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Commit 547512ad authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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ENH: fileOrThing decorator now accepts an "outprefix" argument, which can be 

used as a wildcard - all files which begin with outprefix can be specified
as keyword arguments and LOADed.
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fsl/wrappers/wrapperutils.py
+ 135
− 37
View file @ 547512ad
......@@ -88,7 +88,11 @@ and returned::
import os.path as op
import os
import sys
import glob
import shutil
import fnmatch
import inspect
import logging
import tempfile
import warnings
import functools
......@@ -103,6 +107,9 @@ import fsl.utils.run as run
import fsl.data.image as fslimage
log = logging.getLogger(__name__)
def _update_wrapper(wrapper, wrapped, *args, **kwargs):
"""Replacement for the built-in ``functools.update_wrapper``. This
implementation ensures that the wrapper function has an attribute
......@@ -497,25 +504,31 @@ class _FileOrThing(object):
return self.__output
def __init__(self, func, prepIn, prepOut, load, *things):
def __init__(self, func, prepIn, prepOut, load, *things, outprefix=None):
"""Initialise a ``_FileOrThing`` decorator.
:arg func: The function to be decorated.
:arg func: The function to be decorated.
:arg prepIn: Function which returns a file name to be used in
place of an input argument.
:arg prepIn: Function which returns a file name to be used in
place of an input argument.
:arg prepOut: Function which generates a file name to use for
arguments that were set to :data:`LOAD`.
:arg prepOut: Function which generates a file name to use for
arguments that were set to :data:`LOAD`.
:arg load: Function which is called to load items for arguments
that were set to :data:`LOAD`. Must accept a file path
as its sole argument.
:arg load: Function which is called to load items for arguments
that were set to :data:`LOAD`. Must accept a file path
as its sole argument.
: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
handled.
: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
handled.
: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.
The ``prepIn`` and ``prepOut`` functions must accept the following
positional arguments:
......@@ -527,11 +540,12 @@ class _FileOrThing(object):
- The argument value that was passed in
"""
self.__func = func
self.__prepIn = prepIn
self.__prepOut = prepOut
self.__load = load
self.__things = things
self.__func = func
self.__prepIn = prepIn
self.__prepOut = prepOut
self.__load = load
self.__things = things
self.__outprefix = outprefix
def __call__(self, *args, **kwargs):
......@@ -551,15 +565,17 @@ class _FileOrThing(object):
# function may be relative.
with tempdir.tempdir(changeto=False) as td:
log.debug('Redirecting LOADed outputs to %s', td)
# Replace any things with file names.
# Also get a list of LOAD outputs
args, kwargs, outfiles = self.__prepareArgs(
td, argnames, args, kwargs)
args = self.__prepareArgs(td, argnames, args, kwargs)
args, kwargs, prefix, outfiles, prefixedFiles = args
# Call the function
result = func(*args, **kwargs)
# make a _Reults object to store
# make a _Results object to store
# the output. If we are decorating
# another _FileOrThing, the
# results will get merged together
......@@ -570,11 +586,42 @@ class _FileOrThing(object):
# Load the LOADed outputs
for oname, ofile in outfiles.items():
if not op.exists(ofile): oval = None
else: oval = self.__load(ofile)
log.debug('Loading output %s: %s', oname, ofile)
if op.exists(ofile): oval = self.__load(ofile)
else: oval = None
result[oname] = oval
# Load or move output-prefixed files
if prefix is not None:
prefixDir = op.abspath(op.dirname(prefix))
prefix = op.basename(prefix)
allPrefixed = glob.glob(op.join(td, '{}_*'.format(prefix)))
for filename in allPrefixed:
basename = op.basename(filename)
for argname in prefixedFiles:
if fnmatch.fnmatch(basename, '{}*'.format(argname)):
log.debug('Loading prefixed output %s: %s',
argname, filename)
fval = self.__load(filename)
if argname in result: result[argname].append(fval)
else: result[argname] = [fval]
break
# if file did not match any pattern,
# move it into real prefix
else:
log.debug('Moving prefixed output %s into %s',
filename, prefixDir)
shutil.move(filename, prefixDir)
return result
......@@ -597,34 +644,85 @@ class _FileOrThing(object):
- An updated copy of ``kwargs``.
- The output file prefix that was actually passed in
(it is subsequently modified so that prefixed outputs
are redirected to a temporary location). All prefixed
outputs that are not ``LOAD``ed should be moved into
this directory. ``None`` if there is no output
prefix.
- A dictionary of ``{ name : filename }`` mappings,
for all arguments with a value of ``LOAD``.
- A list ``[ filename ]`` paths, for all
output-prefix arguments with a value of ``LOAD``.
"""
outfiles = dict()
# These containers keep track
# of output files which are to
# be loaded into memory
outfiles = dict()
prefixedFiles = []
allargs = {k : v for k, v in zip(argnames, args)}
allargs.update(kwargs)
# Has an output prefix been specified?
prefix = allargs.get(self.__outprefix, None)
realPrefix = None
# If so, replace it with a new output
# prefix which will redirect all output
# to the temp dir.
#
# Importantly, here we assume that the
# underlying function (and hence the
# underlying command-line tool) will
# accept an output prefix which contains
# a directory path.
if prefix is not None:
realPrefix = prefix
prefix = op.basename(prefix)
allargs[self.__outprefix] = op.join(workdir, prefix)
if len(self.__things) > 0: things = self.__things
else: things = allargs.keys()
for name in things:
for name, val in list(allargs.items()):
val = allargs.get(name, None)
# is this argument referring
# to a prefixd output?
isprefixed = (prefix is not None and
name.startswith(prefix))
if val is None:
if not (isprefixed or name in things):
continue
if val is LOAD:
# Prefixed output files may only
# be given a value of LOAD
if isprefixed and val is not LOAD:
raise ValueError('Cannot specify name of prefixed file - the '
'name is defined by the output prefix')
outfile = self.__prepOut(workdir, name, val)
if val is LOAD:
if outfile is not None:
allargs[ name] = outfile
# this argument refers to an output
# that is generated from the output
# prefix argument, and doesn't map
# directly to an argument of the
# function. So we don't pass it
# through.
if isprefixed:
prefixedFiles.append(name)
allargs.pop(name)
# regular output-file argument
else:
outfile = self.__prepOut(workdir, name, val)
outfiles[name] = outfile
else:
allargs[ name] = outfile
else:
infile = self.__prepIn(workdir, name, val)
if infile is not None:
......@@ -633,10 +731,10 @@ class _FileOrThing(object):
args = [allargs.pop(k) for k in argnames]
kwargs = allargs
return args, kwargs, outfiles
return args, kwargs, realPrefix, outfiles, prefixedFiles
def fileOrImage(*imgargs):
def fileOrImage(*args, **kwargs):
"""Decorator which can be used to ensure that any NIfTI images are saved
to file, and output images can be loaded and returned as ``nibabel``
image objects or :class:`.Image` objects.
......@@ -693,7 +791,7 @@ def fileOrImage(*imgargs):
raise RuntimeError('Cannot handle type: {}'.format(intypes))
def decorator(func):
fot = _FileOrThing(func, prepIn, prepOut, load, *imgargs)
fot = _FileOrThing(func, prepIn, prepOut, load, *args, **kwargs)
def wrapper(*args, **kwargs):
result = fot(*args, **kwargs)
......@@ -705,7 +803,7 @@ def fileOrImage(*imgargs):
return decorator
def fileOrArray(*arrargs):
def fileOrArray(*args, **kwargs):
"""Decorator which can be used to ensure that any Numpy arrays are saved
to text files, and output files can be loaded and returned as Numpy arrays.
"""
......@@ -727,7 +825,7 @@ def fileOrArray(*arrargs):
load = np.loadtxt
def decorator(func):
fot = _FileOrThing(func, prepIn, prepOut, load, *arrargs)
fot = _FileOrThing(func, prepIn, prepOut, load, *args, **kwargs)
def wrapper(*args, **kwargs):
return fot(*args, **kwargs)
......
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