BF - py3k fixes from recent edits

Bytes vs strings
Different level of exception detail in doctests
Change to default floating point division

Author: matthew-brett

nibabel/casting.py

@@ -213,7 +213,7 @@ def as_int(x, check=True):
     2
     >>> as_int(-2.0)
     -2
-    >>> as_int(2.1)
+    >>> as_int(2.1) #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
         ...
     FloatingError: Not an integer: 2.1
@@ -359,5 +359,5 @@ def floor_log2(x):
     rem = abs(x)
     while rem>=2:
         ip += 1
-        rem /= 2
+        rem //= 2
     return ip

nibabel/dft.py

@@ -11,13 +11,14 @@
 import os
 from os.path import join as pjoin
 import tempfile
-import StringIO
 import getpass
 import warnings
 import sqlite3
 
 import numpy
 
+from .py3k import BytesIO
+
 from .nifti1 import Nifti1Header
 
 # Shield optional dicom import
@@ -128,7 +129,7 @@ def as_png(self, index=None, scale_to_slice=True):
             data = data * 255 / (max - min)
         data = data.astype(numpy.uint8)
         im = PIL.Image.fromstring('L', (self.rows, self.columns), data.tostring())
-        s = StringIO.StringIO()
+        s = BytesIO()
         im.save(s, 'PNG')
         return s.getvalue()
 
@@ -191,7 +192,7 @@ def as_nifti(self):
         hdr.set_data_dtype(numpy.int16)
         hdr.set_data_shape((self.columns, self.rows, len(self.storage_instances)))
 
-        s = StringIO.StringIO()
+        s = BytesIO()
         hdr.write_to(s)
 
         return s.getvalue() + data.tostring()

nibabel/ecat.py

@@ -335,11 +335,11 @@ def __getitem__(self, item):
         Examples
         --------
         >>> hdr = EcatHeader()
-        >>> hdr['magic_number'] == 'MATRIX72'
-        True
+        >>> hdr['magic_number'] #23dt next : bytes
+        'MATRIX72'
         '''
         return self._header_data[item].item()
-    
+
     def __setitem__(self, item, value):
         ''' Set values in header data
 

nibabel/optpkg.py

@@ -7,7 +7,7 @@
 else:
     have_nose = True
 
-from .tripwire import TripWire, is_tripwire
+from .tripwire import TripWire
 
 def optional_package(name, trip_msg=None):
     """ Return package-like thing and module setup for package `name`
@@ -47,7 +47,7 @@ def optional_package(name, trip_msg=None):
 
     and
 
-    >>> pkg.some_function()
+    >>> pkg.some_function() #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
         ...
     TripWireError: We need package not_a_package for these functions, but ``import not_a_package`` raised an ImportError

nibabel/tests/test_analyze.py

@@ -15,11 +15,10 @@
 import os
 import re
 import logging
-from StringIO import StringIO
 
 import numpy as np
 
-from ..py3k import BytesIO, asbytes
+from ..py3k import BytesIO, StringIO, asbytes
 from ..volumeutils import array_to_file
 from ..spatialimages import (HeaderDataError, HeaderTypeError)
 from ..analyze import AnalyzeHeader, AnalyzeImage
@@ -449,7 +448,7 @@ def test_scaling():
     assert_array_almost_equal(data, rdata)
     # Writing to integer datatype does, and raises an error
     hdr.set_data_dtype(np.int32)
-    assert_raises(HeaderTypeError, hdr.data_to_fileobj, data, StringIO())
+    assert_raises(HeaderTypeError, hdr.data_to_fileobj, data, BytesIO())
     # unless we aren't scaling, in which case we convert the floats to
     # integers and write
     _write_data(hdr, data, S)

nibabel/tests/test_ecat.py

@@ -10,6 +10,8 @@
 
 import numpy as np
 
+from ..py3k import asbytes
+
 from ..volumeutils import native_code, swapped_code
 from ..ecat import EcatHeader, EcatMlist, EcatSubHeader, EcatImage
 
@@ -34,20 +36,20 @@ def test_header_size(self):
     def test_empty(self):
         hdr = self.header_class()
         assert_true(len(hdr.binaryblock) == 502)
-        assert_true(hdr['magic_number'] == 'MATRIX72')
+        assert_true(hdr['magic_number'] == asbytes('MATRIX72'))
         assert_true(hdr['sw_version'] == 74)
         assert_true(hdr['num_frames'] == 0)
         assert_true(hdr['file_type'] == 0)
         assert_true(hdr['ecat_calibration_factor'] == 1.0)
-        
+
     def test_dtype(self):
         #dtype not specified in header, only in subheaders
         hdr = self.header_class()
         assert_raises(NotImplementedError,
                             hdr.get_data_dtype)
-        
+
     def test_header_codes(self):
-        fid = open(ecat_file)
+        fid = open(ecat_file, 'rb')
         hdr = self.header_class()
         newhdr = hdr.from_fileobj(fid)
         fid.close()
@@ -61,7 +63,7 @@ def test_copy(self):
         assert_true(hdr == hdr2)
         assert_true(not hdr.binaryblock == hdr2._header_data.byteswap().tostring())
         assert_true(hdr.keys() == hdr2.keys())
-         
+
     def test_update(self):
         hdr = self.header_class()
         assert_true(hdr['num_frames'] == 0)
@@ -76,7 +78,7 @@ def test_endianness(self):
         swapped_hdr = self.header_class(endianness=swapped_code)
         assert_true(swapped_hdr.endianness == swapped_code)
         # Example header is big-endian
-        fid = open(ecat_file)
+        fid = open(ecat_file, 'rb')
         file_hdr = native_hdr.from_fileobj(fid)
         fid.close()
         assert_true(file_hdr.endianness == '>')

nibabel/tests/test_wrapstruct.py

@@ -24,14 +24,13 @@
 _field_recoders -> field_recoders
 '''
 import logging
-from StringIO import StringIO
 
 import numpy as np
 
 from ..wrapstruct import WrapStructError, WrapStruct
 from ..batteryrunners import Report
 
-from ..py3k import BytesIO, ZEROB
+from ..py3k import BytesIO, StringIO, asbytes, ZEROB
 from ..volumeutils import swapped_code, native_code, Recoder
 from ..spatialimages import HeaderDataError
 from .. import imageglobals
@@ -59,7 +58,7 @@ def guessed_endian(klass, hdr):
     def default_structarr(klass, endianness=None):
         structarr = super(MyWrapStruct, klass).default_structarr(endianness)
         structarr['an_integer'] = 1
-        structarr['a_str'] = 'a string'
+        structarr['a_str'] = asbytes('a string')
         return structarr
 
     @classmethod
@@ -145,7 +144,7 @@ def test__eq__(self):
     def test_to_from_fileobj(self):
         # Successful write using write_to
         hdr = self.header_class()
-        str_io = StringIO()
+        str_io = BytesIO()
         hdr.write_to(str_io)
         str_io.seek(0)
         hdr2 = self.header_class.from_fileobj(str_io)
@@ -347,7 +346,7 @@ def test_empty(self):
         # Test contents of default header
         hdr = self.header_class()
         assert_equal(hdr['an_integer'], 1)
-        assert_equal(hdr['a_str'], 'a string')
+        assert_equal(hdr['a_str'], asbytes('a string'))
 
     def test_str(self):
         hdr = self.header_class()

nibabel/tripwire.py

@@ -35,7 +35,7 @@ class TripWire(object):
     ...     import silly_module_name
     ... except ImportError:
     ...    silly_module_name = TripWire('We do not have silly_module_name')
-    >>> silly_module_name.do_silly_thing('with silly string')
+    >>> silly_module_name.do_silly_thing('with silly string') #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
         ...
     TripWireError: We do not have silly_module_name