diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index 969dcb3cdf7920f20d8dcb15fd05e6bd6adf03eb..a1405eb59fcef70c45a3a1600bd97c8bfe715670 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -14,7 +14,7 @@ import fsl.utils.assertions as asrt
from . import wrapperutils as wutils
-@wutils.fileOrImage('input', 'output')
+@wutils.fileOrImage('input', 'output', outprefix='output')
@wutils.fslwrapper
def bet(input, output, **kwargs):
"""Wrapper for the ``bet`` command.
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 0ce8c09d5455e529cd828936eacfadd421c30fd0..9b06c982eb8fc44a70c23ef0cb0a78915d201548 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -102,8 +102,9 @@ import six
import nibabel as nib
import numpy as np
-import fsl.utils.tempdir as tempdir
import fsl.utils.run as run
+import fsl.utils.path as fslpath
+import fsl.utils.tempdir as tempdir
import fsl.data.image as fslimage
@@ -504,7 +505,14 @@ class _FileOrThing(object):
return self.__output
- def __init__(self, func, prepIn, prepOut, load, *things, outprefix=None):
+ def __init__(self,
+ func,
+ prepIn,
+ prepOut,
+ load,
+ removeExt,
+ *things,
+ outprefix=None):
"""Initialise a ``_FileOrThing`` decorator.
:arg func: The function to be decorated.
@@ -519,6 +527,9 @@ class _FileOrThing(object):
that were set to :data:`LOAD`. Must accept a file path
as its sole argument.
+ :arg removeExt: Function which can remove a file extension from a file
+ path.
+
:arg things: Names of all arguments which will be handled by
this ``_FileOrThing`` decorator. If not provided,
*all* arguments passed to the function will be
@@ -526,9 +537,8 @@ class _FileOrThing(object):
:arg outprefix: The name of a positional or keyword argument to the
function, which specifies an output file name prefix.
- All other arguments which begin with this prefix (
- more specifically, which begin with ``[prefix]_``)
- may be interpreted as things to load.
+ All other arguments with names that begin with this
+ prefix may be interpreted as things to ``LOAD``.
The ``prepIn`` and ``prepOut`` functions must accept the following
positional arguments:
@@ -544,6 +554,7 @@ class _FileOrThing(object):
self.__prepIn = prepIn
self.__prepOut = prepOut
self.__load = load
+ self.__removeExt = removeExt
self.__things = things
self.__outprefix = outprefix
@@ -570,7 +581,7 @@ class _FileOrThing(object):
# Replace any things with file names.
# Also get a list of LOAD outputs
args = self.__prepareArgs(td, argnames, args, kwargs)
- args, kwargs, prefix, outfiles, prefixedFiles = args
+ args, kwargs, basePrefix, outfiles, prefixes = args
# Call the function
result = func(*args, **kwargs)
@@ -594,29 +605,31 @@ class _FileOrThing(object):
result[oname] = oval
# Load or move output-prefixed files
- if prefix is not None:
+ if basePrefix is not None:
- prefixDir = op.abspath(op.dirname(prefix))
- prefix = op.basename(prefix)
- allPrefixed = glob.glob(op.join(td, '{}_*'.format(prefix)))
+ prefixDir = op.abspath(op.dirname(basePrefix))
+ basePrefix = op.basename(basePrefix)
+ allPrefixed = glob.glob(op.join(td, '{}*'.format(basePrefix)))
for filename in allPrefixed:
basename = op.basename(filename)
- for argname in prefixedFiles:
- if fnmatch.fnmatch(basename, '{}*'.format(argname)):
+ for prefix in prefixes:
+ if fnmatch.fnmatch(basename, '{}*'.format(prefix)):
log.debug('Loading prefixed output %s: %s',
- argname, filename)
-
- fval = self.__load(filename)
+ prefix, filename)
- if argname in result: result[argname].append(fval)
- else: result[argname] = [fval]
+ fval = self.__load(filename)
+ basename = self.__removeExt(basename)
+ result[basename] = fval
break
# if file did not match any pattern,
- # move it into real prefix
+ # move it into the real prefix, where
+ # the function would have saved it
+ # if we had not modified the prefix
+ # (see __prepareArgs)
else:
log.debug('Moving prefixed output %s into %s',
filename, prefixDir)
@@ -691,7 +704,7 @@ class _FileOrThing(object):
for name, val in list(allargs.items()):
# is this argument referring
- # to a prefixd output?
+ # to a prefixed output?
isprefixed = (prefix is not None and
name.startswith(prefix))
@@ -722,6 +735,7 @@ class _FileOrThing(object):
outfiles[name] = outfile
allargs[ name] = outfile
+ # Assumed to be an input file
else:
infile = self.__prepIn(workdir, name, val)
@@ -791,7 +805,13 @@ def fileOrImage(*args, **kwargs):
raise RuntimeError('Cannot handle type: {}'.format(intypes))
def decorator(func):
- fot = _FileOrThing(func, prepIn, prepOut, load, *args, **kwargs)
+ fot = _FileOrThing(func,
+ prepIn,
+ prepOut,
+ load,
+ fslimage.removeExt,
+ *args,
+ **kwargs)
def wrapper(*args, **kwargs):
result = fot(*args, **kwargs)
@@ -825,7 +845,13 @@ def fileOrArray(*args, **kwargs):
load = np.loadtxt
def decorator(func):
- fot = _FileOrThing(func, prepIn, prepOut, load, *args, **kwargs)
+ fot = _FileOrThing(func,
+ prepIn,
+ prepOut,
+ load,
+ fslpath.removeExt,
+ *args,
+ **kwargs)
def wrapper(*args, **kwargs):
return fot(*args, **kwargs)