diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cbec212701b30903cf81d63e499ec97c7a098ffe..8407a74939c4934079eb04022caeb85a1d307ea6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -173,6 +173,12 @@ test:3.8:
<<: *test_template
+test:3.9:
+ stage: test
+ image: pauldmccarthy/fsleyes-py39-wxpy4-gtk3
+ <<: *test_template
+
+
test:build-pypi-dist:
stage: test
image: pauldmccarthy/fsleyes-py36-wxpy4-gtk3
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 4dc7df9ec8ce20b7304ddc0b63307daa567e5018..f8fcd312c170a4eb392ab073b3abb21e8feed939 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,29 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.5.0 (Tuesday 19th January 2021)
+---------------------------------
+
+
+Added
+^^^^^
+
+
+* New ``fsl_anat.tree``, for use with the :mod:`.filetree` package (!264).
+* New :func:`.fsl_prepare_fieldmap` wrapper function (!265).
+* The :class:`.fslmaths` wrapper now supports the ``fslmaths -s`` option
+ via the :meth:`.fslmaths.smooth` method (!271).
+
+
+Fixed
+^^^^^
+
+
+* Windows/WSL-specific workaround to the :func:`fsl.utils.run.run` function to
+ avoid console windows from popping up, when used from a graphical program
+ (!272).
+
+
3.4.0 (Tuesday 20th October 2020)
---------------------------------
diff --git a/COPYRIGHT b/COPYRIGHT
index 2b9a3c28bd9d162848efdb59e6ce0ea744c83a85..ca6e317895149e49a34705663c4c40bbc2277cec 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -1 +1 @@
-Copyright 2016-2020 University of Oxford, Oxford, UK
+Copyright 2016-2021 University of Oxford, Oxford, UK
diff --git a/LICENSE b/LICENSE
index 611fcba5618c84542bbea51bb0329fd035ff3724..29dca5745c25932d5ed83f120fce41be0c17340f 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
The fslpy library
-Copyright 2016-2020 University of Oxford, Oxford, UK.
+Copyright 2016-2021 University of Oxford, Oxford, UK.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
diff --git a/README.rst b/README.rst
index 797b5345ba2bce7dc0b6964649bf6e0d45ff48de..f8b8fd8a118d8b0ee4e3070735c2d56b6d3e7b56 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,7 @@ programming library written in Python. It is used by `FSLeyes
<https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
-``fslpy`` is tested against Python versions 3.5, 3.6 and 3.7.
+``fslpy`` is tested against Python versions 3.6, 3.7, 3.8 and 3.9.
Installation
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index cf75fc505ce80e7db8046133970061fdca4ead90..1e535c8a336de44f3a7d819f067417075eaa16d3 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -286,6 +286,12 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args, **kwargs):
- the command's standard error as a string.
- the command's exit code.
"""
+ if fslplatform.fslwsl:
+ # On Windows this prevents opening of a popup window
+ startupinfo = sp.STARTUPINFO()
+ startupinfo.dwFlags |= sp.STARTF_USESHOWWINDOW
+ kwargs["startupinfo"] = startupinfo
+
proc = sp.Popen(args, stdout=sp.PIPE, stderr=sp.PIPE, **kwargs)
with tempdir.tempdir(changeto=False) as td:
@@ -403,7 +409,7 @@ def wslcmd(cmdpath, *args):
# Check if command exists in WSL (remembering that the command path may include FSLDIR which
# is a Windows path)
cmdpath = fslpath.wslpath(cmdpath)
- retcode = sp.call(["wsl", "test", "-x", cmdpath])
+ _stdout, _stderr, retcode = _realrun(False, None, None, None, "wsl", "test", "-x", cmdpath)
if retcode == 0:
# Form a new argument list and convert any Windows paths in it into WSL paths
wslargs = [fslpath.wslpath(arg) for arg in args]
diff --git a/fsl/version.py b/fsl/version.py
index d15f2d69b6baff5ebd4e06679be3bd27b9deaf96..d094aa68f0e67876293c40f359127f5ea32c5995 100644
--- a/fsl/version.py
+++ b/fsl/version.py
@@ -47,7 +47,7 @@ import re
import string
-__version__ = '3.5.0.dev0'
+__version__ = '3.6.0.dev0'
"""Current version number, as a string. """
diff --git a/tests/test_dicom.py b/tests/test_dicom.py
index e3b444c3c6c535416c86c7a690b5e4e37d2c8d9e..dba678f4868368b514968263f362dafa2759192f 100644
--- a/tests/test_dicom.py
+++ b/tests/test_dicom.py
@@ -29,10 +29,10 @@ pytestmark = pytest.mark.dicomtest
@contextlib.contextmanager
-def install_dcm2niix(version='1.0.20190902'):
+def install_dcm2niix(version='1.0.20201102'):
filenames = {
+ '1.0.20201102' : 'v1.0.20201102/dcm2niix_lnx.zip',
'1.0.20190902' : 'v1.0.20190902/dcm2niix_lnx.zip',
- '1.0.20190410' : 'v1.0.20190410/dcm2niix_11-Apr-2019_lnx.zip',
'1.0.20181125' : 'v1.0.20181125/dcm2niix_25-Nov-2018_lnx.zip',
'1.0.20171017' : 'v1.0.20171017/dcm2niix_18-Oct-2017_lnx.zip',
}
@@ -128,8 +128,9 @@ def test_scanDir():
assert len(series) == 2
for s in series:
- assert (s['PatientName'] == 'MCCARTHY_PAUL' or
- s['PatientName'] == 'MCCARTHY_PAUL_2')
+ assert s['PatientName'] in ('MCCARTHY_PAUL',
+ 'MCCARTHY^PAUL',
+ 'MCCARTHY_PAUL_2')
def test_sersiesCRC():
@@ -158,7 +159,7 @@ def test_sersiesCRC():
def test_loadSeries():
# test a pre-CRC and a post-CRC version
- for version in ('1.0.20190410', '1.0.20190902'):
+ for version in ('1.0.20181125', '1.0.20201102'):
with install_dcm2niix(version):
@@ -170,23 +171,23 @@ def test_loadSeries():
dcmdir = os.getcwd()
series = fsldcm.scanDir(dcmdir)
expShape = (512, 512, 1)
- explens = [1, 1]
- for s, explen in zip(series, explens):
+ for s in series:
imgs = fsldcm.loadSeries(s)
- assert len(imgs) == explen
-
for img in imgs:
assert img.dicomDir == dcmdir
assert img.shape == expShape
assert img[:].shape == expShape
- assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
- img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
+ assert img.getMeta('PatientName') in ('MCCARTHY_PAUL',
+ 'MCCARTHY^PAUL',
+ 'MCCARTHY_PAUL_2')
assert 'PatientName' in img.metaKeys()
assert 'MCCARTHY_PAUL' in img.metaValues() or \
+ 'MCCARTHY^PAUL' in img.metaValues() or \
'MCCARTHY_PAUL_2' in img.metaValues()
assert ('PatientName', 'MCCARTHY_PAUL') in img.metaItems() or \
+ ('PatientName', 'MCCARTHY^PAUL') in img.metaItems() or \
('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()