move comps check to only sqeuclidean

Author: lsqshr

nipype/algorithms/metrics.py

@@ -530,30 +530,29 @@ def _run_interface(self, runtime):
         else:
             msk = np.ones(shape=mapshape)
 
-        # Vectorise both volumes and make the pixel differennce
+        # Flatten both volumes and make the pixel differennce
         mskvector = msk.reshape(-1)
         msk_idxs = np.where(mskvector==1)
         refvector = ref_data.reshape(-1,comps)[msk_idxs].astype(np.float32)
         tstvector = tst_data.reshape(-1,comps)[msk_idxs].astype(np.float32)
         diffvector = (refvector-tstvector)
 
-        # scale the diffrernce
+        # Scale the diffrernce
         if self.inputs.metric == 'sqeuclidean':
             errvector = diffvector**2
+            if (comps > 1):
+                errvector = np.sum(errvector, axis=1)
+            else:
+                errvector = np.squeeze(errvector)
         elif self.inputs.metric == 'euclidean':
             #X = np.hstack((refvector, tstvector))
             errvector = np.linalg.norm(diffvector, axis=1)
 
-        if (comps > 1):
-            errvector = np.sum(errvector, axis=1)
-        else:
-            errvector = np.squeeze(errvector)
-
         errvectorexp = np.zeros_like(mskvector, dtype=np.float32) # The default type is uint8
         errvectorexp[msk_idxs] = errvector
 
         # Get averaged error
-        self._distance = np.average(errvector)
+        self._distance = np.average(errvector) # Only average the masked voxels
 
         errmap = errvectorexp.reshape(mapshape)
 

nipype/algorithms/tests/test_errormap.py

@@ -30,6 +30,7 @@ def test_errormap():
 	errmap = ErrorMap()
 	errmap.inputs.in_tst = os.path.join(tempdir, 'von.nii.gz')
 	errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz')
+	errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz')
 	result = errmap.run()
 	yield assert_equal, result.outputs.distance, 1.125 
 
@@ -57,19 +58,19 @@ def test_errormap():
 	msimg1 = nib.Nifti1Image(msvolume1, np.eye(4))
 
 	msvolume2 = np.zeros(shape=(2,2,2,2))
-	msvolume2[:,:,:,0] = volume2
-	msvolume2[:,:,:,1] = volume3
+	msvolume2[:,:,:,0] = volume3
+	msvolume2[:,:,:,1] = volume1
 	msimg2 = nib.Nifti1Image(msvolume2, np.eye(4))
 
-	nib.save(img1, os.path.join(tempdir, 'von-ray.nii.gz'))
-	nib.save(img2, os.path.join(tempdir, 'alan-ray.nii.gz'))
+	nib.save(msimg1, os.path.join(tempdir, 'von-ray.nii.gz'))
+	nib.save(msimg2, os.path.join(tempdir, 'alan-ray.nii.gz'))
 
 	errmap.inputs.in_tst = os.path.join(tempdir, 'von-ray.nii.gz')
 	errmap.inputs.in_ref = os.path.join(tempdir, 'alan-ray.nii.gz')
 	errmap.inputs.metric = 'sqeuclidean'
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 7.0
+	yield assert_equal, result.outputs.distance, 5.5
 
 	errmap.inputs.metric = 'euclidean'
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 2**0.5 + 6
+	yield assert_equal, result.outputs.distance, np.float32(1.25 * (2**0.5))