# Copyright 2014-2019 The ODL contributors
#
# This file is part of ODL.
#
# This Source Code Form is subject to the terms of the Mozilla Public License,
# v. 2.0. If a copy of the MPL was not distributed with this file, You can
# obtain one at https://mozilla.org/MPL/2.0/.
from __future__ import print_function, division, absolute_import
import numpy as np
__all__ = ('euler_matrix', 'axis_rotation', 'axis_rotation_matrix',
'rotation_matrix_from_to', 'transform_system',
'perpendicular_vector', 'is_inside_bounds')
[docs]
def euler_matrix(phi, theta=None, psi=None):
"""Rotation matrix in 2 and 3 dimensions.
Its rows represent the canonical unit vectors as seen from the
rotated system while the columns are the rotated unit vectors as
seen from the canonical system.
Parameters
----------
phi : float or `array-like`
Either 2D counter-clockwise rotation angle (in radians) or first
Euler angle.
theta, psi : float or `array-like`, optional
Second and third Euler angles in radians. If both are ``None``, a
2D rotation matrix is computed. Otherwise a 3D rotation is computed,
where the default ``None`` is equivalent to ``0.0``.
The rotation is performed in "ZXZ" rotation order, see the
Wikipedia article `Euler angles`_.
Returns
-------
mat : `numpy.ndarray`
Rotation matrix corresponding to the given angles. The
returned array has shape ``(ndim, ndim)`` if all angles represent
single parameters, with ``ndim == 2`` for ``phi`` only and
``ndim == 3`` for 2 or 3 Euler angles.
If any of the angle parameters is an array, the shape of the
returned array is ``broadcast(phi, theta, psi).shape + (ndim, ndim)``.
References
----------
.. _Euler angles:
https://en.wikipedia.org/wiki/Euler_angles#Rotation_matrix
"""
if theta is None and psi is None:
squeeze_out = (np.shape(phi) == ())
ndim = 2
phi = np.array(phi, dtype=float, copy=False, ndmin=1)
theta = psi = 0.0
else:
# `None` broadcasts like a scalar
squeeze_out = (np.broadcast(phi, theta, psi).shape == ())
ndim = 3
phi = np.array(phi, dtype=float, copy=False, ndmin=1)
if theta is None:
theta = 0.0
if psi is None:
psi = 0.0
theta = np.array(theta, dtype=float, copy=False, ndmin=1)
psi = np.array(psi, dtype=float, copy=False, ndmin=1)
ndim = 3
cph = np.cos(phi)
sph = np.sin(phi)
cth = np.cos(theta)
sth = np.sin(theta)
cps = np.cos(psi)
sps = np.sin(psi)
if ndim == 2:
mat = np.array([[cph, -sph],
[sph, cph]])
else:
mat = np.array([
[cph * cps - sph * cth * sps,
-cph * sps - sph * cth * cps,
sph * sth],
[sph * cps + cph * cth * sps,
-sph * sps + cph * cth * cps,
-cph * sth],
[sth * sps + 0 * cph,
sth * cps + 0 * cph,
cth + 0 * (cph + cps)]]) # Make sure all components broadcast
if squeeze_out:
return mat.squeeze()
else:
# Move the `(ndim, ndim)` axes to the end
extra_dims = len(np.broadcast(phi, theta, psi).shape)
newaxes = list(range(2, 2 + extra_dims)) + [0, 1]
return np.transpose(mat, newaxes)
[docs]
def axis_rotation(axis, angle, vectors, axis_shift=(0, 0, 0)):
"""Rotate a vector or an array of vectors around an axis in 3d.
The rotation is computed by `Rodrigues' rotation formula`_.
Parameters
----------
axis : `array-like`, shape ``(3,)``
Rotation axis, assumed to be a unit vector.
angle : float
Angle of the counter-clockwise rotation.
vectors : `array-like`, shape ``(3,)`` or ``(N, 3)``
The vector(s) to be rotated.
axis_shift : `array_like`, shape ``(3,)``, optional
Shift the rotation center by this vector. Note that only shifts
perpendicular to ``axis`` matter.
Returns
-------
rot_vec : `numpy.ndarray`
The rotated vector(s).
References
----------
.. _Rodrigues' rotation formula:
https://en.wikipedia.org/wiki/Rodrigues'_rotation_formula
Examples
--------
Rotating around the third coordinate axis by and angle of 90 degrees:
>>> axis = (0, 0, 1)
>>> rot1 = axis_rotation(axis, angle=np.pi / 2, vectors=(1, 0, 0))
>>> np.allclose(rot1, (0, 1, 0))
True
>>> rot2 = axis_rotation(axis, angle=np.pi / 2, vectors=(0, 1, 0))
>>> np.allclose(rot2, (-1, 0, 0))
True
The rotation can be performed with shifted rotation center. A shift
along the axis does not matter:
>>> rot3 = axis_rotation(axis, angle=np.pi / 2, vectors=(1, 0, 0),
... axis_shift=(0, 0, 2))
>>> np.allclose(rot3, (0, 1, 0))
True
The distance between the rotation center and the vector to be rotated
determines the radius of the rotation circle:
>>> # Rotation center in the point to be rotated, should do nothing
>>> rot4 = axis_rotation(axis, angle=np.pi / 2, vectors=(1, 0, 0),
... axis_shift=(1, 0, 0))
>>> np.allclose(rot4, (1, 0, 0))
True
>>> # Distance 2, thus rotates to (0, 2, 0) in the shifted system,
>>> # resulting in (-1, 2, 0) from shifting back after rotating
>>> rot5 = axis_rotation(axis, angle=np.pi / 2, vectors=(1, 0, 0),
... axis_shift=(-1, 0, 0))
>>> np.allclose(rot5, (-1, 2, 0))
True
Rotation of multiple vectors can be done in bulk:
>>> vectors = [[1, 0, 0], [0, 1, 0]]
>>> rot = axis_rotation(axis, angle=np.pi / 2, vectors=vectors)
>>> np.allclose(rot[0], (0, 1, 0))
True
>>> np.allclose(rot[1], (-1, 0, 0))
True
"""
rot_matrix = axis_rotation_matrix(axis, angle)
vectors = np.asarray(vectors, dtype=float)
if vectors.shape == (3,):
vectors = vectors[None, :]
elif vectors.ndim == 2 and vectors.shape[1] == 3:
pass
else:
raise ValueError('`vectors` must have shape (3,) or (N, 3), got array '
'with shape {}'.format(vectors.shape))
# Get `axis_shift` part that is perpendicular to `axis`
axis_shift = np.asarray(axis_shift, dtype=float)
axis = np.asarray(axis, dtype=float)
axis_shift = axis_shift - axis.dot(axis_shift) * axis
# Shift vectors with the negative of the axis shift to move the rotation
# center to the origin. Then rotate and shift back.
centered_vecs = vectors - axis_shift[None, :]
# Need to transpose the vectors to make the axis of length 3 come first
rot_vecs = rot_matrix.dot(centered_vecs.T).T
return axis_shift[None, :] + rot_vecs
[docs]
def axis_rotation_matrix(axis, angle):
"""Matrix of the rotation around an axis in 3d.
The matrix is computed according to `Rodriguez' rotation formula`_.
Parameters
----------
axis : `array-like`, shape ``(3,)``
Rotation axis, assumed to be a unit vector.
angle : float or `array-like`
Angle(s) of counter-clockwise rotation.
Returns
-------
mat : `numpy.ndarray`, shape ``(3, 3)``
The axis rotation matrix.
References
----------
.. _Rodriguez' rotation formula:
https://en.wikipedia.org/wiki/Rodrigues'_rotation_formula
"""
scalar_out = (np.shape(angle) == ())
axis = np.asarray(axis)
if axis.shape != (3,):
raise ValueError('`axis` shape must be (3,), got {}'
''.format(axis.shape))
angle = np.array(angle, dtype=float, copy=False, ndmin=1)
cross_mat = np.array([[0, -axis[2], axis[1]],
[axis[2], 0, -axis[0]],
[-axis[1], axis[0], 0]])
dy_mat = np.outer(axis, axis)
id_mat = np.eye(3)
cos_ang = np.cos(angle)
sin_ang = np.sin(angle)
# Add extra dimensions for broadcasting
extra_dims = cos_ang.ndim
mat_slc = (None,) * extra_dims + (slice(None), slice(None))
ang_slc = (slice(None),) * extra_dims + (None, None)
# Matrices will have shape (1, ..., 1, ndim, ndim)
cross_mat = cross_mat[mat_slc]
dy_mat = dy_mat[mat_slc]
id_mat = id_mat[mat_slc]
# Angle arrays will have shape (..., 1, 1)
cos_ang = cos_ang[ang_slc]
sin_ang = sin_ang[ang_slc]
axis_mat = cos_ang * id_mat + (1. - cos_ang) * dy_mat + sin_ang * cross_mat
if scalar_out:
return axis_mat.squeeze()
else:
return axis_mat
[docs]
def rotation_matrix_from_to(from_vec, to_vec):
r"""Return a matrix that rotates ``from_vec`` to ``to_vec`` in 2d or 3d.
Since a rotation from one vector to another in 3 dimensions has
(at least) one degree of freedom, this function makes deliberate but
still arbitrary choices to fix these free parameters. See Notes for
details. For the applied formula in 3d, see `this Wikipedia page
about Rodrigues' rotation formula
<https://en.wikipedia.org/wiki/Rodrigues'_rotation_formula>`_.
Parameters
----------
from_vec, to_vec : `array-like`, shape ``(2,)`` or ``(3,)``
Vectors between which the returned matrix rotates. They should not
be very close to zero or collinear.
Returns
-------
matrix : `numpy.ndarray`, shape ``(2, 2)`` or ``(3, 3)``
A matrix rotating ``from_vec`` to ``to_vec``. Note that the
matrix does *not* include scaling, i.e. it is not guaranteed
that ``matrix.dot(from_vec) == to_vec``.
Examples
--------
In two dimensions, rotation is simple:
>>> from_vec, to_vec = [1, 0], [1, 1]
>>> mat = rotation_matrix_from_to(from_vec, to_vec)
>>> to_vec_normalized = np.divide(to_vec, np.linalg.norm(to_vec))
>>> np.allclose(mat.dot([1, 0]), to_vec_normalized)
True
>>> from_vec, to_vec = [1, 0], [-1, 1]
>>> mat = rotation_matrix_from_to(from_vec, to_vec)
>>> to_vec_normalized = np.divide(to_vec, np.linalg.norm(to_vec))
>>> np.allclose(mat.dot([1, 0]), to_vec_normalized)
True
Rotation in 3d by less than ``pi``:
>>> from_vec, to_vec = [1, 0, 0], [-1, 1, 0]
>>> mat = rotation_matrix_from_to(from_vec, to_vec)
>>> to_vec_normalized = np.divide(to_vec, np.linalg.norm(to_vec))
>>> np.allclose(mat.dot([1, 0, 0]), to_vec_normalized)
True
Rotation by more than ``pi``:
>>> from_vec, to_vec = [1, 0, 0], [-1, -1, 0]
>>> mat = rotation_matrix_from_to(from_vec, to_vec)
>>> to_vec_normalized = np.divide(to_vec, np.linalg.norm(to_vec))
>>> np.allclose(mat.dot([1, 0, 0]), to_vec_normalized)
True
Notes
-----
In 3d, the matrix corresponds to a rotation around the normal vector
:math:`\hat n = \hat u \times \hat v`, where :math:`\hat u` and
:math:`\hat v` are the normalized versions of :math:`u`, the
vector from which to rotate, and :math:`v`, the vector to which
should be rotated.
The rotation angle is determined as
:math:`\alpha = \pm \arccos(\langle \hat u, \hat v \rangle)`.
Its sign corresponds to the sign of
:math:`\langle \hat b, \hat v\rangle`, where
:math:`\hat b = \hat n \times \hat u` is the binormal vector.
In the case that :math:`\hat u` and :math:`\hat v` are collinear,
a perpendicular vector is chosen as :math:`\hat n = (1, 0, 0)` if
:math:`v_1 = v_2 = 0`, else :math:`\hat n = (-v_2, v_1, v_3)`.
The angle in this case is :math:`\alpha = 0` if
:math:`\langle \hat u, \hat v \rangle > 0`, otherwise
:math:`\alpha = \pi`.
"""
from_vec, from_vec_in = (np.array(from_vec, dtype=float, copy=True),
from_vec)
to_vec, to_vec_in = np.array(to_vec, dtype=float, copy=True), to_vec
if from_vec.shape not in ((2,), (3,)):
raise ValueError('`from_vec.shape` must be (2,) or (3,), got {}'
''.format(from_vec.shape))
if to_vec.shape not in ((2,), (3,)):
raise ValueError('`to_vec.shape` must be (2,) or (3,), got {}'
''.format(to_vec.shape))
if from_vec.shape != to_vec.shape:
raise ValueError('`from_vec.shape` and `to_vec.shape` not equal: '
'{} != {}'
''.format(from_vec.shape, to_vec.shape))
ndim = len(from_vec)
# Normalize vectors
from_vec_norm = np.linalg.norm(from_vec)
if from_vec_norm < 1e-10:
raise ValueError('`from_vec` {} too close to zero'.format(from_vec_in))
from_vec /= from_vec_norm
to_vec_norm = np.linalg.norm(to_vec)
if to_vec_norm < 1e-10:
raise ValueError('`to_vec` {} too close to zero'.format(to_vec_in))
to_vec /= to_vec_norm
if ndim == 2:
dot = np.dot(from_vec, to_vec)
from_rot = (-from_vec[1], from_vec[0])
if dot == 0:
angle = np.pi / 2 if np.dot(from_rot, to_vec) > 0 else -np.pi / 2
elif np.array_equal(to_vec, -from_vec):
angle = np.pi
else:
angle = (np.sign(np.dot(from_rot, to_vec)) *
np.arccos(np.dot(from_vec, to_vec)))
return np.array([[np.cos(angle), -np.sin(angle)],
[np.sin(angle), np.cos(angle)]])
elif ndim == 3:
# Determine normal
normal = np.cross(from_vec, to_vec)
normal_norm = np.linalg.norm(normal)
if normal_norm < 1e-10:
# Collinear vectors, use perpendicular vector and angle = 0 or pi
normal = perpendicular_vector(from_vec)
angle = 0 if np.dot(from_vec, to_vec) > 0 else np.pi
return axis_rotation_matrix(normal, angle)
else:
# Usual case, determine binormal and sign of rotation angle
normal /= normal_norm
binormal = np.cross(normal, from_vec)
angle = (np.sign(np.dot(binormal, to_vec)) *
np.arccos(np.dot(from_vec, to_vec)))
return axis_rotation_matrix(normal, angle)
else:
raise RuntimeError('bad ndim')
[docs]
def is_rotation_matrix(mat, show_diff=False):
from scipy.linalg import det, norm
dim = mat.shape[0]
if dim != mat.shape[1]:
return False
determ = det(mat)
right_handed = (np.abs(determ - 1.) < 1E-10)
orthonorm_diff = mat * mat.T - np.eye(dim)
diff_norm = norm(orthonorm_diff, 2)
orthonormal = (diff_norm < 1E-10)
if not right_handed or not orthonormal:
if show_diff:
print('matrix S:\n', mat)
print('det(S): ', determ)
print('S*S.T - eye:\n', orthonorm_diff)
print('2-norm of difference: ', diff_norm)
return False
return True
[docs]
def angles_from_matrix(rot_matrix):
if rot_matrix.shape == (2, 2):
theta = np.atan2(rot_matrix[1, 0], rot_matrix[0, 0])
return theta,
elif rot_matrix.shape == (3, 3):
if rot_matrix[2, 2] == 1.: # cannot use last row and column
theta = 0.
# upper-left block is 2d rotation for phi + psi, so one needs
# to be fixed
psi = 0.
phi = np.atan2(rot_matrix[1, 0], rot_matrix[0, 0])
if phi < 0:
phi += 2 * np.pi # in [0, 2pi)
else:
phi = np.atan2(rot_matrix[0, 2], -rot_matrix[1, 2])
psi = np.atan2(rot_matrix[2, 0], rot_matrix[2, 1])
theta = np.acos(rot_matrix[2, 2])
if phi < 0. or psi < 0.:
phi += np.pi
psi += np.pi
theta = -theta
return phi, theta, psi
else:
raise ValueError('shape of `rot_matrix` must be (2, 2) or (3, 3), '
'got {}'.format(rot_matrix.shape))
[docs]
def to_lab_sys(vec_in_local_coords, local_sys):
vec_in_local_coords = np.array(vec_in_local_coords)
trafo_matrix = np.matrix(local_sys).T
return np.dot(trafo_matrix, vec_in_local_coords)
[docs]
def to_local_sys(vec_in_lab_coords, local_sys):
vec_in_lab_coords = np.array(vec_in_lab_coords)
trafo_matrix = np.matrix(local_sys)
return np.dot(trafo_matrix, vec_in_lab_coords)
[docs]
def perpendicular_vector(vec):
"""Return a vector perpendicular to ``vec``.
Parameters
----------
vec : `array-like`
Vector(s) of arbitrary length. The axis along the vector components
must come last.
Returns
-------
perp_vec : `numpy.ndarray`
Array of same shape as ``vec`` such that ``dot(vec, perp_vec) == 0``
(along the last axis if there are multiple vectors).
Examples
--------
Works in 2d:
>>> perpendicular_vector([0, 1])
array([-1., 0.])
>>> np.allclose(perpendicular_vector([1, 0]), [0, 1]) # would print -0
True
And in 3d:
>>> perpendicular_vector([0, 1, 0])
array([-1., 0., 0.])
>>> perpendicular_vector([0, 0, 1])
array([ 1., 0., 0.])
>>> np.allclose(perpendicular_vector([1, 0, 0]), [0, 1, 0])
True
The function is vectorized, i.e., it can be called with multiple
vectors at once (additional axes being added to the left):
>>> perpendicular_vector([[0, 1, 0],
... [0, 0, 1]]) # 2 vectors
array([[-1., 0., 0.],
[ 1., 0., 0.]])
>>> vecs = np.zeros((2, 3, 3))
>>> vecs[..., 1] = 1 # (2, 3) array of vectors (0, 1, 0)
>>> perpendicular_vector(vecs)
array([[[-1., 0., 0.],
[-1., 0., 0.],
[-1., 0., 0.]],
<BLANKLINE>
[[-1., 0., 0.],
[-1., 0., 0.],
[-1., 0., 0.]]])
"""
squeeze_out = (np.ndim(vec) == 1)
vec = np.array(vec, dtype=float, copy=False, ndmin=2)
if np.any(np.all(vec == 0, axis=-1)):
raise ValueError('zero vector')
result = np.zeros(vec.shape)
cond = np.any(vec[..., :2] != 0, axis=-1)
result[cond, 0] = -vec[cond, 1]
result[cond, 1] = vec[cond, 0]
result[~cond, 0] = 1
result /= np.linalg.norm(result, axis=-1, keepdims=True)
if squeeze_out:
result = result.squeeze()
return result
[docs]
def is_inside_bounds(value, params):
"""Return ``True`` if ``value`` is contained in ``params``.
This method supports broadcasting in the sense that for
``params.ndim >= 2``, if more than one value is given, the inputs
are broadcast against each other.
Parameters
----------
value : `array-like`
Value(s) to be checked. For several inputs, the final bool
tells whether all inputs pass the check or not.
params : `IntervalProd`
Set in which the value is / the values are supposed to lie.
Returns
-------
is_inside_bounds : bool
``True`` is all values lie in ``params``, ``False`` otherwise.
Examples
--------
Check a single point:
>>> params = odl.IntervalProd([0, 0], [1, 2])
>>> is_inside_bounds([0, 0], params)
True
>>> is_inside_bounds([0, -1], params)
False
Using broadcasting:
>>> pts_ax0 = np.array([0, 0, 1, 0, 1])[:, None]
>>> pts_ax1 = np.array([2, 0, 1])[None, :]
>>> is_inside_bounds([pts_ax0, pts_ax1], params)
True
>>> pts_ax1 = np.array([-2, 1])[None, :]
>>> is_inside_bounds([pts_ax0, pts_ax1], params)
False
"""
if value in params:
# Single parameter
return True
else:
if params.ndim == 1:
return params.contains_all(np.ravel(value))
else:
# Flesh out and flatten to check bounds
bcast_value = np.broadcast_arrays(*value)
stacked_value = np.vstack(bcast_value)
flat_value = stacked_value.reshape(params.ndim, -1)
return params.contains_all(flat_value)
if __name__ == '__main__':
from odl.util.testutils import run_doctests
run_doctests()