diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index f469af4873effcb400a9ef2f3a181c98100f96f7..3fb7d979eb9848ed8c4a878a53edd6b0c39eb052 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -21,7 +21,6 @@
import sys
import logging
-import warnings
import threading
import contextlib
import collections
@@ -129,7 +128,7 @@ def run(*args, **kwargs):
argument.
An exception is raised if the command returns a non-zero exit code, unless
- the ``ret`` option is set to ``True``.
+ the ``exitcode`` option is set to ``True``.
:arg stdout: Must be passed as a keyword argument. Defaults to ``True``.
If ``True``, standard output is captured and returned.
@@ -162,8 +161,8 @@ def run(*args, **kwargs):
- stderr: Optional file-like object to which the command's
standard error stream can be forwarded.
- - cmd: Optional file-like object to which the command itself
- is logged.
+ - cmd: Optional file-like object to which the command
+ itself is logged.
:returns: If ``submit`` is provided, the return value of
:func:`.fslsub` is returned. Otherwise returns a single
@@ -323,11 +322,11 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
def runfsl(*args, **kwargs):
- """Call a FSL command and return its output.
-
+ """Call a FSL command and return its output.
+
This function searches for the command in the following
locations (ordered by priority):
-
+
1. ``FSL_PREFIX``
2. ``$FSLDEVDIR/bin``
3. ``$FSLDIR/bin``
@@ -342,7 +341,7 @@ def runfsl(*args, **kwargs):
prefixes.append(op.join(fslplatform.fsldevdir, 'bin'))
if fslplatform.fsldir is not None:
prefixes.append(op.join(fslplatform.fsldir, 'bin'))
-
+
if not prefixes:
raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index 31660d122addd1f30fb0de857a97219d64f350f0..895f0aa88365fc5044d95fcae7694ee3dc87ed64 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -4,6 +4,7 @@
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
#
"""This module provides the :func:`bet` function, a wrapper for the FSL
`BET <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET>`_ command.
@@ -58,7 +59,7 @@ def bet(input, output, **kwargs):
cmd = ['bet', input, output]
# The 'centre' argument requires three co-ordinates and can't be passed
- # as a single value, so needs to be handled separately. Assume it is
+ # as a single value, so needs to be handled separately. Assume it is
# passed as a Python sequence
centre = kwargs.pop("c", None)
if centre is not None:
diff --git a/fsl/wrappers/eddy.py b/fsl/wrappers/eddy.py
index 3419c99d133045a4b34762e85de4d1e5f24528d1..53a90b9ca263984a1be1b168f6ea6a2c02e4e865 100644
--- a/fsl/wrappers/eddy.py
+++ b/fsl/wrappers/eddy.py
@@ -4,6 +4,7 @@
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Martin Craig <martin.craig@eng.ox.a.uk>
#
"""This module provides wrapper functions for the FSL `TOPUP
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup>`_ and `EDDY
@@ -15,6 +16,7 @@ estimation and eddy-current distortion correction.
eddy_cuda
topup
+ applytopup
"""
@@ -93,8 +95,8 @@ def applytopup(imain, datain, index, **kwargs):
asrt.assertIsNifti(imain)
cmd = [
- 'applytopup', '--imain={}'.format(imain),
- '--inindex={}'.format(index),
+ 'applytopup', '--imain={}'.format(imain),
+ '--inindex={}'.format(index),
'--datain={}'.format(datain),
]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
diff --git a/fsl/wrappers/fast.py b/fsl/wrappers/fast.py
index b1cd712ac99e9e45d2e97f74f5dae5b38c6e80c0..5dbe2a412c4b3bbf30a7ce9c707a16de06bc8af8 100644
--- a/fsl/wrappers/fast.py
+++ b/fsl/wrappers/fast.py
@@ -45,7 +45,11 @@ def fast(imgs, out='fast', **kwargs):
}
cmd = ['fast', '-v', '--out=%s' % out]
- cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
+ cmd += wutils.applyArgStyle('--=',
+ valmap=valmap,
+ argmap=argmap,
+ singlechar_args=True,
+ **kwargs)
cmd += imgs
return cmd
diff --git a/fsl/wrappers/fsl_anat.py b/fsl/wrappers/fsl_anat.py
index a1ea260c137049a0dd26b1a84dbbd3184dc1e78c..868dacb70d206fe5a9b53907668cc7641513bf52 100644
--- a/fsl/wrappers/fsl_anat.py
+++ b/fsl/wrappers/fsl_anat.py
@@ -46,6 +46,10 @@ def fsl_anat(img, out='fsl_anat', **kwargs):
if smoothing is not None:
cmd += ['-s', str(smoothing)]
- cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
+ cmd += wutils.applyArgStyle('--=',
+ valmap=valmap,
+ argmap=argmap,
+ singlechar_args=True,
+ **kwargs)
return cmd
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 2bda19793ffca266038421e734738b55743604e4..88db1dc92b7774cc683aedbd6e55dbeef25fb032 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -4,6 +4,7 @@
# functions.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
#
"""This module contains functions and decorators used by the FSL wrapper
functions.
@@ -159,7 +160,12 @@ def cmdwrapper(func):
submit = kwargs.pop('submit', None)
log = kwargs.pop('log', {'tee' : True})
cmd = func(*args, **kwargs)
- return run.run(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
+ return run.run(cmd,
+ stderr=stderr,
+ log=log,
+ submit=submit,
+ stdout=stdout,
+ exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -175,7 +181,12 @@ def fslwrapper(func):
submit = kwargs.pop('submit', None)
log = kwargs.pop('log', {'tee' : True})
cmd = func(*args, **kwargs)
- return run.runfsl(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
+ return run.runfsl(cmd,
+ stderr=stderr,
+ log=log,
+ submit=submit,
+ stdout=stdout,
+ exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -197,7 +208,12 @@ generated command line arguments.
"""
-def applyArgStyle(style, valsep=None, argmap=None, valmap=None, singlechar_args=False, **kwargs):
+def applyArgStyle(style,
+ valsep=None,
+ argmap=None,
+ valmap=None,
+ singlechar_args=False,
+ **kwargs):
"""Turns the given ``kwargs`` into command line options. This function
is intended to be used to automatically generate command line options
from arguments passed into a Python function.
@@ -256,8 +272,9 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, singlechar_args=
The argument for any options not specified in the ``valmap``
will be converted into strings.
- :arg singlechar_args: If True, single character arguments always take a single
- hyphen prefix (e.g. -h) regardless of the style
+ :arg singlechar_args: If True, single character arguments always take a
+ single hyphen prefix (e.g. -h) regardless of the
+ style.
:arg kwargs: Arguments to be converted into command-line options.
@@ -284,8 +301,10 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, singlechar_args=
if valmap is None: valmap = {}
def fmtarg(arg):
- if style in ('-', '-=') or (singlechar_args and len(arg) == 1): arg = '-{}'.format(arg)
- elif style in ('--', '--='): arg = '--{}'.format(arg)
+ if style in ('-', '-=') or (singlechar_args and len(arg) == 1):
+ arg = '-{}'.format(arg)
+ elif style in ('--', '--='):
+ arg = '--{}'.format(arg)
return arg
# always returns a sequence
@@ -1007,9 +1026,11 @@ def fileOrArray(*args, **kwargs):
return decorator
+
def fileOrText(*args, **kwargs):
- """Decorator which can be used to ensure that any text output (e.g. log file are saved
- to text files, and output files can be loaded and returned as strings.
+ """Decorator which can be used to ensure that any text output (e.g. log
+ file) are saved to text files, and output files can be loaded and returned
+ as strings.
"""
def prepIn(workdir, name, val):