Merge pull request #638 from ANTsX/ants_read_warp_transform

Ants read warp transform

ants/core/ants_transform_io.py

@@ -253,6 +253,10 @@ def transform_from_displacement_field(field):
     """
     if not isinstance(field, iio.ANTsImage):
         raise ValueError("field must be ANTsImage type")
+    if field.dimension < 2 or field.dimension > 3:
+        raise ValueError("Unsupported displacement field dimension: %i" % field.dimension)
+    if field.components != field.dimension:
+        raise ValueError("Displacement field must have same number of components as the image dimension")
     libfn = utils.get_lib_fn("antsTransformFromDisplacementField")
     field = field.clone("float")
     txptr = libfn(field.pointer)
@@ -263,6 +267,7 @@ def transform_from_displacement_field(field):
         pointer=txptr,
     )
 
+
 def transform_to_displacement_field(xfrm, ref):
     """
     Convert displacement field ANTsTransform to displacement field
@@ -299,6 +304,7 @@ def transform_to_displacement_field(xfrm, ref):
     field_ptr = libfn(xfrm.pointer, ref.pointer)
     return iio2.from_pointer(field_ptr)
 
+
 def read_transform(filename, precision="float"):
     """
     Read a transform from file
@@ -329,7 +335,9 @@ def read_transform(filename, precision="float"):
     if not os.path.exists(filename):
         raise ValueError("filename does not exist!")
 
-    # intentionally ignore dimension
+    if filename.endswith('.nii') or filename.endswith('.nii.gz'):
+        return transform_from_displacement_field(iio2.image_read(filename))
+
     libfn1 = utils.get_lib_fn("getTransformDimensionFromFile")
     dimensionUse = libfn1(filename)
 
@@ -377,7 +385,7 @@ def write_transform(transform, filename):
     """
     if not isinstance(transform, tio.ANTsTransform):
         raise Exception('Only ANTsTransform instances can be written to file. Check that you are not passing in a filepath to a saved transform.')
-    
+
     filename = os.path.expanduser(filename)
     libfn = utils.get_lib_fn("writeTransform")
     libfn(transform.pointer, filename)

tests/test_core_ants_transform_io.py

@@ -31,17 +31,17 @@ def setUp(self):
         self.txs = [tx2d, tx3d]
         self.pixeltypes = ['unsigned char', 'unsigned int', 'float']
 
-        self.matrix_offset_types = ['AffineTransform', 
+        self.matrix_offset_types = ['AffineTransform',
                                     'CenteredAffineTransform',
                                     'Euler2DTransform',
                                     'Euler3DTransform',
                                     'Rigid2DTransform',
                                     'QuaternionRigidTransform',
                                     'Similarity2DTransform',
                                     'CenteredSimilarity2DTransform',
-                                    'Similarity3DTransform', 
+                                    'Similarity3DTransform',
                                     'CenteredRigid2DTransform',
-                                    'CenteredEuler3DTransform', 
+                                    'CenteredEuler3DTransform',
                                     'Rigid3DTransform']
 
     def tearDown(self):
@@ -95,16 +95,27 @@ def test_read_write_transform(self):
         # file doesnt exist
         with self.assertRaises(Exception):
             ants.read_transform('blah-blah.mat')
-
+
+    def test_from_displacement_components(self):
+        vec_np = np.ndarray((2,2,3), dtype=np.float32)
+        vec = ants.from_numpy(vec_np, origin=(0,0), spacing=(1,1), has_components=True)
+        # should get ValueError here because the 2D vector field has 3 components
+        with self.assertRaises(ValueError):
+            ants.transform_from_displacement_field(vec)
+        vec_np = np.ndarray((2,2,2,3), dtype=np.float32)
+        vec = ants.from_numpy(vec_np, origin=(0,0,0), spacing=(1,1,1), has_components=True)
+        # should work here because the 3D vector field has 3 components
+        tx = ants.transform_from_displacement_field(vec)
+
     def test_from_displacement(self):
         fi = ants.image_read(ants.get_ants_data('r16') )
         mi = ants.image_read(ants.get_ants_data('r64') )
         fi = ants.resample_image(fi,(60,60),1,0)
         mi = ants.resample_image(mi,(60,60),1,0) # speed up
         mytx = ants.registration(fixed=fi, moving=mi, type_of_transform = ('SyN') )
-        vec = ants.image_read( mytx['fwdtransforms'][0] )
-        atx = ants.transform_from_displacement_field( vec )
-        
+        # read transform, which calls transform_from_displacement_field
+        atx = ants.read_transform( mytx['fwdtransforms'][0] )
+
     def test_to_displacement(self):
         fi = ants.image_read(ants.get_ants_data('r16') )
         mi = ants.image_read(ants.get_ants_data('r64') )
@@ -113,11 +124,11 @@ def test_to_displacement(self):
         mytx = ants.registration(fixed=fi, moving=mi, type_of_transform = ('SyN') )
         vec = ants.image_read( mytx['fwdtransforms'][0] )
         atx = ants.transform_from_displacement_field( vec )
-        field = ants.transform_to_displacement_field( atx, fi )   
-        
+        field = ants.transform_to_displacement_field( atx, fi )
+
     def test_catch_error(self):
         with self.assertRaises(Exception):
-            ants.write_transform(123, 'test.mat') 
+            ants.write_transform(123, 'test.mat')
 
 
 if __name__ == '__main__':