def test_save3():
# A test to ensure that when a file is saved, the affine
# and the data agree. In this case, things don't agree:
# i) the pixdim is off
# ii) makes the affine off
step = np.array([3.45,2.3,4.5,6.9])
shape = (13,5,7,3)
mni_xyz = mni_csm(3).coord_names
cmap = AT(CS('jkli'),
CS(('t',) + mni_xyz[::-1]),
from_matvec(np.diag([0,3,5,1]), step))
data = np.random.standard_normal(shape)
img = api.Image(data, cmap)
# with InTemporaryDirectory():
with InTemporaryDirectory():
save_image(img, TMP_FNAME)
tmp = load_image(TMP_FNAME)
# Detach image from file so we can delete it
data = tmp.get_data().copy()
img2 = api.Image(data, tmp.coordmap, tmp.metadata)
del tmp
assert_equal(tuple([img.shape[l] for l in [3,2,1,0]]), img2.shape)
a = np.transpose(np.asarray(img), [3,2,1,0])
assert_false(np.allclose(img.affine, img2.affine))
assert_true(np.allclose(a, img2.get_data()))
def test_save4():
# Same as test_save3 except we have reordered the 'ijk' input axes.
shape = (13,5,7,3)
step = np.array([3.45,2.3,4.5,6.9])
# When the input coords are in the 'ljki' order, the affines get
# rearranged. Note that the 'start' below, must be 0 for
# non-spatial dimensions, because we have no way to store them in
# most cases. For example, a 'start' of [1,5,3,1] would be lost on
# reload
mni_xyz = mni_csm(3).coord_names
cmap = AT(CS('tkji'),
CS((('t',) + mni_xyz[::-1])),
from_matvec(np.diag([2., 3, 5, 1]), step))
data = np.random.standard_normal(shape)
img = api.Image(data, cmap)
with InTemporaryDirectory():
save_image(img, TMP_FNAME)
tmp = load_image(TMP_FNAME)
data = tmp.get_data().copy()
# Detach image from file so we can delete it
img2 = api.Image(data, tmp.coordmap, tmp.metadata)
del tmp
P = np.array([[0,0,0,1,0],
[0,0,1,0,0],
[0,1,0,0,0],
[1,0,0,0,0],
[0,0,0,0,1]])
res = np.dot(P, np.dot(img.affine, P.T))
# the step part of the affine should be set correctly
assert_array_almost_equal(res[:4,:4], img2.affine[:4,:4])
# start in the spatial dimensions should be set correctly
assert_array_almost_equal(res[:3,-1], img2.affine[:3,-1])
# start in the time dimension should be 3.45 as in img, because NIFTI stores
# the time offset in hdr[``toffset``]
assert_not_equal(res[3,-1], img2.affine[3,-1])
assert_equal(res[3,-1], 3.45)
# shapes should be reversed because img has coordinates reversed
assert_equal(img.shape[::-1], img2.shape)
# data should be transposed because coordinates are reversed
assert_array_almost_equal(
np.transpose(np.asarray(img2),[3,2,1,0]),
np.asarray(img))
# coordinate names should be reversed as well
assert_equal(img2.coordmap.function_domain.coord_names,
img.coordmap.function_domain.coord_names[::-1])
assert_equal(img2.coordmap.function_domain.coord_names,
('i', 'j', 'k', 't'))
def test_save4():
# Same as test_save3 except we have reordered the 'ijk' input axes.
shape = (13, 5, 7, 3)
step = np.array([3.45, 2.3, 4.5, 6.9])
# When the input coords are in the 'ljki' order, the affines get
# rearranged. Note that the 'start' below, must be 0 for
# non-spatial dimensions, because we have no way to store them in
# most cases. For example, a 'start' of [1,5,3,1] would be lost on
# reload
mni_xyz = mni_csm(3).coord_names
cmap = AT(CS('tkji'), CS((('t', ) + mni_xyz[::-1])),
from_matvec(np.diag([2., 3, 5, 1]), step))
data = np.random.standard_normal(shape)
img = api.Image(data, cmap)
with InTemporaryDirectory():
save_image(img, TMP_FNAME)
tmp = load_image(TMP_FNAME)
data = tmp.get_data().copy()
# Detach image from file so we can delete it
img2 = api.Image(data, tmp.coordmap, tmp.metadata)
del tmp
P = np.array([[0, 0, 0, 1, 0], [0, 0, 1, 0, 0], [0, 1, 0, 0, 0],
[1, 0, 0, 0, 0], [0, 0, 0, 0, 1]])
res = np.dot(P, np.dot(img.affine, P.T))
# the step part of the affine should be set correctly
assert_array_almost_equal(res[:4, :4], img2.affine[:4, :4])
# start in the spatial dimensions should be set correctly
assert_array_almost_equal(res[:3, -1], img2.affine[:3, -1])
# start in the time dimension should be 3.45 as in img, because NIFTI stores
# the time offset in hdr[``toffset``]
assert_not_equal(res[3, -1], img2.affine[3, -1])
assert_equal(res[3, -1], 3.45)
# shapes should be reversed because img has coordinates reversed
assert_equal(img.shape[::-1], img2.shape)
# data should be transposed because coordinates are reversed
assert_array_almost_equal(np.transpose(img2.get_data(), [3, 2, 1, 0]),
img.get_data())
# coordinate names should be reversed as well
assert_equal(img2.coordmap.function_domain.coord_names,
img.coordmap.function_domain.coord_names[::-1])
assert_equal(img2.coordmap.function_domain.coord_names,
('i', 'j', 'k', 't'))
def test_save3():
# A test to ensure that when a file is saved, the affine
# and the data agree. In this case, things don't agree:
# i) the pixdim is off
# ii) makes the affine off
step = np.array([3.45, 2.3, 4.5, 6.9])
shape = (13, 5, 7, 3)
mni_xyz = mni_csm(3).coord_names
cmap = AT(CS('jkli'), CS(('t', ) + mni_xyz[::-1]),
from_matvec(np.diag([0, 3, 5, 1]), step))
data = np.random.standard_normal(shape)
img = api.Image(data, cmap)
# with InTemporaryDirectory():
with InTemporaryDirectory():
save_image(img, TMP_FNAME)
tmp = load_image(TMP_FNAME)
# Detach image from file so we can delete it
data = tmp.get_data().copy()
img2 = api.Image(data, tmp.coordmap, tmp.metadata)
del tmp
assert_equal(tuple([img.shape[l] for l in [3, 2, 1, 0]]), img2.shape)
a = np.transpose(img.get_data(), [3, 2, 1, 0])
assert_false(np.allclose(img.affine, img2.affine))
assert_true(np.allclose(a, img2.get_data()))
