bop_toolkit
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thodan
Fix missing identity in get_symmetry_transformations
Without this fix, the identity transformation is only included for the discrete transformations, but missing from the continuous transformations:
>>> import json
>>> from bop_toolkit_lib.misc import get_symmetry_transformations
>>> from numpy import pi
# before this PR:
>>> model_info_discrete = json.loads('{ "symmetries_discrete": [[-1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1]] }')
>>> get_symmetry_transformations(model_info_discrete, pi / 4)
[{'R': array([[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]]),
't': array([[0],
[0],
[0]])},
{'R': array([[-1, 0, 0],
[ 0, -1, 0],
[ 0, 0, 1]]),
't': array([[0],
[0],
[0]])}]
>>> model_info_continuous = json.loads('{ "symmetries_continuous": [{"axis": [1, 0, 0], "offset": [0, 0, 0]}] }')
>>> get_symmetry_transformations(model_info_continuous, pi / 4)
[{'R': array([[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 6.123234e-17, -1.000000e+00],
[ 0.000000e+00, 1.000000e+00, 6.123234e-17]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1.0000000e+00, 0.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, -1.0000000e+00, -1.2246468e-16],
[ 0.0000000e+00, 1.2246468e-16, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1.0000000e+00, 0.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, -1.8369702e-16, 1.0000000e+00],
[ 0.0000000e+00, -1.0000000e+00, -1.8369702e-16]]),
't': array([[0.],
[0.],
[0.]])}]
>>> model_info_both = json.loads('{ "symmetries_discrete": [[1, 0, 0, 0, 0, -1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1]], "symmetries_continuous": [{"axis": [0, 0, 1], "offset": [0, 0, 0]}] }')
>>> get_symmetry_transformations(model_info_both, pi / 4)
[{'R': array([[ 6.123234e-17, -1.000000e+00, 0.000000e+00],
[ 1.000000e+00, 6.123234e-17, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.0000000e+00, -1.2246468e-16, 0.0000000e+00],
[ 1.2246468e-16, -1.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, 1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.8369702e-16, 1.0000000e+00, 0.0000000e+00],
[-1.0000000e+00, -1.8369702e-16, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, 1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 6.123234e-17, 1.000000e+00, 0.000000e+00],
[ 1.000000e+00, -6.123234e-17, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, -1.000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.0000000e+00, 1.2246468e-16, 0.0000000e+00],
[ 1.2246468e-16, 1.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.8369702e-16, -1.0000000e+00, 0.0000000e+00],
[-1.0000000e+00, 1.8369702e-16, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])}]
# after this PR:
>>> get_symmetry_transformations(model_info_discrete, pi / 4)
[{'R': array([[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]]),
't': array([[0],
[0],
[0]])},
{'R': array([[-1, 0, 0],
[ 0, -1, 0],
[ 0, 0, 1]]),
't': array([[0],
[0],
[0]])}]
>>> get_symmetry_transformations(model_info_continuous, pi / 4)
[{'R': array([[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1.000000e+00, 0.000000e+00, 0.000000e+00],
[ 0.000000e+00, 6.123234e-17, -1.000000e+00],
[ 0.000000e+00, 1.000000e+00, 6.123234e-17]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1.0000000e+00, 0.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, -1.0000000e+00, -1.2246468e-16],
[ 0.0000000e+00, 1.2246468e-16, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1.0000000e+00, 0.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, -1.8369702e-16, 1.0000000e+00],
[ 0.0000000e+00, -1.0000000e+00, -1.8369702e-16]]),
't': array([[0.],
[0.],
[0.]])}]
>>> get_symmetry_transformations(model_info_both, pi / 4)
[{'R': array([[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 6.123234e-17, -1.000000e+00, 0.000000e+00],
[ 1.000000e+00, 6.123234e-17, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, 1.000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.0000000e+00, -1.2246468e-16, 0.0000000e+00],
[ 1.2246468e-16, -1.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, 1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.8369702e-16, 1.0000000e+00, 0.0000000e+00],
[-1.0000000e+00, -1.8369702e-16, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, 1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 1., 0., 0.],
[ 0., -1., 0.],
[ 0., 0., -1.]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[ 6.123234e-17, 1.000000e+00, 0.000000e+00],
[ 1.000000e+00, -6.123234e-17, 0.000000e+00],
[ 0.000000e+00, 0.000000e+00, -1.000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.0000000e+00, 1.2246468e-16, 0.0000000e+00],
[ 1.2246468e-16, 1.0000000e+00, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])},
{'R': array([[-1.8369702e-16, -1.0000000e+00, 0.0000000e+00],
[-1.0000000e+00, 1.8369702e-16, 0.0000000e+00],
[ 0.0000000e+00, 0.0000000e+00, -1.0000000e+00]]),
't': array([[0.],
[0.],
[0.]])}]
