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Evan Edmond
fslpy
Commits
dab1d398
Commit
dab1d398
authored
Feb 25, 2020
by
Martin Craig
Committed by
Paul McCarthy
Apr 22, 2020
Browse files
Moved fsl command code out of main run function for clarity
parent
cced3d12
Changes
1
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Inline
Side-by-side
fsl/utils/run.py
View file @
dab1d398
...
...
@@ -362,24 +362,9 @@ def runfsl(*args, **kwargs):
for
prefix
in
prefixes
:
cmdpath
=
op
.
join
(
prefix
,
args
[
0
])
if
fslplatform
.
fslwsl
:
# We want to run the command from FSL installed in the Windows Subsystem for Linux
# First we check it exists in WSL (translating Windows path separators to Unix)
# Then we convert any Windows paths in the arguments (e.g. temp files) to the
# corresponding WSL Unix paths (C:/ -> /mnt/c)
# Then we prepend important environment variables - note that it seems we cannot
# use WSLENV for this due to its insistance on path mapping.
# Finally we append the command and its arguments
cmdpath
=
cmdpath
.
replace
(
"
\\
"
,
"/"
)
retcode
=
sp
.
call
([
"wsl"
,
"test"
,
"-x"
,
cmdpath
])
if
retcode
==
0
:
args
[
0
]
=
cmdpath
args
=
[
wslpath
(
arg
)
for
arg
in
args
]
args
=
[
"wsl"
,
"PATH=$PATH:%s/bin"
%
fslplatform
.
fsldir
,
"FSLDIR=%s"
%
fslplatform
.
fsldir
,
"FSLOUTPUTTYPE=%s"
%
os
.
environ
.
get
(
"FSLOUTPUTTYPE"
,
"NIFTI_GZ"
)
]
+
args
wslargs
=
wslcmd
(
cmdpath
,
*
args
)
if
wslargs
is
not
None
:
args
=
wslargs
break
elif
op
.
isfile
(
cmdpath
):
args
[
0
]
=
cmdpath
...
...
@@ -393,6 +378,40 @@ def runfsl(*args, **kwargs):
return
run
(
*
args
,
**
kwargs
)
def
wslcmd
(
cmdpath
,
*
args
):
"""
Convert a command + arguments into an equivalent set of arguments that will run the command
under Windows Subsystem for Linux
:param cmdpath: Fully qualified path to the command. This is essentially a WSL path not a Windows
one since FSLDIR is specified as a WSL path, however it may have backslashes
as path separators due to previous use of ``os.path.join``
:param args: Sequence of command arguments (the first of which is the unqualified command name)
:return: If ``cmdpath`` exists and is executable in WSL, return a sequence of command arguments
which when executed will run the command in WSL. Windows paths in the argument list will
be converted to WSL paths. If ``cmdpath`` was not executable in WSL, returns None
"""
# Check if command exists in WSL (translating Windows path separators to Unix as os.path.join
# may have inserted some backslashes)
cmdpath
=
cmdpath
.
replace
(
"
\\
"
,
"/"
)
retcode
=
sp
.
call
([
"wsl"
,
"test"
,
"-x"
,
cmdpath
])
if
retcode
==
0
:
# Form a new argument list and convert any Windows paths in it into WSL paths
wslargs
=
[
wslpath
(
arg
)
for
arg
in
args
]
wslargs
[
0
]
=
cmdpath
# Prepend important environment variables - note that it seems we cannot
# use WSLENV for this due to its insistance on path mapping.
return
[
"wsl"
,
"PATH=$PATH:%s/bin"
%
fslplatform
.
fsldir
,
"FSLDIR=%s"
%
fslplatform
.
fsldir
,
"FSLOUTPUTTYPE=%s"
%
os
.
environ
.
get
(
"FSLOUTPUTTYPE"
,
"NIFTI_GZ"
)
]
+
wslargs
else
:
# Command was not found in WSL with this path
return
None
def
wslpath
(
patharg
):
"""
Convert a command line argument containing a Windows path to the equivalent WSL path (e.g. ``c:
\\
Users`` -> ``/mnt/c/Users``)
...
...
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