fixed bug with create sphere and mask

Former-commit-id: b9f8116

Author: ljchang

nltools/data.py

@@ -87,8 +87,8 @@ def __init__(self, data=None, Y=None, X=None, mask=None, output_file=None, **kwa
                 if type(mask) is str:
                     if os.path.isfile(mask):
                         mask = nib.load(mask)
-            else:
-                raise ValueError("mask is not a nibabel instance")
+                else:
+                    raise ValueError("mask is not a nibabel instance or a valid file name")
             self.mask = mask
         else:
             self.mask = nib.load(os.path.join(get_resource_path(),'MNI152_T1_2mm_brain_mask.nii.gz'))

nltools/mask.py

@@ -82,9 +82,9 @@ def sphere(r, p, mask):
         coordinates = [coordinates]
     if (type(radius)) is list and (type(coordinates) is list) and (len(radius) == len(coordinates)):
         A = np.zeros_like(mask.get_data())
-        A = Brain_Data(nib.Nifti1Image(A,affine=mask.get_affine()))
+        A = Brain_Data(nib.Nifti1Image(A,affine=mask.affine),mask=mask)
         for i in xrange(len(radius)):
-            A = A + Brain_Data(sphere(radius[i], coordinates[i], mask))
+            A = A + Brain_Data(sphere(radius[i], coordinates[i], mask),mask=mask)
             # B,translation_affine = sphere(radius[i], coordinates[i], mask)
             # A = np.add(A, B)
             # A = np.add(A, sphere(radius[i], coordinates[i], mask))