Created the apply transfomr workflow.

1) Added a function to load the saved affine matrix from the text file.
2) Added the import of ndimage from scipy in the test_parzenhist.py file.
3) Created a new workflow file apply_transform.

dipy/align/tests/test_parzenhist.py

@@ -1,5 +1,6 @@
 import numpy as np
 import scipy as sp
+from scipy import ndimage
 from functools import reduce
 from operator import mul
 from dipy.core.ndindex import ndindex

dipy/io/image.py

@@ -1,7 +1,6 @@
 from __future__ import division, print_function, absolute_import
-
-import nibabel as nib
 import numpy as np
+import nibabel as nib
 
 
 def load_nifti(fname, return_img=False, return_voxsize=False,
@@ -37,3 +36,13 @@ def save_affine_matrix(fname, affine):
         The object containing the affine matrix.
     """
     np.savetxt(fname, affine)
+
+
+def load_affine_matrix(fname):
+    """
+        Parameters
+        ---------
+        fname : str
+            The file containing the saved affine matrix.
+    """
+    return np.loadtxt(fname)

dipy/workflows/apply_transform.py

@@ -0,0 +1,47 @@
+from dipy.workflows.workflow import Workflow
+
+from dipy.align.imaffine import AffineMap
+import nibabel as nib
+import numpy as np
+from os.path import join as pjoin
+from os import path
+from dipy.io.image import save_nifti, load_affine_matrix
+
+
+class ApplyTransformFlow(Workflow):
+
+    def run(self, reference_image_file, moving_image_files, affine_matrix_file,
+            out_file='transformed.nii.gz'):
+
+        """
+        Parameters
+        ----------
+        reference_image_file : string
+            Path to the static image file.
+
+        moving_image_files : string
+            Location of the file or folder containing the images to be transformed.
+
+        affine_matrix_file : string
+            The text file containing the affine matrix for transformation.
+
+        out_file : string, optional
+            Name of the transformed file. (default 'transformed.nii.gz')
+        """
+
+        io = self.get_io_iterator()
+
+        for ref_image_file, mov_images, affine_matrix_file, out_file in io:
+
+            ref_image = nib.load(ref_image_file)
+            static_grid2world = ref_image.affine
+
+            image = nib.load(mov_images)
+            image_data = np.array(image.get_data())
+
+            affine_matrix = load_affine_matrix(affine_matrix_file)
+
+            img_transformation = AffineMap(affine=affine_matrix, domain_grid_shape=image_data.shape)
+            transformed = img_transformation.transform(image_data)
+
+            save_nifti(pjoin(path.split(mov_images)[1]+out_file), transformed, affine=static_grid2world)