enh: initialize AFNI's displacements fields loader

Author: oesteban

nitransforms/io/afni.py

@@ -4,7 +4,12 @@
 from nibabel.affines import obliquity, voxel_sizes
 
 from ..patched import shape_zoom_affine
-from .base import BaseLinearTransformList, LinearParameters, TransformFileError
+from .base import (
+    BaseLinearTransformList,
+    DisplacementsField,
+    LinearParameters,
+    TransformFileError,
+)
 
 LPS = np.diag([-1, -1, 1, 1])
 OBLIQUITY_THRESHOLD_DEG = 0.01
@@ -119,5 +124,29 @@ def from_string(cls, string):
         return _self
 
 
+class AFNIDisplacementsField(DisplacementsField):
+    """A data structure representing displacements fields."""
+
+    @classmethod
+    def from_image(cls, imgobj):
+        """Import a displacements field from a NIfTI file."""
+        _hdr = imgobj.header.copy()
+        _shape = _hdr.get_data_shape()
+
+        if (
+            len(_shape) != 5 or
+            _shape[-2] != 1 or
+            not _shape[-1] in (2, 3)
+        ):
+            raise TransformFileError(
+                'Displacements field "%s" does not come from AFNI.' %
+                imgobj.file_map['image'].filename)
+
+        _field = np.squeeze(np.asanyarray(imgobj.dataobj))
+        _field[..., (0, 1)] *= -1.0
+
+        return imgobj.__class__(_field, imgobj.affine, _hdr)
+
+
 def _is_oblique(affine, thres=OBLIQUITY_THRESHOLD_DEG):
     return (obliquity(affine).min() * 180 / pi) > thres

nitransforms/io/base.py

@@ -157,6 +157,21 @@ def from_string(cls, string):
         raise NotImplementedError
 
 
+class DisplacementsField:
+    """A data structure representing displacements fields."""
+
+    @classmethod
+    def from_filename(cls, filename):
+        """Import a displacements field from a NIfTI file."""
+        imgobj = loadimg(str(filename))
+        return cls.from_image(imgobj)
+
+    @classmethod
+    def from_image(cls, imgobj):
+        """Import a displacements field from a nibabel image object."""
+        raise NotImplementedError
+
+
 def _read_mat(byte_stream):
     mjv, _ = get_matfile_version(byte_stream)
     if mjv == 0:

nitransforms/io/itk.py

@@ -4,7 +4,13 @@
 from scipy.io import savemat as _save_mat
 from nibabel.loadsave import load as loadimg
 from nibabel.affines import from_matvec
-from .base import BaseLinearTransformList, LinearParameters, _read_mat, TransformFileError
+from .base import (
+    BaseLinearTransformList,
+    DisplacementsField,
+    LinearParameters,
+    TransformFileError,
+    _read_mat,
+)
 
 LPS = np.diag([-1, -1, 1, 1])
 
@@ -249,15 +255,9 @@ def from_string(cls, string):
         return _self
 
 
-class ITKDisplacementsField:
+class ITKDisplacementsField(DisplacementsField):
     """A data structure representing displacements fields."""
 
-    @classmethod
-    def from_filename(cls, filename):
-        """Import a displacements field from a NIfTI file."""
-        imgobj = loadimg(str(filename))
-        return cls.from_image(imgobj)
-
     @classmethod
     def from_image(cls, imgobj):
         """Import a displacements field from a NIfTI file."""

nitransforms/tests/test_nonlinear.py

@@ -58,16 +58,14 @@ def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool
     fieldmap[..., axis] = -10.0
 
     _hdr = nii.header.copy()
-    _hdr.set_intent('vector')
+    if sw_tool in ('itk', ):
+        _hdr.set_intent('vector')
     _hdr.set_data_dtype('float32')
 
     xfm_fname = 'warp.nii.gz'
     field = nb.Nifti1Image(fieldmap, nii.affine, _hdr)
     field.to_filename(xfm_fname)
 
-    xfm = DisplacementsFieldTransform(
-        ITKDisplacementsField.from_image(field))
-
     # Then apply the transform and cross-check with software
     cmd = APPLY_NONLINEAR_CMD[sw_tool](
         transform=os.path.abspath(xfm_fname),