Merge pull request #182 from bpinsard/enh/output_displacement_field

FIX: Output displacement fields

Author: oesteban

nitransforms/io/afni.py

@@ -209,6 +209,17 @@ def from_image(cls, imgobj):
 
         return imgobj.__class__(field, imgobj.affine, hdr)
 
+    @classmethod
+    def to_image(cls, imgobj):
+        """Export a displacements field from a nibabel object."""
+
+        hdr = imgobj.header.copy()
+
+        warp_data = imgobj.get_fdata().reshape(imgobj.shape[:3] + (1, imgobj.shape[-1]))
+        warp_data[..., (0, 1)] *= -1
+
+        return imgobj.__class__(warp_data, imgobj.affine, hdr)
+
 
 def _is_oblique(affine, thres=OBLIQUITY_THRESHOLD_DEG):
     """

nitransforms/io/base.py

@@ -146,6 +146,17 @@ def from_image(cls, imgobj):
         """Import a displacements field from a nibabel image object."""
         raise NotImplementedError
 
+    @classmethod
+    def to_filename(cls, img, filename):
+        """Export a displacements field to a NIfTI file."""
+        imgobj = cls.to_image(img)
+        imgobj.to_filename(filename)
+
+    @classmethod
+    def to_image(cls, imgobj):
+        """Export a displacements field image from a nitransforms image object."""
+        raise NotImplementedError
+
 
 def _ensure_image(img):
     if isinstance(img, (str, Path)):

nitransforms/io/fsl.py

@@ -190,6 +190,17 @@ def from_image(cls, imgobj):
 
         return imgobj.__class__(field, imgobj.affine, hdr)
 
+    @classmethod
+    def to_image(cls, imgobj):
+        """Export a displacements field from a nibabel object."""
+
+        hdr = imgobj.header.copy()
+
+        warp_data = imgobj.get_fdata()
+        warp_data[..., 0] *= -1
+
+        return imgobj.__class__(warp_data, imgobj.affine, hdr)
+
 
 def _fsl_aff_adapt(space):
     """

nitransforms/io/itk.py

@@ -352,6 +352,18 @@ def from_image(cls, imgobj):
 
         return imgobj.__class__(field, imgobj.affine, hdr)
 
+    @classmethod
+    def to_image(cls, imgobj):
+        """Export a displacements field from a nibabel object."""
+
+        hdr = imgobj.header.copy()
+        hdr.set_intent("vector")
+
+        warp_data = imgobj.get_fdata().reshape(imgobj.shape[:3] + (1, imgobj.shape[-1]))
+        warp_data[..., (0, 1)] *= -1
+
+        return imgobj.__class__(warp_data, imgobj.affine, hdr)
+
 
 class ITKCompositeH5:
     """A data structure for ITK's HDF5 files."""