diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 94b90a11186a7c6ef1c11515731b73b64355675a..3d4d505204e049c862039cbce1b1bc2921687e6d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,14 +1,17 @@
-# Keeping this commented out until CI is working
-#
-# test:2.7:
-# image: python2.7
-# script:
-# - cat requirements.txt | xargs -n 1 pip install
-# - python setup.py test
+test:2.7:
+ image: fsleyes-py27
+ script:
+ - cat requirements.txt | xargs -n 1 pip install
+ - pip install scipy
+ - pip install coverage
+ - su -s /bin/bash -c "xvfb-run python setup.py test" nobody
+ - coverage report -m
-
-# test:3.5:
-# image: python3.5
-# script:
-# - cat requirements.txt | xargs -n 1 pip install
-# - python setup.py test
+test:3.6:
+ image: fsleyes-py36
+ script:
+ - cat requirements.txt | xargs -n 1 pip install
+ - pip install scipy
+ - pip install coverage
+ - su -s /bin/bash -c "xvfb-run python setup.py test" nobody
+ - coverage report -m
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 81c6fb5d046992f63b3358481b25eafb85e8c52a..3673975f3eb8a0c96125c9fe18c8c061ee7f2b19 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -16,16 +16,17 @@ Development model
developers are free to choose their own development workflow in their own
repositories.
-- A separate branch is created for each release. Hotfixes may be added to
- these release branches.
-
- Merge requests will not be accepted unless:
-
+
- All existing tests pass (or have been updated as needed).
- New tests have been written to cover newly added features.
- Code coverage is as close to 100% as possible.
- Coding conventions are adhered to (unless there is good reason not to).
+- A separate branch is created for each release. Hotfixes may be added to
+ these release branches. Hotfixes should be merged into the master branch,
+ and then cherry-picked onto the release branch(es).
+
Version number
--------------
@@ -40,13 +41,16 @@ numbers::
- The ``patch`` number is incremented on bugfixes and minor
(backwards-compatible) changes.
-
+
- The ``minor`` number is incremented on feature additions and/or
backwards-compatible changes.
- The ``major`` number is incremented on major feature additions, and
backwards-incompatible changes.
+Additionally, a single letter (``a``, ``b``, ``c``, etc) may be appended
+to the version number, indicating a hotfix release.
+
Testing
-------
@@ -78,7 +82,7 @@ Configure your text editor to use:
- `flake8 <http://flake8.pycqa.org/en/latest/>`_: This checks your code for
adherence to the `PEP8 <https://www.python.org/dev/peps/pep-0008/>`_ coding
standard.
-
+
- `pylint <https://www.pylint.org/>`_: This checks that your code follows
other good conventions.
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 9f6b9fe8df68f665233dadd9fac579521f8ea80f..2a10b1214c89b092e91d7ec4728408e9f08f3c86 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -308,6 +308,58 @@ class AtlasRegistry(notifier.Notifier):
fslsettings.write('fsl.data.atlases', atlases)
+class AtlasLabel(object):
+ """The ``AtlasLabel`` class is used by the :class:`AtlasDescription` class
+ as a container object used for storing atlas label information.
+
+ An ``AtlasLabel`` instance contains the following attributes:
+
+ ========= ==============================================================
+ ``name`` Region name
+ ``index`` For probabilistic atlases, the volume index into the 4D atlas
+ image that corresponds to this region. For label atlases, the
+ value of voxels that are in this region. For summary images of
+ probabilistic atlases, add 1 to this value to get the
+ corresponding voxel values.
+ ``x`` X coordinate of the region in world space
+ ``y`` Y coordinate of the region in world space
+ ``z`` Z coordinate of the region in world space
+ ========= ==============================================================
+
+ .. note:: The ``x``, ``y`` and ``z`` label coordinates are pre-calculated
+ centre-of-gravity coordinates, as listed in the atlas xml file.
+ They are in the coordinate system defined by the transformation
+ matrix for the first image in the ``images`` list of the atlas
+ XML file (typically MNI152 space).
+ """
+
+ def __init__(self, name, index, x, y, z):
+ self.name = name
+ self.index = index
+ self.x = x
+ self.y = y
+ self.z = z
+
+
+ def __eq__(self, other):
+ """Compares the ``index`` of this ``AtlasLabel`` with another.
+ """
+ return self.index == other.index
+
+
+ def __neq__(self, other):
+ """Compares the ``index`` of this ``AtlasLabel`` with another.
+ """
+ return self.index != other.index
+
+
+ def __lt__(self, other):
+ """Compares this ``AtlasLabel`` with another by their ``index``
+ attribute.
+ """
+ return self.index < other.index
+
+
class AtlasDescription(object):
"""An ``AtlasDescription`` instance parses and stores the information
stored in the FSL XML file that describes a single FSL atlas. An XML
@@ -393,30 +445,9 @@ class AtlasDescription(object):
``numpy`` arrays), one for each image in ``images``,
defining the voxel to world coordinate transformations.
- ``labels`` A list of ``AtlasLabel`` objects, describing each
+ ``labels`` A list of :class`AtlasLabel` objects, describing each
region / label in the atlas.
================= ======================================================
-
- Each ``AtlasLabel`` instance in the ``labels`` list contains the
- following attributes:
-
- ========= ==============================================================
- ``name`` Region name
- ``index`` For probabilistic atlases, the volume index into the 4D atlas
- image that corresponds to this region. For label atlases, the
- value of voxels that are in this region. For summary images of
- probabilistic atlases, add 1 to this value to get the
- corresponding voxel values.
- ``x`` X coordinate of the region in world space
- ``y`` Y coordinate of the region in world space
- ``z`` Z coordinate of the region in world space
- ========= ==============================================================
-
- .. note:: The ``x``, ``y`` and ``z`` label coordinates are pre-calculated
- centre-of-gravity coordinates, as listed in the atlas xml file.
- They are in the coordinate system defined by the transformation
- matrix for the first image in the ``images`` list.(typically
- MNI152 space).
"""
@@ -471,11 +502,6 @@ class AtlasDescription(object):
self.pixdims .append(i.pixdim[:3])
self.xforms .append(i.voxToWorldMat)
- # A container object used for
- # storing atlas label information
- class AtlasLabel(object):
- pass
-
labels = data.findall('label')
self.labels = []
@@ -488,14 +514,14 @@ class AtlasDescription(object):
for i, label in enumerate(labels):
- al = AtlasLabel()
- al.name = label.text
- al.index = int( label.attrib['index'])
- al.x = float(label.attrib['x'])
- al.y = float(label.attrib['y'])
- al.z = float(label.attrib['z'])
+ name = label.text
+ index = int( label.attrib['index'])
+ x = float(label.attrib['x'])
+ y = float(label.attrib['y'])
+ z = float(label.attrib['z'])
+ al = AtlasLabel(name, index, x, y, z)
- coords[i] = (al.x, al.y, al.z)
+ coords[i] = (x, y, z)
self.labels.append(al)
@@ -507,7 +533,6 @@ class AtlasDescription(object):
# Update the coordinates
# in our label objects
for i, label in enumerate(self.labels):
-
label.x, label.y, label.z = coords[i]
diff --git a/fsl/data/image.py b/fsl/data/image.py
index f44c3bec5539e84f24a8ee9285fd713499b687aa..1166cd53c4b1cce2246ac04301f1acce781bc0da 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -34,6 +34,7 @@ and file names:
import os
import os.path as op
+import string
import logging
import six
@@ -290,6 +291,33 @@ class Nifti(notifier.Notifier):
return origShape, shape, pixdims
+ def strval(self, key):
+ """Returns the specified NIFTI header field, converted to a python
+ string, correctly null-terminated, and with non-printable characters
+ removed.
+
+ This method is used to sanitise some NIFTI header fields. The default
+ Python behaviour for converting a sequence of bytes to a string is to
+ strip all termination characters (bytes with value of ``0x00``) from
+ the end of the sequence.
+
+ This default behaviour does not handle the case where a sequence of
+ bytes which did contain a long string is subsequently overwritten with
+ a shorter string - the short string will be terminated, but that
+ termination character will be followed by the remainder of the
+ original string.
+ """
+
+ val = self.header[key]
+
+ try: val = bytes(val).partition(b'\0')[0]
+ except: val = bytes(val)
+
+ val = val.decode('ascii')
+
+ return ''.join([c for c in val if c in string.printable]).strip()
+
+
@property
def niftiVersion(self):
"""Returns the NIFTI file version:
@@ -662,7 +690,8 @@ class Image(Nifti):
loadData=True,
calcRange=True,
indexed=False,
- threaded=False):
+ threaded=False,
+ **kwargs):
"""Create an ``Image`` object with the given image data or file name.
:arg image: A string containing the name of an image file to load,
@@ -706,6 +735,9 @@ class Image(Nifti):
:arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
separate thread for data range calculation. Defaults
to ``False``. Ignored if ``loadData`` is ``True``.
+
+ All other arguments are passed through to the ``nibabel.load`` function
+ (if it is called).
"""
nibImage = None
@@ -735,7 +767,7 @@ class Image(Nifti):
# Otherwise we let nibabel
# manage the file reference(s)
else:
- nibImage = nib.load(image)
+ nibImage = nib.load(image, **kwargs)
dataSource = image
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 71cdd829425ada0d346005d9fa9b7d403457f795..0bd260a3481925d5e3e792d5b2c5d39a82d5f440 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -84,27 +84,26 @@ def isWidgetAlive(widget):
"""Returns ``True`` if the given ``wx.Window`` object is "alive" (i.e.
has not been destroyed), ``False`` otherwise. Works in both wxPython
and wxPython/Phoenix.
+
+ .. warning:: Don't try to test whether a ``wx.MenuItem`` has been
+ destroyed, as it will probably result in segmentation
+ faults. Check the parent ``wx.Menu`` instead.
"""
import wx
- if platform.wxFlavour == WX_PHOENIX:
- return bool(widget)
- elif platform.wxFlavour == WX_PYTHON:
- try:
- # GetId seems to be available on all wx
- # objects, despite not being documented.
- #
- # I was originally calling IsEnabled,
- # but this causes segfaults if called
- # on a wx.MenuItem from within an
- # event handler on that menu item!
- widget.GetId()
- return True
-
- except wx.PyDeadObjectError:
- return False
+ if platform.wxFlavour == platform.WX_PHOENIX:
+ excType = RuntimeError
+ elif platform.wxFlavour == platform.WX_PYTHON:
+ excType = wx.PyDeadObjectError
+
+ try:
+ widget.GetParent()
+ return True
+
+ except excType:
+ return False
class Platform(notifier.Notifier):
@@ -146,6 +145,7 @@ class Platform(notifier.Notifier):
self.isWidgetAlive = isWidgetAlive
self.__inSSHSession = False
+ self.__inVNCSession = False
self.__glVersion = None
self.__glRenderer = None
self.__glIsSoftware = None
@@ -163,17 +163,14 @@ class Platform(notifier.Notifier):
except ImportError:
self.__canHaveGui = False
+ # If one of the SSH_/VNC environment
+ # variables is set, then we're probably
+ # running over SSH/VNC.
+ sshVars = ['SSH_CLIENT', 'SSH_TTY']
+ vncVars = ['VNCDESKTOP', 'X2GO_SESSION', 'NXSESSIONID']
- # If one of the SSH_ environment
- # variables is set, and we're
- # not running in a VNC session,
- # then we're probably running
- # over SSH.
- inSSH = 'SSH_CLIENT' in os.environ or \
- 'SSH_TTY' in os.environ
- inVNC = 'VNCDESKTOP' in os.environ
-
- self.__inSSHSession = inSSH and not inVNC
+ self.__inSSHSession = any(s in os.environ for s in sshVars)
+ self.__inVNCSession = any(v in os.environ for v in vncVars)
@property
@@ -220,6 +217,19 @@ class Platform(notifier.Notifier):
return self.__inSSHSession
+ @property
+ def inVNCSession(self):
+ """``True`` if this application is running over a VNC (or similar)
+ session, ``False`` otherwise. Currently, the following remote desktop
+ environments are detected:
+
+ - VNC
+ - x2go
+ - NoMachine
+ """
+ return self.__inVNCSession
+
+
@property
def wxPlatform(self):
"""One of :data:`WX_UNKNOWN`, :data:`WX_MAC_COCOA`,
@@ -353,9 +363,6 @@ class Platform(notifier.Notifier):
# necessary.
self.__glIsSoftware = any((
'software' in value,
- 'mesa' in value,
- 'gallium' in value,
- 'llvmpipe' in value,
'chromium' in value,
))
diff --git a/fsl/utils/settings.py b/fsl/utils/settings.py
index 5fd3207c827698d2cf3ade58446867be35c19f48..491198adb5f86729e93e9b7d80859b6e8047f35a 100644
--- a/fsl/utils/settings.py
+++ b/fsl/utils/settings.py
@@ -373,9 +373,9 @@ class Settings(object):
with open(configFile, 'rb') as f:
return pickle.load(f)
except:
- log.warning('Unable to load stored {} configuration file '
- '{}'.format(self.__configID, configFile),
- exc_info=True)
+ log.debug('Unable to load stored {} configuration file '
+ '{}'.format(self.__configID, configFile),
+ exc_info=True)
return {}
diff --git a/requirements.txt b/requirements.txt
index 83de75e266e952ae485cb15e388b0863a408a996..dd852d16ed620cb5d8943efe4fb353c716e49865 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,4 +2,4 @@ six>=1.10.0,<2.0
numpy>=1.11.1,<2.0
nibabel>=2.1,<3.0
indexed_gzip>=0.3.3,<0.4
-wxPython>=3.0.2.0,<=4.0
+wxPython>=3.0.2.0,<=4.0.0a2
diff --git a/setup.py b/setup.py
index c793739fa383707ced42d2984d0953777a1325d7..459dc01e149a193f1d1dee7ee04b1857f304877a 100644
--- a/setup.py
+++ b/setup.py
@@ -102,11 +102,11 @@ setup(
install_requires=install_requires,
setup_requires=['pytest-runner'],
- tests_require=['pytest',
- 'mock',
+ tests_require=['mock',
'pytest-cov',
'pytest-html',
- 'pytest-runner'],
+ 'pytest-runner',
+ 'pytest'],
test_suite='tests',
cmdclass={'doc' : doc},
diff --git a/tests/test_callfsl.py b/tests/test_callfsl.py
index 28481b33c33267042a2828e84c1c7a802d7b85ad..e137160e46e341d0d9744aaafa3b8bdfe8e3885a 100644
--- a/tests/test_callfsl.py
+++ b/tests/test_callfsl.py
@@ -10,7 +10,9 @@ import os.path as op
import subprocess as sp
import numpy as np
+import nibabel as nib
+import mock
import pytest
import fsl.utils.callfsl as callfsl
@@ -24,6 +26,17 @@ def setup_module():
raise Exception('FSLDIR is not set - callfsl tests cannot be run')
+# mock subprocess.check_output command
+# which expects 'fslstats -m filename'
+# or 'fslinfo ...'
+def mock_check_output(args):
+ if args[0].endswith('fslinfo'):
+ return 'info'
+
+ img = nib.load(args[-2])
+ return str(img.get_data().mean())
+
+
def test_callfsl():
with tests.testdir() as testdir:
@@ -35,12 +48,16 @@ def test_callfsl():
# Pass a single string
cmd = 'fslstats {} -m'.format(fname)
- result = callfsl.callFSL(cmd)
- assert np.isclose(float(result), img.mean())
- # Or pass a list of args
- result = callfsl.callFSL(*cmd.split())
- assert np.isclose(float(result), img.mean())
+ with mock.patch('fsl.utils.callfsl.sp.check_output',
+ mock_check_output):
+ result = callfsl.callFSL(cmd)
+
+ assert np.isclose(float(result), img.mean())
+
+ # Or pass a list of args
+ result = callfsl.callFSL(*cmd.split())
+ assert np.isclose(float(result), img.mean())
# Bad commands
badcmds = ['fslblob', 'fslstats notafile']
@@ -51,7 +68,9 @@ def test_callfsl():
# No FSL - should crash
cmd = 'fslinfo {}'.format(fname)
- callfsl.callFSL(cmd)
+ with mock.patch('fsl.utils.callfsl.sp.check_output',
+ mock_check_output):
+ callfsl.callFSL(cmd)
fslplatform.fsldir = None
with pytest.raises(Exception):
callfsl.callFSL(cmd)
diff --git a/tests/test_image.py b/tests/test_image.py
index 19f7eea86db037a40e71d267cecf358792590762..22568f92620f97f7117d628af3217ac4e1acd6d7 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -56,7 +56,7 @@ def make_image(filename=None,
xform = np.eye(4)
for i, p in enumerate(pixdims):
xform[i, i] = p
-
+
data = np.array(np.random.random(dims) * 100, dtype=dtype)
if imgtype == 0: img = nib.AnalyzeImage(data, xform, hdr)
@@ -68,7 +68,7 @@ def make_image(filename=None,
if op.splitext(filename)[1] == '':
if imgtype == 0: filename = '{}.img'.format(filename)
else: filename = '{}.nii'.format(filename)
-
+
nib.save(img, filename)
return img
@@ -95,7 +95,7 @@ def test_load():
'ambiguous.img',
'ambiguous.img.gz',
'notnifti.nii.gz']
-
+
shouldPass = ['compressed',
'compressed.nii.gz',
@@ -121,12 +121,12 @@ def test_load():
testdir = tempfile.mkdtemp()
for f in toCreate:
-
+
if f.startswith('notnifti'):
make_dummy_file(op.join(testdir, f))
else:
make_random_image(op.join(testdir, f))
-
+
# Not raising an error means the test passes
try:
for fname in shouldPass:
@@ -164,7 +164,7 @@ def test_create():
assert img.niftiVersion == 1
for imgType in [0, 1, 2]:
-
+
nimg = make_image(imgtype=imgType, pixdims=(5, 6, 7))
nhdr = nimg.header
@@ -189,13 +189,13 @@ def test_create():
img = fslimage.Image(nimg)
assert img.niftiVersion == imgtype
assert np.all(np.isclose(img.pixdim, (2, 3, 4)))
-
+
finally:
shutil.rmtree(testdir)
def test_bad_create():
-
+
class BadThing(object):
pass
@@ -204,7 +204,7 @@ def test_bad_create():
fslimage.Image(
np.random.random((10, 10, 10)),
header=BadThing())
-
+
# Bad data
with pytest.raises(Exception):
fslimage.Image(BadThing())
@@ -221,18 +221,18 @@ def test_bad_create():
with pytest.raises(Exception):
fslimage.Image(np.random.random(10, 10, 10),
xform=np.eye(3))
-
+
with pytest.raises(Exception):
fslimage.Image(np.random.random(10, 10, 10),
xform=np.eye(5))
-def test_Image_atts_analyze(): _test_Image_atts(0)
+def test_Image_atts_analyze(): _test_Image_atts(0)
def test_Image_atts_nifti1(): _test_Image_atts(1)
def test_Image_atts_nifti2(): _test_Image_atts(2)
def _test_Image_atts(imgtype):
"""Test that basic Nifti/Image attributes are correct. """
-
+
testdir = tempfile.mkdtemp()
allowedExts = fslimage.ALLOWED_EXTENSIONS
fileGroups = fslimage.FILE_GROUPS
@@ -259,17 +259,17 @@ def _test_Image_atts(imgtype):
tests = it.product(dims, pixdims, dtypes)
tests = list(tests)
paths = ['test{:03d}'.format(i) for i in range(len(tests))]
-
+
for path, atts in zip(paths, tests):
dims, pixdims, dtype = atts
ndims = len(dims)
- pixdims = pixdims[:ndims]
+ pixdims = pixdims[:ndims]
path = op.abspath(op.join(testdir, path))
make_image(path, imgtype, dims, pixdims, dtype)
-
+
try:
for path, atts in zip(paths, tests):
@@ -295,12 +295,12 @@ def _test_Image_atts(imgtype):
fileGroups=fileGroups)
finally:
shutil.rmtree(testdir)
-
-def test_Image_atts2_analyze(): _test_Image_atts2(0)
+
+def test_Image_atts2_analyze(): _test_Image_atts2(0)
def test_Image_atts2_nifti1(): _test_Image_atts2(1)
def test_Image_atts2_nifti2(): _test_Image_atts2(2)
def _test_Image_atts2(imgtype):
-
+
# See fsl.utils.constants for the meanings of these codes
xyzUnits = [0, 1, 2, 3]
timeUnits = [8, 16, 24, 32, 40, 48]
@@ -392,7 +392,7 @@ def test_addExt():
for path in toCreate:
path = op.abspath(op.join(testdir, path))
- make_random_image(path)
+ make_random_image(path)
try:
for path, mustExist, expected in tests:
@@ -456,14 +456,14 @@ def test_defaultExt():
os.environ['FSLOUTPUTTYPE'] = o
assert fslimage.defaultExt() == e
-
+
def test_Image_orientation_analyze_neuro(): _test_Image_orientation(0, 'neuro')
def test_Image_orientation_analyze_radio(): _test_Image_orientation(0, 'radio')
def test_Image_orientation_nifti1_neuro(): _test_Image_orientation(1, 'neuro')
def test_Image_orientation_nifti1_radio(): _test_Image_orientation(1, 'radio')
def test_Image_orientation_nifti2_neuro(): _test_Image_orientation(2, 'neuro')
-def test_Image_orientation_nifti2_radio(): _test_Image_orientation(2, 'radio')
+def test_Image_orientation_nifti2_radio(): _test_Image_orientation(2, 'radio')
def _test_Image_orientation(imgtype, voxorient):
"""Test the Nifti.isNeurological and Nifti.getOrientation methods. """
@@ -493,7 +493,7 @@ def _test_Image_orientation(imgtype, voxorient):
expectvox0Orientation = constants.ORIENT_R2L
expectvox1Orientation = constants.ORIENT_P2A
expectvox2Orientation = constants.ORIENT_I2S
-
+
elif voxorient == 'neuro':
expectNeuroTest = True
expectvox0Orientation = constants.ORIENT_L2R
@@ -534,7 +534,7 @@ def test_Image_sqforms_nifti1_nosqform(): _test_Image_sqforms(1, 1, 0)
def test_Image_sqforms_nifti2_normal(): _test_Image_sqforms(2, 1, 1)
def test_Image_sqforms_nifti2_nosform(): _test_Image_sqforms(2, 0, 1)
def test_Image_sqforms_nifti2_noqform(): _test_Image_sqforms(2, 1, 0)
-def test_Image_sqforms_nifti2_nosqform(): _test_Image_sqforms(2, 0, 0)
+def test_Image_sqforms_nifti2_nosqform(): _test_Image_sqforms(2, 0, 0)
def _test_Image_sqforms(imgtype, sformcode, qformcode):
"""Test the Nifti.getXFormCode method, and the voxToWorldMat/worldToVoxMat
attributes for NIFTI images with the given sform/qform code combination.
@@ -587,7 +587,7 @@ def _test_Image_sqforms(imgtype, sformcode, qformcode):
with pytest.raises(ValueError):
image.getXFormCode('badcode')
-
+
try:
assert np.all(np.isclose(image.voxToWorldMat, expAffine))
assert np.all(np.isclose(image.worldToVoxMat, invExpAffine))
@@ -601,10 +601,10 @@ def _test_Image_sqforms(imgtype, sformcode, qformcode):
shutil.rmtree(testdir)
-def test_Image_changeXform_analyze(): _test_Image_changeXform(0)
+def test_Image_changeXform_analyze(): _test_Image_changeXform(0)
def test_Image_changeXform_nifti1(): _test_Image_changeXform(1)
def test_Image_changeXform_nifti1_nosqform(): _test_Image_changeXform(1, 0, 0)
-def test_Image_changeXform_nifti2(): _test_Image_changeXform(2)
+def test_Image_changeXform_nifti2(): _test_Image_changeXform(2)
def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
"""Test changing the Nifti.voxToWorldMat attribute. """
@@ -641,7 +641,7 @@ def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
if imgtype > 0:
expSformCode = image.get_sform(coded=True)[1]
expQformCode = image.get_qform(coded=True)[1]
-
+
if sformcode == 0:
expSformCode = constants.NIFTI_XFORM_ALIGNED_ANAT
else:
@@ -654,7 +654,7 @@ def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
assert img.saveState
if imgtype == 0:
- # ANALYZE affine is not editable
+ # ANALYZE affine is not editable
with pytest.raises(Exception):
img.voxToWorldMat = newXform
return
@@ -679,7 +679,7 @@ def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
def test_Image_changeData_analyze(seed): _test_Image_changeData(0)
def test_Image_changeData_nifti1(seed): _test_Image_changeData(1)
-def test_Image_changeData_nifti2(seed): _test_Image_changeData(2)
+def test_Image_changeData_nifti2(seed): _test_Image_changeData(2)
def _test_Image_changeData(imgtype):
"""Test that changing image data triggers notification, and also causes
the dataRange attribute to be updated.
@@ -687,13 +687,13 @@ def _test_Image_changeData(imgtype):
testdir = tempfile.mkdtemp()
imagefile = op.join(testdir, 'image')
-
+
make_image(imagefile, imgtype)
img = fslimage.Image(imagefile)
notified = {}
-
+
def randvox():
return (np.random.randint(0, img.shape[0]),
np.random.randint(0, img.shape[1]),
@@ -773,7 +773,7 @@ def _test_Image_2D(imgtype):
# which happens when you create
# an XY slice with fslroi. This
# should still be read in as a
- # 3D image.
+ # 3D image.
testdims = [(10, 20),
(10, 20, 1),
(10, 1, 20),
@@ -787,9 +787,9 @@ def _test_Image_2D(imgtype):
for shape in testdims:
pixdim = [2] * len(shape)
-
+
imagefile = op.join(testdir, 'image')
-
+
make_image(imagefile, imgtype, shape, pixdim)
image = fslimage.Image(imagefile)
@@ -831,9 +831,9 @@ def test_Image_voxelsToScaledVoxels():
if itype > 0 and pixdims[0] > 0:
xf[0, 0] = -pixdims[0]
xf[0, 3] = pixdims[0] * (dims[0] - 1)
-
+
return xf
-
+
for imgType, dim, pixdim in it.product(imgTypes, dims, pixdims):
nimg = make_image(imgtype=imgType, dims=dim, pixdims=pixdim)
img = fslimage.Image(nimg)
@@ -842,7 +842,7 @@ def test_Image_voxelsToScaledVoxels():
result = img.voxelsToScaledVoxels()
assert np.all(np.isclose(result, expected))
-
+
def test_Image_sameSpace():
@@ -853,7 +853,7 @@ def test_Image_sameSpace():
pixdims = [(2, 2, 2, 1),
(2, 3, 4, 1)]
- for (imgType,
+ for (imgType,
dim1,
dim2,
pixdim1,
@@ -885,8 +885,8 @@ def _test_Image_save(imgtype):
if rvox not in rvoxes:
rvoxes.append(rvox)
return rvoxes
-
-
+
+
testdir = tempfile.mkdtemp()
if imgtype == 0:
filename = op.join(testdir, 'blob.img')
@@ -904,11 +904,13 @@ def _test_Image_save(imgtype):
try:
make_image(filename, imgtype)
- img = fslimage.Image(filename)
+ # Using mmap can cause a "Bus error"
+ # under docker. No idea why.
+ img = fslimage.Image(filename, mmap=False)
randvoxes = randvoxes(5)
randvals = [np.random.random() for i in range(5)]
-
+
for (x, y, z), v in zip(randvoxes, randvals):
img[x, y, z] = v
@@ -937,7 +939,7 @@ def _test_Image_save(imgtype):
# Load the image back in
img2 = fslimage.Image(img.dataSource)
-
+
assert img.saveState
assert img.dataSource == expDataSource
@@ -945,8 +947,8 @@ def _test_Image_save(imgtype):
assert np.all(np.isclose(img.voxToWorldMat, xform))
for (x, y, z), v in zip(randvoxes, randvals):
- assert np.isclose(img[x, y, z], v)
-
+ assert np.isclose(img[x, y, z], v)
+
finally:
shutil.rmtree(testdir)