TEST: Added acceptance test for qform code being '2' after parrec2nii.

Author: JasperVanDenBosch

nibabel/tests/test_parrec2nii.py

@@ -1,16 +1,30 @@
 """ Tests for the parrec2nii exe code
 """
 import imp, numpy
+from numpy.testing import (assert_almost_equal,
+                           assert_array_equal)
+from nose.tools import assert_equal
 from mock import Mock, MagicMock
 from numpy import array as npa
+from test_parrec import EG_PAR, VARY_PAR
+from os.path import dirname, join, isfile, basename
+from ..tmpdirs import InTemporaryDirectory
 
 AN_OLD_AFFINE = numpy.array(
     [[-3.64994708, 0., 1.83564171, 123.66276611],
      [0., -3.75, 0., 115.617],
      [0.86045705, 0., 7.78655376, -27.91161211],
      [0., 0., 0., 1.]])
 
+PAR_AFFINE = numpy.array(
+[[  -3.64994708,    0.  ,          1.83564171,  107.63076611],
+ [   0.        ,    3.75,          0.        , -118.125     ],
+ [   0.86045705,    0.  ,          7.78655376,  -58.25061211],
+ [   0.        ,    0.  ,          0.        ,    1.        ]])
+
 def test_parrec2nii_sets_qform_with_code2():
+    """Unit test that ensures that set_qform() is called on the new header.
+    """
     parrec2nii = imp.load_source('parrec2nii', 'bin/parrec2nii')
     parrec2nii.verbose.switch = False
 
@@ -43,4 +57,35 @@ def test_parrec2nii_sets_qform_with_code2():
 
     infile = 'nonexistent.PAR'
     parrec2nii.proc_file(infile, opts)
-    nhdr.set_qform.assert_called_with(pr_hdr.get_affine(), code=2)    
+    nhdr.set_qform.assert_called_with(pr_hdr.get_affine(), code=2)
+
+def test_parrec2nii_save_load_qform_code():
+    """Tests that after parrec2nii saves file, it has the qform 'code'
+    set to '2', which means 'aligned', so that other software, e.g. FSL
+    picks up the qform.
+    """
+    import nibabel
+    parrec2nii = imp.load_source('parrec2nii', 'bin/parrec2nii')
+    parrec2nii.verbose.switch = False
+
+    opts = Mock()
+    opts.outdir = None
+    opts.scaling = 'off'
+    opts.minmax = [1, 1]
+    opts.store_header = False
+    opts.bvs = False
+    opts.vol_info = False
+    opts.dwell_time = False
+    opts.compressed = False
+
+    with InTemporaryDirectory() as pth:
+        opts.outdir = pth
+        for fname in [EG_PAR, VARY_PAR]:
+            parrec2nii.proc_file(fname, opts)
+            outfname = join(pth, basename(fname)).replace('.PAR', '.nii')
+            assert isfile(outfname)
+            img = nibabel.load(outfname)
+            assert_almost_equal(img.get_affine(), PAR_AFFINE, 4)
+            assert_array_equal(img.header['qform_code'], 2)
+            assert_array_equal(img.header['sform_code'], 2)
+