Initial commit for the image registration code.

1) Developed a new workflow for image registration.
2) Developed a testing script for the workflow to replicate and validate run time output and error.

Future Work

1) Link the test script for automated execution in Nose.
2) Create a function to replicate error behavior for wrong input.
3) Add few more checks for validating the format and type of input parameters in the workflow.

dipy/io/image.py

@@ -1,6 +1,7 @@
 from __future__ import division, print_function, absolute_import
 
 import nibabel as nib
+import numpy as np
 
 
 def load_nifti(fname, return_img=False, return_voxsize=False,
@@ -24,3 +25,17 @@ def load_nifti(fname, return_img=False, return_voxsize=False,
 def save_nifti(fname, data, affine, hdr=None):
     result_img = nib.Nifti1Image(data, affine, header=hdr)
     result_img.to_filename(fname)
+
+
+def save_affine_matrix(fname, affine):
+
+    """
+    Parameters
+    ---------
+    fname : str
+        File path to save the affine matrix.
+    affine : numpy array
+        The object containing the affine matrix.
+    """
+    np.savetxt(fname, affine)
+

dipy/workflows/tests/test_image_registration.py

@@ -0,0 +1,109 @@
+import os.path
+from os.path import join as pjoin
+import shutil
+import numpy as np
+import numpy.testing as npt
+
+from time import sleep
+
+from nibabel.tmpdirs import TemporaryDirectory
+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.image_registration import ImageRegistrationFlow
+
+folder_path = '/Users/schmuck/Documents/register_workflow_test/test'
+
+def test_image_registration():
+
+    image_registeration_flow = ImageRegistrationFlow()
+
+    with TemporaryDirectory() as temp_out_dir:
+
+        static, moving, static_g2w, moving_g2w, smask, mmask, M = setup_random_transform(
+            transform=regtransforms[('TRANSLATION', 3)], rfactor=2.0)
+
+        save_nifti(pjoin(folder_path,'mask.nii.gz'),data=smask,affine=static_g2w)
+
+        save_nifti(pjoin(temp_out_dir,'b0.nii.gz'), data=static,
+                   affine=static_g2w)
+        save_nifti(pjoin(temp_out_dir,'t1.nii.gz'), data=moving,
+                   affine=moving_g2w)
+
+        static_image_file = pjoin(temp_out_dir,'b0.nii.gz')
+        moving_image_file = pjoin(temp_out_dir,'t1.nii.gz')
+
+        out_moved = pjoin(temp_out_dir, "com_moved.nii.gz")
+        out_affine = pjoin(temp_out_dir, "com_affine.txt")
+
+        image_registeration_flow.run(str(static_image_file),
+                                     str(moving_image_file),
+                                     transform='com',
+                                     out_dir=temp_out_dir
+                                     ,out_moved=out_moved,
+                                     out_affine=out_affine)
+
+        npt.assert_equal(os.path.exists(out_moved), True)
+        npt.assert_equal(os.path.exists(out_affine), True)
+
+        out_moved = pjoin(temp_out_dir, "trans_moved.nii.gz")
+        out_affine = pjoin(temp_out_dir, "trans_affine.txt")
+
+        print('trans')
+        image_registeration_flow.run(str(static_image_file),
+                                     str(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)
+
+        out_moved = pjoin(temp_out_dir, "rigid_moved.nii.gz")
+        out_affine = pjoin(temp_out_dir, "rigid_affine.txt")
+
+        image_registeration_flow.run(str(static_image_file),
+                                     str(moving_image_file),
+                                     transform='rigid',
+                                     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)
+
+        out_moved = pjoin(temp_out_dir, "affine_moved.nii.gz")
+        out_affine = pjoin(temp_out_dir, "affine_affine.txt")
+
+        print('affine')
+
+        image_registeration_flow.run(str(static_image_file),
+                                     str(moving_image_file),
+                                     transform='affine',
+                                     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)
+
+        copy_output(temp_out_dir,folder_path)
+
+
+def copy_output(temp_directory_path, folder_path):
+
+    out_files = list(glob(pjoin(temp_directory_path,'*.nii.gz')) + glob(pjoin(temp_directory_path,'*.txt')))
+
+    for out_file in out_files:
+        shutil.copy(out_file, folder_path)
+
+
+if __name__ == '__main__':
+    test_image_registration()