Commit ef9ce000 authored by Paul McCarthy's avatar Paul McCarthy 🚵
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Merge branch 'enh/fslmaths' into 'master'

Enh/fslmaths

See merge request fsl/fslpy!304
parents 31a53f4b 4f7d2f77
Pipeline #9998 canceled with stages
in 3 minutes and 22 seconds
......@@ -4,4 +4,5 @@ Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
Martin Craig <martin.craig@eng.ox.ac.uk>
Taylor Hanayik <taylor.hanayik@ndcn.ox.ac.uk>
Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
\ No newline at end of file
Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
Christoph Arthofer <christoph.arthofer@ndcn.oxc.ac.uk>
\ No newline at end of file
......@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
3.6.4 (Tuesday 3rd August 2021)
-------------------------------
Added
^^^^^
* New :meth:`.fslmaths.kernel` and :meth:`.fslmaths.fmeanu` options on the
:class:`.fslmaths` wrapper (!304).
3.6.3 (Wednesday 28th July 2021)
--------------------------------
......
......@@ -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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