def test_ijkml_to_utzyx():
# This should raise a warning about the last 2 axes not being in
# order, and one about the loss of information from a non-diagonal
# matrix, and also one about the nifti output coordinates.
input_coords = CoordinateSystem('ijkml', 'input')
output_coords = CoordinateSystem('utzyx', 'output')
cmap = Affine(np.identity(6), input_coords, output_coords)
newcmap, order = niref.coerce_coordmap(cmap)
yield assert_equal, newcmap.input_coords.name, 'input-reordered'
yield assert_equal, newcmap.output_coords.name, 'output-reordered'
yield assert_equal, order, (0,1,2,4,3)
# Generate an affine that matches the order of the input coords 'ijkml'
ndim = cmap.ndim[0]
perm = np.zeros((ndim+1,ndim+1))
perm[-1,-1] = 1
for i, j in enumerate(order):
perm[i,j] = 1
r = np.zeros_like(perm)
r[5, 5] = 1.0
# The rotation part (5x5) of the newcmap affine will be flipped
# vertically to account for the reverse order of the output coords
# 'utzyx'
r[:5, :5] = np.flipud(perm[:5,:5])
yield assert_true, np.allclose(newcmap.affine, r)
X = np.arange(10, 15)
Xr = [X[i] for i in order]
yield assert_true, np.allclose(np.fliplr(newcmap(Xr)), cmap(X))
def test_general_coercion():
# General test of coormap coercion
cmap = Affine(
np.eye(4),
CoordinateSystem('ijk'),
CoordinateSystem('xyz'))
ncmap, order = niref.coerce_coordmap(cmap)
yield assert_equal, ncmap.output_coords, cmap.output_coords
yield assert_equal, order, (0, 1, 2)
cmap = CoordinateMap(
lambda x : x,
CoordinateSystem('ijk'),
CoordinateSystem('xyz'))
yield assert_raises, ValueError, niref.coerce_coordmap, cmap
cmap = Affine(
np.array([[1,0,0],[0,1,0],[0,0,1],[0,0,1]]),
CoordinateSystem('ij'),
CoordinateSystem('xyz'))
yield assert_raises, ValueError, niref.coerce_coordmap, cmap
cmap = Affine(
np.eye(4),
CoordinateSystem('ijq'),
CoordinateSystem('xyz'))
yield assert_raises, ValueError, niref.coerce_coordmap, cmap
cmap = Affine(
np.eye(4),
CoordinateSystem('ijk'),
CoordinateSystem('xyq'))
yield assert_raises, ValueError, niref.coerce_coordmap, cmap
# Space order should not matter if no time reordering required
cmap = Affine(
np.eye(4),
CoordinateSystem('kji'),
CoordinateSystem('xyz'))
ncmap, order = niref.coerce_coordmap(cmap)
yield assert_equal, ncmap.output_coords, cmap.output_coords
yield assert_equal, order, (0, 1, 2)
yield assert_array_equal, np.eye(4), ncmap.affine
# Even if time is present but in the right place
cmap = Affine(
np.eye(5),
CoordinateSystem('kjil'),
CoordinateSystem('xyzt'))
ncmap, order = niref.coerce_coordmap(cmap)
yield assert_equal, ncmap.output_coords, cmap.output_coords
yield assert_equal, order, (0, 1, 2, 3)
yield assert_array_equal, np.eye(5), ncmap.affine
def test_iljk_to_xyzt():
# this should raise a warning about the first three input
# coordinates, and one about the last axis not being in the
# correct order. this also will give a warning about the pixdim.
# ninput_axes = list('iljk')
input_coords = CoordinateSystem('iljk', 'input')
output_coords = CoordinateSystem('xyzt', 'output')
cmap = Affine(np.identity(5), input_coords, output_coords)
newcmap, order = niref.coerce_coordmap(cmap)
aff = np.array([[ 1, 0, 0, 0, 0,],
[ 0, 0, 1, 0, 0,],
[ 0, 0, 0, 1, 0,],
[ 0, 1, 0, 0, 0,],
[ 0, 0, 0, 0, 1,]])
yield assert_equal, newcmap.affine, aff
yield assert_equal, newcmap.input_coords.name, 'input-reordered'
# order should match a reorder to 'ijkl'
yield assert_equal, order, (0,2,3,1)
def test_ijkml_to_xyztu():
# This should raise a warning about the last 2 axes not being in
# order, and one about the loss of information from a non-diagonal
# matrix. This also means that the pixdim will be wrong
input_coords = CoordinateSystem('ijkml', 'input')
output_coords = CoordinateSystem('xyztu', 'output')
cmap = Affine(np.identity(6), input_coords, output_coords)
newcmap, order = niref.coerce_coordmap(cmap)
yield assert_equal, newcmap.input_coords.name, 'input-reordered'
yield assert_equal, order, (0,1,2,4,3)
# build an affine xform that should match newcmap.affine
ndim = cmap.ndim[0]
perm = np.zeros((ndim+1,ndim+1))
perm[-1,-1] = 1
for i, j in enumerate(order):
perm[i,j] = 1
B = np.dot(np.identity(6), perm)
yield assert_true, np.allclose(newcmap.affine, B)
# Compare applying the original cmap to a vector against applying
# the reordered cmap to a reordered vector.
X = np.arange(10, 15)
Xr = [X[i] for i in order]
yield assert_true, np.allclose(newcmap(Xr), cmap(X))
