Merge pull request #1309 from chrisfilo/fix/distance

Added support for nan images and turned off memory mapping in Distance calculation.

Author: chrisgorgo

nipype/algorithms/metrics.py

@@ -105,12 +105,12 @@ def _eucl_min(self, nii1, nii2):
                 set2_coordinates.T[point2, :])
 
     def _eucl_cog(self, nii1, nii2):
-        origdata1 = nii1.get_data().astype(np.bool)
-        cog_t = np.array(center_of_mass(origdata1)).reshape(-1, 1)
+        origdata1 = np.logical_and(nii1.get_data() != 0, np.logical_not(np.isnan(nii1.get_data())))
+        cog_t = np.array(center_of_mass(origdata1.copy())).reshape(-1, 1)
         cog_t = np.vstack((cog_t, np.array([1])))
         cog_t_coor = np.dot(nii1.affine, cog_t)[:3, :]
 
-        origdata2 = nii2.get_data().astype(np.bool)
+        origdata2 = np.logical_and(nii2.get_data() != 0, np.logical_not(np.isnan(nii2.get_data())))
         (labeled_data, n_labels) = label(origdata2)
 
         cogs = np.ones((4, n_labels))
@@ -181,8 +181,9 @@ def _eucl_max(self, nii1, nii2):
         return np.max(mins)
 
     def _run_interface(self, runtime):
-        nii1 = nb.load(self.inputs.volume1)
-        nii2 = nb.load(self.inputs.volume2)
+        # there is a bug in some scipy ndimage methods that gets tripped by memory mapped objects
+        nii1 = nb.load(self.inputs.volume1, mmap=False)
+        nii2 = nb.load(self.inputs.volume2, mmap=False)
 
         if self.inputs.method == "eucl_min":
             self._distance, self._point1, self._point2 = self._eucl_min(