Merge pull request #279 from matthew-brett/parrec-as-uint

MRG: PAR / REC data are unsigned 8 or 16 bit integers

Consensus seems to be that REC data is in uint format - see 
#275

Raise error for data width other than 8 or 16 bit because we haven't any examples to know what these are.

Author: matthew-brett

nibabel/parrec.py

@@ -74,6 +74,17 @@
 different order.
 
 We call the PAR file's axis system "PSL" (Posterior, Superior, Left)
+
+#########
+Data type
+#########
+
+It seems that everyone agrees that Philips stores REC data in little-endian
+format - see https://github.com/nipy/nibabel/issues/274
+
+Philips XML header files, and some previous experience, suggest that the REC
+data is always stored as 8 or 16 bit unsigned integers - see
+https://github.com/nipy/nibabel/issues/275
 """
 from __future__ import print_function, division
 
@@ -556,8 +567,12 @@ def __init__(self, info, image_defs, permit_truncated=False):
         # functionality
         # dtype
         bitpix = self._get_unique_image_prop('image pixel size')
-        # REC data always little endian?
-        dt = np.dtype('int' + str(bitpix)).newbyteorder('<')
+        if bitpix not in (8, 16):
+            raise PARRECError('Only 8- and 16-bit data supported (not %s)'
+                              'please report this to the nibabel developers'
+                              % bitpix)
+        # REC data always little endian
+        dt = np.dtype('uint' + str(bitpix)).newbyteorder('<')
         Header.__init__(self,
                         data_dtype=dt,
                         shape=self._calc_data_shape(),

nibabel/tests/test_parrec.py

@@ -124,7 +124,7 @@
     dict(
         fname = EG_PAR,
         shape = (64, 64, 9, 3),
-        dtype = np.int16,
+        dtype = np.uint16,
         # We disagree with Philips about the right affine, for the moment, so
         # use our own affine as determined from a previous load in nibabel
         affine = AN_OLD_AFFINE,
@@ -146,7 +146,7 @@ def test_top_level_load():
 def test_header():
     hdr = PARRECHeader(HDR_INFO, HDR_DEFS)
     assert_equal(hdr.get_data_shape(), (64, 64, 9, 3))
-    assert_equal(hdr.get_data_dtype(), np.dtype('<i2'))
+    assert_equal(hdr.get_data_dtype(), np.dtype('<u2'))
     assert_equal(hdr.get_zooms(), (3.75, 3.75, 8.0, 2.0))
     assert_equal(hdr.get_data_offset(), 0)
     si = np.array([np.unique(x) for x in hdr.get_data_scaling()]).ravel()
@@ -534,3 +534,11 @@ class TestPARRECImage(tsi.MmapImageMixin):
 
     def write_image(self):
         return parrec.load(EG_PAR), EG_PAR
+
+
+def test_bitpix():
+    # Check errors for other than 8, 16 bit
+    hdr_defs = HDR_DEFS.copy()
+    for pix_size in (24, 32):
+        hdr_defs['image pixel size'] = pix_size
+        assert_raises(PARRECError, PARRECHeader, HDR_INFO, hdr_defs)

nibabel/tests/test_scripts.py

@@ -95,7 +95,7 @@ def test_parrec2nii():
         run_command(['parrec2nii', in_fname])
         img = load(out_froot)
         assert_equal(img.shape, (64, 64, 9, 3))
-        assert_equal(img.get_data_dtype(), np.dtype(np.int16))
+        assert_equal(img.get_data_dtype(), np.dtype(np.uint16))
         # Check against values from Philips converted nifti image
         data = img.get_data()
         assert_true(np.allclose(