Merge branch 'master' into sandbox

Author: effigies

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."""

nitransforms/nonlinear.py

@@ -173,13 +173,17 @@ def map(self, x, inverse=False):
                     ijk.T,
                     order=3,
                     mode="constant",
-                    cval=0,
+                    cval=np.nan,
                     prefilter=True,
                 )
                 for i in range(self.reference.ndim)
             )
         ).T
 
+        # Set NaN values back to the original coordinates value = no displacement
+        new_map[np.isnan(new_map)] = x[np.isnan(new_map)]
+        return new_map
+
     def __matmul__(self, b):
         """
         Compose with a transform on the right.