diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index a5b9df816f9605edf62b8daa62d082142a898057..ba3ce9a647a7c026a501ffc845eaa0b69a65c29b 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -166,8 +166,8 @@ def run(*args, **kwargs):
- stderr: Optional file-like object to which the command's
standard error stream can be forwarded.
- - cmd: If ``True``, the command itself is logged to the
- standard output stream(s).
+ - 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
@@ -194,7 +194,7 @@ def run(*args, **kwargs):
tee = log .get('tee', False)
logStdout = log .get('stdout', None)
logStderr = log .get('stderr', None)
- logCmd = log .get('cmd', False)
+ logCmd = log .get('cmd', None)
args = _prepareArgs(args)
if not bool(submit):
@@ -272,8 +272,8 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
:arg logStderr: Optional file-like object to which the command's standard
error stream can be forwarded.
- :arg logCmd: If ``True``, the command itself is logged to the standard
- output stream(s).
+ :arg logCmd: Optional file-like object to which the command itself is
+ logged.
:arg args: Command to run
@@ -308,15 +308,13 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
if logStdout is not None: outstreams.append(logStdout)
if logStderr is not None: errstreams.append(logStderr)
- # log the command to
- # stdout if requested
- if logCmd:
+ # log the command if requested
+ if logCmd is not None:
cmd = ' '.join(args) + '\n'
- for o in outstreams:
- if 'b' in getattr(o, 'mode', 'w'):
- o.write(cmd.encode('utf-8'))
- else:
- o.write(cmd)
+ if 'b' in getattr(logCmd, 'mode', 'w'):
+ logCmd.write(cmd.encode('utf-8'))
+ else:
+ logCmd.write(cmd)
stdoutt = _forwardStream(proc.stdout, *outstreams)
stderrt = _forwardStream(proc.stderr, *errstreams)
@@ -340,23 +338,35 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
def runfsl(*args, **kwargs):
- """Call a FSL command and return its output. This function simply prepends
- ``$FSLDIR/bin/`` to the command before passing it to :func:`run`.
+ """Call a FSL command and return its output.
+
+ This function searches for the command in the following
+ locations (ordered by priority):
+
+ 1. ``FSL_PREFIX``
+ 2. ``$FSLDEVDIR/bin``
+ 3. ``$FSLDIR/bin``
+
+ If found, the full path to the command is then passed to :func:`run`.
"""
-
- prefix = None
+ prefixes = []
if FSL_PREFIX is not None:
- prefix = FSL_PREFIX
- elif fslplatform.fsldevdir is not None:
- prefix = op.join(fslplatform.fsldevdir, 'bin')
- elif fslplatform.fsldir is not None:
- prefix = op.join(fslplatform.fsldir, 'bin')
- else:
+ prefixes.append(FSL_PREFIX)
+ if fslplatform.fsldevdir is not None:
+ prefixes.append(op.join(fslplatform.fsldevdir, 'bin'))
+ if fslplatform.fsldir is not None:
+ prefixes.append(op.join(fslplatform.fsldir, 'bin'))
+
+ if not prefixes:
raise FSLNotPresent('$FSLDIR is not set - FSL cannot be found!')
- args = _prepareArgs(args)
- args[0] = op.join(prefix, args[0])
+ args = _prepareArgs(args)
+ for prefix in prefixes:
+ cmdpath = op.join(prefix, args[0])
+ if op.isfile(cmdpath):
+ args[0] = cmdpath
+ break
return run(*args, **kwargs)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 3a0297a3ef7af4574087ff3e4f3ace977d1b8d3f..b37413ed3678a5fbd84f9056bdae2d52f76a64dd 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -80,8 +80,10 @@ from .wrapperutils import (LOAD,) # noqa
from .bet import (bet, # noqa
robustfov)
from .eddy import (eddy_cuda, # noqa
- topup)
+ topup,
+ applytopup)
from .fast import (fast,) # noqa
+from .fsl_anat import (fsl_anat,) # noqa
from .flirt import (flirt, # noqa
invxfm,
applyxfm,
diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index 09282f117b26374ab99a40420976fa0c1771dc8d..e20ee3fb13cb0070aca3b742b1946d34511106db 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -35,6 +35,7 @@ def bet(input, output, **kwargs):
'robust' : 'R',
'fracintensity' : 'f',
'seg' : 'n',
+ 'centre' : 'c',
}
valmap = {
@@ -55,6 +56,14 @@ 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
+ # passed as a Python sequence
+ centre = kwargs.pop("c", None)
+ if centre is not None:
+ cmd += ['c', ] + list(centre)
+
cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
diff --git a/fsl/wrappers/eddy.py b/fsl/wrappers/eddy.py
index ae5c7bb4f0075c65fa363970237b26baf7797bd1..3419c99d133045a4b34762e85de4d1e5f24528d1 100644
--- a/fsl/wrappers/eddy.py
+++ b/fsl/wrappers/eddy.py
@@ -61,8 +61,8 @@ def eddy_cuda(imain, mask, index, acqp, bvecs, bvals, out, **kwargs):
return cmd
-@wutils.fileOrImage('imain', 'fout', 'iout')
-@wutils.fileOrArray('datain')
+@wutils.fileOrImage('imain', 'fout', 'iout', outprefix='out')
+@wutils.fileOrArray('datain', outprefix='out')
@wutils.fslwrapper
def topup(imain, datain, **kwargs):
"""Wrapper for the ``topup`` command."""
@@ -78,3 +78,25 @@ def topup(imain, datain, **kwargs):
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
+
+@wutils.fileOrImage('imain', 'out')
+@wutils.fileOrArray('datain')
+@wutils.fslwrapper
+def applytopup(imain, datain, index, **kwargs):
+ """Wrapper for the ``applytopup`` command."""
+
+ valmap = {
+ 'verbose' : wutils.SHOW_IF_TRUE
+ }
+
+ asrt.assertFileExists(datain)
+ asrt.assertIsNifti(imain)
+
+ cmd = [
+ 'applytopup', '--imain={}'.format(imain),
+ '--inindex={}'.format(index),
+ '--datain={}'.format(datain),
+ ]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+
+ return cmd
diff --git a/fsl/wrappers/fast.py b/fsl/wrappers/fast.py
index a944ea77ad31f2c8487c2e8e4aec2e3b8aea1b77..b1cd712ac99e9e45d2e97f74f5dae5b38c6e80c0 100644
--- a/fsl/wrappers/fast.py
+++ b/fsl/wrappers/fast.py
@@ -33,12 +33,19 @@ def fast(imgs, out='fast', **kwargs):
asrt.assertIsNifti(*imgs)
+ valmap = {
+ 'nobias' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ 'Prior' : wutils.SHOW_IF_TRUE,
+ 'segments' : wutils.SHOW_IF_TRUE,
+ }
+
argmap = {
'n_classes' : 'class',
}
cmd = ['fast', '-v', '--out=%s' % out]
- cmd += wutils.applyArgStyle('--=', argmap=argmap, **kwargs)
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
cmd += imgs
return cmd
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index cac769bf26f428d4bed62d830ec661cf43b8dd74..8b5d1d526dc6a893441204d788d58b7302d59260 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -59,14 +59,15 @@ def flirt(src, ref, **kwargs):
return cmd
-def applyxfm(src, ref, mat, out, interp='spline'):
+def applyxfm(src, ref, mat, out, interp='spline', **kwargs):
"""Convenience function which runs ``flirt -applyxfm ...``."""
return flirt(src,
ref,
out=out,
applyxfm=True,
init=mat,
- interp=interp)
+ interp=interp,
+ **kwargs)
@wutils.fileOrArray()
diff --git a/fsl/wrappers/fnirt.py b/fsl/wrappers/fnirt.py
index bd457337357694e3bb869ef8a0c516cebd1c7cb1..f4ca120fceebed4cdd97310087a1f816e544a979 100644
--- a/fsl/wrappers/fnirt.py
+++ b/fsl/wrappers/fnirt.py
@@ -27,12 +27,12 @@ from . import wrapperutils as wutils
'refout', 'refmask', 'inmask')
@wutils.fileOrArray('aff')
@wutils.fslwrapper
-def fnirt(src, ref, **kwargs):
+def fnirt(src, **kwargs):
"""Wrapper for the ``fnirt`` command."""
- asrt.assertIsNifti(src, ref)
+ asrt.assertIsNifti(src)
- cmd = ['fnirt', '--in={}'.format(src), '--ref={}'.format(ref)]
+ cmd = ['fnirt', '--in={}'.format(src)]
cmd += wutils.applyArgStyle('--=', **kwargs)
return cmd
@@ -41,7 +41,7 @@ def fnirt(src, ref, **kwargs):
@wutils.fileOrImage('src', 'ref', 'out', 'warp', 'mask')
@wutils.fileOrArray('premat', 'postmat')
@wutils.fslwrapper
-def applywarp(src, ref, out, warp, **kwargs):
+def applywarp(src, ref, out, **kwargs):
"""Wrapper for the ``applywarp`` command. """
valmap = {
@@ -55,8 +55,7 @@ def applywarp(src, ref, out, warp, **kwargs):
cmd = ['applywarp',
'--in={}'.format(src),
'--ref={}'.format(ref),
- '--out={}'.format(out),
- '--warp={}'.format(warp)]
+ '--out={}'.format(out)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
@@ -76,7 +75,7 @@ def invwarp(warp, ref, out, **kwargs):
'verbose' : wutils.SHOW_IF_TRUE,
}
- asrt.assertIsNifti(warp, ref, out)
+ asrt.assertIsNifti(warp, ref)
cmd = ['invwarp',
'--warp={}'.format(warp),
@@ -88,7 +87,7 @@ def invwarp(warp, ref, out, **kwargs):
return cmd
-@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap')
+@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap', 'jacobian')
@wutils.fileOrArray('premat', 'midmat', 'postmat')
@wutils.fslwrapper
def convertwarp(out, ref, **kwargs):
@@ -99,7 +98,6 @@ def convertwarp(out, ref, **kwargs):
'rel' : wutils.SHOW_IF_TRUE,
'absout' : wutils.SHOW_IF_TRUE,
'relout' : wutils.SHOW_IF_TRUE,
- 'jacobian' : wutils.SHOW_IF_TRUE,
'jstats' : wutils.SHOW_IF_TRUE,
'constrainj' : wutils.SHOW_IF_TRUE,
'verbose' : wutils.SHOW_IF_TRUE,
@@ -107,5 +105,4 @@ def convertwarp(out, ref, **kwargs):
cmd = ['convertwarp', '--ref={}'.format(ref), '--out={}'.format(out)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
-
return cmd
diff --git a/fsl/wrappers/fsl_anat.py b/fsl/wrappers/fsl_anat.py
new file mode 100644
index 0000000000000000000000000000000000000000..a1ea260c137049a0dd26b1a84dbbd3184dc1e78c
--- /dev/null
+++ b/fsl/wrappers/fsl_anat.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+#
+# fsl_anat.py - Wrapper for the FSL_ANAT command.
+#
+# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
+#
+"""This module provides the :func:`fsl_anat` function, a wrapper for the FSL
+`FSL_ANAT <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat>`_ command.
+"""
+
+import six
+
+import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
+
+@wutils.fileOrImage('img', outprefix='out')
+@wutils.fslwrapper
+def fsl_anat(img, out='fsl_anat', **kwargs):
+ """Wrapper for the ``fsl_anat`` command.
+
+ :arg img: Input structural image
+ :arg out: Output directory name
+ """
+ asrt.assertIsNifti(img)
+
+ valmap = {
+ 'strongbias' : wutils.SHOW_IF_TRUE,
+ 'weakbias' : wutils.SHOW_IF_TRUE,
+ 'noreorient' : wutils.SHOW_IF_TRUE,
+ 'nocrop' : wutils.SHOW_IF_TRUE,
+ 'nobias' : wutils.SHOW_IF_TRUE,
+ 'noreg' : wutils.SHOW_IF_TRUE,
+ 'nononlinreg' : wutils.SHOW_IF_TRUE,
+ 'noseg' : wutils.SHOW_IF_TRUE,
+ 'nosubcortseg' : wutils.SHOW_IF_TRUE,
+ 'nosearch' : wutils.SHOW_IF_TRUE,
+ 'nocleanup' : wutils.SHOW_IF_TRUE,
+ }
+
+ argmap = {
+ }
+
+ img_type = kwargs.pop("img_type", "T1")
+ cmd = ['fsl_anat', '-i', img, '-o', out, '-t', img_type]
+ smoothing = kwargs.pop("bias_smoothing", None)
+ if smoothing is not None:
+ cmd += ['-s', str(smoothing)]
+
+ 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 6728a23272696f295227291d723101cd366e7be5..cf452d9eee82a56d5a498beba9a159dc652a11b9 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -152,11 +152,13 @@ def cmdwrapper(func):
:func:`fsl.utils.run.run` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
+ stdout = kwargs.pop('stdout', True)
+ stderr = kwargs.pop('stderr', False)
+ exitcode = kwargs.pop('exitcode', False)
submit = kwargs.pop('submit', None)
- stderr = kwargs.pop('stderr', True)
log = kwargs.pop('log', {'tee' : True})
cmd = func(*args, **kwargs)
- return run.run(cmd, stderr=stderr, log=log, submit=submit)
+ return run.run(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -166,11 +168,13 @@ def fslwrapper(func):
:func:`fsl.utils.run.runfsl` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
+ stdout = kwargs.pop('stdout', True)
+ stderr = kwargs.pop('stderr', False)
+ exitcode = kwargs.pop('exitcode', False)
submit = kwargs.pop('submit', None)
- stderr = kwargs.pop('stderr', True)
log = kwargs.pop('log', {'tee' : True})
cmd = func(*args, **kwargs)
- return run.runfsl(cmd, stderr=stderr, log=log, submit=submit)
+ return run.runfsl(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -192,7 +196,7 @@ generated command line arguments.
"""
-def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **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.
@@ -251,6 +255,9 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
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 kwargs: Arguments to be converted into command-line options.
:returns: A list containing the generated command-line options.
@@ -276,7 +283,7 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
if valmap is None: valmap = {}
def fmtarg(arg):
- if 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
@@ -303,11 +310,12 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
for k, v in kwargs.items():
+ if v is None: continue
+
k = argmap.get(k, k)
mapv = valmap.get(k, fmtval(v))
k = fmtarg(k)
-
if mapv in (SHOW_IF_TRUE, HIDE_IF_TRUE):
if (mapv is SHOW_IF_TRUE and v) or \
(mapv is HIDE_IF_TRUE and not v):
@@ -849,7 +857,6 @@ class _FileOrThing(object):
for prefixed in it.chain(*allPrefixed):
fullpath = prefixed
prefixed = op.relpath(prefixed, workdir)
-
for prefPat, prefName in prefixes.items():
if not fnmatch.fnmatch(prefixed, '{}*'.format(prefPat)):
continue
@@ -862,10 +869,17 @@ class _FileOrThing(object):
# not of the correct type.
fval = self.__load(fullpath)
if fval is not None:
- prefixed = self.__removeExt(prefixed)
+ noext = self.__removeExt(prefixed)
prefPat = prefPat.replace('\\', '\\\\')
- prefixed = re.sub('^' + prefPat, prefName, prefixed)
- result[prefixed] = fval
+ noext = re.sub('^' + prefPat, prefName, noext)
+ # If there is already an item in result with the
+ # name (stripped of prefix), then instead store
+ # the result with the full prefixed name
+ if noext not in result:
+ result[noext] = fval
+ else:
+ withext = re.sub('^' + prefPat, prefName, prefixed)
+ result[withext] = fval
break
return result
@@ -887,8 +901,11 @@ def fileOrImage(*args, **kwargs):
infile = None
- if isinstance(val, (fslimage.Image, nib.nifti1.Nifti1Image)):
- intypes.append(type(val))
+ if isinstance(val, fslimage.Image):
+ intypes.append(fslimage.Image)
+
+ elif isinstance(val, nib.nifti1.Nifti1Image):
+ intypes.append(nib.nifti1.Nifti1Image)
if isinstance(val, fslimage.Image):
val = val.nibImage