From c68da9a3529024090f73069d23ee78d2c5ccc685 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 11 May 2018 16:25:38 +0100
Subject: [PATCH] ENH: fileOrImage works with fsl.data.images.
---
fsl/wrappers/wrapperutils.py | 33 ++++++++++++++++++++++++++++++---
1 file changed, 30 insertions(+), 3 deletions(-)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index ee056553f..a1bc938d9 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -635,13 +635,25 @@ class _FileOrThing(object):
def fileOrImage(*imgargs):
"""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.
+ image objects or :class:`.Image` objects.
"""
+ # keep track of the input argument
+ # types on each call, so we know
+ # whether to return a fsl.Image or
+ # a nibabel image
+ intypes = []
+
def prepIn(workdir, name, val):
infile = None
+ if isinstance(val, (fslimage.Image, nib.nifti1.Nifti1Image)):
+ intypes.append(type(val))
+
+ if isinstance(val, fslimage.Image):
+ val = val.nibImage
+
if isinstance(val, nib.nifti1.Nifti1Image):
infile = val.get_filename()
@@ -661,13 +673,28 @@ def fileOrImage(*imgargs):
# create an independent in-memory
# copy of the image file
img = nib.load(path)
- return nib.nifti1.Nifti1Image(img.get_data(), None, img.header)
+
+ # if any arguments were fsl images,
+ # that takes precedence.
+ if fslimage.Image in intypes:
+ return fslimage.Image(img.get_data(), header=img.header)
+ # but if all inputs were file names,
+ # nibabel takes precedence
+ elif nib.nifti1.Nifti1Image in intypes or len(intypes) == 0:
+ return nib.nifti1.Nifti1Image(img.get_data(), None, img.header)
+
+ # this function should not be called
+ # under any other circumstances
+ else:
+ raise RuntimeError('Cannot handle type: {}'.format(intypes))
def decorator(func):
fot = _FileOrThing(func, prepIn, prepOut, load, *imgargs)
def wrapper(*args, **kwargs):
- return fot(*args, **kwargs)
+ result = fot(*args, **kwargs)
+ intypes[:] = []
+ return result
return _update_wrapper(wrapper, func)
--
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