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Commit 26b41155 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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ENH: _FileOrThing supports output prefix with a directory

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fsl/wrappers/wrapperutils.py
+ 105
− 72
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......@@ -85,20 +85,22 @@ and returned::
"""
import os.path as op
import os
import sys
import glob
import shutil
import random
import string
import fnmatch
import inspect
import logging
import tempfile
import warnings
import functools
import collections
import itertools as it
import os.path as op
import os
import re
import sys
import glob
import shutil
import random
import string
import fnmatch
import inspect
import logging
import tempfile
import warnings
import functools
import collections
import six
import nibabel as nib
......@@ -585,66 +587,13 @@ 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, basePrefix, outfiles, prefixes = args
args, kwargs, outprefix, outfiles, prefixes = args
# Call the function
result = func(*args, **kwargs)
# make a _Results object to store
# the output. If we are decorating
# another _FileOrThing, the
# results will get merged together
# into a single _Results dict.
if not isinstance(result, _FileOrThing._Results):
result = _FileOrThing._Results(result)
# Load the LOADed outputs
for oname, ofile in outfiles.items():
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 basePrefix is not None:
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 prefPat, prefName in prefixes.items():
if fnmatch.fnmatch(basename, '{}*'.format(prefPat)):
log.debug('Loading prefixed output %s [%s]: %s',
prefPat, prefName, filename)
# if the load function returns
# None, this file is probably
# not of the correct type.
fval = self.__load(filename)
if fval is not None:
basename = self.__removeExt(basename)
basename = basename.replace(prefPat, prefName)
result[basename] = fval
break
# if file did not match any pattern,
# 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)
shutil.move(filename, prefixDir)
return result
return self.__generateResult(
td, result, outprefix, outfiles, prefixes)
def __prepareArgs(self, workdir, argnames, args, kwargs):
......@@ -718,8 +667,14 @@ class _FileOrThing(object):
prefixedFiles[prefix] = self.__outprefix
realPrefix = prefix
prefix = op.basename(prefix)
allargs[self.__outprefix] = op.join(workdir, prefix)
fakePrefix = op.join(workdir, prefix)
allargs[self.__outprefix] = fakePrefix
pdir = op.dirname(fakePrefix)
if pdir != '' and not op.exists(pdir):
os.makedirs(pdir)
if len(self.__things) > 0: things = self.__things
else: things = allargs.keys()
......@@ -771,12 +726,90 @@ class _FileOrThing(object):
if infile is not None:
allargs[name] = infile
if realPrefix is not None and len(prefixedFiles) == 0:
allargs[self.__outprefix] = realPrefix
args = [allargs.pop(k) for k in argnames]
kwargs = allargs
return args, kwargs, realPrefix, outfiles, prefixedFiles
def __generateResult(
self, workdir, result, outprefix, outfiles, prefixes):
"""Loads function outputs and returns a :class:`_Results` object.
Called by :meth:`__call__` after the decorated function has been
called. Figures out what files should be loaded, and loads them into
a ``_Results`` object.
:arg workdir: Directory which contains the function outputs.
:arg result: Function return value.
:arg outprefix: Original output prefix that was passed into the
function (or ``None`` if one wasn't passed)
:arg outfiles: Dictionary containing output files to be loaded (see
:meth:`__prepareArgs`).
:arg prefixes: Dictionary containing output-prefix patterns to be
loaded (see :meth:`__prepareArgs`).
:returns: A ``_Results`` object containing all loaded outputs.
"""
# make a _Results object to store
# the output. If we are decorating
# another _FileOrThing, the
# results will get merged together
# into a single _Results dict.
if not isinstance(result, _FileOrThing._Results):
result = _FileOrThing._Results(result)
# Load the LOADed outputs
for oname, ofile in outfiles.items():
log.debug('Loading output %s: %s', oname, ofile)
if op.exists(ofile): oval = self.__load(ofile)
else: oval = None
result[oname] = oval
# No output prefix - we're done
if outprefix is None or len(prefixes) == 0:
return result
# Load or move output-prefixed files.
# Find all files with a name that
# matches the prefix that was passed
# in (recursing into matching sub-
# directories too).
allPrefixed = glob.glob(op.join(workdir, '{}*'.format(outprefix)))
allPrefixed = [fslpath.allFiles(f) if op.isdir(f) else [f]
for f in allPrefixed]
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
log.debug('Loading prefixed output %s [%s]: %s',
prefPat, prefName, prefixed)
# if the load function returns
# None, this file is probably
# not of the correct type.
fval = self.__load(fullpath)
if fval is not None:
prefixed = self.__removeExt(prefixed)
prefixed = re.sub('^' + prefPat, prefName, prefixed)
result[prefixed] = fval
break
return result
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``
......
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