From c53e61224442ad3122bb069e98c69108b253560e Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sat, 28 Mar 2020 17:21:19 +0000
Subject: [PATCH] RF: Loaded wrapper outputs are named sensibly when possible
---
fsl/wrappers/wrapperutils.py | 31 ++++++++++++++++++-------------
1 file changed, 18 insertions(+), 13 deletions(-)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index a2bc3cd65..150ef0ae9 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -604,8 +604,10 @@ class FileOrThing(object):
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.
+ that were set to :data:`LOAD`. Must accept the
+ following arguments:
+ - the name of the argument
+ - path to the file to be loaded
:arg removeExt: Function which can remove a file extension from a file
path.
@@ -760,7 +762,7 @@ class FileOrThing(object):
- A dictionary of ``{ name : filename }`` mappings,
for all arguments with a value of ``LOAD``.
- - A dictionary ``{ filepat : replstr }`` paths, for
+ - A dictionary of ``{ filepat : replstr }`` paths, for
all output-prefix arguments with a value of ``LOAD``.
"""
@@ -925,7 +927,7 @@ class FileOrThing(object):
log.debug('Loading output %s: %s', oname, ofile)
- if op.exists(ofile): oval = self.__load(ofile)
+ if op.exists(ofile): oval = self.__load(oname, ofile)
else: oval = None
result[oname] = oval
@@ -953,21 +955,23 @@ class FileOrThing(object):
log.debug('Loading prefixed output %s [%s]: %s',
prefPat, prefName, prefixed)
+ noext = self.__removeExt(prefixed)
+ prefPat = prefPat.replace('\\', '\\\\')
+ noext = re.sub('^' + prefPat, prefName, noext)
+ withext = re.sub('^' + prefPat, prefName, prefixed)
+
# if the load function returns
# None, this file is probably
# not of the correct type.
- fval = self.__load(fullpath)
+ fval = self.__load(noext, fullpath)
if fval is not None:
- noext = self.__removeExt(prefixed)
- prefPat = prefPat.replace('\\', '\\\\')
- 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
@@ -1014,7 +1018,7 @@ def fileOrImage(*args, **kwargs):
def prepOut(workdir, name, val):
return op.join(workdir, '{}.nii.gz'.format(name))
- def load(path):
+ def load(name, path):
if not fslimage.looksLikeImage(path):
return None
@@ -1027,7 +1031,8 @@ def fileOrImage(*args, **kwargs):
# if any arguments were fsl images,
# that takes precedence.
if fslimage.Image in intypes:
- return fslimage.Image(data, header=img.header)
+ return fslimage.Image(data, header=img.header, name=name)
+
# but if all inputs were file names,
# nibabel takes precedence
elif nib.nifti1.Nifti1Image in intypes or len(intypes) == 0:
@@ -1076,7 +1081,7 @@ def fileOrArray(*args, **kwargs):
def prepOut(workdir, name, val):
return op.join(workdir, '{}.txt'.format(name))
- def load(path):
+ def load(_, path):
try: return np.loadtxt(path)
except Exception: return None
@@ -1141,7 +1146,7 @@ def fileOrText(*args, **kwargs):
def prepOut(workdir, name, val):
return op.join(workdir, '{}.txt'.format(name))
- def load(path):
+ def load(_, path):
try:
with open(path, "r") as f:
return f.read()
--
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