diff --git a/tests/test_image.py b/tests/test_image.py
index 00a2cc749fa056288de6164648f8b82763205e35..841e1620ffde74b403131758e271de393ad94177 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -10,8 +10,6 @@
import os
import os.path as op
import itertools as it
-import tempfile
-import shutil
import pytest
@@ -27,10 +25,10 @@ import fsl.data.imagewrapper as imagewrapper
import fsl.utils.path as fslpath
import fsl.utils.transform as transform
+from fsl.utils.tempdir import tempdir
+
from . import make_random_image
from . import make_dummy_file
-from . import testdir
-from . import tempdir
def make_image(filename=None,
@@ -121,17 +119,17 @@ def test_load():
('notnifti', ImageFileError),
('notnifti.nii.gz', ImageFileError)]
- testdir = tempfile.mkdtemp()
- for f in toCreate:
+ with tempdir() as testdir:
- if f.startswith('notnifti'):
- make_dummy_file(op.join(testdir, f))
- else:
- make_random_image(op.join(testdir, f))
+ 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:
+ # Not raising an error means the test passes
for fname in shouldPass:
fslimage.Image(op.join(testdir, fname))
@@ -139,8 +137,6 @@ def test_load():
for fname, exc in shouldRaise:
with pytest.raises(exc):
fslimage.Image(op.join(testdir, fname))
- finally:
- shutil.rmtree(testdir)
def test_create():
@@ -180,8 +176,7 @@ def test_create():
assert np.all(np.isclose(img.pixdim, (2, 3, 4)))
for imgtype in [0, 1, 2]:
- testdir = tempfile.mkdtemp()
- try:
+ with tempdir() as testdir:
fname = op.join(testdir, 'myimage')
nimg = make_image(fname, imgtype, pixdims=(2, 3, 4))
@@ -193,9 +188,6 @@ def test_create():
assert img.niftiVersion == imgtype
assert np.all(np.isclose(img.pixdim, (2, 3, 4)))
- finally:
- shutil.rmtree(testdir)
-
def test_bad_create():
@@ -236,7 +228,6 @@ 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
@@ -268,17 +259,17 @@ def _test_Image_atts(imgtype):
tests = list(tests)
paths = ['test{:03d}'.format(i) for i in range(len(tests))]
- for path, atts in zip(paths, tests):
+ with tempdir() as testdir:
- dims, pixdims, dtype = atts
+ for path, atts in zip(paths, tests):
- ndims = len(dims)
- pixdims = pixdims[:ndims]
+ dims, pixdims, dtype = atts
- path = op.abspath(op.join(testdir, path))
- make_image(path, imgtype, dims, pixdims, dtype)
+ ndims = len(dims)
+ pixdims = pixdims[:ndims]
- try:
+ path = op.abspath(op.join(testdir, path))
+ make_image(path, imgtype, dims, pixdims, dtype)
for path, atts in zip(paths, tests):
@@ -305,8 +296,7 @@ def _test_Image_atts(imgtype):
allowedExts=allowedExts,
mustExist=True,
fileGroups=fileGroups)
- finally:
- shutil.rmtree(testdir)
+
def test_Image_atts2_analyze(): _test_Image_atts2(0)
def test_Image_atts2_nifti1(): _test_Image_atts2(1)
@@ -390,7 +380,6 @@ def test_addExt():
"""Test the addExt function. """
default = fslimage.defaultExt()
- testdir = tempfile.mkdtemp()
toCreate = [
'compressed.nii.gz',
@@ -429,11 +418,13 @@ def test_addExt():
('ambiguous.img.gz', True, 'ambiguous.img.gz'),
('ambiguous.hdr.gz', True, 'ambiguous.hdr.gz')]
- for path in toCreate:
- path = op.abspath(op.join(testdir, path))
- make_random_image(path)
- try:
+ with tempdir() as testdir:
+
+ for path in toCreate:
+ path = op.abspath(op.join(testdir, path))
+ make_random_image(path)
+
for path, mustExist, expected in tests:
path = op.abspath(op.join(testdir, path))
@@ -445,8 +436,6 @@ def test_addExt():
with pytest.raises(fslimage.PathError):
path = op.join(testdir, 'ambiguous')
fslimage.addExt(path, mustExist=True)
- finally:
- shutil.rmtree(testdir)
def test_removeExt():
@@ -506,45 +495,43 @@ 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. """
- testdir = tempfile.mkdtemp()
- imagefile = op.join(testdir, 'image')
-
- # an image with RAS voxel storage order
- # (affine has a positive determinant)
- # is said to be "neurological", whereas
- # an image with LAS voxel storage order
- # (negative determinant - x axis must
- # be flipped to bring it into RAS nifti
- # world coordinates)) is said to be
- # "radiological". The make_image function
- # forms the affine from these pixdims.
- if voxorient == 'neuro': pixdims = ( 1, 1, 1)
- elif voxorient == 'radio': pixdims = (-1, 1, 1)
-
- make_image(imagefile, imgtype, (10, 10, 10), pixdims, np.float32)
-
- image = fslimage.Image(imagefile)
-
- # analyze images are always assumed to be
- # stored in radiological (LAS) orientation
- if imgtype == 0:
- expectNeuroTest = False
- expectvox0Orientation = constants.ORIENT_R2L
- expectvox1Orientation = constants.ORIENT_P2A
- expectvox2Orientation = constants.ORIENT_I2S
-
- elif voxorient == 'neuro':
- expectNeuroTest = True
- expectvox0Orientation = constants.ORIENT_L2R
- expectvox1Orientation = constants.ORIENT_P2A
- expectvox2Orientation = constants.ORIENT_I2S
- else:
- expectNeuroTest = False
- expectvox0Orientation = constants.ORIENT_R2L
- expectvox1Orientation = constants.ORIENT_P2A
- expectvox2Orientation = constants.ORIENT_I2S
-
- try:
+ with tempdir() as testdir:
+ imagefile = op.join(testdir, 'image')
+
+ # an image with RAS voxel storage order
+ # (affine has a positive determinant)
+ # is said to be "neurological", whereas
+ # an image with LAS voxel storage order
+ # (negative determinant - x axis must
+ # be flipped to bring it into RAS nifti
+ # world coordinates)) is said to be
+ # "radiological". The make_image function
+ # forms the affine from these pixdims.
+ if voxorient == 'neuro': pixdims = ( 1, 1, 1)
+ elif voxorient == 'radio': pixdims = (-1, 1, 1)
+
+ make_image(imagefile, imgtype, (10, 10, 10), pixdims, np.float32)
+
+ image = fslimage.Image(imagefile)
+
+ # analyze images are always assumed to be
+ # stored in radiological (LAS) orientation
+ if imgtype == 0:
+ expectNeuroTest = False
+ expectvox0Orientation = constants.ORIENT_R2L
+ expectvox1Orientation = constants.ORIENT_P2A
+ expectvox2Orientation = constants.ORIENT_I2S
+
+ elif voxorient == 'neuro':
+ expectNeuroTest = True
+ expectvox0Orientation = constants.ORIENT_L2R
+ expectvox1Orientation = constants.ORIENT_P2A
+ expectvox2Orientation = constants.ORIENT_I2S
+ else:
+ expectNeuroTest = False
+ expectvox0Orientation = constants.ORIENT_R2L
+ expectvox1Orientation = constants.ORIENT_P2A
+ expectvox2Orientation = constants.ORIENT_I2S
assert image.isNeurological() == expectNeuroTest
@@ -562,9 +549,6 @@ def _test_Image_orientation(imgtype, voxorient):
assert image.getOrientation(1, affine) == expectvox1Orientation
assert image.getOrientation(2, affine) == expectvox2Orientation
- finally:
- shutil.rmtree(testdir)
-
def test_Image_sqforms_nifti1_normal(): _test_Image_sqforms(1, 1, 1)
def test_Image_sqforms_nifti1_nosform(): _test_Image_sqforms(1, 0, 1)
@@ -579,55 +563,54 @@ def _test_Image_sqforms(imgtype, sformcode, qformcode):
attributes for NIFTI images with the given sform/qform code combination.
"""
- testdir = tempfile.mkdtemp()
+ with tempdir() as testdir:
- imagefile = op.abspath(op.join(testdir, 'image.nii.gz'))
+ imagefile = op.abspath(op.join(testdir, 'image.nii.gz'))
- # For an image with no s/q form, we expect the
- # fallback affine - a simple scaling matrix.
- # We add some offsets to the actual affine so
- # we can distinguish it from the fallback affine.
- scaleMat = np.diag([2, 2, 2, 1])
- invScaleMat = np.diag([0.5, 0.5, 0.5, 1])
- affine = np.array(scaleMat)
- affine[:3, 3] = [25, 20, 20]
- invAffine = npla.inv(affine)
+ # For an image with no s/q form, we expect the
+ # fallback affine - a simple scaling matrix.
+ # We add some offsets to the actual affine so
+ # we can distinguish it from the fallback affine.
+ scaleMat = np.diag([2, 2, 2, 1])
+ invScaleMat = np.diag([0.5, 0.5, 0.5, 1])
+ affine = np.array(scaleMat)
+ affine[:3, 3] = [25, 20, 20]
+ invAffine = npla.inv(affine)
- image = make_image(imagefile, imgtype, (10, 10, 10), (2, 2, 2), np.float32)
+ image = make_image(imagefile, imgtype, (10, 10, 10), (2, 2, 2), np.float32)
- image.set_sform(affine, sformcode)
- image.set_qform(affine, qformcode)
- image.update_header()
+ image.set_sform(affine, sformcode)
+ image.set_qform(affine, qformcode)
+ image.update_header()
- nib.save(image, imagefile)
+ nib.save(image, imagefile)
- # No s or qform - we expect the fallback affine
- if sformcode == 0 and qformcode == 0:
- expAffine = scaleMat
- invExpAffine = invScaleMat
- expCode = constants.NIFTI_XFORM_UNKNOWN
- expOrient = constants.ORIENT_UNKNOWN
+ # No s or qform - we expect the fallback affine
+ if sformcode == 0 and qformcode == 0:
+ expAffine = scaleMat
+ invExpAffine = invScaleMat
+ expCode = constants.NIFTI_XFORM_UNKNOWN
+ expOrient = constants.ORIENT_UNKNOWN
- # No sform, but valid qform - expect the affine
- elif sformcode == 0 and qformcode > 0:
- expAffine = affine
- invExpAffine = invAffine
- expCode = qformcode
- expOrient = constants.ORIENT_L2R
+ # No sform, but valid qform - expect the affine
+ elif sformcode == 0 and qformcode > 0:
+ expAffine = affine
+ invExpAffine = invAffine
+ expCode = qformcode
+ expOrient = constants.ORIENT_L2R
- # Valid sform (qform irrelevant) - expect the affine
- elif sformcode > 0:
- expAffine = affine
- invExpAffine = invAffine
- expCode = sformcode
- expOrient = constants.ORIENT_L2R
+ # Valid sform (qform irrelevant) - expect the affine
+ elif sformcode > 0:
+ expAffine = affine
+ invExpAffine = invAffine
+ expCode = sformcode
+ expOrient = constants.ORIENT_L2R
- image = fslimage.Image(imagefile)
+ image = fslimage.Image(imagefile)
- with pytest.raises(ValueError):
- image.getXFormCode('badcode')
+ with pytest.raises(ValueError):
+ image.getXFormCode('badcode')
- try:
assert np.all(np.isclose(image.voxToWorldMat, expAffine))
assert np.all(np.isclose(image.worldToVoxMat, invExpAffine))
@@ -636,8 +619,6 @@ def _test_Image_sqforms(imgtype, sformcode, qformcode):
assert image.getXFormCode('qform') == qformcode
assert image.getOrientation(0, image.voxToWorldMat) == expOrient
- finally:
- shutil.rmtree(testdir)
def test_Image_changeXform_analyze(): _test_Image_changeXform(0)
@@ -647,47 +628,45 @@ def test_Image_changeXform_nifti2(): _test_Image_changeXform(2)
def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
"""Test changing the Nifti.voxToWorldMat attribute. """
- testdir = tempfile.mkdtemp()
- imagefile = op.join(testdir, 'image')
+ with tempdir() as testdir:
+ imagefile = op.join(testdir, 'image')
- image = make_image(imagefile, imgtype)
+ image = make_image(imagefile, imgtype)
- if imgtype > 0:
-
- if sformcode is not None: image.set_sform(image.affine, sformcode)
- if qformcode is not None: image.set_qform(image.affine, qformcode)
- image.update_header()
- nib.save(image, imagefile)
+ if imgtype > 0:
- notified = {}
+ if sformcode is not None: image.set_sform(image.affine, sformcode)
+ if qformcode is not None: image.set_qform(image.affine, qformcode)
+ image.update_header()
+ nib.save(image, imagefile)
- def onXform(*a):
- notified['xform'] = True
+ notified = {}
- def onSave(*a):
- notified['save'] = True
+ def onXform(*a):
+ notified['xform'] = True
- img = fslimage.Image(imagefile)
+ def onSave(*a):
+ notified['save'] = True
- img.register('name1', onXform, 'transform')
- img.register('name2', onSave, 'saveState')
+ img = fslimage.Image(imagefile)
- newXform = np.array([[5, 0, 0, 10],
- [0, 2, 0, 23],
- [0, 0, 14, 5],
- [0, 0, 0, 1]])
+ img.register('name1', onXform, 'transform')
+ img.register('name2', onSave, 'saveState')
- if imgtype > 0:
- expSformCode = image.get_sform(coded=True)[1]
- expQformCode = image.get_qform(coded=True)[1]
+ newXform = np.array([[5, 0, 0, 10],
+ [0, 2, 0, 23],
+ [0, 0, 14, 5],
+ [0, 0, 0, 1]])
- if sformcode == 0:
- expSformCode = constants.NIFTI_XFORM_ALIGNED_ANAT
- else:
- expSformCode = constants.NIFTI_XFORM_ANALYZE
- expQformCode = constants.NIFTI_XFORM_ANALYZE
+ if imgtype > 0:
+ expSformCode = image.get_sform(coded=True)[1]
+ expQformCode = image.get_qform(coded=True)[1]
- try:
+ if sformcode == 0:
+ expSformCode = constants.NIFTI_XFORM_ALIGNED_ANAT
+ else:
+ expSformCode = constants.NIFTI_XFORM_ANALYZE
+ expQformCode = constants.NIFTI_XFORM_ANALYZE
# Image state should initially be saved
assert img.saveState
@@ -712,8 +691,6 @@ def _test_Image_changeXform(imgtype, sformcode=None, qformcode=None):
assert np.all(np.isclose(img.worldToVoxMat, invx))
assert img.getXFormCode('sform') == expSformCode
assert img.getXFormCode('qform') == expQformCode
- finally:
- shutil.rmtree(testdir)
def test_Image_changeData_analyze(seed): _test_Image_changeData(0)
@@ -724,48 +701,52 @@ def _test_Image_changeData(imgtype):
the dataRange attribute to be updated.
"""
- testdir = tempfile.mkdtemp()
- imagefile = op.join(testdir, 'image')
-
- make_image(imagefile, imgtype)
+ with tempdir() as testdir:
+ imagefile = op.join(testdir, 'image')
- img = fslimage.Image(imagefile)
+ make_image(imagefile, imgtype)
- notified = {}
+ img = fslimage.Image(imagefile)
- def randvox():
- return (np.random.randint(0, img.shape[0]),
- np.random.randint(0, img.shape[1]),
- np.random.randint(0, img.shape[2]))
+ notified = {}
- def onData(*a):
- notified['data'] = True
+ def randvox():
+ return (np.random.randint(0, img.shape[0]),
+ np.random.randint(0, img.shape[1]),
+ np.random.randint(0, img.shape[2]))
- def onSaveState(*a):
- notified['save'] = True
+ def onData(*a):
+ notified['data'] = True
- def onDataRange(*a):
- notified['dataRange'] = True
+ def onSaveState(*a):
+ notified['save'] = True
- img.register('name1', onData, 'data')
- img.register('name2', onSaveState, 'saveState')
- img.register('name3', onDataRange, 'dataRange')
+ def onDataRange(*a):
+ notified['dataRange'] = True
- # Calculate the actual data range
- data = img.nibImage.get_data()
- dmin = data.min()
- dmax = data.max()
- drange = dmax - dmin
+ img.register('name1', onData, 'data')
+ img.register('name2', onSaveState, 'saveState')
+ img.register('name3', onDataRange, 'dataRange')
- try:
+ # Calculate the actual data range
+ data = img.nibImage.get_data()
+ dmin = data.min()
+ dmax = data.max()
+ drange = dmax - dmin
assert img.saveState
assert np.all(np.isclose(img.dataRange, (dmin, dmax)))
- # random value within the existing data range
- randval = dmin + np.random.random() * drange
- rx, ry, rz = randvox()
- img[rx, ry, rz] = randval
+ # random value within the existing data range,
+ # making sure not to overwite the min or max
+ randval = dmin + np.random.random() * drange
+
+ while True:
+ rx, ry, rz = randvox()
+ if not (np.isclose(img[rx, ry, rz], dmin) or
+ np.isclose(img[rx, ry, rz], dmax)):
+ img[rx, ry, rz] = randval
+ break
assert np.isclose(img[rx, ry, rz], randval)
assert notified.get('data', False)
@@ -808,17 +789,12 @@ def _test_Image_changeData(imgtype):
assert np.isclose(img[maxx, maxy, maxz], newdmax)
assert np.all(np.isclose(img.dataRange, (newdmin, newdmax)))
- finally:
- shutil.rmtree(testdir)
-
def test_Image_2D_analyze(): _test_Image_2D(0)
def test_Image_2D_nifti1(): _test_Image_2D(1)
def test_Image_2D_nifti2(): _test_Image_2D(2)
def _test_Image_2D(imgtype):
- testdir = tempfile.mkdtemp()
-
# The first shape tests when the
# nifti dim0 field is set to 2,
# which happens when you create
@@ -833,7 +809,7 @@ def _test_Image_2D(imgtype):
(10, 1, 20, 5),
(1, 10, 20, 5)]
- try:
+ with tempdir() as testdir:
for shape in testdims:
@@ -858,9 +834,6 @@ def _test_Image_2D(imgtype):
assert tuple(map(float, shape)) == tuple(map(float, image[:].shape))
assert tuple(map(float, pixdim)) == tuple(map(float, image .pixdim))
- finally:
- shutil.rmtree(testdir)
-
def test_Image_5D_analyze(): _test_Image_5D(0)
def test_Image_5D_nifti1(): _test_Image_5D(1)
@@ -878,7 +851,7 @@ def _test_Image_5D(imgtype):
for dims in testdims:
- with testdir() as td:
+ with tempdir() as td:
path = op.join(td, 'test.nii')
@@ -970,21 +943,20 @@ def _test_Image_save(imgtype):
return rvoxes
- testdir = tempfile.mkdtemp()
- if imgtype == 0:
- filename = op.join(testdir, 'blob.img')
- filename2 = op.join(testdir, 'blob_copy.img')
- else:
- filename = op.join(testdir, 'blob.nii')
- filename2 = op.join(testdir, 'blob_copy.nii')
+ with tempdir() as testdir:
+ if imgtype == 0:
+ filename = op.join(testdir, 'blob.img')
+ filename2 = op.join(testdir, 'blob_copy.img')
+ else:
+ filename = op.join(testdir, 'blob.nii')
+ filename2 = op.join(testdir, 'blob_copy.nii')
- xform = np.eye(4)
- xform[:3, 3] = [-10, 20, 30]
- xform[ 0, 0] = 33
- xform[ 1, 1] = 55
- xform[ 2, 2] = 38
+ xform = np.eye(4)
+ xform[:3, 3] = [-10, 20, 30]
+ xform[ 0, 0] = 33
+ xform[ 1, 1] = 55
+ xform[ 2, 2] = 38
- try:
make_image(filename, imgtype)
# Using mmap can cause a "Bus error"
@@ -1033,13 +1005,9 @@ def _test_Image_save(imgtype):
assert np.isclose(img[x, y, z], v)
- finally:
- shutil.rmtree(testdir)
-
-
def test_image_resample(seed):
- with testdir() as td:
+ with tempdir() as td:
fname = op.join(td, 'test.nii')