Merge pull request #575 from pauldmccarthy/make_qform_sform_codes_int

Force sform/qform codes to be ints, rather than numpy types.

Author: effigies

doc/source/nifti_images.rst

@@ -237,7 +237,7 @@ You can get the affine and the code using the ``coded=True`` argument to
 (array([[  -2.  ,    0.  ,    0.  ,  117.86],
        [  -0.  ,    1.97,   -0.36,  -35.72],
        [   0.  ,    0.32,    2.17,   -7.25],
-       [   0.  ,    0.  ,    0.  ,    1.  ]]), array(1, dtype=int16))
+       [   0.  ,    0.  ,    0.  ,    1.  ]]), 1)
 
 You can set the sform with the ``set_sform()`` method of the header and
 the image.
@@ -256,7 +256,7 @@ Set the affine and code using the ``code`` parameter to ``set_sform()``:
 (array([[ 3.,  0.,  0.,  0.],
        [ 0.,  4.,  0.,  0.],
        [ 0.,  0.,  5.,  0.],
-       [ 0.,  0.,  0.,  1.]]), array(4, dtype=int16))
+       [ 0.,  0.,  0.,  1.]]), 4)
 
 The qform affine
 ================
@@ -276,7 +276,7 @@ the sform: ``get_qform()``, ``set_qform()``.
 (array([[  -2.  ,    0.  ,    0.  ,  117.86],
        [  -0.  ,    1.97,   -0.36,  -35.72],
        [   0.  ,    0.32,    2.17,   -7.25],
-       [   0.  ,    0.  ,    0.  ,    1.  ]]), array(1, dtype=int16))
+       [   0.  ,    0.  ,    0.  ,    1.  ]]), 1)
 
 The qform also has a corresponding ``qform_code`` with the same interpretation
 as the `sform_code`.
@@ -332,7 +332,7 @@ respectively:
 (array([[ 2.,  0.,  0.,  0.],
         [ 0.,  2.,  0.,  0.],
         [ 0.,  0.,  2.,  0.],
-        [ 0.,  0.,  0.,  1.]]), array(2, dtype=int16))
+        [ 0.,  0.,  0.,  1.]]), 2)
 >>> img.get_qform(coded=True)
 (None, 0)
 

nibabel/freesurfer/mghformat.py

@@ -251,7 +251,7 @@ def get_zooms(self):
         -------
         z : tuple
            tuple of header zoom values
-           
+
         .. _mghformat: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat#line-82
         '''
         # Do not return time zoom (TR) if 3D image

nibabel/nifti1.py

@@ -911,7 +911,7 @@ def get_qform(self, coded=False):
             Qform code. Only returned if `coded` is True.
         """
         hdr = self._structarr
-        code = hdr['qform_code']
+        code = int(hdr['qform_code'])
         if code == 0 and coded:
             return None, 0
         quat = self.get_qform_quaternion()
@@ -1054,7 +1054,7 @@ def get_sform(self, coded=False):
             Sform code. Only returned if `coded` is True.
         """
         hdr = self._structarr
-        code = hdr['sform_code']
+        code = int(hdr['sform_code'])
         if code == 0 and coded:
             return None, 0
         out = np.eye(4)

nibabel/tests/test_nifti1.py

@@ -12,6 +12,8 @@
 import warnings
 import struct
 
+import six
+
 import numpy as np
 
 from nibabel import nifti1 as nifti1
@@ -595,7 +597,7 @@ def test_intents(self):
         assert_raises(HeaderDataError, ehdr.set_intent, 999, (1,),
                       allow_unknown=True)
         assert_raises(HeaderDataError, ehdr.set_intent, 999, (1,2),
-                      allow_unknown=True) 
+                      allow_unknown=True)
 
     def test_set_slice_times(self):
         hdr = self.header_class()
@@ -900,6 +902,23 @@ def test_set_sform(self):
         img.set_sform(new_affine, 2)
         assert_array_almost_equal(img.affine, new_affine)
 
+    def test_sqform_code_type(self):
+        # make sure get_s/qform returns codes as integers
+        img = self.image_class(np.zeros((2, 3, 4)), None)
+        assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
+        assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
+        img.set_sform(None, 3)
+        img.set_qform(None, 3)
+        assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
+        assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
+        img.set_sform(None, 2.0)
+        img.set_qform(None, 4.0)
+        assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
+        assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
+        img.set_sform(None, img.get_sform(coded=True)[1])
+        img.set_qform(None, img.get_qform(coded=True)[1])
+
+
     def test_hdr_diff(self):
         # Check an offset beyond data does not raise an error
         img = self.image_class(np.zeros((2, 3, 4)), np.eye(4))