Commit c7fe1d5d authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Added kernel and fmeanu options to fslmaths

parent 31a53f4b
......@@ -163,6 +163,16 @@ class fslmaths(object):
self.__args.extend(("-bptf", hp_sigma, lp_sigma))
return self
def kernel(self, kernel='3D'):
"""2D or (default) 3D kernel"""
self.__args.extend(("-kernel", kernel))
return self
def fmeanu(self):
"""Mean filtering, kernel weighted, un-normalised (gives edge effects)"""
self.__args.append("-fmeanu")
return self
def run(self, output=None):
"""Save output of operations to image. Set ``output`` to a filename to have
the result saved to file, or omit ``output`` entirely to have the
......
......@@ -291,14 +291,15 @@ def test_fslmaths():
.fillh().ero().dilM().dilF().add('addim').sub('subim') \
.mul('mulim').div('divim').mas('masim').rem('remim') \
.thr('thrim').uthr('uthrim').inm('inmim').bptf(1, 10) \
.smooth(sigma=6).run('output')
.smooth(sigma=6).kernel('3D').fmeanu().run('output')
expected = [cmd, 'input',
'-abs', '-bin', '-binv', '-recip', '-Tmean', '-Tstd',
'-Tmin', '-Tmax', '-fillh', '-ero', '-dilM', '-dilF',
'-add addim', '-sub subim', '-mul mulim', '-div divim',
'-mas masim', '-rem remim', '-thr thrim', '-uthr uthrim',
'-inm inmim', '-bptf 1 10', '-s 6', 'output']
'-inm inmim', '-bptf 1 10', '-s 6', '-kernel 3D', '-fmeanu',
'output']
expected = ' '.join(expected)
assert result.stdout[0] == expected
......
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