RF: Derive affine in SpatialImage.transpose

Return original image if no transform is to be made

Author: effigies

nibabel/funcs.py

@@ -10,8 +10,7 @@
 ''' Processor functions for images '''
 import numpy as np
 
-from .orientations import (io_orientation, inv_ornt_aff,
-                           OrientationError)
+from .orientations import io_orientation, OrientationError
 from .loadsave import load
 
 
@@ -206,24 +205,14 @@ def as_closest_canonical(img, enforce_diag=False):
        already has the correct data ordering, we just return `img`
        unmodified.
     '''
-    aff = img.affine
-    ornt = io_orientation(aff)
-    if np.all(ornt == [[0, 1],
-                       [1, 1],
-                       [2, 1]]):  # canonical already
-        # however, the affine may not be diagonal
-        if enforce_diag and not _aff_is_diag(aff):
-            raise OrientationError('Transformed affine is not diagonal')
-        return img
-    shape = img.shape
-    t_aff = inv_ornt_aff(ornt, shape)
-    out_aff = np.dot(aff, t_aff)
-    # check if we are going to end up with something diagonal
-    if enforce_diag and not _aff_is_diag(aff):
+    # Get the image class to transform the data for us
+    img = img.transpose(io_orientation(img.affine))
+
+    # however, the affine may not be diagonal
+    if enforce_diag and not _aff_is_diag(img.affine):
         raise OrientationError('Transformed affine is not diagonal')
 
-    # Get the image class to transform the data for us
-    return img.transpose(ornt, out_aff)
+    return img
 
 
 def _aff_is_diag(aff):

nibabel/nifti1.py

@@ -27,7 +27,6 @@
 from .spm99analyze import SpmAnalyzeHeader
 from .casting import have_binary128
 from .pydicom_compat import have_dicom, pydicom as pdcm
-from .orientations import apply_orientation
 
 # nifti1 flat header definition for Analyze-like first 348 bytes
 # first number in comments indicates offset in file header in bytes
@@ -1970,23 +1969,39 @@ def set_sform(self, affine, code=None, **kwargs):
             else:
                 self._affine[:] = self._header.get_best_affine()
 
-    def transpose(self, ornt, new_aff):
-        # Override the default SpatialImage method so that we update dim_info
-        t_arr = apply_orientation(self.get_data(), ornt)
+    def transpose(self, ornt):
+        """Apply an orientation change and return a new image
+
+        If image already has orientation, return the original image, unchanged
+
+        Parameters
+        ----------
+        ornt : (n,2) orientation array
+           orientation transform. ``ornt[N,1]` is flip of axis N of the
+           array implied by `shape`, where 1 means no flip and -1 means
+           flip.  For example, if ``N==0`` and ``ornt[0,1] == -1``, and
+           there's an array ``arr`` of shape `shape`, the flip would
+           correspond to the effect of ``np.flipud(arr)``.  ``ornt[:,0]`` is
+           the transpose that needs to be done to the implied array, as in
+           ``arr.transpose(ornt[:,0])``
+        """
+        img = super(Nifti1Pair, self).transpose(ornt)
+
+        if img is self:
+            return img
 
         # Also apply the transform to the dim_info fields
-        new_hdr = self.header.copy()
-        new_dim = list(new_hdr.get_dim_info())
+        new_dim = list(img.header.get_dim_info())
         for idx, value in enumerate(new_dim):
             # For each value, leave as None if it was that way,
             # otherwise check where we have mapped it to
             if value is None:
                 continue
             new_dim[idx] = np.where(ornt[:, 0] == idx)[0]
 
-        new_hdr.set_dim_info(*new_dim)
+        img.header.set_dim_info(*new_dim)
 
-        return self.__class__(t_arr, new_aff, new_hdr)
+        return img
 
 
 class Nifti1Image(Nifti1Pair):

nibabel/spatialimages.py

@@ -141,7 +141,7 @@
 from .viewers import OrthoSlicer3D
 from .volumeutils import shape_zoom_affine
 from .deprecated import deprecate_with_version
-from .orientations import apply_orientation
+from .orientations import apply_orientation, inv_ornt_aff
 
 
 class HeaderDataError(Exception):
@@ -486,9 +486,11 @@ def orthoview(self):
                              title=self.get_filename())
 
 
-    def transpose(self, ornt, new_aff):
+    def transpose(self, ornt):
         """Apply an orientation change and return a new image
 
+        If image already has orientation, return the original image, unchanged
+
         Parameters
         ----------
         ornt : (n,2) orientation array
@@ -506,6 +508,10 @@ def transpose(self, ornt, new_aff):
         when re-orienting an image.
         """
 
+        if np.array_equal(ornt, [[0, 1], [1, 1], [2, 1]]):
+            return self
+
         t_arr = apply_orientation(self.get_data(), ornt)
+        new_aff = self.affine.dot(inv_ornt_aff(ornt, self.shape))
 
         return self.__class__(t_arr, new_aff, self.header)