diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index e4a4c51961c74c23554fca53cb3fd0394000467b..f469af4873effcb400a9ef2f3a181c98100f96f7 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -162,8 +162,8 @@ 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
@@ -179,7 +179,7 @@ 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):
@@ -257,8 +257,8 @@ 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
@@ -293,15 +293,13 @@ 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)
@@ -325,23 +323,35 @@ 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..31660d122addd1f30fb0de857a97219d64f350f0 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', ] + [str(v) for v in 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 d3fc2db2379224aa1f3582a1c8e6a96afc8ac164..2bda19793ffca266038421e734738b55743604e4 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -153,11 +153,13 @@ def cmdwrapper(func):
:func:`fsl.utils.run.run` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
- submit = kwargs.pop('submit', None)
+ stdout = kwargs.pop('stdout', True)
stderr = kwargs.pop('stderr', True)
+ exitcode = kwargs.pop('exitcode', False)
+ 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)
+ return run.run(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -167,11 +169,13 @@ def fslwrapper(func):
:func:`fsl.utils.run.runfsl` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
- submit = kwargs.pop('submit', None)
+ stdout = kwargs.pop('stdout', True)
stderr = kwargs.pop('stderr', True)
+ exitcode = kwargs.pop('exitcode', False)
+ 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)
+ return run.runfsl(cmd, stderr=stderr, log=log, submit=submit, stdout=stdout, exitcode=exitcode)
return _update_wrapper(wrapper, func)
@@ -193,7 +197,7 @@ 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.
@@ -252,6 +256,9 @@ 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.
@@ -277,7 +284,7 @@ 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
@@ -304,11 +311,12 @@ 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):
@@ -850,7 +858,6 @@ 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
@@ -863,10 +870,17 @@ 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
@@ -888,8 +902,11 @@ 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
@@ -989,3 +1006,43 @@ def fileOrArray(*args, **kwargs):
return _update_wrapper(wrapper, func)
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.
+ """
+
+ def prepIn(workdir, name, val):
+
+ infile = None
+
+ if isinstance(val, six.string_types):
+ with tempfile.NamedTemporaryFile(mode='w', suffix='.txt') as f:
+ f.write(val)
+ infile = f.name
+ return infile
+
+ def prepOut(workdir, name, val):
+ return op.join(workdir, '{}.txt'.format(name))
+
+ def load(path):
+ try:
+ with open(path, "r") as f:
+ return f.read()
+ except Exception: return None
+
+ def decorator(func):
+ fot = _FileOrThing(func,
+ prepIn,
+ prepOut,
+ load,
+ fslpath.removeExt,
+ *args,
+ **kwargs)
+
+ def wrapper(*args, **kwargs):
+ return fot(*args, **kwargs)
+
+ return _update_wrapper(wrapper, func)
+
+ return decorator
diff --git a/tests/__init__.py b/tests/__init__.py
index 4960e909532e5d5f1a970fd9f44368ed23c7d31e..06bd6b5b7095dade252133f67754b9dd7c66f2cb 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -35,7 +35,7 @@ logging.getLogger().setLevel(logging.WARNING)
@contextlib.contextmanager
-def mockFSLDIR():
+def mockFSLDIR(**kwargs):
oldfsldir = fslplatform.fsldir
oldfsldevdir = fslplatform.fsldevdir
@@ -45,6 +45,12 @@ def mockFSLDIR():
fsldir = op.join(td, 'fsl')
bindir = op.join(fsldir, 'bin')
os.makedirs(bindir)
+ for subdir, files in kwargs.items():
+ subdir = op.join(fsldir, subdir)
+ if not op.isdir(subdir):
+ os.makedirs(subdir)
+ for fname in files:
+ touch(op.join(subdir, fname))
fslplatform.fsldir = fsldir
fslplatform.fsldevdir = None
diff --git a/tests/test_run.py b/tests/test_run.py
index bc77a46fd14f494a4269ecb90d2749a5bace5ab5..422222fb9b6454982197ee04720a561bf1da5868 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -353,20 +353,22 @@ def test_run_logcmd():
exit 0
""").strip()
- expstdout = './script.sh 1 2 3\noutput 1 2 3\n'
+ expcmd = './script.sh 1 2 3\n'
+ expstdout = 'output 1 2 3\n'
with tempdir.tempdir():
mkexec('script.sh', test_script)
- stdout = run.run('./script.sh 1 2 3', log={'cmd' : True})
- assert stdout == expstdout
- mkexec('script.sh', test_script)
- stdout = run.run('./script.sh 1 2 3', log={'cmd' : True})
- assert stdout == expstdout
+ with open('my_stdout', 'wt') as stdoutf:
+ stdout = run.run('./script.sh 1 2 3',
+ log={'cmd' : stdoutf})
+
+ assert stdout == expstdout
+ assert open('my_stdout', 'rt').read() == expcmd
with open('my_stdout', 'wt') as stdoutf:
stdout = run.run('./script.sh 1 2 3',
- log={'cmd' : True, 'stdout' : stdoutf})
+ log={'cmd' : stdoutf, "stdout" : stdoutf})
assert stdout == expstdout
- assert open('my_stdout', 'rt').read() == expstdout
+ assert open('my_stdout', 'rt').read() == expcmd + expstdout
diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
index af2a95fb6df0c7254ebde60625ccc2264ebdaa2e..b1517b32cd69fcc26d39409a58311961b422cdd9 100644
--- a/tests/test_wrappers.py
+++ b/tests/test_wrappers.py
@@ -39,7 +39,7 @@ def checkResult(cmd, base, args, stripdir=None):
def test_bet():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('bet',)) as fsldir:
bet = op.join(fsldir, 'bin', 'bet')
result = fw.bet('input', 'output', mask=True, c=(10, 20, 30))
expected = (bet + ' input output', ('-m', '-c 10 20 30'))
@@ -47,7 +47,7 @@ def test_bet():
def test_robustfov():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('robustfov',)) as fsldir:
rfov = op.join(fsldir, 'bin', 'robustfov')
result = fw.robustfov('input', 'output', b=180)
expected = (rfov + ' -i input', ('-r output', '-b 180'))
@@ -55,7 +55,7 @@ def test_robustfov():
def test_eddy_cuda():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('eddy_cuda',)) as fsldir:
eddy = op.join(fsldir, 'bin', 'eddy_cuda')
result = fw.eddy_cuda('imain', 'mask', 'index', 'acqp',
'bvecs', 'bvals', 'out', dont_mask_output=True)
@@ -72,7 +72,7 @@ def test_eddy_cuda():
def test_topup():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('topup',)) as fsldir:
topup = op.join(fsldir, 'bin', 'topup')
result = fw.topup('imain', 'datain', minmet=1)
expected = topup + ' --imain=imain --datain=datain --minmet=1'
@@ -80,7 +80,7 @@ def test_topup():
def test_flirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('flirt',)) as fsldir:
flirt = op.join(fsldir, 'bin', 'flirt')
result = fw.flirt('src', 'ref', usesqform=True, anglerep='euler')
expected = (flirt + ' -in src -ref ref',
@@ -89,7 +89,7 @@ def test_flirt():
def test_applyxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('flirt',)) as fsldir:
flirt = op.join(fsldir, 'bin', 'flirt')
result = fw.applyxfm('src', 'ref', 'mat', 'out', interp='trilinear')
expected = (flirt + ' -in src -ref ref',
@@ -101,7 +101,7 @@ def test_applyxfm():
def test_invxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convert_xfm',)) as fsldir:
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.invxfm('mat', 'output')
expected = cnvxfm + ' -omat output -inverse mat'
@@ -109,7 +109,7 @@ def test_invxfm():
def test_concatxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convert_xfm',)) as fsldir:
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.concatxfm('mat1', 'mat2', 'output')
expected = cnvxfm + ' -omat output -concat mat2 mat1'
@@ -117,7 +117,7 @@ def test_concatxfm():
def test_mcflirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('mcflirt',)) as fsldir:
mcflirt = op.join(fsldir, 'bin', 'mcflirt')
result = fw.mcflirt('input', out='output', cost='normcorr', dof=12)
expected = (mcflirt + ' -in input',
@@ -128,28 +128,29 @@ def test_mcflirt():
def test_fnirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fnirt',)) as fsldir:
fnirt = op.join(fsldir, 'bin', 'fnirt')
- result = fw.fnirt('src', 'ref', iout='iout', fout='fout',
+ result = fw.fnirt('src', ref='ref', iout='iout', fout='fout',
subsamp=(8, 6, 4, 2))
- expected = (fnirt + ' --in=src --ref=ref',
- ('--iout=iout',
+ expected = (fnirt + ' --in=src',
+ ('--ref=ref',
+ '--iout=iout',
'--fout=fout',
'--subsamp=8,6,4,2'))
assert checkResult(result.output[0], *expected)
def test_applywarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('applywarp',)) as fsldir:
applywarp = op.join(fsldir, 'bin', 'applywarp')
- result = fw.applywarp('src', 'ref', 'out', 'warp', abs=True, super=True)
- expected = (applywarp + ' --in=src --ref=ref --out=out --warp=warp',
- ('--abs', '--super'))
+ result = fw.applywarp('src', 'ref', 'out', warp='warp', abs=True, super=True)
+ expected = (applywarp + ' --in=src --ref=ref --out=out',
+ ('--warp=warp', '--abs', '--super'))
assert checkResult(result.output[0], *expected)
def test_invwarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('invwarp',)) as fsldir:
invwarp = op.join(fsldir, 'bin', 'invwarp')
result = fw.invwarp('warp', 'ref', 'out',
rel=True, noconstraint=True)
@@ -159,16 +160,16 @@ def test_invwarp():
def test_convertwarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convertwarp',)) as fsldir:
cnvwarp = op.join(fsldir, 'bin', 'convertwarp')
- result = fw.convertwarp('out', 'ref', absout=True, jacobian=True)
+ result = fw.convertwarp('out', 'ref', absout=True, jacobian='jacobian')
expected = (cnvwarp + ' --ref=ref --out=out',
- ('--absout', '--jacobian'))
+ ('--absout', '--jacobian=jacobian'))
assert checkResult(result.output[0], *expected)
def test_fugue():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fugue',)) as fsldir:
fugue = op.join(fsldir, 'bin', 'fugue')
result = fw.fugue(input='input', warp='warp',
median=True, dwell=10)
@@ -181,7 +182,7 @@ def test_fugue():
def test_sigloss():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('sigloss',)) as fsldir:
sigloss = op.join(fsldir, 'bin', 'sigloss')
result = fw.sigloss('input', 'sigloss', mask='mask', te=0.5)
expected = (sigloss + ' --in input --sigloss sigloss',
@@ -190,7 +191,7 @@ def test_sigloss():
def test_melodic():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('melodic',)) as fsldir:
melodic = op.join(fsldir, 'bin', 'melodic')
result = fw.melodic('input', dim=50, mask='mask', Oall=True)
expected = (melodic + ' --in=input',
@@ -199,7 +200,7 @@ def test_melodic():
def test_fsl_regfilt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fsl_regfilt',)) as fsldir:
regfilt = op.join(fsldir, 'bin', 'fsl_regfilt')
result = fw.fsl_regfilt('input', 'output', 'design',
filter=(1, 2, 3, 4), vn=True)
@@ -210,7 +211,7 @@ def test_fsl_regfilt():
def test_fslreorient2std():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslreorient2std',)) as fsldir:
r2std = op.join(fsldir, 'bin', 'fslreorient2std')
result = fw.fslreorient2std('input', 'output')
expected = r2std + ' input output'
@@ -218,7 +219,7 @@ def test_fslreorient2std():
def test_fslroi():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslroi',)) as fsldir:
fslroi = op.join(fsldir, 'bin', 'fslroi')
result = fw.fslroi('input', 'output', 1, 10)
@@ -235,7 +236,7 @@ def test_fslroi():
def test_slicer():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('slicer',)) as fsldir:
slicer = op.join(fsldir, 'bin', 'slicer')
result = fw.slicer('input1', 'input2', i=(20, 100), x=(20, 'x.png'))
expected = slicer + ' input1 input2 -i 20 100 -x 20 x.png'
@@ -243,7 +244,7 @@ def test_slicer():
def test_cluster():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('cluster',)) as fsldir:
cluster = op.join(fsldir, 'bin', 'cluster')
result = fw.cluster('input', 'thresh',
fractional=True, osize='osize')
@@ -253,7 +254,7 @@ def test_cluster():
def test_fslmaths():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslmaths',)) as fsldir:
cmd = op.join(fsldir, 'bin', 'fslmaths')
result = fw.fslmaths('input') \
.abs().bin().binv().recip().Tmean().Tstd().Tmin().Tmax() \
@@ -274,7 +275,7 @@ def test_fslmaths():
# TODO test LOAD output
def test_fast():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fast',)) as fsldir:
cmd = op.join(fsldir, 'bin', 'fast')
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 29e569c9f011cea38e9ceaf0ec1dde42eedd7785..54cf16f4c44b06af65dae7df906f095768ef1388 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -598,7 +598,7 @@ def test_fslwrapper():
def func(a, b):
return ['func', str(a), str(b)]
- with run.dryrun(), mockFSLDIR() as fsldir:
+ with run.dryrun(), mockFSLDIR(bin=('func',)) as fsldir:
expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
assert func(1, 2)[0] == expected