add SimpleITK.Image to ANTsImage conversion (#726)

* add sitk_to_ants

* move test to test_utils.py, install SimpleITK so test runs in coverage

---------

Co-authored-by: Bryn Lloyd <12702862+dyollb@users.noreply.github.com>

.github/workflows/code-coverage.yml

@@ -20,6 +20,9 @@ jobs:
       - name: Install coverage
         run: python -m pip install coverage
 
+      - name: Install optional dependencies
+        run: python -m pip install SimpleITK
+
       - name: Unit tests
         run: tests/run_tests.sh -c
 

ants/utils/__init__.py

@@ -11,4 +11,5 @@
 from .mni2tal import mni2tal
 from .ndimage_to_list import ndimage_to_list, list_to_ndimage
 from .nifti_to_ants import nifti_to_ants
-from .scalar_rgb_vector import rgb_to_vector, vector_to_rgb, scalar_to_rgb
+from .scalar_rgb_vector import rgb_to_vector, vector_to_rgb, scalar_to_rgb
+from .sitk_to_ants import from_sitk, to_sitk

ants/utils/nifti_to_ants.py

@@ -1,7 +1,5 @@
 __all__ = ["nifti_to_ants"]
 
-import os
-from tempfile import mkstemp
 import numpy as np
 import ants
 

ants/utils/sitk_to_ants.py

@@ -0,0 +1,63 @@
+import numpy as np
+import ants
+
+
+def from_sitk(sitk_image: "SimpleITK.Image") -> ants.ANTsImage:
+    """
+    Converts a given SimpleITK image into an ANTsPy image
+
+    Parameters
+    ----------
+        img: SimpleITK.Image
+
+    Returns
+    -------
+        ants_image: ANTsImage
+    """
+    import SimpleITK as sitk
+
+    ndim = sitk_image.GetDimension()
+
+    if ndim < 3:
+        print("Dimensionality is less than 3.")
+        return None
+
+    direction = np.asarray(sitk_image.GetDirection()).reshape((3, 3))
+    spacing = list(sitk_image.GetSpacing())
+    origin = list(sitk_image.GetOrigin())
+
+    data = sitk.GetArrayViewFromImage(sitk_image)
+
+    ants_img: ants.ANTsImage = ants.from_numpy(
+        data=data.ravel(order="F").reshape(data.shape[::-1]),
+        origin=origin,
+        spacing=spacing,
+        direction=direction,
+    )
+
+    return ants_img
+
+
+def to_sitk(ants_image: ants.ANTsImage) -> "SimpleITK.Image":
+    """
+    Converts a given ANTsPy image into an SimpleITK image
+
+    Parameters
+    ----------
+        ants_image: ANTsImage
+
+    Returns
+    -------
+        img: SimpleITK.Image
+    """
+
+    import SimpleITK as sitk
+
+    data = ants_image.view()
+    shape = ants_image.shape
+
+    sitk_img = sitk.GetImageFromArray(data.ravel(order="F").reshape(shape[::-1]))
+    sitk_img.SetOrigin(ants_image.origin)
+    sitk_img.SetSpacing(ants_image.spacing)
+    sitk_img.SetDirection(ants_image.direction.flatten())
+    return sitk_img

tests/test_utils.py

@@ -4,12 +4,17 @@
 
 import os
 import unittest
+from tempfile import TemporaryDirectory
 
 from common import run_tests
 
 import numpy.testing as nptest
 import numpy as np
 import pandas as pd
+try:
+    import SimpleITK as sitk
+except ImportError:
+    sitk = None
 
 import ants
 
@@ -994,5 +999,49 @@ def test_channels_first(self):
         self.assertTrue(np.allclose(img3.numpy()[:,:,1], img4.numpy()[1,:,:]))
 
 
+@unittest.skipIf(sitk is None, "SimpleITK is not installed")
+class TestModule_sitk_to_ants(unittest.TestCase):
+    def setUp(self):
+        shape = (32, 24, 16)
+        self.img = sitk.GetImageFromArray(np.arange(np.prod(shape), dtype=float).reshape(shape))
+        self.img.SetSpacing([0.5, 0.5, 2.0])
+        self.img.SetOrigin([1.2, 5.7, -3.4])
+        self.img.SetDirection(sitk.VersorTransform([1, 0, 0], 0.5).GetMatrix())
+
+    def tearDown(self):
+        pass
+
+    def test_from_sitk(self):
+        ants_img = ants.from_sitk(self.img)
+
+        with TemporaryDirectory() as temp_dir:
+            temp_fpath = os.path.join(temp_dir, "img.nrrd")
+            ants.image_write(ants_img, temp_fpath)
+            img = sitk.ReadImage(temp_fpath)
+
+        nptest.assert_equal(
+            sitk.GetArrayViewFromImage(self.img), sitk.GetArrayViewFromImage(img)
+        )
+        nptest.assert_almost_equal(self.img.GetOrigin(), img.GetOrigin())
+        nptest.assert_almost_equal(self.img.GetSpacing(), img.GetSpacing())
+        nptest.assert_almost_equal(self.img.GetDirection(), img.GetDirection())
+
+    def test_ito_sitk(self):
+        with TemporaryDirectory() as temp_dir:
+            temp_fpath = os.path.join(temp_dir, "img.nrrd")
+            sitk.WriteImage(self.img, temp_fpath)
+            ants_img = ants.image_read(temp_fpath)
+
+        img = ants.to_sitk(ants_img)
+
+        nptest.assert_equal(
+            sitk.GetArrayViewFromImage(self.img), sitk.GetArrayViewFromImage(img)
+        )
+        nptest.assert_almost_equal(self.img.GetOrigin(), img.GetOrigin())
+        nptest.assert_almost_equal(self.img.GetSpacing(), img.GetSpacing())
+        nptest.assert_almost_equal(self.img.GetDirection(), img.GetDirection())
+
+
+
 if __name__ == "__main__":
     run_tests()