Merge pull request #51 from smoia/enh/fsl-displacementfield

ENH: I/O of FSL displacements fields

Author: oesteban

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] *= -1.0
+
+        return imgobj.__class__(field, imgobj.affine, hdr)
+
+
 def _fsl_aff_adapt(space):
     """
     Adapt FSL affines.

nitransforms/nonlinear.py

@@ -77,14 +77,15 @@ def map(self, x, inverse=False):
 
     @classmethod
     def from_filename(cls, filename, fmt="X5"):
-        if fmt == "afni":
-            _factory = io.afni.AFNIDisplacementsField
-        elif fmt == "itk":
-            _factory = io.itk.ITKDisplacementsField
-        else:
-            raise NotImplementedError
-
-        return cls(_factory.from_filename(filename))
+        _factory = {
+            "afni": io.afni.AFNIDisplacementsField,
+            "itk": io.itk.ITKDisplacementsField,
+            "fsl": io.fsl.FSLDisplacementsField,
+        }
+        if fmt not in _factory:
+            raise NotImplementedError(f"Unsupported format <{fmt}>")
+
+        return cls(_factory[fmt].from_filename(filename))
 
 
 load = DisplacementsFieldTransform.from_filename

nitransforms/tests/data/ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz

@@ -12,6 +12,7 @@
 from ..nonlinear import DisplacementsFieldTransform, load as nlload
 from ..io.itk import ITKDisplacementsField
 
+
 TESTS_BORDER_TOLERANCE = 0.05
 APPLY_NONLINEAR_CMD = {
     "itk": """\
@@ -22,6 +23,9 @@
 3dNwarpApply -nwarp {transform} -source {moving} \
 -master {reference} -interp NN -prefix resampled.nii.gz
 """.format,
+    'fsl': """\
+applywarp -i {moving} -r {reference} -o resampled.nii.gz \
+-w {transform} --interp=nn""".format,
 }
 
 
@@ -59,7 +63,10 @@ def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool
     os.chdir(str(tmp_path))
     nii = get_testdata[image_orientation]
     nii.to_filename("reference.nii.gz")
-    fieldmap = np.zeros((*nii.shape[:3], 1, 3), dtype="float32")
+    fieldmap = np.zeros(
+        (*nii.shape[:3], 1, 3) if sw_tool != "fsl" else (*nii.shape[:3], 3),
+        dtype="float32",
+    )
     fieldmap[..., axis] = -10.0
 
     _hdr = nii.header.copy()