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FSL
fslpy
Commits
7f02d3b1
Commit
7f02d3b1
authored
Aug 02, 2021
by
Christoph Arthofer
Committed by
Paul McCarthy
Aug 03, 2021
Browse files
Added kernel and fmeanu options to fslmaths
parent
7d6d1346
Changes
2
Hide whitespace changes
Inline
Side-by-side
fsl/wrappers/fslmaths.py
View file @
7f02d3b1
...
...
@@ -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
...
...
tests/test_wrappers/test_wrappers.py
View file @
7f02d3b1
...
...
@@ -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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