def test_nifti_extensions():
nim = load(image_file)
# basic checks of the available extensions
ext = nim.extra['extensions']
ok_(len(ext) == 2)
ok_(ext.count('comment') == 2)
ok_(ext.count('afni') == 0)
ok_(ext.get_codes() == [6, 6])
ok_((ext.get_sizeondisk() - 4) % 16 == 0)
# first extension should be short one
ok_(ext[0].get_content() == 'extcomment1')
# add one
afniext = Nifti1Extension('afni', '<xml></xml>')
ext.append(afniext)
ok_(ext.get_codes() == [6, 6, 4])
ok_(ext.count('comment') == 2)
ok_(ext.count('afni') == 1)
ok_((ext.get_sizeondisk() - 4) % 16 == 0)
# delete one
del ext[1]
ok_(ext.get_codes() == [6, 4])
ok_(ext.count('comment') == 1)
ok_(ext.count('afni') == 1)
def load(filename, *args, **kwargs):
''' Load file given filename, guessing at file type
Parameters
----------
filename : string or file-like
specification of filename or file to load
*args
**kwargs
arguments to pass to image load function
Returns
-------
img : ``SpatialImage``
Image of guessed type
'''
# Try and guess file type from filename
if isinstance(filename, basestring):
fname = filename
for ending in ('.gz', '.bz2'):
if filename.endswith(ending):
fname = fname[:-len(ending)]
break
if fname.endswith('.nii'):
return nifti1.load(filename, *args, **kwargs)
if fname.endswith('.mnc'):
return minc.load(filename, *args, **kwargs)
# Not a string, or not recognized as nii or mnc
try:
files = nifti1.Nifti1Image.filespec_to_files(filename)
except ValueError:
raise RuntimeError('Cannot work out file type of "%s"' %
filename)
hdr = nifti1.Nifti1Header.from_fileobj(
vu.allopen(files['header']),
check=False)
magic = hdr['magic']
if magic in ('ni1', 'n+1'):
return nifti1.load(filename, *args, **kwargs)
return spm2.load(filename, *args, **kwargs)
def test_loadsavecycle():
nim = load(image_file)
# ensure we have extensions
ok_(nim.extra.has_key('extensions'))
ok_(len(nim.extra['extensions']))
# write into the air ;-)
stio = StringIO()
files = {'header': stio, 'image': stio}
nim.to_files(files)
stio.seek(0)
# reload
lnim = Nifti1Image.from_files(files)
ok_(lnim.extra.has_key('extensions'))
ok_(nim.extra['extensions'] == lnim.extra['extensions'])
