Added FSL Displacement field class and a FSL warp

Author: smoia

nitransforms/io/fsl.py

@@ -9,6 +9,7 @@
 from .base import (
     BaseLinearTransformList,
     LinearParameters,
+    DisplacementsField,
     TransformFileError,
     _ensure_image,
 )
@@ -171,6 +172,26 @@ def from_filename(cls, filename):
         return _self
 
 
+class FSLDisplacementsField(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) != 4 or not shape[-1] in (2, 3):
+            raise TransformFileError(
+                'Displacements field "%s" does not come from FSL.' %
+                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 _fsl_aff_adapt(space):
     """
     Adapt FSL affines.