = 0
+
         if isdefined(self.inputs.mask_index):
             if self.inputs.mask_index < len(self.inputs.mask_files):
                 self.inputs.mask_files = [
@@ -519,6 +525,9 @@ def _run_interface(self, runtime):
                             imgseries.shape))
 
         if isdefined(self.inputs.mask_files):
+            if (not isdefined(self.inputs.mask_index) and
+              not isdefined(self.inputs.merge_method)):
+                self.inputs.mask_index = 0
             if isdefined(self.inputs.mask_index):
                 if self.inputs.mask_index < len(self.inputs.mask_files):
                     self.inputs.mask_files = [

nipype/algorithms/tests/test_compcor.py

@@ -110,8 +110,7 @@ def test_tcompcor_merge_intersect_masks(self):
         for method in ['union', 'intersect']:
             TCompCor(realigned_file=self.realigned_file,
                      mask_files=self.mask_files,
-                     merge_method=method,
-                     mask_index=Undefined).run()
+                     merge_method=method).run()
             if method == 'union':
                 assert np.array_equal(nb.load('mask.nii').get_data(),
                                      ([[[0,0],[0,0]],[[0,0],[1,0]]]))
@@ -120,7 +119,6 @@ def test_tcompcor_merge_intersect_masks(self):
                                       ([[[0,0],[0,0]],[[0,1],[0,0]]]))
 
     def test_tcompcor_index_mask(self):
-        print(len(self.mask_files))
         TCompCor(realigned_file=self.realigned_file,
                  mask_files=self.mask_files,
                  mask_index=1).run()