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Commit 7a9afbce authored by Paul McCarthy's avatar Paul McCarthy
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Python 2/3 (and other minor) test updates

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tests/__init__.py
+ 11
− 12
View file @ 7a9afbce
......@@ -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)
......
tests/test_async.py
+ 14
− 14
View file @ 7a9afbce
......@@ -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)
......
tests/test_featdesign.py
+ 11
− 15
View file @ 7a9afbce
......@@ -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)
tests/test_image_advanced.py
+ 21
− 21
View file @ 7a9afbce
......@@ -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)
......
tests/test_immv_imcp.py
+ 53
− 47
View file @ 7a9afbce
......@@ -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)
......
tests/test_melodicimage.py
+ 10
− 9
View file @ 7a9afbce
......@@ -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)
......
tests/test_transform.py
+ 43
− 33
View file @ 7a9afbce
......@@ -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]
......
tests/test_vest.py
+ 18
− 18
View file @ 7a9afbce
......@@ -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'),
......
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