1) Apply transform code is integrated with the align.py file.

2) Wrote the test cases for the apply transform for automated testing.
3) Did manual testing of the apply transform workflow.

dipy/workflows/align.py

@@ -567,7 +567,4 @@ def run(self, reference_image_file, moving_image_files, affine_matrix_file,
             img_transformation = AffineMap(affine=affine_matrix, domain_grid_shape=image_data.shape)
             transformed = img_transformation.transform(image_data)
 
-            if out_file == 'transformed.nii.gz':
-                save_nifti(pjoin(path.split(moving_image_file)[1]+out_file), transformed, affine=static_grid2world)
-            else:
-                save_nifti(out_file, transformed, affine=static_grid2world)
+            save_nifti(out_dir+out_file, transformed, affine=static_grid2world)

dipy/workflows/tests/test_align.py

@@ -1,5 +1,8 @@
 import numpy.testing as npt
+import numpy as np
 
+
+from time import sleep
 import nibabel as nib
 from nibabel.tmpdirs import TemporaryDirectory
 
@@ -8,15 +11,14 @@
 
 import os.path
 from os.path import join as pjoin
-import shutil
 
 from dipy.align.tests.test_parzenhist import setup_random_transform
 from dipy.align.transforms import (Transform,
                                    regtransforms)
 from dipy.io.image import save_nifti
-from glob import glob
 
 from dipy.workflows.align import ImageRegistrationFlow
+from dipy.workflows.align import ApplyTransformFlow
 
 
 def test_reslice():
@@ -156,3 +158,62 @@ def test_err():
         test_affine()
         test_err()
 
+
+def test_apply_transform():
+    with TemporaryDirectory() as temp_out_dir:
+
+        factors = {
+            ('TRANSLATION', 3): (2.0, None, np.array([2.3, 4.5, 1.7])),
+            ('RIGID', 3): (0.1, None, np.array([0.1, 0.15, -0.11, 2.3, 4.5,
+                                                1.7])),
+            ('AFFINE', 3): (0.1, None, np.array([0.99, -0.05, 0.03, 1.3,
+                                                 0.05, 0.99, -0.10, 2.5,
+                                                 -0.07, 0.10, 0.99, -1.4]))}
+
+        for i in factors.keys():
+            static, moving, static_g2w, moving_g2w, \
+            smask, mmask, M = setup_random_transform(
+                transform=regtransforms[i], rfactor=factors[i][0])
+
+            some = str(i[0]) + '_static.nii.gz'
+            one =  str(i[0]) + '_moving.nii.gz'
+
+            save_nifti(pjoin(temp_out_dir, some), data=static,
+                       affine=static_g2w)
+
+            save_nifti(pjoin(temp_out_dir, one), data=moving,
+                       affine=moving_g2w)
+
+
+        static_image_file = pjoin(temp_out_dir, 'TRANSLATION_static.nii.gz')
+        moving_image_file = pjoin(temp_out_dir, 'TRANSLATION_moving.nii.gz')
+
+        out_moved = pjoin(temp_out_dir, "trans_moved.nii.gz")
+        out_affine = pjoin(temp_out_dir, "trans_affine.txt")
+
+        image_registeration_flow = ImageRegistrationFlow()
+
+        image_registeration_flow.run(static_image_file,
+                                     moving_image_file,
+                                     transform='trans',
+                                     out_dir=temp_out_dir,
+                                     out_moved=out_moved,
+                                     out_affine=out_affine,
+                                     level_iters=[100, 10, 1])
+
+        npt.assert_equal(os.path.exists(out_moved), True)
+        npt.assert_equal(os.path.exists(out_affine), True)
+
+
+        apply_trans = ApplyTransformFlow()
+        two = pjoin(temp_out_dir,'*moving*')
+        apply_trans.run(static_image_file, two, out_affine)
+
+        npt.assert_equal(os.path.exists(pjoin(temp_out_dir,'transformed.nii.gz')), True)
+
+
+if __name__ == "__main__":
+        test_reslice()
+        test_image_registration()
+        test_apply_transform()
+