diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cc43a5a9719687566b48b3348d6cf4c662c07018..92cb04a711f882e5303d4a5c96f0e195b1dfce3f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -171,10 +171,10 @@ test:3.9:
<<: *test_template
-test:3.10:
- stage: test
- image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
- <<: *test_template
+# test:3.10:
+# stage: test
+# image: pauldmccarthy/fsleyes-py310-wxpy4-gtk3
+# <<: *test_template
test:build-pypi-dist:
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1d1ae7c2123250837e0a6e0b705f828a7ff91e55..2bc89f66edcd4c40216443cf517fee1f6a5b9c97 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,8 +2,8 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
-3.8.0 (Under development)
--------------------------
+3.7.1 (Friday 12th November 2021)
+---------------------------------
Changed
@@ -11,7 +11,15 @@ Changed
* BIDS and ``dcm2niix`` ``.json`` sidecar files with control characters
- are now accepted.
+ are now accepted (!312).
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue with temporary input files created by :mod:`fsl.wrappers`
+ functions not being deleted (!313).
3.7.0 (Friday 20th August 2021)
@@ -23,7 +31,7 @@ Added
* New :mod:`fsl.wrappers.fsl_sub` wrapper function for the ``fsl_sub``
- command.
+ command (!309).
Changed
@@ -32,19 +40,19 @@ Changed
* Performance of the :mod:`.imglob`, :mod:`.imln`, :mod:`imtest`, :mod:`.imrm`
and :mod:`.remove_ext` scripts has been improved, by re-organising them to
- avoid unnecessary and expensive imports such as ``numpy``.
+ avoid unnecessary and expensive imports such as ``numpy`` (!310).
* The default behaviour of the :func:`fsl.utils.run.run` function (and hence
that of all :mod:`fsl.wrappers` functions) has been changed so that the
standard output and error of the called command is now forwarded to the
calling Python process, in addition to being returned from ``run`` as
strings. In other words, the default behaviour of ``run('cmd')``, is now
equivalent to ``run('cmd', log={"tee":True})``. The previous default
- behaviour can be achieved with ``run('cmd', log={"tee":False})``.
+ behaviour can be achieved with ``run('cmd', log={"tee":False})`` (!309).
* The :func:`fsl.utils.run.run` and :func:`fsl.utils.run.runfsl` functions
(and hence all :mod:`fsl.wrappers` functions) have been modified to use
``fsl.wrappers.fsl_sub`` instead of ``fsl.utils.fslsub.submit``. This is an
internal change which should not affect the usage of the ``run``, ``runfsl``
- or wrapper functions.
+ or wrapper functions (!309).
Deprecated
@@ -53,10 +61,10 @@ Deprecated
* :class:`fsl.utils.fslsub.SubmitParams` and :func:`fsl.utils.fslsub.submit`
have been deprecated in favour of using the ``fsl.wrappers.fsl_sub`` wrapper
- function.
+ function (!309).
* The :func:`fsl.utils.fslsub.info` function has been deprecated in favour of
using the ``fsl_sub.report`` function, from the separate `fsl_sub
- <https://git.fmrib.ox.ac.uk/fsl/fsl_sub>`_ Python library.
+ <https://git.fmrib.ox.ac.uk/fsl/fsl_sub>`_ Python library (!309).
3.6.4 (Tuesday 3rd August 2021)
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index ac647674bfa4c1161f8b5e8ed62e8268a9940518..8a5fa0eb424230684c2af013aed8f0479384cb11 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -1046,9 +1046,16 @@ def fileOrImage(*args, **kwargs):
# in-memory image - we have
# to save it out to a file
- if infile is None:
- hd, infile = tempfile.mkstemp(fslimage.defaultExt())
+ if infile is None or not op.exists(infile):
+ hd, infile = tempfile.mkstemp(fslimage.defaultExt(),
+ dir=workdir)
os.close(hd)
+
+ # Create a copy of the input image and
+ # save that, so the original doesn't
+ # get associated with the temp file
+ val = nib.nifti1.Nifti1Image(
+ np.asanyarray(val.dataobj), None, val.header)
val.to_filename(infile)
return infile
@@ -1110,7 +1117,7 @@ def fileOrArray(*args, **kwargs):
infile = None
if isinstance(val, np.ndarray):
- hd, infile = tempfile.mkstemp('.txt')
+ hd, infile = tempfile.mkstemp('.txt', dir=workdir)
os.close(hd)
np.savetxt(infile, val, fmt='%0.18f')
@@ -1176,6 +1183,7 @@ def fileOrText(*args, **kwargs):
if not isinstance(val, pathlib.Path):
with tempfile.NamedTemporaryFile(mode='w',
suffix='.txt',
+ dir=workdir,
delete=False) as f:
f.write(val)
infile = f.name
diff --git a/tests/test_wrappers/test_wrapperutils.py b/tests/test_wrappers/test_wrapperutils.py
index e8acaf135e77899a2aaf6631fdc684a65f15b6c8..d3ac883decdcf3fda47e84383f5d134dbf492d02 100644
--- a/tests/test_wrappers/test_wrapperutils.py
+++ b/tests/test_wrappers/test_wrapperutils.py
@@ -876,3 +876,61 @@ def test_cmdwrapper_cmdonly_assert():
assert func()[0].strip() == 'hello'
os.remove('file')
assert func(cmdonly=True) == ['echo', 'hello']
+
+
+def test_fileOrArray_all_tempfiles_cleared():
+
+ tempfiles = []
+
+ @wutils.fileOrArray('in_', 'out')
+ def array(in_, out):
+ tempfiles.extend((in_, out))
+ i = np.loadtxt(in_)
+ i = i + 1
+ np.savetxt(out, i)
+
+ arr = np.array([[1, 2], [ 3, 4]])
+ arrout = array(arr, wutils.LOAD).out
+
+ assert np.all(np.isclose(arrout, arr + 1))
+ assert len(tempfiles) == 2
+ assert not any(op.exists(f) for f in tempfiles)
+
+
+def test_fileOrImage_all_tempfiles_cleared():
+
+ tempfiles = []
+
+ @wutils.fileOrImage('in_', 'out')
+ def image(in_, out):
+ tempfiles.extend((in_, out))
+ i = nib.load(in_)
+ i = nib.Nifti1Image(i.get_fdata() + 1, np.eye(4))
+ i.to_filename(out)
+
+ arr = np.array([[1, 2], [ 3, 4]])
+ img = nib.nifti1.Nifti1Image(arr, np.eye(4))
+ imgout = image(img, wutils.LOAD).out
+
+ assert np.all(np.isclose(imgout.get_fdata(), img.get_fdata() + 1))
+ assert len(tempfiles) == 2
+ assert not any(op.exists(f) for f in tempfiles)
+
+
+def test_fileOrText_all_tempfiles_cleared():
+
+ tempfiles = []
+
+ @wutils.fileOrText('in_', 'out')
+ def text(in_, out):
+ tempfiles.extend((in_, out))
+ with open(in_, 'rt') as inf, open(out, 'wt') as outf:
+ outf.write(inf.read())
+ outf.write('456')
+
+ txt = '123'
+ txtout = text( txt, wutils.LOAD).out
+
+ assert txtout == '123456'
+ assert len(tempfiles) == 2
+ assert not any(op.exists(f) for f in tempfiles)