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Christoph Arthofer
fslpy
Commits
c17195b5
Commit
c17195b5
authored
Jun 23, 2021
by
Paul McCarthy
🚵
Browse files
Merge branch 'rf/fast-wrapper' into 'master'
Rf/fast wrapper See merge request fsl/fslpy!299
parents
ed5f7e53
e5811b42
Changes
3
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CHANGELOG.rst
View file @
c17195b5
...
...
@@ -3,7 +3,7 @@ order.
3.6.
1
(
Thur
sday 2
7th April
2021)
3.6.
2
(
Wedne
sday 2
3rd June
2021)
--------------------------------
...
...
@@ -11,6 +11,18 @@ Changed
^^^^^^^
* The ``fsl.wrappers.fast`` wrapper passes ``-v`` to ``fast`` if ``v=True`` or
``verbose=True`` is specified.
3.6.1 (Thursday 27th May 2021)
------------------------------
Changed
^^^^^^^
* Removed the ``dataclasses`` backport from requirements (!297).
...
...
fsl/wrappers/fast.py
View file @
c17195b5
...
...
@@ -50,7 +50,7 @@ def fast(imgs, out='fast', **kwargs):
'n_classes'
:
'class'
,
}
cmd
=
[
'fast'
,
'-v'
,
'--out=%s'
%
out
]
cmd
=
[
'fast'
,
'--out=%s'
%
out
]
cmd
+=
wutils
.
applyArgStyle
(
'--='
,
valmap
=
valmap
,
argmap
=
argmap
,
...
...
tests/test_wrappers/test_wrappers.py
View file @
c17195b5
...
...
@@ -327,13 +327,16 @@ def test_fast():
cmd
=
op
.
join
(
fsldir
,
'bin'
,
'fast'
)
result
=
fw
.
fast
(
'input'
,
'myseg'
,
n_classes
=
3
)
expected
=
[
cmd
,
'-v'
,
'--out=myseg'
,
'--class=3'
,
'input'
]
expected
=
[
cmd
,
'--out=myseg'
,
'--class=3'
,
'input'
]
assert
result
.
stdout
[
0
]
==
' '
.
join
(
expected
)
result
=
fw
.
fast
((
'in1'
,
'in2'
,
'in3'
),
'myseg'
,
n_classes
=
3
)
expected
=
[
cmd
,
'-v'
,
'--out=myseg'
,
'--class=3'
,
'in1'
,
'in2'
,
'in3'
]
expected
=
[
cmd
,
'--out=myseg'
,
'--class=3'
,
'in1'
,
'in2'
,
'in3'
]
assert
result
.
stdout
[
0
]
==
' '
.
join
(
expected
)
result
=
fw
.
fast
((
'in1'
,
'in2'
,
'in3'
),
'myseg'
,
n_classes
=
3
,
verbose
=
True
)
expected
=
[
cmd
,
'--out=myseg'
,
'--class=3'
,
'--verbose'
,
'in1'
,
'in2'
,
'in3'
]
assert
result
.
stdout
[
0
]
==
' '
.
join
(
expected
)
...
...
@@ -390,10 +393,10 @@ def test_tbss():
def
test_fsl_prepare_fieldmap
():
with
asrt
.
disabled
(),
run
.
dryrun
(),
mockFSLDIR
(
bin
=
(
'fsl_prepare_fieldmap'
,))
as
fsldir
:
fpf
=
op
.
join
(
fsldir
,
'bin'
,
'fsl_prepare_fieldmap'
)
result
=
fw
.
fsl_prepare_fieldmap
(
phase_image
=
'ph'
,
magnitude_image
=
'mag'
,
out_image
=
'out'
,
deltaTE
=
2.46
,
nocheck
=
True
)
result
=
fw
.
fsl_prepare_fieldmap
(
phase_image
=
'ph'
,
magnitude_image
=
'mag'
,
out_image
=
'out'
,
deltaTE
=
2.46
,
nocheck
=
True
)
expected
=
(
fpf
,
(
'SIEMENS'
,
'ph'
,
'mag'
,
'out'
,
'2.46'
,
'--nocheck'
))
assert
checkResult
(
result
.
stdout
[
0
],
*
expected
)
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