BF - set pixdims from affine when initializing image with affine; thanks to Satra for pointing out the need

Author: matthew-brett

nibabel/nifti1.py

@@ -1376,8 +1376,13 @@ def update_header(self):
         hdr = self._header
         hdr['magic'] = 'ni1'
         if not self._affine is None:
+            # Set affine into sform
             hdr.set_sform(self._affine, code='aligned')
+            # Make qform 'unknown', set voxel sizes from affine
             hdr['qform_code'] = 0
+            RZS = self._affine[:3, :3]
+            zooms = np.sqrt(np.sum(RZS * RZS, axis=0))
+            hdr['pixdim'][1:4] = zooms
 
 
 class Nifti1Image(Nifti1Pair):

nibabel/tests/test_nifti1.py

@@ -628,24 +628,29 @@ def test_affines_init():
     hdr = img.get_header()
     assert_equal(hdr['qform_code'], 0)
     assert_equal(hdr['sform_code'], 2)
+    assert_array_equal(hdr.get_zooms(), [2, 3, 4])
     # This is also true for affines with header passed
     qaff = np.diag([3, 4, 5, 1])
     saff = np.diag([6, 7, 8, 1])
     hdr.set_qform(qaff, code='scanner')
     hdr.set_sform(saff, code='talairach')
+    assert_array_equal(hdr.get_zooms(), [3, 4, 5])
     img = Nifti1Image(arr, aff, hdr)
     new_hdr = img.get_header()
     # Again affine is sort of anonymous space
     assert_equal(new_hdr['qform_code'], 0)
     assert_equal(new_hdr['sform_code'], 2)
     assert_array_equal(new_hdr.get_sform(), aff)
+    assert_array_equal(new_hdr.get_zooms(), [2, 3, 4])
     # But if no affine passed, codes and matrices stay the same
     img = Nifti1Image(arr, None, hdr)
     new_hdr = img.get_header()
     assert_equal(new_hdr['qform_code'], 1) # scanner
     assert_array_equal(new_hdr.get_qform(), qaff)
     assert_equal(new_hdr['sform_code'], 3) # Still talairach
     assert_array_equal(new_hdr.get_sform(), saff)
+    # Pixdims as in the original header
+    assert_array_equal(new_hdr.get_zooms(), [3, 4, 5])