RF+BF - non-doctests now all pass on py3k

Author: matthew-brett

nibabel/batteryrunners.py

@@ -211,8 +211,17 @@ def __init__(self,
         self.problem_msg = problem_msg
         self.fix_msg = fix_msg
 
-    def __cmp__(self, other):
-        ''' Compare two BatteryRunner-like objects
+    def __getstate__(self):
+        """ State that defines object
+
+        Returns
+        -------
+        tup : tuple
+        """
+        return self.error, self.problem_level, self.problem_msg, self.fix_msg
+
+    def __eq__(self, other):
+        ''' are two BatteryRunner-like objects equal?
 
         Parameters
         ----------
@@ -229,7 +238,14 @@ def __cmp__(self, other):
         >>> rep == rep3
         False
         '''
-        return cmp(self.__dict__, other.__dict__)
+        return self.__getstate__() == other.__getstate__()
+
+    def __ne__(self, other):
+        """ are two BatteryRunner-like objects not equal?
+
+        See docstring for __eq__
+        """
+        return not self == other
 
     def __str__(self):
         ''' Printable string for object '''

nibabel/externals/netcdf.py

@@ -731,7 +731,7 @@ def _pack_int(self, value):
     _pack_int32 = _pack_int
 
     def _unpack_int(self):
-        return fromstring(self.fp.read(4), '>i')[0]
+        return int(fromstring(self.fp.read(4), '>i')[0])
     _unpack_int32 = _unpack_int
 
     def _pack_int64(self, value):

nibabel/externals/tests/__init__.py

@@ -0,0 +1 @@
+# Make externals tests a package

nibabel/externals/tests/data/example_1.nc

@@ -0,0 +1,120 @@
+''' Tests for netcdf '''
+
+import os
+from os.path import join as pjoin, dirname
+import shutil
+import tempfile
+from glob import glob
+
+import numpy as np
+
+from ...py3k import BytesIO, asbytes
+from ..netcdf import netcdf_file
+
+from nose.tools import assert_true, assert_false, assert_equal, assert_raises
+
+TEST_DATA_PATH = pjoin(dirname(__file__), 'data')
+
+N_EG_ELS = 11 # number of elements for example variable
+VARTYPE_EG = 'b' # var type for example variable
+
+
+def make_simple(*args, **kwargs):
+    f = netcdf_file(*args, **kwargs)
+    f.history = 'Created for a test'
+    f.createDimension('time', N_EG_ELS)
+    time = f.createVariable('time', VARTYPE_EG, ('time',))
+    time[:] = np.arange(N_EG_ELS)
+    time.units = 'days since 2008-01-01'
+    f.flush()
+    return f
+
+
+def gen_for_simple(ncfileobj):
+    ''' Generator for example fileobj tests '''
+    yield assert_equal, ncfileobj.history, asbytes('Created for a test')
+    time = ncfileobj.variables['time']
+    yield assert_equal, time.units, asbytes('days since 2008-01-01')
+    yield assert_equal, time.shape, (N_EG_ELS,)
+    yield assert_equal, time[-1], N_EG_ELS-1
+
+
+def test_read_write_files():
+    # test round trip for example file
+    cwd = os.getcwd()
+    try:
+        tmpdir = tempfile.mkdtemp()
+        os.chdir(tmpdir)
+        f = make_simple('simple.nc', 'w')
+        f.close()
+        # To read the NetCDF file we just created::
+        f = netcdf_file('simple.nc')
+        # Using mmap is the default
+        yield assert_true, f.use_mmap
+        for testargs in gen_for_simple(f):
+            yield testargs
+        f.close()
+        # Now without mmap
+        f = netcdf_file('simple.nc', mmap=False)
+        # Using mmap is the default
+        yield assert_false, f.use_mmap
+        for testargs in gen_for_simple(f):
+            yield testargs
+        f.close()
+        # To read the NetCDF file we just created, as file object, no
+        # mmap.  When n * n_bytes(var_type) is not divisible by 4, this
+        # raised an error in pupynere 1.0.12 and scipy rev 5893, because
+        # calculated vsize was rounding up in units of 4 - see
+        # http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html
+        fobj = open('simple.nc', 'rb')
+        f = netcdf_file(fobj)
+        # by default, don't use mmap for file-like
+        yield assert_false, f.use_mmap
+        for testargs in gen_for_simple(f):
+            yield testargs
+        f.close()
+    except:
+        os.chdir(cwd)
+        shutil.rmtree(tmpdir)
+        raise
+    os.chdir(cwd)
+    shutil.rmtree(tmpdir)
+
+
+def test_read_write_sio():
+    eg_sio1 = BytesIO()
+    f1 = make_simple(eg_sio1, 'w')
+    str_val = eg_sio1.getvalue()
+    f1.close()
+    eg_sio2 = BytesIO(str_val)
+    f2 = netcdf_file(eg_sio2)
+    for testargs in gen_for_simple(f2):
+        yield testargs
+    f2.close()
+    # Test that error is raised if attempting mmap for sio
+    eg_sio3 = BytesIO(str_val)
+    yield assert_raises, ValueError, netcdf_file, eg_sio3, 'r', True
+    # Test 64-bit offset write / read
+    eg_sio_64 = BytesIO()
+    f_64 = make_simple(eg_sio_64, 'w', version=2)
+    str_val = eg_sio_64.getvalue()
+    f_64.close()
+    eg_sio_64 = BytesIO(str_val)
+    f_64 = netcdf_file(eg_sio_64)
+    for testargs in gen_for_simple(f_64):
+        yield testargs
+    yield assert_equal, f_64.version_byte, 2
+    # also when version 2 explicitly specified
+    eg_sio_64 = BytesIO(str_val)
+    f_64 = netcdf_file(eg_sio_64, version=2)
+    for testargs in gen_for_simple(f_64):
+        yield testargs
+    yield assert_equal, f_64.version_byte, 2
+
+
+def test_read_example_data():
+    # read any example data files
+    for fname in glob(pjoin(TEST_DATA_PATH, '*.nc')):
+        f = netcdf_file(fname, 'r')
+        f = netcdf_file(fname, 'r', mmap=False)
+

nibabel/externals/tests/test_netcdf.py

@@ -7,6 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # module imports
+from .py3k import asbytes
 from .filename_parser import types_filenames, splitext_addext
 from . import volumeutils as vu
 from . import spm2analyze as spm2
@@ -44,7 +45,7 @@ def load(filename):
         hdr = nifti1.Nifti1Header.from_fileobj(
             vu.allopen(filenames['header']),
             check=False)
-        if hdr['magic'] in ('ni1', 'n+1'):
+        if hdr['magic'] in (asbytes('ni1'), asbytes('n+1')):
             # allow goofy nifti single magic for pair
             klass = nifti1.Nifti1Pair
         else:

nibabel/loadsave.py

@@ -10,6 +10,7 @@
 
 from .externals.netcdf import netcdf_file
 
+from .py3k import asbytes, asstr
 from .spatialimages import SpatialImage
 
 _dt_dict = {
@@ -52,7 +53,7 @@ def __init__(self, mincfile):
         # We don't currently support irregular spacing
         # http://www.bic.mni.mcgill.ca/software/minc/minc1_format/node15.html
         for dim in self._dims:
-            if dim.spacing != 'regular__':
+            if dim.spacing != asbytes('regular__'):
                 raise ValueError('Irregular spacing not supported')
         self._spatial_dims = [name for name in self._dim_names
                              if name.endswith('space')]
@@ -64,7 +65,7 @@ def get_data_dtype(self):
         elif typecode == 'd':
             dtt = np.dtype(np.float64)
         else:
-            signtype = self._image.signtype
+            signtype = asstr(self._image.signtype)
             dtt = _dt_dict[(typecode, signtype)]
         return np.dtype(dtt).newbyteorder('>')
 

nibabel/minc.py

@@ -11,7 +11,7 @@
 import numpy as np
 import numpy.linalg as npl
 
-from .py3k import ZEROB, ints2bytes, asbytes
+from .py3k import ZEROB, ints2bytes, asbytes, asstr
 from .volumeutils import Recoder, make_dt_codes, endian_codes
 from .spatialimages import HeaderDataError, ImageFileError
 from .batteryrunners import Report
@@ -276,9 +276,11 @@ def __repr__(self):
         s = "Nifti1Extension('%s', '%s')" % (code, self._content)
         return s
 
-    def __cmp__(self, other):
-        return cmp((self._code, self._content),
-                   (other._code, other._content))
+    def __eq__(self, other):
+        return (self._code, self._content) == (other._code, other._content)
+
+    def __ne__(self, other):
+        return not self == other
 
     def write_to(self, fileobj, byteswap):
         ''' Write header extensions to fileobj
@@ -919,7 +921,7 @@ def get_intent(self, code_repr='label'):
             raise TypeError('repr can be "label" or "code"')
         n_params = len(recoder.parameters[code])
         params = (float(hdr['intent_p%d' % (i+1)]) for i in range(n_params))
-        return label, tuple(params), str(hdr['intent_name'])
+        return label, tuple(params), np.asscalar(hdr['intent_name'])
 
     def set_intent(self, code, params=(), name=''):
         ''' Set the intent code, parameters and name
@@ -1281,7 +1283,8 @@ def _chk_qfac(hdr, fix=False):
     @staticmethod
     def _chk_magic_offset(hdr, fix=False):
         rep = Report(HeaderDataError)
-        magic = hdr['magic']
+        # for ease of later string formatting, use scalar of byte string
+        magic = np.asscalar(hdr['magic'])
         offset = hdr['vox_offset']
         if magic == asbytes('n+1'): # one file
             if offset >= 352:
@@ -1304,7 +1307,8 @@ def _chk_magic_offset(hdr, fix=False):
                 rep.fix_msg = 'setting to minimum value of 352'
         elif magic != asbytes('ni1'): # two files
             # unrecognized nii magic string, oh dear
-            rep.problem_msg = 'magic string "%s" is not valid' % magic
+            rep.problem_msg = ('magic string "%s" is not valid' %
+                               asstr(magic))
             rep.problem_level = 45
             if fix:
                 rep.fix_msg = 'leaving as is, but future errors are likely'

nibabel/nifti1.py

@@ -11,7 +11,7 @@
 from os.path import join as pjoin
 import shutil
 from tempfile import mkdtemp
-from ..py3k import BytesIO
+from ..py3k import BytesIO, asbytes
 
 import numpy as np
 
@@ -103,7 +103,7 @@ def test_save_load_endian():
     m_img2 = round_trip(mixed_img)
     assert_equal(m_img2.get_header().endianness, native_code)
     assert_array_equal(m_img2.get_data(), data)
-    
+
 
 def test_save_load():
     shape = (2, 4, 6)
@@ -156,12 +156,12 @@ def test_two_to_one():
     affine[:3,3] = [3,2,1]
     # single file format
     img = ni1.Nifti1Image(data, affine)
-    assert_equal(img.get_header()['magic'], 'n+1')
+    assert_equal(img.get_header()['magic'], asbytes('n+1'))
     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()['magic'], asbytes('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())
@@ -171,7 +171,7 @@ def test_two_to_one():
     pimg.file_map['header'].fileobj = hsio
     pimg.to_file_map()
     # the offset remains the same
-    assert_equal(pimg.get_header()['magic'], 'ni1')
+    assert_equal(pimg.get_header()['magic'], asbytes('ni1'))
     assert_equal(pimg.get_header()['vox_offset'], 352)
     assert_array_equal(pimg.get_data(), data)
     # same for from_image, going from single image to pair format