Merge branch 'enh/wrappers_support_fsl_image' into 'master'

Support fsl data image in wrappers

See merge request fsl/fslpy!53

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)
 -----------------------------
 

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

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

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)
 

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'])
+        atlas_parser.parse_args(['fake'])
\ No newline at end of file

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():