diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e27bff36738b3e8750437885fb49a2af12abe6fe..63302ceedba7fac56d09169f04a99a6185972b2b 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+1.8.1 (Friday May 11th 2018)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.fileOrImage` decorator function now accepts :class:`.Image`
+ objects as well as ``nibabel`` image objects.
+
+
1.8.0 (Thursday May 3rd 2018)
-----------------------------
diff --git a/README.rst b/README.rst
index d711e110d35de0cbc2fa089ca9806319a9dcdc85..d753da3bacd2f6c2cc7be43c0a140dda97dc0686 100644
--- a/README.rst
+++ b/README.rst
@@ -48,12 +48,10 @@ Some extra dependencies are listed in `requirements.txt
on the mesh.
+If you are using Linux, need to install wxPython first, as binaries are not
+available on PyPI. Change the URL for your specific platform::
-To install these additional dependencies, you first need to install wxPython,
-which is still in pre-relaes.
-
- - **macOS**: ``pip install --pre wxPython``
- - **Linux** (change the URL for your specific platform): ``pip install --only-binary wxpython -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython``
+ pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
The ``rtree`` library also assumes that ``libspatialindex`` is installed on
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 5dee416cdfa12ee400e45ebe788a5da444f4c3b1..251f98c2d5a4db188f9bb8e4c8dd424512f60840 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -42,6 +42,7 @@ the following labels (this convention has been inherited from `nibabel
* *DOC*: for all kinds of documentation related commits
* *TEST*: for adding or changing tests
* *MAINT*: for administrative/maintenance changes
+ * *CI*: for continuous-integration changes
Version number
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index ee056553f59d5b6cfb62592f1f5c9dd7f37e75c1..a1bc938d96ba57ddd95956a45c139fc348f3cb18 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)
diff --git a/tests/test_parse_data.py b/tests/test_parse_data.py
index 77a8dce24a3c3081e0eae1af79dbc0db6dc8ca85..ac2d0e36b885653e2edf6c8d847d81f394348cdd 100644
--- a/tests/test_parse_data.py
+++ b/tests/test_parse_data.py
@@ -15,6 +15,7 @@ from fsl.data.atlases import Atlas
from pytest import raises
from .test_image import make_image
import os
+import pytest
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -115,6 +116,7 @@ def test_image_out():
assert args.image_out == 'test.surf.gii' + extension
+@pytest.mark.fsltest
def test_atlas():
atlas_parser = argparse.ArgumentParser('reads an atlas')
atlas_parser.add_argument('atlas', type=parse_data.Atlas)
@@ -123,4 +125,4 @@ def test_atlas():
assert isinstance(args.atlas, Atlas)
with raises(SystemExit):
- atlas_parser.parse_args(['fake'])
\ No newline at end of file
+ atlas_parser.parse_args(['fake'])
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 3e35d91e2f989b2ef5b80a995de6d179b3349ffc..b5c393e78d92c1360576a1dbe309cb5587898ce7 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -21,6 +21,7 @@ import nibabel as nib
import fsl.utils.tempdir as tempdir
import fsl.utils.run as run
import fsl.utils.fslsub as fslsub
+import fsl.data.image as fslimage
import fsl.wrappers.wrapperutils as wutils
@@ -284,6 +285,28 @@ def test_fileOrImage():
assert np.all(nib.load('output.nii').get_data() == expected)
os.remove('output.nii')
+ # fslimage, file, load
+ result = func(fslimage.Image(img1), img2='img2.nii',
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # fslimage, fslimage, load
+ result = func(fslimage.Image(img1), img2=fslimage.Image(img2),
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # fslimage, nib.image, load
+ result = func(fslimage.Image(img1), img2=img2,
+ output=wutils.LOAD)['output']
+ assert isinstance(result, fslimage.Image)
+ assert np.all(result[:].squeeze() == expected)
+
+ # nib.image, nib.image, load
+ result = func(img1, img2=img2, output=wutils.LOAD)['output']
+ assert isinstance(result, nib.nifti1.Nifti1Image)
+ assert np.all(result.get_data()[:] == expected)
def test_chained_fileOrImageAndArray():