ENH: Add explicit identity linear transform.

ants/registration/registration.py

@@ -1621,8 +1621,8 @@ def label_image_registration(fixed_label_images,
         of the moving image.
 
     type_of_linear_transform : string
-        Use label images with the centers of mass to a calculate linear
-        transform of type 'rigid', 'similarity', or 'affine'.
+        Use label images with the centers of mass to a calculate linear 
+        transform of type 'identity', 'rigid', 'similarity', or 'affine'.
 
     type_of_deformable_transform : string
         Only works with deformable-only transforms, specifically the family
@@ -1707,7 +1707,7 @@ def label_image_registration(fixed_label_images,
     if output_prefix == "" or output_prefix is None or len(output_prefix) == 0:
         output_prefix = mktemp()
 
-    allowable_linear_transforms = ['rigid', 'similarity', 'affine']
+    allowable_linear_transforms = ['rigid', 'similarity', 'affine', 'identity']  
     if not type_of_linear_transform in allowable_linear_transforms:
         raise ValueError("Unrecognized linear transform.")
 
@@ -1729,6 +1729,8 @@ def label_image_registration(fixed_label_images,
         if len(common_label_ids[i]) == 0:
             raise ValueError("No common labels for image pair " + str(i))
 
+    deformable_multivariate_extras = list()
+
     if verbose:
         print("Total number of labels: " + str(total_number_of_labels))
 
@@ -1739,7 +1741,7 @@ def label_image_registration(fixed_label_images,
     ##############################
 
     linear_xfrm = None
-    if type_of_linear_transform is not None:
+    if type_of_linear_transform != 'identity':
 
         if verbose:
             print("\n\nComputing linear transform.\n")
@@ -1749,8 +1751,6 @@ def label_image_registration(fixed_label_images,
 
         fixed_centers_of_mass = np.zeros((total_number_of_labels, image_dimension))
         moving_centers_of_mass = np.zeros((total_number_of_labels, image_dimension))
-        deformable_multivariate_extras = list()
-
         count = 0
         for i in range(len(common_label_ids)):
             for j in range(len(common_label_ids[i])):
@@ -1783,6 +1783,16 @@ def label_image_registration(fixed_label_images,
 
     if do_deformable:
 
+        if type_of_linear_transform == "identity":
+            for i in range(len(common_label_ids)):
+                for j in range(len(common_label_ids[i])):
+                    label = common_label_ids[i][j]
+                    fixed_single_label_image = ants.threshold_image(fixed_label_images[i], label, label, 1, 0)
+                    moving_single_label_image = ants.threshold_image(moving_label_images[i], label, label, 1, 0)
+                    deformable_multivariate_extras.append(["MSQ", fixed_single_label_image, 
+                                                        moving_single_label_image, 
+                                                        label_image_weights[i], 0])
+
         if verbose:
             print("\n\nComputing deformable transform using images.\n")
 
@@ -1940,13 +1950,20 @@ def label_image_registration(fixed_label_images,
 
     find_inverse_warps = np.where([re.search("[0-9]InverseWarp.nii.gz", ff) for ff in all_xfrms])[0]
     find_forward_warps = np.where([re.search("[0-9]Warp.nii.gz", ff) for ff in all_xfrms])[0]
-
-    if len(find_inverse_warps) > 0:
-        fwdtransforms = [all_xfrms[find_forward_warps[0]], linear_xfrm_file]
-        invtransforms = [linear_xfrm_file, all_xfrms[find_inverse_warps[0]]]
+
+    fwdtransforms = []
+    invtransforms = []
+    if linear_xfrm is not None:
+        if len(find_inverse_warps) > 0:
+            fwdtransforms = [all_xfrms[find_forward_warps[0]], linear_xfrm_file]
+            invtransforms = [linear_xfrm_file, all_xfrms[find_inverse_warps[0]]]
+        else:
+            fwdtransforms = [linear_xfrm_file]
+            invtransforms = [linear_xfrm_file]                     
     else:
-        fwdtransforms = [linear_xfrm_file]
-        invtransforms = [linear_xfrm_file]
+        if len(find_inverse_warps) > 0:
+            fwdtransforms = [all_xfrms[find_forward_warps[0]]]
+            invtransforms = [all_xfrms[find_inverse_warps[0]]]
 
     if verbose:
         print("\n\nResulting transforms")