diff --git a/README.md b/README.md
index a63ac35a54eebcad5f8603229aaa6fe2197ad6fa..a3ab1ba2fc53104b2e61fb65808ad41e3a2094d4 100644
--- a/README.md
+++ b/README.md
@@ -35,8 +35,10 @@ guide](doc/contributing.rst).
Tests
-----
-To run the tests, install `pytest` and `pytest-cov`, and then run:
+To run the tests, install `mock`, `pytest`, `pytest-runner`, `pytest-html`,
+and `pytest-cov`, and then run:
python setup.py test
-A code coverage report will be generated in `htmlcov/`.
+A test report will be generated at `report.html`, and a code coverage report
+will be generated in `htmlcov/`.
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index db1925fa46e88b69ffe596070cdf765291bc0e18..9f6b9fe8df68f665233dadd9fac579521f8ea80f 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -40,6 +40,8 @@ load an atlas image, which will be one of the following atlas-specific
"""
+from __future__ import division
+
import xml.etree.ElementTree as et
import os.path as op
import glob
@@ -521,11 +523,11 @@ class AtlasDescription(object):
return self.atlasID != other.atlasID
- def __cmp__(self, other):
+ def __lt__(self, other):
"""Compares this ``AtlasDescription`` with another by their ``name``
attribute.
"""
- return cmp(self.name.lower(), other.name.lower())
+ return self.name.lower() < other.name.lower()
class Atlas(fslimage.Image):
@@ -559,8 +561,10 @@ class Atlas(fslimage.Image):
res = resolution
reses = np.concatenate(atlasDesc.pixdims)
- if resolution is None: imageIdx = np.argmin(reses) / 3
- else: imageIdx = np.argmin(np.abs(reses - res)) / 3
+ if resolution is None: imageIdx = np.argmin(reses)
+ else: imageIdx = np.argmin(np.abs(reses - res))
+
+ imageIdx = imageIdx // 3
if isLabel: imageFile = atlasDesc.summaryImages[imageIdx]
else: imageFile = atlasDesc.images[ imageIdx]
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index ee5843064b0d2c9bccc93dd4322be98f5f51f2a4..ed8d905994e98a1c6a240230cab56307f6a6b5b8 100644
--- a/fsl/data/featdesign.py
+++ b/fsl/data/featdesign.py
@@ -540,7 +540,7 @@ def getFirstLevelEVs(featDir, settings, designMat):
# above, about the voxelwise
# confound EV locations, holds
startIdx = len(evs) + 1
- if voxConfLocs != range(startIdx, startIdx + len(voxConfFiles)):
+ if voxConfLocs != list(range(startIdx, startIdx + len(voxConfFiles))):
raise FSFError('Unsupported voxelwise confound ordering '
'({} -> {})'.format(startIdx, voxConfLocs))
@@ -640,26 +640,11 @@ def loadDesignMat(designmat):
:arg designmat: Path to the ``design.mat`` file.
"""
- matrix = None
-
log.debug('Loading FEAT design matrix from {}'.format(designmat))
- with open(designmat, 'rt') as f:
-
- while True:
- line = f.readline()
-
- # readline returns an empty string at EOF
- if line == '':
- break
-
- # Matrix data starts after "/Matrix"
- if line.strip() == '/Matrix':
- break
-
- matrix = np.loadtxt(f, ndmin=2)
+ matrix = np.loadtxt(designmat, comments='/', ndmin=2)
- if matrix is None or matrix.size == 0:
+ if matrix is None or matrix.size == 0 or len(matrix.shape) != 2:
raise FSFError('{} does not appear to be a '
'valid design.mat file'.format(designmat))
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 1b93982be91d51ba32da528a555d9030faddb9b1..f44c3bec5539e84f24a8ee9285fd713499b687aa 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -470,8 +470,8 @@ class Nifti(notifier.Notifier):
elif qform_code != constants.NIFTI_XFORM_UNKNOWN: code = qform_code
# Invalid values
- if code > 4: code = constants.NIFTI_XFORM_UNKNOWN
- elif code < 0: code = constants.NIFTI_XFORM_UNKNOWN
+ if code not in range(5):
+ code = constants.NIFTI_XFORM_UNKNOWN
return int(code)
@@ -836,7 +836,7 @@ class Image(Nifti):
self.__nibImage = None
self.__imageWrapper = None
- if self.__fileobj is not None:
+ if getattr(self, '__fileobj', None) is not None:
self.__fileobj.close()
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 810624daaccd695c857f0b1f90ccd989e7207b55..81658f594817ad90b3f4f9c7fd7fecbd9949e0a2 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -415,7 +415,7 @@ class ImageWrapper(notifier.Notifier):
"""
shape = self.__image.shape
- slices = zip([0] * len(shape), shape)
+ slices = [[0, s] for s in shape]
return sliceCovered(slices, self.__coverage)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index e34ebf2a7b3bedaee0ef80c629c5b23a794fa577..2a9c47df7bdacc938cbcef57bf459b05529f8db1 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -221,7 +221,6 @@ def loadVTKPolydataFile(infile):
for i in range(nVertices):
vertLine = lines[i + 5]
- vertices[i, :] = map(float, vertLine.split())
vertices[i, :] = [float(w) for w in vertLine.split()]
indexOffset = 0
@@ -232,7 +231,6 @@ def loadVTKPolydataFile(infile):
start = indexOffset
end = indexOffset + polygonLengths[i]
- indices[start:end] = map(int, polyLine[1:])
indices[start:end] = [int(w) for w in polyLine[1:]]
indexOffset += polygonLengths[i]
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
index 938a83c384746540cf77bce76dd089e64591d4aa..a8e8efa0e41a39336b4acecb6ab7709c1c14ac04 100644
--- a/fsl/utils/async.py
+++ b/fsl/utils/async.py
@@ -290,8 +290,11 @@ def _wxIdleLoop(ev):
except queue.Empty:
# Make sure that we get called periodically,
- # if EVT_IDLE decides to stop firing.
- _idleTimer.Start(_idleCallRate, wx.TIMER_ONE_SHOT)
+ # if EVT_IDLE decides to stop firing. If
+ # _idleTimer is None, then idleReset has
+ # probably been called.
+ if _idleTimer is not None:
+ _idleTimer.Start(_idleCallRate, wx.TIMER_ONE_SHOT)
return
now = time.time()
diff --git a/pytest.ini b/pytest.ini
index 599c0c249814ef8da3a0efca547b52e16dcdb48b..4352354c39baad6c64cc31779521515065481c51 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,3 +1,3 @@
[pytest]
testpaths = tests
-addopts = -v --niters=50 --cov=fsl --cov-report=html
+addopts = -s -v --niters=50 --cov=fsl --cov-report=html --html=report.html
diff --git a/requirements.txt b/requirements.txt
index 6370b5c227e5a96c814bccef79407d3bc5bb98bf..a35583e56da774621c9fee8dfcc693f2ffacd962 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
six>=1.10.0,<2.0
numpy>=1.11.1,<2.0
nibabel>=2.1,<3.0
-indexed_gzip>=0.3.1,<0.4
+indexed_gzip>=0.3.2,<0.4
wxPython>=3.0.2.0,<=4.0
diff --git a/setup.py b/setup.py
index a83332d4a2c721261bb158086934d247e3aec18a..c793739fa383707ced42d2984d0953777a1325d7 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ with open(op.join(basedir, "fsl", "version.py")) as f:
for line in f:
if line.startswith('__version__'):
exec(line, version)
- break
+ break
with open(op.join(basedir, 'README.md'), 'rt') as f:
readme = f.read()
@@ -45,9 +45,9 @@ with open(op.join(basedir, 'README.md'), 'rt') as f:
class doc(Command):
"""Build the API documentation. """
-
+
user_options = []
-
+
def initialize_options(self):
pass
@@ -64,12 +64,12 @@ class doc(Command):
env = dict(os.environ)
ppath = [op.join(pkgutil.get_loader('fsl').filename, '..')]
-
+
env['PYTHONPATH'] = op.pathsep.join(ppath)
print('Building documentation [{}]'.format(destdir))
- sp.call(['sphinx-build', docdir, destdir], env=env)
+ sp.call(['sphinx-build', docdir, destdir], env=env)
setup(
@@ -102,7 +102,11 @@ setup(
install_requires=install_requires,
setup_requires=['pytest-runner'],
- tests_require=['pytest', 'mock', 'pytest-cov', 'pytest-runner'],
+ tests_require=['pytest',
+ 'mock',
+ 'pytest-cov',
+ 'pytest-html',
+ 'pytest-runner'],
test_suite='tests',
cmdclass={'doc' : doc},
diff --git a/tests/__init__.py b/tests/__init__.py
index 106f41767bf137ee895d693d7ad727967dfdef2e..0d5e4affcc5fe572197a5c79c9a6363590e2ef59 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -24,15 +24,14 @@ def testdir(contents=None):
if contents is not None:
contents = [op.join(*c.split('/')) for c in contents]
- print(contents)
-
+
class ctx(object):
def __init__(self, contents):
self.contents = contents
-
+
def __enter__(self):
-
+
self.testdir = tempfile.mkdtemp()
if self.contents is not None:
@@ -55,7 +54,7 @@ def make_dummy_files(paths):
def make_dummy_file(path, contents=None):
"""Makes a plain text file. Returns a hash of the file contents. """
dirname = op.dirname(path)
-
+
if not op.exists(dirname):
os.makedirs(dirname)
@@ -148,8 +147,8 @@ def make_mock_feat_analysis(featdir,
src = featdir
dest = op.join(testdir, op.basename(featdir))
- featdir = dest
-
+ featdir = dest
+
shutil.copytree(src, dest)
if indata:
@@ -184,18 +183,18 @@ def make_mock_feat_analysis(featdir,
if copes:
files = glob.glob(op.join(featdir, 'stats', 'cope*nii.gz'))
otherFiles .extend(files)
- otherShapes.extend([shape] * len(files))
+ otherShapes.extend([shape] * len(files))
if zstats:
files = glob.glob(op.join(featdir, 'stats', 'zstat*nii.gz'))
otherFiles .extend(files)
- otherShapes.extend([shape] * len(files))
-
+ otherShapes.extend([shape] * len(files))
+
if residuals:
files = glob.glob(op.join(featdir, 'stats', 'res4d.nii.gz'))
otherFiles .extend(files)
- otherShapes.extend([shape4D])
-
+ otherShapes.extend([shape4D])
+
if clustMasks:
files = glob.glob(op.join(featdir, 'cluster_mask*nii.gz'))
otherFiles .extend(files)
diff --git a/tests/test_async.py b/tests/test_async.py
index 9a2e03d56b0aaf4db299eaf2d694da1636ab0f14..3e7819d4013e0d91c76d3852b092ab4a621c52f7 100644
--- a/tests/test_async.py
+++ b/tests/test_async.py
@@ -59,7 +59,7 @@ def _run_with_wx(func, *args, **kwargs):
frame.Destroy()
_wxapp.ExitMainLoop()
wx.CallLater(finishingDelay, finish)
-
+
frame.Show()
wx.CallLater(startingDelay, wrap)
@@ -69,7 +69,7 @@ def _run_with_wx(func, *args, **kwargs):
if raised[0] and propagateRaise:
raise raised[0]
-
+
return result[0]
@@ -100,8 +100,8 @@ def _test_run():
taskRun[0] = True
def errtask():
- taskRun[0] = True
- raise Exception('Task crashed!')
+ taskRun[0] = True
+ raise Exception('Task which was supposed to crash crashed!')
def onFinish():
onFinishCalled[0] = True
@@ -127,7 +127,7 @@ def _test_run():
taskRun[ 0] = False
onFinishCalled[0] = False
-
+
t = async.run(errtask, onFinish, onError)
if t is not None:
@@ -157,7 +157,7 @@ def test_idle():
called[0] = arg == 1 and kwarg1 == 2
def errtask(arg, kwarg1=None):
- raise Exception('Task crashed!')
+ raise Exception('Task which was supposed to crash crashed!')
assert async.getIdleTimeout() > 0
@@ -173,10 +173,10 @@ def test_idle():
# Run a crashing task directly
with pytest.raises(Exception):
- async.idle(errtask)
+ async.idle(errtask, 1, kwarg1=2)
# Run a crashing task on idle loop - error should not propagate
- _run_with_wx(async.idle, errtask)
+ _run_with_wx(async.idle, errtask, 1, kwarg1=2)
def test_inidle():
@@ -413,7 +413,7 @@ def _test_wait():
if t is not None:
t.join()
-
+
_wait_for_idle_loop_to_clear()
assert all(threadtaskscalled)
@@ -449,7 +449,7 @@ def test_TaskThread_onFinish():
taskCalled[0] = True
def onFinish():
- onFinishCalled[0] = True
+ onFinishCalled[0] = True
tt = async.TaskThread()
tt.start()
@@ -488,7 +488,7 @@ def test_TaskThread_isQueued():
time.sleep(0.3)
tt.stop()
- tt.join()
+ tt.join()
assert queued
assert called[0]
@@ -517,7 +517,7 @@ def test_TaskThread_dequeue():
time.sleep(0.3)
tt.stop()
- tt.join()
+ tt.join()
assert not called[0]
@@ -542,7 +542,7 @@ def test_TaskThread_TaskVeto():
time.sleep(0.5)
tt.stop()
- tt.join()
+ tt.join()
assert taskCalled[0]
assert not onFinishCalled[0]
@@ -579,7 +579,7 @@ def test_mutex():
t[0].method2start = None
t[0].method1end = None
t[0].method2end = None
-
+
t1 = threading.Thread(target=thread1)
t2 = threading.Thread(target=thread2)
diff --git a/tests/test_featdesign.py b/tests/test_featdesign.py
index c1f6a21010580b5882d239666d31fd36dd1ae51e..f685ff712364c6338faaade5af3cea151ccc87a5 100644
--- a/tests/test_featdesign.py
+++ b/tests/test_featdesign.py
@@ -68,7 +68,7 @@ with the following commands:
- 2 temporal derivative EVs
- 1 voxelwise EV
- 6 Standard motion parameters
- - 2 contrasts - one on each stimulus EV
+ - 2 contrasts - one on each stimulus EV
`1stlevel_3.feat`
- 45 time points
@@ -99,7 +99,7 @@ with the following commands:
- Shape (10, 10, 10)
- Three subjects
- Two copes
- - One main EV - group average
+ - One main EV - group average
"""
@@ -145,7 +145,7 @@ for i, featdir in enumerate(featdirs):
def test_FEATFSFDesign():
for featdir in TEST_ANALYSES.keys():
-
+
nev = TEST_ANALYSES[featdir]['nevs']
shape = TEST_ANALYSES[featdir]['shape']
desshape = TEST_ANALYSES[featdir]['designShape']
@@ -306,16 +306,14 @@ def test_getFirstLevelEVs_3():
(featdesign.MotionParameterEV, {'index' : 29, 'motionIndex' : 23}),
(featdesign.ConfoundEV, {'index' : 30, 'confIndex' : 0}),
(featdesign.ConfoundEV, {'index' : 31, 'confIndex' : 1})]
-
+
evs = featdesign.getFirstLevelEVs(featdir, settings, matrix)
-
+
assert len(evs) == 32
for i, (evtype, atts) in enumerate(expected):
- print(i, evs[i])
-
assert isinstance(evs[i], evtype)
for k, v in atts.items():
assert getattr(evs[i], k) == v
@@ -330,17 +328,15 @@ def test_getFirstLevelEVs_realdata():
(featdesign.TemporalDerivativeEV, {'index' : 3})]
evs = featdesign.getFirstLevelEVs(featdir, settings, matrix)
-
+
assert len(evs) == 4
for i, (evtype, atts) in enumerate(expected):
- print(i, evs[i])
-
assert isinstance(evs[i], evtype)
for k, v in atts.items():
assert getattr(evs[i], k) == v
-
+
def test_getHigherLevelEVs_1():
@@ -355,8 +351,8 @@ def test_getHigherLevelEVs_1():
assert isinstance(evs[0], featdesign.NormalEV)
assert evs[0].index == 0
assert evs[0].origIndex == 0
-
-
+
+
def test_getHigherLevelEVs_2():
@@ -386,9 +382,9 @@ def test_loadDesignMat():
assert mat.shape == shape
nonfile = op.join(datadir, 'non-existent-file')
- badfile = op.join(datadir, '1stlevel_1.feat', 'design.fsf')
+ badfile = op.join(datadir, '1stlevel_1.feat', 'design.fsf')
with pytest.raises(Exception):
featdesign.loadDesignMat(nonfile)
with pytest.raises(Exception):
- featdesign.loadDesignMat(badfile)
+ featdesign.loadDesignMat(badfile)
diff --git a/tests/test_image_advanced.py b/tests/test_image_advanced.py
index 58b60e2751fd4a60ff597629ef4be4e4f514521b..a8401b92d4239f782ebd0959f7b7ef4bcd04f126 100644
--- a/tests/test_image_advanced.py
+++ b/tests/test_image_advanced.py
@@ -16,18 +16,18 @@ import fsl.data.image as fslimage
def test_image_indexed_threaded( ): _test_image_indexed(True)
-def test_image_indexed_unthreaded(): _test_image_indexed(False)
+def test_image_indexed_unthreaded(): _test_image_indexed(False)
def _test_image_indexed(threaded):
with tests.testdir() as testdir:
-
+
filename = op.join(testdir, 'image.nii.gz')
# Data range grows with volume
data = np.zeros((100, 100, 100, 50))
for vol in range(data.shape[-1]):
data[..., vol] = vol
-
+
fslimage.Image(data).save(filename)
img = fslimage.Image(
@@ -45,7 +45,7 @@ def _test_image_indexed(threaded):
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
-
+
assert img.dataRange == (0, vol)
end1 = time.time()
@@ -66,7 +66,7 @@ def test_image_indexed_read4D_unthreaded(seed):
def _test_image_indexed_read4D(threaded):
with tests.testdir() as testdir:
-
+
filename = op.join(testdir, 'image.nii.gz')
# Data range grows with volume
@@ -74,7 +74,7 @@ def _test_image_indexed_read4D(threaded):
data = np.zeros((50, 50, 50, nvols))
for vol in range(nvols):
data[..., vol] = vol
-
+
fslimage.Image(data).save(filename)
img = fslimage.Image(
@@ -82,15 +82,15 @@ def _test_image_indexed_read4D(threaded):
loadData=False,
calcRange=False,
indexed=True,
- threaded=threaded)
+ threaded=threaded)
# Test reading slice through
# 4D (e.g. voxel time course)
- #
+ #
# n.b. This is SUPER SLOW!!
voxels = tests.random_voxels((50, 50, 50), 5)
for i, xyz in enumerate(voxels):
-
+
x, y, z = [int(v) for v in xyz]
data = img[x, y, z, :]
@@ -98,21 +98,21 @@ def _test_image_indexed_read4D(threaded):
img.getImageWrapper().getTaskThread().waitUntilIdle()
assert np.all(data == np.arange(nvols))
-
+
def test_image_indexed_save_threaded( ): _test_image_indexed_save(True)
-def test_image_indexed_save_unthreaded(): _test_image_indexed_save(False)
+def test_image_indexed_save_unthreaded(): _test_image_indexed_save(False)
def _test_image_indexed_save(threaded):
with tests.testdir() as testdir:
-
+
filename = op.join(testdir, 'image.nii.gz')
# Data range grows with volume
data = np.zeros((100, 100, 100, 50))
for vol in range(data.shape[-1]):
data[..., vol] = vol
-
+
fslimage.Image(data).save(filename)
img = fslimage.Image(
@@ -149,7 +149,7 @@ def _test_image_indexed_save(threaded):
# get rebuilt to this point
img[..., 0]
img[..., 40]
-
+
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
@@ -162,8 +162,8 @@ def _test_image_indexed_save(threaded):
img.getImageWrapper().getTaskThread().waitUntilIdle()
# make sure we got the modified data
- assert img.dataRange == (0, 49)
-
+ assert img.dataRange == (0, 49)
+
# Finally, reload, and verify the change
img = fslimage.Image(filename)
@@ -229,8 +229,8 @@ def _test_image_calcRange(threaded):
img.calcRange(np.prod(img.shape) * img.dtype.itemsize + 1)
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
- assert img.dataRange == (0, 10)
-
+ assert img.dataRange == (0, 10)
+
# Check that calcRange(smallnum) will
# calculate the range of the first slice
img = fslimage.Image(data, **kwargs)
@@ -252,15 +252,15 @@ def _test_image_calcRange(threaded):
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
assert img.dataRange == (0, 10)
-
+
# Check that calcRange(numBiggerThanImage)
# will calculate the full range
img = fslimage.Image(data, **kwargs)
img.calcRange(np.prod(img.shape) * img.dtype.itemsize + 1)
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
- assert img.dataRange == (0, 10)
-
+ assert img.dataRange == (0, 10)
+
# Check that calcRange(smallnum) will
# calculate the range of the first volume
img = fslimage.Image(data, **kwargs)
diff --git a/tests/test_immv_imcp.py b/tests/test_immv_imcp.py
index 6b6f030fb322f70ed825db23a6e3790cf9811741..37b8639d36ec8436fc257762efe85aa690d2f4fd 100644
--- a/tests/test_immv_imcp.py
+++ b/tests/test_immv_imcp.py
@@ -12,7 +12,7 @@ from __future__ import print_function
import os
import os.path as op
import shutil
-import subprocess as sp
+import subprocess as sp
import tempfile
import logging
@@ -35,6 +35,12 @@ from . import looks_like_image
from . import cleardir
+real_print = print
+
+def print(*args, **kwargs):
+ pass
+
+
def makeImage(filename):
return hash(make_random_image(filename).get_data().tobytes())
@@ -106,18 +112,18 @@ def checkFilesToExpect(files, outdir, outputType, datahashes):
def test_imcp_script_shouldPass(move=False):
-
+
# The imcp/immv scripts should honour the
- # FSLOUTPUTTYPE env var. If it is unset
+ # FSLOUTPUTTYPE env var. If it is unset
# or invalid - '' in this case), they
# should produce .nii.gz
outputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', '']
-
+
# Test tuples have the following structure (each
# item is a string which will be split on spaces):
- #
+ #
# (files_to_create, imcp_args, files_to_expect)
#
# The files_to_expect is a list of
@@ -134,26 +140,26 @@ def test_imcp_script_shouldPass(move=False):
('a.nii', 'a b.nii', 'b'),
('a.nii', 'a.nii b.nii', 'b'),
('a.nii', 'a .', 'a'),
- ('a.nii', 'a.nii .', 'a'),
+ ('a.nii', 'a.nii .', 'a'),
('a.nii', 'a b.hdr', 'b'),
('a.nii', 'a b.img', 'b'),
('a.nii', 'a b.nii.gz', 'b'),
('a.nii', 'a.nii b.hdr', 'b'),
('a.nii', 'a.nii b.img', 'b'),
- ('a.nii', 'a.nii b.nii.gz', 'b'),
-
+ ('a.nii', 'a.nii b.nii.gz', 'b'),
+
('a.nii.gz', 'a b', 'b'),
('a.nii.gz', 'a.nii.gz b', 'b'),
('a.nii.gz', 'a b.nii.gz', 'b'),
('a.nii.gz', 'a.nii.gz b.nii.gz', 'b'),
('a.nii.gz', 'a .', 'a'),
- ('a.nii.gz', 'a.nii.gz .', 'a'),
+ ('a.nii.gz', 'a.nii.gz .', 'a'),
('a.nii.gz', 'a b.hdr', 'b'),
('a.nii.gz', 'a b.img', 'b'),
('a.nii.gz', 'a b.nii', 'b'),
('a.nii.gz', 'a.nii.gz b.hdr', 'b'),
('a.nii.gz', 'a.nii.gz b.img', 'b'),
- ('a.nii.gz', 'a.nii.gz b.nii', 'b'),
+ ('a.nii.gz', 'a.nii.gz b.nii', 'b'),
('a.img', 'a b', 'b'),
('a.img', 'a b.img', 'b'),
@@ -166,8 +172,8 @@ def test_imcp_script_shouldPass(move=False):
('a.img', 'a.hdr b', 'b'),
('a.img', 'a.hdr b.img', 'b'),
('a.img', 'a.hdr b.hdr', 'b'),
- ('a.img', 'a.hdr .', 'a'),
-
+ ('a.img', 'a.hdr .', 'a'),
+
('a.img', 'a b.nii', 'b'),
('a.img', 'a b.nii.gz', 'b'),
('a.img', 'a .', 'a'),
@@ -191,7 +197,7 @@ def test_imcp_script_shouldPass(move=False):
('a.img b.img', 'a.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr b .', 'a b'),
('a.img b.img', 'a.hdr b.img .', 'a b'),
- ('a.img b.img', 'a.hdr b.hdr .', 'a b'),
+ ('a.img b.img', 'a.hdr b.hdr .', 'a b'),
('a.nii.gz b.nii.gz', 'a b .', 'a b'),
('a.nii.gz b.nii.gz', 'a b.nii.gz .', 'a b'),
@@ -226,7 +232,7 @@ def test_imcp_script_shouldPass(move=False):
('a.img', 'a.hdr a .', 'a'),
('a.img', 'a.hdr a.img .', 'a'),
('a.img', 'a.hdr a.hdr .', 'a'),
-
+
('a.img b.img', 'a a b b .', 'a b'),
('a.img b.img', 'a a b b.img .', 'a b'),
('a.img b.img', 'a a b b.hdr .', 'a b'),
@@ -262,7 +268,7 @@ def test_imcp_script_shouldPass(move=False):
('a.img b.img', 'a.img a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b.img .', 'a b'),
- ('a.img b.img', 'a.img a.hdr b.img b.hdr .', 'a b'),
+ ('a.img b.img', 'a.img a.hdr b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a b b .', 'a b'),
('a.img b.img', 'a.hdr a b b.img .', 'a b'),
('a.img b.img', 'a.hdr a b b.hdr .', 'a b'),
@@ -297,18 +303,18 @@ def test_imcp_script_shouldPass(move=False):
('a.img a.nii.gz a.nii ', 'a.img a.nii.gz a.nii .', 'a'),
('a.img a.nii a.nii.gz', 'a.img a.nii a.nii.gz .', 'a'),
('a.nii.gz a.img a.nii ', 'a.nii.gz a.img a.nii .', 'a'),
- ('a.nii.gz a.nii a.img ', 'a.nii.gz a.nii a.img .', 'a'),
+ ('a.nii.gz a.nii a.img ', 'a.nii.gz a.nii a.img .', 'a'),
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
-
+
try:
for outputType in outputTypes:
-
+
os.environ['FSLOUTPUTTYPE'] = outputType
-
+
for files_to_create, imcp_args, files_to_expect in tests:
imageHashes = []
@@ -333,7 +339,7 @@ def test_imcp_script_shouldPass(move=False):
else: imcp_script.main(imcp_args)
print('indir after: ', os.listdir(indir))
- print('outdir after: ', os.listdir(outdir))
+ print('outdir after: ', os.listdir(outdir))
checkFilesToExpect(
files_to_expect, outdir, outputType, imageHashes)
@@ -346,11 +352,11 @@ def test_imcp_script_shouldPass(move=False):
cleardir(indir)
cleardir(outdir)
-
+
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
-
+
def test_imcp_script_shouldFail(move=False):
@@ -361,11 +367,11 @@ def test_imcp_script_shouldFail(move=False):
# - ambiguous inputs
# - input is incomplete pair (e.g. .hdr
# without corresponding .img)
-
+
# a.img
# a.hdr
# a.nii
- #
+ #
# FAIL: imcp a dest
# (files_to_create, imcp_args[, preproc])
@@ -397,7 +403,7 @@ def test_imcp_script_shouldFail(move=False):
('a.img', 'a.hdr b', 'rm indir/a.hdr'),
('a.img', 'a b', 'rm indir/a.img'),
('a.img', 'a.img b', 'rm indir/a.img'),
- ('a.img', 'a.hdr b', 'rm indir/a.img'),
+ ('a.img', 'a.hdr b', 'rm indir/a.img'),
]
if move:
@@ -410,13 +416,13 @@ def test_imcp_script_shouldFail(move=False):
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
-
+
try:
for test in tests:
files_to_create = test[0]
imcp_args = test[1]
-
+
if len(test) == 3: preproc = test[2]
else: preproc = None
@@ -455,9 +461,9 @@ def test_imcp_script_shouldFail(move=False):
def test_immv_script_shouldPass():
test_imcp_script_shouldPass(move=True)
-
+
def test_immv_script_shouldFail():
- test_imcp_script_shouldFail(move=True)
+ test_imcp_script_shouldFail(move=True)
def test_imcp_shouldPass(move=False):
@@ -473,7 +479,7 @@ def test_imcp_shouldPass(move=False):
# imgp src.img dest -> dest.nii.gz
# imgp src.img dest.nii -> dest.nii.gz
- #
+ #
# (files_to_create,
# [( imcp_args, files_which_should_exist),
# ...
@@ -524,9 +530,9 @@ def test_imcp_shouldPass(move=False):
('file.nii file.nii', 'file.nii'),
# TODO both img/nii files
- ]),
-
-
+ ]),
+
+
('file.nii', [
('file file', 'file.nii'),
('file file.nii', 'file.nii'),
@@ -545,7 +551,7 @@ def test_imcp_shouldPass(move=False):
('file.nii.gz .', 'file.nii.gz'),
]),
-
+
('file.nii file.blob', [
('file file', 'file.nii'),
('file file.nii', 'file.nii'),
@@ -553,8 +559,8 @@ def test_imcp_shouldPass(move=False):
('file.nii file', 'file.nii'),
('file.nii file.nii', 'file.nii'),
('file.nii .', 'file.nii'),
- ]),
-
+ ]),
+
('file.nii file.nii.gz', [
('file.nii file', 'file.nii'),
@@ -577,11 +583,11 @@ def test_imcp_shouldPass(move=False):
('001.img 002.img 003.img', [
-
+
('001 002 003 .', '001.img 002.img 003.img'),
('001.img 002.img 003.img .', '001.img 002.img 003.img'),
('001.hdr 002.hdr 003.hdr .', '001.img 002.img 003.img'),
-
+
('001.img 002 003 .', '001.img 002.img 003.img'),
('001.hdr 002 003 .', '001.img 002.img 003.img'),
@@ -591,13 +597,13 @@ def test_imcp_shouldPass(move=False):
('001 003 .', '001.img 003.img'),
('001.img 003.img .', '001.img 003.img'),
('001.hdr 003.hdr .', '001.img 003.img'),
-
+
('001.img 003 .', '001.img 003.img'),
('001.hdr 003 .', '001.img 003.img'),
('001.img 003.img .', '001.img 003.img'),
- ('001.hdr 003.hdr .', '001.img 003.img'),
- ]),
+ ('001.hdr 003.hdr .', '001.img 003.img'),
+ ]),
]
@@ -609,7 +615,7 @@ def test_imcp_shouldPass(move=False):
for files_to_create, tests in shouldPass:
files_to_create = files_to_create.split()
-
+
for imcp_args, should_exist in tests:
should_exist = should_exist.split()
@@ -636,7 +642,7 @@ def test_imcp_shouldPass(move=False):
print(' src: {}'.format(src))
src = op.join(indir, src)
-
+
if move: imcp.immv(src, op.join(outdir, imcp_dest), overwrite=True)
else: imcp.imcp(src, op.join(outdir, imcp_dest), overwrite=True)
@@ -655,15 +661,15 @@ def test_imcp_shouldPass(move=False):
if move:
for f in should_exist:
assert not op.exists(op.join(indir, f))
-
+
for f in os.listdir(indir):
try: os.remove(op.join(indir, f))
except: pass
-
+
for f in os.listdir(outdir):
os.remove(op.join(outdir, f))
-
-
+
+
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
diff --git a/tests/test_melodicimage.py b/tests/test_melodicimage.py
index 7122d6f2dd8482d8a42a13ca366b628b20ddfb62..95853b759dc91cea992e299940a5c9d3e41c550f 100644
--- a/tests/test_melodicimage.py
+++ b/tests/test_melodicimage.py
@@ -5,6 +5,7 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+from __future__ import division
import os.path as op
@@ -52,8 +53,8 @@ def _create_dummy_melodic_analysis(basedir,
# rows=frequencies
# columns=ICs
if timepoints % 2: nfreqs = int(np.ceil(timepoints / 2.0))
- else: nfreqs = timepoints / 2
-
+ else: nfreqs = timepoints // 2
+
ftmixdata = np.zeros((nfreqs, nics))
for ic in range(nics):
@@ -63,7 +64,7 @@ def _create_dummy_melodic_analysis(basedir,
np.savetxt(mixfile, mixdata)
np.savetxt(ftmixfile, ftmixdata)
fslimage.Image(icimg).save(icfile)
-
+
if with_data:
dataimg = np.zeros(list(shape4D[:3]) + [timepoints])
for t in range(timepoints):
@@ -71,7 +72,7 @@ def _create_dummy_melodic_analysis(basedir,
hdr = nib.nifti1.Nifti1Header()
hdr['pixdim'][4] = tr
-
+
img = fslimage.Image(dataimg, header=hdr, xform=np.eye(4))
img.save(datafile)
@@ -105,8 +106,8 @@ def test_MelodicImage_create():
meldir = _create_dummy_melodic_analysis(testdir)
icfile = op.join(meldir, 'melodic_IC.nii.gz')
icfilenosuf = op.join(meldir, 'melodic_IC')
-
- # Should be able to specify the
+
+ # Should be able to specify the
# melodic dir, or the IC image
meli.MelodicImage(meldir)
meli.MelodicImage(icfile)
@@ -129,7 +130,7 @@ def test_MelodicImage_atts():
assert img.getTopLevelAnalysisDir() == mela.getTopLevelAnalysisDir(meldir)
assert img.getDataFile() == mela.getDataFile(meldir)
assert img.getMeanFile() == mela.getMeanFile(meldir)
-
+
def test_MelodicImage_componentData():
with tests.testdir() as testdir:
@@ -153,7 +154,7 @@ def test_MelodicImage_tr():
img = meli.MelodicImage(meldir)
assert img.tr == 1
-
+
# Otherwise, it should be set to the datafile tr
with tests.testdir() as testdir:
meldir = _create_dummy_melodic_analysis(testdir, tr=5)
@@ -166,7 +167,7 @@ def test_MelodicImage_tr():
cbCalled = [False]
def trChanged(*a):
cbCalled[0] = True
-
+
meldir = _create_dummy_melodic_analysis(testdir, with_data=False)
img = meli.MelodicImage(meldir)
diff --git a/tests/test_transform.py b/tests/test_transform.py
index ddf6fc6c7a74929accd1ad8977655edb89f0b365..e8b2d342210ce3be368b6b5bdc1af0b114330d2e 100644
--- a/tests/test_transform.py
+++ b/tests/test_transform.py
@@ -5,11 +5,16 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+
+from __future__ import division
+
import glob
import os.path as op
import itertools as it
import numpy as np
+import six
+
import pytest
import fsl.utils.transform as transform
@@ -22,9 +27,20 @@ datadir = op.join(op.dirname(__file__), 'testdata')
def readlines(filename):
with open(filename, 'rt') as f:
lines = f.readlines()
- lines = [l.strip() for l in lines]
- lines = [l for l in lines if not l.startswith('#')]
- lines = [l for l in lines if l != '']
+ lines = [l.strip() for l in lines]
+ lines = [l for l in lines if not l.startswith('#')]
+ lines = [l for l in lines if l != '']
+
+ # numpy.genfromtxt is busted in python 3.
+ # Pass it [str, str, ...], and it complains:
+ #
+ # TypeError: must be str or None, not bytes
+ #
+ # Pass it [bytes, bytes, ...], and it works
+ # fine.
+ if six.PY3:
+ lines = [l.encode('ascii') for l in lines]
+
return lines
@@ -33,7 +49,7 @@ def test_invert():
testfile = op.join(datadir, 'test_transform_test_invert.txt')
testdata = np.loadtxt(testfile)
- nmatrices = testdata.shape[0] / 4
+ nmatrices = testdata.shape[0] // 4
for i in range(nmatrices):
@@ -45,19 +61,18 @@ def test_invert():
def test_concat():
-
+
testfile = op.join(datadir, 'test_transform_test_concat.txt')
lines = readlines(testfile)
- ntests = len(lines) / 4
+ ntests = len(lines) // 4
tests = []
for i in range(ntests):
ilines = lines[i * 4:i * 4 + 4]
-
data = np.genfromtxt(ilines)
- ninputs = data.shape[1] / 4 - 1
+ ninputs = data.shape[1] // 4 - 1
inputs = []
@@ -79,12 +94,12 @@ def test_scaleOffsetXform():
testfile = op.join(datadir, 'test_transform_test_scaleoffsetxform.txt')
lines = readlines(testfile)
- ntests = len(lines) / 5
+ ntests = len(lines) // 5
for i in range(ntests):
-
+
lineoff = i * 5
- scales, offsets = lines[lineoff].split(',')
+ scales, offsets = lines[lineoff].decode('ascii').split(',')
scales = [float(s) for s in scales .split()]
offsets = [float(o) for o in offsets.split()]
@@ -102,13 +117,13 @@ def test_compose_and_decompose():
testfile = op.join(datadir, 'test_transform_test_compose.txt')
lines = readlines(testfile)
- ntests = len(lines) / 4
+ ntests = len(lines) // 4
for i in range(ntests):
xform = lines[i * 4: i * 4 + 4]
xform = np.genfromtxt(xform)
-
+
scales, offsets, rotations = transform.decompose(xform)
result = transform.compose(scales, offsets, rotations)
@@ -127,11 +142,11 @@ def test_compose_and_decompose():
def test_axisBounds():
testfile = op.join(datadir, 'test_transform_test_axisBounds.txt')
lines = readlines(testfile)
- ntests = len(lines) / 6
+ ntests = len(lines) // 6
def readTest(testnum):
tlines = lines[testnum * 6: testnum * 6 + 6]
- params = [p.strip() for p in tlines[0].split(',')]
+ params = [p.strip() for p in tlines[0].decode('ascii').split(',')]
shape = [int(s) for s in params[0].split()]
origin = params[1]
boundary = None if params[2] == 'None' else params[2]
@@ -140,7 +155,7 @@ def test_axisBounds():
expected = (expected[:3], expected[3:])
return shape, origin, boundary, xform, expected
-
+
allAxes = list(it.chain(
range(0, 1, 2),
it.permutations((0, 1, 2), 1),
@@ -151,11 +166,6 @@ def test_axisBounds():
shape, origin, boundary, xform, expected = readTest(i)
- print('Test {}'.format(i))
- print(' shape {}'.format(shape))
- print(' origin {}'.format(origin))
- print(' boundary {}'.format(boundary))
-
for axes in allAxes:
result = transform.axisBounds(shape,
xform,
@@ -168,7 +178,7 @@ def test_axisBounds():
assert np.all(np.isclose(exp, result))
- # Do some parameter checks on
+ # Do some parameter checks on
# the first test in the file
# which has origin == centre
for i in range(ntests):
@@ -186,7 +196,7 @@ def test_axisBounds():
with pytest.raises(ValueError):
transform.axisBounds(shape, xform, origin='Blag', boundary=boundary)
with pytest.raises(ValueError):
- transform.axisBounds(shape, xform, origin=origin, boundary='Blufu')
+ transform.axisBounds(shape, xform, origin=origin, boundary='Blufu')
def test_transform():
@@ -214,19 +224,19 @@ def test_transform():
it.permutations((0, 1, 2), 1),
it.permutations((0, 1, 2), 2),
it.permutations((0, 1, 2), 3)))
-
+
for i, testfile in enumerate(testfiles):
-
+
lines = readlines(testfile)
xform = np.genfromtxt(lines[:4])
expected = np.genfromtxt(lines[ 4:])
result = transform.transform(testcoords, xform)
-
+
assert np.all(np.isclose(expected, result))
if not is_orthogonal(xform):
continue
-
+
for axes in allAxes:
atestcoords = testcoords[:, axes]
aexpected = expected[ :, axes]
@@ -241,26 +251,26 @@ def test_transform():
coords = badcoords[:, :3]
with pytest.raises(IndexError):
- transform.transform(coords, badxform)
+ transform.transform(coords, badxform)
with pytest.raises(ValueError):
transform.transform(badcoords, xform)
-
+
with pytest.raises(ValueError):
transform.transform(badcoords.reshape(5, 2, 4), xform)
with pytest.raises(ValueError):
- transform.transform(badcoords.reshape(5, 2, 4), xform, axes=1)
+ transform.transform(badcoords.reshape(5, 2, 4), xform, axes=1)
with pytest.raises(ValueError):
transform.transform(badcoords[:, (1, 2, 3)], xform, axes=[1, 2])
def test_flirtMatrixToSform():
-
+
testfile = op.join(datadir, 'test_transform_test_flirtMatrixToSform.txt')
lines = readlines(testfile)
- ntests = len(lines) / 18
+ ntests = len(lines) // 18
for i in range(ntests):
tlines = lines[i * 18: i * 18 + 18]
@@ -282,7 +292,7 @@ def test_flirtMatrixToSform():
def test_sformToFlirtMatrix():
testfile = op.join(datadir, 'test_transform_test_flirtMatrixToSform.txt')
lines = readlines(testfile)
- ntests = len(lines) / 18
+ ntests = len(lines) // 18
for i in range(ntests):
tlines = lines[i * 18: i * 18 + 18]
diff --git a/tests/test_vest.py b/tests/test_vest.py
index bdd60133ba2fee797bf32bffce3f912a4db9e528..84638a3ce0227fb00b9dbec438cc112cee05e47e 100644
--- a/tests/test_vest.py
+++ b/tests/test_vest.py
@@ -19,11 +19,11 @@ import fsl.data.vest as vest
testfile1 = """%!VEST-LUT
%%BeginInstance
<<
-/SavedInstanceClassName /ClassLUT
-/PseudoColorMinimum 0.00
-/PseudoColorMaximum 1.00
-/PseudoColorMinControl /Low
-/PseudoColorMaxControl /High
+/SavedInstanceClassName /ClassLUT
+/PseudoColorMinimum 0.00
+/PseudoColorMaximum 1.00
+/PseudoColorMinControl /Low
+/PseudoColorMaxControl /High
/PseudoColormap [
<-color{0.00,0.00,0.00}->
<-color{0.01,0.01,0.01}->
@@ -47,11 +47,11 @@ testfile1Colours = np.array([
testfile2 = """%!VEST-LUT
%%BeginInstance
<<
-/SavedInstanceClassName /ClassLUT
-/PseudoColorMinimum 0.00
-/PseudoColorMaximum 1.00
-/PseudoColorMinControl /Low
-/PseudoColorMaxControl /High
+/SavedInstanceClassName /ClassLUT
+/PseudoColorMinimum 0.00
+/PseudoColorMaximum 1.00
+/PseudoColorMinControl /Low
+/PseudoColorMaxControl /High
/PseudoColormap [
<-color{0.0,0.0,0.0}->
]
@@ -78,16 +78,16 @@ testfile3 = """%!VEST-LUT
testfile3Colours = np.array([
[0.0, 0.0, 0.0],
[0.5, 0.2, 0.6]])
-
+
testfile4 = """%!VEST-LUT
%%BeginInstance
<<
-/SavedInstanceClassName /ClassLUT
-/PseudoColorMinimum 0.00
-/PseudoColorMaximum 1.00
-/PseudoColorMinControl /Low
-/PseudoColorMaxControl /High
+/SavedInstanceClassName /ClassLUT
+/PseudoColorMinimum 0.00
+/PseudoColorMaximum 1.00
+/PseudoColorMinControl /Low
+/PseudoColorMaxControl /High
/PseudoColormap [
<-color{0.0,1.0,5.0}->
<-color{1.0,2.0,4.0}->
@@ -119,7 +119,7 @@ def _createFiles(testdir):
for name, text in zip(names, texts):
filename = op.join(testdir, '{}.txt'.format(name))
with open(filename, 'wt') as f:
- f.write(text)
+ f.write(text)
@@ -142,7 +142,7 @@ def test_looksLikeVestLutFile():
def test_loadVestLutFile():
-
+
testdir = tempfile.mkdtemp()
testfiles = [
op.join(testdir, 'testfile1.txt'),