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Evan Edmond
fslpy
Commits
d211ea51
Commit
d211ea51
authored
Aug 20, 2021
by
Paul McCarthy
🚵
Browse files
STY: Address/suppress lint
parent
adcd481c
Changes
3
Hide whitespace changes
Inline
Side-by-side
fsl/utils/run.py
View file @
d211ea51
...
...
@@ -52,17 +52,16 @@ class FSLNotPresent(Exception):
"""Error raised by the :func:`runfsl` function when ``$FSLDIR`` cannot
be found.
"""
pass
@
contextlib
.
contextmanager
def
dryrun
(
*
args
):
def
dryrun
(
*
_
):
"""Context manager which causes all calls to :func:`run` to be logged but
not executed. See the :data:`DRY_RUN` flag.
The returned standard output will be equal to ``' '.join(args)``.
"""
global
DRY_RUN
global
DRY_RUN
# pylint: disable=global-statement
oldval
=
DRY_RUN
DRY_RUN
=
True
...
...
@@ -184,16 +183,16 @@ def run(*args, **kwargs):
returnExitcode
=
kwargs
.
pop
(
'exitcode'
,
False
)
submit
=
kwargs
.
pop
(
'submit'
,
{})
cmdonly
=
kwargs
.
pop
(
'cmdonly'
,
False
)
log
=
kwargs
.
pop
(
'log'
,
None
)
log
g
=
kwargs
.
pop
(
'log'
,
None
)
args
=
prepareArgs
(
args
)
if
log
is
None
:
log
=
{}
if
log
g
is
None
:
log
g
=
{}
tee
=
log
.
get
(
'tee'
,
False
)
logStdout
=
log
.
get
(
'stdout'
,
None
)
logStderr
=
log
.
get
(
'stderr'
,
None
)
logCmd
=
log
.
get
(
'cmd'
,
None
)
tee
=
log
g
.
get
(
'tee'
,
False
)
logStdout
=
log
g
.
get
(
'stdout'
,
None
)
logStderr
=
log
g
.
get
(
'stderr'
,
None
)
logCmd
=
log
g
.
get
(
'cmd'
,
None
)
if
not
bool
(
submit
):
submit
=
None
...
...
@@ -394,25 +393,32 @@ def runfsl(*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
"""
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 (remembering that the command path may include FSLDIR which
# is a Windows path)
# Check if command exists in WSL (remembering
# that the command path may include FSLDIR
# which is a Windows path)
cmdpath
=
fslpath
.
wslpath
(
cmdpath
)
_stdout
,
_stderr
,
retcode
=
_realrun
(
False
,
None
,
None
,
None
,
"wsl"
,
"test"
,
"-x"
,
cmdpath
)
_stdout
,
_stderr
,
retcode
=
_realrun
(
False
,
None
,
None
,
None
,
"wsl"
,
"test"
,
"-x"
,
cmdpath
)
if
retcode
==
0
:
# Form a new argument list and convert any Windows paths in it into WSL paths
# Form a new argument list and convert
# any Windows paths in it into WSL paths
wslargs
=
[
fslpath
.
wslpath
(
arg
)
for
arg
in
args
]
wslargs
[
0
]
=
cmdpath
local_fsldir
=
fslpath
.
wslpath
(
fslplatform
.
fsldir
)
...
...
@@ -420,8 +426,10 @@ def wslcmd(cmdpath, *args):
local_fsldevdir
=
fslpath
.
wslpath
(
fslplatform
.
fsldevdir
)
else
:
local_fsldevdir
=
None
# Prepend important environment variables - note that it seems we cannot
# use WSLENV for this due to its insistance on path mapping. FIXME FSLDEVDIR?
# Prepend important environment variables -
# note that it seems we cannot use WSLENV
# for this due to its insistance on path
# mapping. FIXME FSLDEVDIR?
local_path
=
"$PATH"
if
local_fsldevdir
:
local_path
+=
":%s/bin"
%
local_fsldevdir
...
...
fsl/wrappers/__init__.py
View file @
d211ea51
#!/usr/bin/env python
#
# pylint: disable=unused-import
# flake8: noqa: F401
#
# __init__.py - Wrappers for FSL command-line tools.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
...
...
@@ -79,37 +82,37 @@ decorators.
"""
from
.wrapperutils
import
(
LOAD
,)
# noqa
from
.bet
import
(
bet
,
# noqa
robustfov
)
from
.eddy
import
(
eddy_cuda
,
# noqa
topup
,
applytopup
)
from
.fast
import
(
fast
,)
# noqa
from
.fsl_anat
import
(
fsl_anat
,)
# noqa
from
.fsl_sub
import
(
fsl_sub
,)
# noqa
from
.flirt
import
(
flirt
,
# noqa
invxfm
,
applyxfm
,
applyxfm4D
,
concatxfm
,
mcflirt
)
from
.fnirt
import
(
fnirt
,
# noqa
applywarp
,
invwarp
,
convertwarp
)
from
.fslmaths
import
(
fslmaths
,)
# noqa
from
.fslstats
import
(
fslstats
,)
# noqa
from
.fugue
import
(
fugue
,
# noqa
prelude
,
sigloss
,
fsl_prepare_fieldmap
)
from
.melodic
import
(
melodic
,
# noqa
fsl_regfilt
)
from
.misc
import
(
fslreorient2std
,
# noqa
fslroi
,
slicer
,
cluster
,
gps
)
from
.epi_reg
import
epi_reg
from
.
import
tbss
# noqa
from
fsl.wrappers
.wrapperutils
import
(
LOAD
,)
from
fsl.wrappers
.bet
import
(
bet
,
robustfov
)
from
fsl.wrappers
.eddy
import
(
eddy_cuda
,
topup
,
applytopup
)
from
fsl.wrappers
.fast
import
(
fast
,)
from
fsl.wrappers
.fsl_anat
import
(
fsl_anat
,)
from
fsl.wrappers
.fsl_sub
import
(
fsl_sub
,)
from
fsl.wrappers
.flirt
import
(
flirt
,
invxfm
,
applyxfm
,
applyxfm4D
,
concatxfm
,
mcflirt
)
from
fsl.wrappers
.fnirt
import
(
fnirt
,
applywarp
,
invwarp
,
convertwarp
)
from
fsl.wrappers
.fslmaths
import
(
fslmaths
,)
from
fsl.wrappers
.fslstats
import
(
fslstats
,)
from
fsl.wrappers
.fugue
import
(
fugue
,
prelude
,
sigloss
,
fsl_prepare_fieldmap
)
from
fsl.wrappers
.melodic
import
(
melodic
,
fsl_regfilt
)
from
fsl.wrappers
.misc
import
(
fslreorient2std
,
fslroi
,
slicer
,
cluster
,
gps
)
from
fsl.wrappers
.epi_reg
import
epi_reg
from
fsl.wrappers
import
tbss
fsl/wrappers/wrapperutils.py
View file @
d211ea51
...
...
@@ -441,7 +441,7 @@ file should be loaded into memory and returned as a Python object.
"""
class
FileOrThing
(
object
)
:
class
FileOrThing
:
"""Decorator which ensures that certain arguments which are passed into the
decorated function are always passed as file names. Both positional and
keyword arguments can be specified.
...
...
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