RF+BF - gradual cleanup of py3k test errors; still 10 E 15 F to fix

Author: matthew-brett

nibabel/nifti1.py

@@ -308,7 +308,7 @@ def write_to(self, fileobj, byteswap):
         fileobj.write(self._mangle(self._content))
         # be nice and zero out remaining part of the extension till the
         # next 16 byte border
-        fileobj.write('\x00' * (extstart + rawsize - fileobj.tell()))
+        fileobj.write(ZEROB * (extstart + rawsize - fileobj.tell()))
 
 
 # NIfTI header extension type codes (ECODE)
@@ -428,7 +428,7 @@ def from_fileobj(klass, fileobj, size, byteswap):
                 raise HeaderDataError(
                         'extension size is not a multiple of 16 bytes')
             # read extension itself; esize includes the 8 bytes already read
-            evalue = fileobj.read(esize - 8)
+            evalue = fileobj.read(int(esize - 8))
             if not len(evalue) == esize - 8:
                 raise HeaderDataError('failed to read extension content')
             # note that we read a full extension

nibabel/tests/test_batteryrunners.py

@@ -10,7 +10,7 @@
 
 '''
 
-from StringIO import StringIO
+from ..py3k import StringIO
 
 import logging
 
@@ -92,7 +92,7 @@ def test_init_basic():
 def test_init_report():
     rep = Report()
     assert_equal(rep, Report(Exception, 0, '', ''))
-    
+
 
 def test_report_strings():
     rep = Report()
@@ -107,21 +107,21 @@ def test_report_strings():
     rep.problem_level = 30
     rep.write_raise(str_io)
     assert_equal(str_io.getvalue(), 'Level 30: msg; fix\n')
-    str_io.truncate(0)
+    str_io.truncate(0); str_io.seek(0)
     # No fix string, no fix message
     rep.fix_msg = ''
     rep.write_raise(str_io)
     assert_equal(str_io.getvalue(), 'Level 30: msg\n')
     rep.fix_msg = 'fix'
-    str_io.truncate(0)
+    str_io.truncate(0); str_io.seek(0)
     # If we drop the level, nothing goes to the log
     rep.problem_level = 20
     rep.write_raise(str_io)
     assert_equal(str_io.getvalue(), '')
     # Unless we set the default log level in the call
     rep.write_raise(str_io, log_level=20)
     assert_equal(str_io.getvalue(), 'Level 20: msg; fix\n')
-    str_io.truncate(0)
+    str_io.truncate(0); str_io.seek(0)
     # If we set the error level down this low, we raise an error
     assert_raises(ValueError, rep.write_raise, str_io, 20)
     # But the log level wasn't low enough to do a log entry
@@ -131,7 +131,7 @@ def test_report_strings():
     assert_raises(ValueError, rep.write_raise, str_io, 20, 20)
     assert_equal(str_io.getvalue(), 'Level 20: msg; fix\n')
     # If there's no error, we can't raise
-    str_io.truncate(0)
+    str_io.truncate(0); str_io.seek(0)
     rep.error = None
     rep.write_raise(str_io, 20)
     assert_equal(str_io.getvalue(), '')
@@ -148,7 +148,7 @@ def test_logging():
     rep.problem_level = 30
     rep.log_raise(logger)
     assert_equal(str_io.getvalue(), 'msg; fix\n')
-    str_io.truncate(0)
+    str_io.truncate(0); str_io.seek(0)
 
 
 def test_checks():

nibabel/tests/test_binary.py

@@ -84,13 +84,10 @@ def test_general_init(self):
 
     def test_mappingness(self):
         hdr = self.header_class()
-        if sys.version_info[0] >= 3:
-            print('Skipping due to numpy python 3 bug')
-        else:
-            assert_raises(ValueError,
-                        hdr.__setitem__,
-                        'nonexistent key',
-                        0.1)
+        assert_raises(ValueError,
+                    hdr.__setitem__,
+                    'nonexistent key',
+                    0.1)
         hdr_dt = hdr.structarr.dtype
         keys = hdr.keys()
         assert_equal(keys, list(hdr))

nibabel/tests/test_image_load_save.py

@@ -11,7 +11,7 @@
 from os.path import join as pjoin
 import shutil
 from tempfile import mkdtemp
-from StringIO import StringIO
+from ..py3k import BytesIO
 
 import numpy as np
 
@@ -42,7 +42,7 @@
 
 def round_trip(img):
     # round trip a nifti single
-    sio = StringIO()
+    sio = BytesIO()
     img.file_map['image'].fileobj = sio
     img.to_file_map()
     img2 = Nifti1Image.from_file_map(img.file_map)
@@ -157,16 +157,16 @@ def test_two_to_one():
     # single file format
     img = ni1.Nifti1Image(data, affine)
     assert_equal(img.get_header()['magic'], 'n+1')
-    str_io = StringIO()
+    str_io = BytesIO()
     img.file_map['image'].fileobj = str_io
     # check that the single format vox offset is set correctly
     img.to_file_map()
     assert_equal(img.get_header()['magic'], 'n+1')
     assert_equal(img.get_header()['vox_offset'], 352)
     # make a new pair image, with the single image header
     pimg = ni1.Nifti1Pair(data, affine, img.get_header())
-    isio = StringIO()
-    hsio = StringIO()
+    isio = BytesIO()
+    hsio = BytesIO()
     pimg.file_map['image'].fileobj = isio
     pimg.file_map['header'].fileobj = hsio
     pimg.to_file_map()
@@ -178,7 +178,7 @@ def test_two_to_one():
     ana_img = ana.AnalyzeImage.from_image(img)
     assert_equal(ana_img.get_header()['vox_offset'], 352)
     # back to the single image, save it again to a stringio
-    str_io = StringIO()
+    str_io = BytesIO()
     img.file_map['image'].fileobj = str_io
     img.to_file_map()
     assert_equal(img.get_header()['vox_offset'], 352)
@@ -206,7 +206,7 @@ def test_negative_load_save():
     hdr = ni1.Nifti1Header()
     hdr.set_data_dtype(np.int16)
     img = Nifti1Image(data, affine, hdr)
-    str_io = StringIO()
+    str_io = BytesIO()
     img.file_map['image'].fileobj = str_io
     img.to_file_map()
     str_io.seek(0)

nibabel/tests/test_nifti1.py

@@ -10,7 +10,7 @@
 from __future__ import with_statement
 import os
 
-from StringIO import StringIO
+from ..py3k import BytesIO, ZEROB
 
 import numpy as np
 
@@ -56,7 +56,7 @@ def test_empty(self):
         assert_equal(hdr['vox_offset'], 0)
 
     def test_from_eg_file(self):
-        hdr = Nifti1Header.from_fileobj(open(self.example_file))
+        hdr = Nifti1Header.from_fileobj(open(self.example_file, 'rb'))
         assert_equal(hdr.endianness, '<')
         assert_equal(hdr['magic'], 'ni1')
         assert_equal(hdr['sizeof_hdr'], 348)
@@ -169,9 +169,9 @@ def test_binblock_is_file(self):
         # the case of the single file version of the header, we need to append
         # the extension string (4 0s)
         hdr = self.header_class()
-        str_io = StringIO()
+        str_io = BytesIO()
         hdr.write_to(str_io)
-        assert_equal(str_io.getvalue(), hdr.binaryblock + '\x00' * 4)
+        assert_equal(str_io.getvalue(), hdr.binaryblock + ZEROB * 4)
 
 
 class TestNifti1Image(tana.TestAnalyzeImage):
@@ -407,7 +407,7 @@ def test_nifti1_images():
     img = Nifti1Image(data, affine)
     assert_equal(img.get_shape(), shape)
     img.set_data_dtype(npt)
-    stio = StringIO()
+    stio = BytesIO()
     img.file_map['image'].fileobj = stio
     img.to_file_map()
     img2 = Nifti1Image.from_file_map(img.file_map)
@@ -491,7 +491,7 @@ def test_loadsave_cycle():
     exts_container = hdr.extensions
     assert_true(len(exts_container) > 0)
     # write into the air ;-)
-    stio = StringIO()
+    stio = BytesIO()
     nim.file_map['image'].fileobj = stio
     nim.to_file_map()
     stio.seek(0)
@@ -516,7 +516,7 @@ def test_loadsave_cycle():
     assert_equal(wnim.get_data_dtype(), np.int16)
     assert_equal(wnim.get_header().get_slope_inter(), (2, 8))
     # write into the air again ;-)
-    stio = StringIO()
+    stio = BytesIO()
     wnim.file_map['image'].fileobj = stio
     wnim.to_file_map()
     stio.seek(0)
@@ -605,7 +605,7 @@ def test_load_pixdims():
     assert_array_equal(img_hdr.get_zooms(), [2,3,4])
     # Save to stringio
     fm = Nifti1Image.make_file_map()
-    fm['image'].fileobj = StringIO()
+    fm['image'].fileobj = BytesIO()
     simg.to_file_map(fm)
     # Load again
     re_simg = Nifti1Image.from_file_map(fm)

nibabel/tests/test_orientations.py

@@ -107,19 +107,20 @@ def same_transform(taff, ornt, shape):
 
 def test_apply():
     # most tests are in ``same_transform`` above, via the
-    # test_io_orientations. 
+    # test_io_orientations
     a = np.arange(24).reshape((2,3,4))
-    # Test 4D
+    # Test 4D with an example orientation
+    ornt = OUT_ORNTS[-1]
     t_arr = apply_orientation(a[:,:,:,None], ornt)
     assert_equal(t_arr.ndim, 4)
     # Orientation errors
     assert_raises(OrientationError,
-                        apply_orientation,
-                        a[:,:,1], ornt)
+                  apply_orientation,
+                  a[:,:,1], ornt)
     assert_raises(OrientationError,
-                        apply_orientation,
-                        a,
-                        [[0,1],[np.nan,np.nan],[2,1]])
+                  apply_orientation,
+                  a,
+                  [[0,1],[np.nan,np.nan],[2,1]])
 
 
 def test_flip_axis():

nibabel/tests/test_spm99analyze.py

@@ -6,10 +6,11 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-from StringIO import StringIO
 
 import numpy as np
 
+from ..py3k import BytesIO
+
 from numpy.testing import assert_array_equal, assert_array_almost_equal, dec
 
 # Decorator to skip tests requiring save / load if scipy not available for mat
@@ -43,7 +44,7 @@ def test_scaling(self):
         hdr = self.header_class()
         hdr.set_data_shape((1,2,3))
         hdr.set_data_dtype(np.int16)
-        S3 = StringIO()
+        S3 = BytesIO()
         data = np.arange(6, dtype=np.float64).reshape((1,2,3))
         # This uses scaling
         hdr.data_to_fileobj(data, S3)

nibabel/tests/test_trackvis.py

@@ -1,9 +1,8 @@
 ''' Testing trackvis module '''
 
-from StringIO import StringIO
-
 import numpy as np
 
+from ..py3k import BytesIO
 from .. import trackvis as tv
 from ..volumeutils import swapped_code
 
@@ -14,7 +13,7 @@
 
 def test_write():
     streams = []
-    out_f = StringIO()
+    out_f = BytesIO()
     tv.write(out_f, [], {})
     assert_equal(out_f.getvalue(), tv.empty_header().tostring())
     out_f.truncate(0)
@@ -48,7 +47,7 @@ def test_write_scalars_props():
     scalars = np.arange(N*M).reshape((N,M)) + 100
     props = np.arange(P) + 1000
     # If scalars not same size for each point, error
-    out_f = StringIO()
+    out_f = BytesIO()
     streams = [(points, None, None),
                (points, scalars, None)]
     assert_raises(tv.DataError, tv.write, out_f, streams)
@@ -109,7 +108,7 @@ def streamlist_equal(streamlist1, streamlist2):
 
 
 def test_round_trip():
-    out_f = StringIO()
+    out_f = BytesIO()
     xyz0 = np.tile(np.arange(5).reshape(5,1), (1, 3))
     xyz1 = np.tile(np.arange(5).reshape(5,1) + 10, (1, 3))
     streams = [(xyz0, None, None), (xyz1, None, None)]
@@ -135,7 +134,7 @@ def test_round_trip():
     streams3, hdr = tv.read(out_f, as_generator=True)
     # Now we need a new file object, because we're still using the old one for
     # our generator
-    out_f_write = StringIO()
+    out_f_write = BytesIO()
     tv.write(out_f_write, streams3, {})
     # and re-read just to check
     out_f_write.seek(0)
@@ -217,7 +216,7 @@ def test_tv_class():
     assert_true(isinstance(tvf.header, np.ndarray))
     assert_equal(tvf.endianness, tv.native_code)
     assert_equal(tvf.filename, None)
-    out_f = StringIO()
+    out_f = BytesIO()
     tvf.to_file(out_f)
     assert_equal(out_f.getvalue(), tv.empty_header().tostring())
     out_f.truncate(0)