def test_applyDeformation_premat():
src2ref = affine.compose(
np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3),
[0, 0, 0])
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
refdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(refdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world')
# First try a down-sampled version
# of the original source image
altsrc, xf = resample.resample(src, (5, 5, 5), origin='corner')
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# Now try a down-sampled ROI
# of the original source image
altsrc = roi.roi(src, [(2, 9), (2, 9), (2, 9)])
altsrc, xf = resample.resample(altsrc, (4, 4, 4))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# down-sampled and offset ROI
# of the original source image
altsrc = roi.roi(src, [(-5, 8), (-5, 8), (-5, 8)])
altsrc, xf = resample.resample(altsrc, (6, 6, 6))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
def test_linear_altsrc(seed):
with tempdir.tempdir():
src2ref = _random_affine()
src = _random_image(np.eye(4), (20, 20, 20))
ref = _random_image(src2ref)
x5.writeLinearX5('xform.x5', src2ref, src, ref)
src.save('src')
ref.save('ref')
srclo, xf = resample.resample(src, (10, 10, 10))
srclo = fslimage.Image(srclo, xform=xf)
srchi, xf = resample.resample(src, (40, 40, 40))
srchi = fslimage.Image(srchi, xform=xf)
srcoff = roi.roi(src, [(-10, 10), (-10, 10), (-10, 10)])
srclo.save('srclo')
srchi.save('srchi')
srcoff.save('srcoff')
fsl_apply_x5.main('src xform.x5 out'.split())
fsl_apply_x5.main('srclo xform.x5 outlo'.split())
fsl_apply_x5.main('srchi xform.x5 outhi'.split())
fsl_apply_x5.main('srcoff xform.x5 outoff'.split())
out = fslimage.Image('out')
outlo = fslimage.Image('outlo')
outhi = fslimage.Image('outhi')
outoff = fslimage.Image('outoff')
exp = resample.resampleToReference(src, ref, matrix=src2ref)[0]
explo = resample.resampleToReference(srclo, ref, matrix=src2ref)[0]
exphi = resample.resampleToReference(srchi, ref, matrix=src2ref)[0]
expoff = resample.resampleToReference(srcoff, ref, matrix=src2ref)[0]
assert out.sameSpace(ref)
assert outlo.sameSpace(ref)
assert outhi.sameSpace(ref)
assert outoff.sameSpace(ref)
assert np.all(np.isclose(out.data, exp))
assert np.all(np.isclose(outlo.data, explo))
assert np.all(np.isclose(outhi.data, exphi))
assert np.all(np.isclose(outoff.data, expoff))
def test_roi():
# inshape, bounds, expected outshape, expected affine offset
tests = [
# 3D image, 3D roi
([10, 10, 10], [(0, 10), (0, 10), (0, 10)], [10, 10, 10], [0, 0, 0]),
([10, 10, 10], [(1, 10), (1, 10), (1, 10)], [9, 9, 9], [1, 1, 1]),
([10, 10, 10], [(1, 9), (1, 9), (1, 9)], [8, 8, 8], [1, 1, 1]),
([10, 10, 10], [(3, 5), (3, 5), (3, 5)], [2, 2, 2], [3, 3, 3]),
([10, 10, 10], [(4, 5), (4, 5), (4, 5)], [1, 1, 1], [4, 4, 4]),
# 4D image, 3D roi
([10, 10, 10, 10], [(0, 10), (0, 10), (0, 10)], [10, 10, 10,
10], [0, 0, 0]),
([10, 10, 10, 10], [(1, 10), (1, 10), (1, 10)], [9, 9, 9,
10], [1, 1, 1]),
([10, 10, 10, 10], [(1, 9), (1, 9), (1, 9)], [8, 8, 8, 10], [1, 1, 1]),
([10, 10, 10, 10], [(3, 5), (3, 5), (3, 5)], [2, 2, 2, 10], [3, 3, 3]),
([10, 10, 10, 10], [(4, 5), (4, 5), (4, 5)], [1, 1, 1, 10], [4, 4, 4]),
# 4D image, 4D roi
([10, 10, 10, 10], [(0, 10), (0, 10), (0, 10),
(0, 10)], [10, 10, 10, 10], [0, 0, 0]),
([10, 10, 10, 10], [(1, 10), (1, 10), (1, 10),
(1, 10)], [9, 9, 9, 9], [1, 1, 1]),
([10, 10, 10, 10], [(1, 9), (1, 9), (1, 9), (1, 9)], [8, 8, 8,
8], [1, 1, 1]),
([10, 10, 10, 10], [(3, 5), (3, 5), (3, 5), (3, 5)], [2, 2, 2,
2], [3, 3, 3]),
([10, 10, 10, 10], [(4, 5), (4, 5), (4, 5), (4, 5)], [1, 1,
1], [4, 4, 4]),
# expanding FOV
([10, 10, 10], [(-5, 15), (0, 10), (0, 10)], [20, 10, 10], [-5, 0, 0]),
([10, 10, 10], [(-5, 15), (-5, 15), (0, 10)], [20, 20,
10], [-5, -5, 0]),
([10, 10, 10], [(-5, 15), (-5, 10), (-5, 15)], [20, 15,
20], [-5, -5, -5]),
([10, 10, 10], [(-5, 15), (3, 7), (0, 10)], [20, 4, 10], [-5, 3, 0]),
]
for inshape, bounds, outshape, offset in tests:
data = np.random.randint(1, 10, inshape)
image = fslimage.Image(data, xform=np.eye(4))
result = roi.roi(image, bounds)
expaff = np.eye(4)
expaff[:3, 3] = offset
assert np.all(list(result.shape) == list(outshape))
assert np.all(np.isclose(result.voxToWorldMat, expaff))
oldslc = []
newslc = []
for (lo, hi), oldlen in zip(bounds, inshape):
oldslc.append(slice(max(lo, 0), min(hi, oldlen)))
if len(oldslc) < len(inshape):
for d in inshape[len(oldslc):]:
oldslc.append(slice(0, d))
for (lo, hi), slc in zip(bounds, oldslc):
if lo < 0: newlo = -lo
else: newlo = 0
oldlen = slc.stop - slc.start
newslc.append(slice(newlo, newlo + oldlen))
if len(newslc) > len(outshape):
newslc = newslc[:len(outshape)]
assert np.all(data[tuple(oldslc)] == result.data[tuple(newslc)])
# Error on:
# - not enough bounds
# - too many bounds
# - hi >= lo
data = np.random.randint(1, 10, (10, 10, 10))
image = fslimage.Image(data, xform=np.eye(4))
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (0, 10), (0, 10), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(5, 5), (0, 10), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(6, 5), (0, 10), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (5, 5), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (6, 5), (0, 10)])
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (0, 10), (5, 5)])
with pytest.raises(ValueError):
roi.roi(image, [(0, 10), (0, 10), (6, 5)])
def test_nonlinear_altsrc(seed):
with tempdir.tempdir():
src2ref = _random_affine()
ref2src = affine.invert(src2ref)
src = _random_image(np.eye(4), (20, 20, 20))
ref = _random_image(src2ref, (20, 20, 20))
field = _affine_field(src, ref, ref2src, 'world', 'world')
x5.writeNonLinearX5('xform.x5', field)
src.save('src')
ref.save('ref')
# use origin=corner so that the
# resampled variants are exactly
# aligned in the world coordinate
# system
srclo, xf = resample.resample(src, (10, 10, 10),
origin='corner',
smooth=False)
srclo = fslimage.Image(srclo, xform=xf)
srchi, xf = resample.resample(src, (40, 40, 40),
origin='corner',
smooth=False)
srchi = fslimage.Image(srchi, xform=xf)
srcoff = roi.roi(src, [(-10, 10), (-10, 10), (-10, 10)])
srclo.save('srclo')
srchi.save('srchi')
srcoff.save('srcoff')
fsl_apply_x5.main('src xform.x5 out'.split())
fsl_apply_x5.main('srclo xform.x5 outlo'.split())
fsl_apply_x5.main('srchi xform.x5 outhi'.split())
fsl_apply_x5.main('srcoff xform.x5 outoff'.split())
out = fslimage.Image('out')
outlo = fslimage.Image('outlo')
outhi = fslimage.Image('outhi')
outoff = fslimage.Image('outoff')
exp, x1 = resample.resampleToReference(src,
ref,
matrix=src2ref,
mode='constant',
smooth=False)
explo, x2 = resample.resampleToReference(srclo,
ref,
matrix=src2ref,
mode='constant',
smooth=False)
exphi, x3 = resample.resampleToReference(srchi,
ref,
matrix=src2ref,
mode='constant',
smooth=False)
expoff, x4 = resample.resampleToReference(srcoff,
ref,
matrix=src2ref,
mode='constant',
smooth=False)
assert out.sameSpace(ref)
assert outlo.sameSpace(ref)
assert outhi.sameSpace(ref)
assert outoff.sameSpace(ref)
# We get boundary cropping,
# so ignore edge slices
out = out.data[1:-1, 1:-1, 1:-1]
outlo = outlo.data[1:-1, 1:-1, 1:-1]
outhi = outhi.data[1:-1, 1:-1, 1:-1]
outoff = outoff.data[:9, :9, :9]
exp = exp[1:-1, 1:-1, 1:-1]
explo = explo[1:-1, 1:-1, 1:-1]
exphi = exphi[1:-1, 1:-1, 1:-1]
expoff = expoff[:9, :9, :9]
tol = dict(atol=1e-3, rtol=1e-3)
assert np.all(np.isclose(out, exp, **tol))
assert np.all(np.isclose(outlo, explo, **tol))
assert np.all(np.isclose(outhi, exphi, **tol))
assert np.all(np.isclose(outoff, expoff, **tol))
def copyImage(overlayList,
displayCtx,
overlay,
createMask=False,
copy4D=True,
copyDisplay=True,
name=None,
roi=None,
channel=None,
data=None):
"""Creates a copy of the given :class:`.Image` overlay, and inserts it
into the :class:`.OverlayList`.
:arg overlayList: The :class:`.OverlayList`.
:arg displayCtx: The :class:`.DisplayContext`.
:arg overlay: The :class:`.Image` to be copied.
:arg createMask: If ``True``, the copy will be an empty ``Image`` the
same shape as the ``overlay``.
:arg copy4D: If ``True``, and the ``overlay`` is 4D, the copy will
also be 4D. Otherwise, the current 3D voluem is copied.
:arg copyDisplay: If ``True``, the copy will inherit the display settings
of the ``overlay``. Otherwise, the copy will be
initialised with default display settings.
:arg name: If provided, will be used as the :attr:`.Display.name`
of the copy. Otherwise the copy will be given a name.
:arg roi: If provided, the copy will be cropped to the low/high
voxel bounds specified in the image. Must be a sequence
of tuples, containing the low/high bounds for each voxel
dimension. For 4D images, the bounds for the fourth
dimension are optional. If ``roi`` specifies more than
three dimensions, but ``copy4D is False``, the additional
dimensions are ignored.
:arg channel: If provided, and if the image is complex or multi-valued
(RGB(A)), only this channel is copied. Otherwise the
image and data type are copied as-is. For complex images,
valid values are ``'real'`` or ``'imag'``; for multi-
valued images, valid values are ``'R'``, ``'G'``, ``'B'``
or ``'A'``.
:arg data: If provided, is used as the image data for the new copy.
Must match the shape dictated by the other arguments
(i.e. ``copy4D`` and ``roi``). If ``data`` is provided,
the ``createMask`` argument is ignored.
:returns: The newly created :class:`.Image` object.
Note that the ``roi`` and ``copy4D`` options do not support images with
more than four dimensions.
"""
ovlIdx = overlayList.index(overlay)
opts = displayCtx.getOpts(overlay)
is4D = len(overlay.shape) > 3
isROI = roi is not None
copy4D = copy4D and is4D
createMask = createMask and (data is None)
# Initialise the roi indices if one wasn't
# provided - we will use the indices
# regardless of whether an ROI was passed
# in or not
if roi is None:
roi = [(0, s) for s in overlay.shape]
# Adjust the roi to index a
# specific volume if requested
if not copy4D:
roi = list(roi[:3]) + [(i, i + 1) for i in opts.index()[3:]]
if name is None:
name = '{}_copy'.format(overlay.name)
# If an ROI is not specified, we slice
# the image data, either including all
# volumes, or the currently selected volume
if not isROI:
slc = tuple(slice(lo, hi) for lo, hi in roi)
imgdata = overlay[slc]
xform = overlay.voxToWorldMat
# if an ROI is specified, we use the
# fsl.utils.image.roi module to generate
# an ROI and the adjusted voxel-to-world
# affine
else:
roi = imgroi.roi(overlay, roi)
imgdata = roi.data
xform = roi.voxToWorldMat
if channel is not None:
if overlay.iscomplex:
if channel == 'real': imgdata = imgdata.real
elif channel == 'imag': imgdata = imgdata.imag
else:
raise ValueError('Invalid value for channel: '
'{}'.format(channel))
elif overlay.nvals > 1:
if channel not in 'RGBA':
raise ValueError('Invalid value for channel: '
'{}'.format(channel))
imgdata = imgdata[channel]
if createMask:
data = np.zeros(imgdata.shape, dtype=imgdata.dtype)
elif data is None:
data = np.copy(imgdata)
copy = fslimage.Image(data, xform=xform, header=overlay.header, name=name)
overlayList.insert(ovlIdx + 1, copy)
# Copy the Display/DisplayOpts settings
if copyDisplay:
# Don't override the name
# that we set above
dispexcl = ('name', )
# And don't clobber the transform, and related,
# properties, as it is (typically) automatically
# controlled via the DisplayContext.displaySpace
optexcl = ('transform', 'bounds')
copyDisplayProperties(displayCtx,
overlay,
copy,
displayExclude=dispexcl,
optExclude=optexcl)
return copy