# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
# transformations.py
# Copyright (c) 2006, Christoph Gohlke
# Copyright (c) 2006-2010, The Regents of the University of California
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"""
Homogeneous Transformation Matrices and Quaternions --- :mod:`MDAnalysis.lib.transformations`
==============================================================================================
A library for calculating 4x4 matrices for translating, rotating, reflecting,
scaling, shearing, projecting, orthogonalizing, and superimposing arrays of
3D homogeneous coordinates as well as for converting between rotation matrices,
Euler angles, and quaternions. Also includes an Arcball control object and
functions to decompose transformation matrices.
:Authors:
`Christoph Gohlke <http://www.lfd.uci.edu/~gohlke/>`__,
Laboratory for Fluorescence Dynamics, University of California, Irvine
:Version: 2010.05.10
:Licence: BSD 3-clause
Requirements
------------
* `Python 2.6 or 3.1 <http://www.python.org>`__
* `Numpy 1.4 <http://numpy.scipy.org>`__
* `transformations.c 2010.04.10 <http://www.lfd.uci.edu/~gohlke/>`__
(optional implementation of some functions in C)
Notes
-----
The API is not stable yet and is expected to change between revisions.
This Python code is not optimized for speed. Refer to the transformations.c
module for a faster implementation of some functions.
Documentation in HTML format can be generated with epydoc.
Matrices (M) can be inverted using ``numpy.linalg.inv(M)``, concatenated using
``numpy.dot(M0, M1)``, or used to transform homogeneous coordinates (v) using
``numpy.dot(M, v)`` for shape ``(4, *)`` "point of arrays", respectively
``numpy.dot(v, M.T)`` for shape ``(*, 4)`` "array of points".
Use the transpose of transformation matrices for OpenGL ``glMultMatrixd()``.
Calculations are carried out with ``numpy.float64`` precision.
Vector, point, quaternion, and matrix function arguments are expected to be
"array like", i.e. tuple, list, or numpy arrays.
Return types are numpy arrays unless specified otherwise.
Angles are in radians unless specified otherwise.
Quaternions w+ix+jy+kz are represented as ``[w, x, y, z]``.
A triple of Euler angles can be applied/interpreted in 24 ways, which can
be specified using a 4 character string or encoded 4-tuple:
- *Axes 4-string*: e.g. 'sxyz' or 'ryxy'
- first character : rotations are applied to 's'tatic or 'r'otating frame
- remaining characters : successive rotation axis 'x', 'y', or 'z'
- *Axes 4-tuple*: e.g. (0, 0, 0, 0) or (1, 1, 1, 1)
- inner axis: code of axis ('x':0, 'y':1, 'z':2) of rightmost matrix.
- parity : even (0) if inner axis 'x' is followed by 'y', 'y' is followed
by 'z', or 'z' is followed by 'x'. Otherwise odd (1).
- repetition : first and last axis are same (1) or different (0).
- frame : rotations are applied to static (0) or rotating (1) frame.
.. rubric:: References
.. footbibliography::
Examples
--------
>>> from MDAnalysis.lib.transformations import *
>>> import numpy as np
>>> alpha, beta, gamma = 0.123, -1.234, 2.345
>>> origin, xaxis, yaxis, zaxis = (0, 0, 0), (1, 0, 0), (0, 1, 0), (0, 0, 1)
>>> I = identity_matrix()
>>> Rx = rotation_matrix(alpha, xaxis)
>>> Ry = rotation_matrix(beta, yaxis)
>>> Rz = rotation_matrix(gamma, zaxis)
>>> R = concatenate_matrices(Rx, Ry, Rz)
>>> euler = euler_from_matrix(R, 'rxyz')
>>> np.allclose([alpha, beta, gamma], euler)
True
>>> Re = euler_matrix(alpha, beta, gamma, 'rxyz')
>>> is_same_transform(R, Re)
True
>>> al, be, ga = euler_from_matrix(Re, 'rxyz')
>>> is_same_transform(Re, euler_matrix(al, be, ga, 'rxyz'))
True
>>> qx = quaternion_about_axis(alpha, xaxis)
>>> qy = quaternion_about_axis(beta, yaxis)
>>> qz = quaternion_about_axis(gamma, zaxis)
>>> q = quaternion_multiply(qx, qy)
>>> q = quaternion_multiply(q, qz)
>>> Rq = quaternion_matrix(q)
>>> is_same_transform(R, Rq)
True
>>> S = scale_matrix(1.23, origin)
>>> T = translation_matrix((1, 2, 3))
>>> Z = shear_matrix(beta, xaxis, origin, zaxis)
>>> R = random_rotation_matrix(np.random.rand(3))
>>> M = concatenate_matrices(T, R, Z, S)
>>> scale, shear, angles, trans, persp = decompose_matrix(M)
>>> np.allclose(scale, 1.23)
True
>>> np.allclose(trans, (1, 2, 3))
True
>>> np.allclose(shear, (0, math.tan(beta), 0))
True
>>> is_same_transform(R, euler_matrix(axes='sxyz', *angles))
True
>>> M1 = compose_matrix(scale, shear, angles, trans, persp)
>>> is_same_transform(M, M1)
True
Functions
---------
.. See `help(MDAnalysis.lib.transformations)` for a listing of functions or
.. the online help.
.. versionchanged:: 0.11.0
Transformations library moved from MDAnalysis.core.transformations to
MDAnalysis.lib.transformations
"""
import sys
import os
import warnings
import math
import numpy as np
from numpy.linalg import norm
from .mdamath import angle as vecangle
from MDAnalysis.lib.util import no_copy_shim
def identity_matrix():
"""Return 4x4 identity/unit matrix.
>>> from MDAnalysis.lib.transformations import identity_matrix
>>> import numpy as np
>>> I = identity_matrix()
>>> np.allclose(I, np.dot(I, I))
True
>>> np.sum(I), np.trace(I)
(4.0, 4.0)
>>> np.allclose(I, np.identity(4, dtype=np.float64))
True
"""
return np.identity(4, dtype=np.float64)
def translation_matrix(direction):
"""Return matrix to translate by direction vector.
>>> from MDAnalysis.lib.transformations import translation_matrix
>>> import numpy as np
>>> v = np.random.random(3) - 0.5
>>> np.allclose(v, translation_matrix(v)[:3, 3])
True
"""
M = np.identity(4)
M[:3, 3] = direction[:3]
return M
[docs]
def translation_from_matrix(matrix):
"""Return translation vector from translation matrix.
>>> from MDAnalysis.lib.transformations import (translation_matrix,
... translation_from_matrix)
>>> import numpy as np
>>> v0 = np.random.random(3) - 0.5
>>> v1 = translation_from_matrix(translation_matrix(v0))
>>> np.allclose(v0, v1)
True
"""
return np.array(matrix, copy=False)[:3, 3].copy()
def reflection_matrix(point, normal):
"""Return matrix to mirror at plane defined by point and normal vector.
>>> from MDAnalysis.lib.transformations import reflection_matrix
>>> import numpy as np
>>> v0 = np.random.random(4) - 0.5
>>> v0[3] = 1.0
>>> v1 = np.random.random(3) - 0.5
>>> R = reflection_matrix(v0, v1)
>>> np.allclose(2., np.trace(R))
True
>>> np.allclose(v0, np.dot(R, v0))
True
>>> v2 = v0.copy()
>>> v2[:3] += v1
>>> v3 = v0.copy()
>>> v2[:3] -= v1
>>> np.allclose(v2, np.dot(R, v3))
True
"""
normal = unit_vector(normal[:3])
M = np.identity(4)
M[:3, :3] -= 2.0 * np.outer(normal, normal)
M[:3, 3] = (2.0 * np.dot(point[:3], normal)) * normal
return M
[docs]
def reflection_from_matrix(matrix):
"""Return mirror plane point and normal vector from reflection matrix.
>>> from MDAnalysis.lib.transformations import (reflection_matrix,
... reflection_from_matrix, is_same_transform)
>>> import numpy as np
>>> v0 = np.random.random(3) - 0.5
>>> v1 = np.random.random(3) - 0.5
>>> M0 = reflection_matrix(v0, v1)
>>> point, normal = reflection_from_matrix(M0)
>>> M1 = reflection_matrix(point, normal)
>>> is_same_transform(M0, M1)
True
"""
M = np.array(matrix, dtype=np.float64, copy=False)
# normal: unit eigenvector corresponding to eigenvalue -1
l, V = np.linalg.eig(M[:3, :3])
i = np.where(abs(np.real(l) + 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no unit eigenvector corresponding to eigenvalue -1")
normal = np.real(V[:, i[0]]).squeeze()
# point: any unit eigenvector corresponding to eigenvalue 1
l, V = np.linalg.eig(M)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
point = np.real(V[:, i[-1]]).squeeze()
point /= point[3]
return point, normal
def rotation_matrix(angle, direction, point=None):
"""Return matrix to rotate about axis defined by point and direction.
>>> from MDAnalysis.lib.transformations import (rotation_matrix,
... is_same_transform)
>>> import random, math
>>> import numpy as np
>>> R = rotation_matrix(math.pi/2.0, [0, 0, 1], [1, 0, 0])
>>> np.allclose(np.dot(R, [0, 0, 0, 1]), [ 1., -1., 0., 1.])
True
>>> angle = (random.random() - 0.5) * (2*math.pi)
>>> direc = np.random.random(3) - 0.5
>>> point = np.random.random(3) - 0.5
>>> R0 = rotation_matrix(angle, direc, point)
>>> R1 = rotation_matrix(angle-2*math.pi, direc, point)
>>> is_same_transform(R0, R1)
True
>>> R0 = rotation_matrix(angle, direc, point)
>>> R1 = rotation_matrix(-angle, -direc, point)
>>> is_same_transform(R0, R1)
True
>>> I = np.identity(4, np.float64)
>>> np.allclose(I, rotation_matrix(math.pi*2, direc))
True
>>> np.allclose(2., np.trace(rotation_matrix(math.pi/2,
... direc, point)))
True
"""
sina = math.sin(angle)
cosa = math.cos(angle)
direction = unit_vector(direction[:3])
# rotation matrix around unit vector
R = np.array(
(
(cosa, 0.0, 0.0),
(0.0, cosa, 0.0),
(0.0, 0.0, cosa)), dtype=np.float64)
R += np.outer(direction, direction) * (1.0 - cosa)
direction *= sina
R += np.array(
((0.0, -direction[2], direction[1]),
(direction[2], 0.0, -direction[0]),
(-direction[1], direction[0], 0.0)), dtype=np.float64)
M = np.identity(4)
M[:3, :3] = R
if point is not None:
# rotation not around origin
point = np.array(point[:3], dtype=np.float64, copy=no_copy_shim)
M[:3, 3] = point - np.dot(R, point)
return M
[docs]
def rotation_from_matrix(matrix):
"""Return rotation angle and axis from rotation matrix.
>>> from MDAnalysis.lib.transformations import (rotation_matrix,
... is_same_transform, rotation_from_matrix)
>>> import random, math
>>> import numpy as np
>>> angle = (random.random() - 0.5) * (2*math.pi)
>>> direc = np.random.random(3) - 0.5
>>> point = np.random.random(3) - 0.5
>>> R0 = rotation_matrix(angle, direc, point)
>>> angle, direc, point = rotation_from_matrix(R0)
>>> R1 = rotation_matrix(angle, direc, point)
>>> is_same_transform(R0, R1)
True
"""
R = np.array(matrix, dtype=np.float64, copy=False)
R33 = R[:3, :3]
# direction: unit eigenvector of R33 corresponding to eigenvalue of 1
l, W = np.linalg.eig(R33.T)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
direction = np.real(W[:, i[-1]]).squeeze()
# point: unit eigenvector of R33 corresponding to eigenvalue of 1
l, Q = np.linalg.eig(R)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
point = np.real(Q[:, i[-1]]).squeeze()
point /= point[3]
# rotation angle depending on direction
cosa = (np.trace(R33) - 1.0) / 2.0
if abs(direction[2]) > 1e-8:
sina = (R[1, 0] + (cosa - 1.0) * direction[0] * direction[1]) / direction[2]
elif abs(direction[1]) > 1e-8:
sina = (R[0, 2] + (cosa - 1.0) * direction[0] * direction[2]) / direction[1]
else:
sina = (R[2, 1] + (cosa - 1.0) * direction[1] * direction[2]) / direction[0]
angle = math.atan2(sina, cosa)
return angle, direction, point
def scale_matrix(factor, origin=None, direction=None):
"""Return matrix to scale by factor around origin in direction.
Use factor -1 for point symmetry.
>>> from MDAnalysis.lib.transformations import scale_matrix
>>> import random
>>> import numpy as np
>>> v = (np.random.rand(4, 5) - 0.5) * 20.0
>>> v[3] = 1.0
>>> S = scale_matrix(-1.234)
>>> np.allclose(np.dot(S, v)[:3], -1.234*v[:3])
True
>>> factor = random.random() * 10 - 5
>>> origin = np.random.random(3) - 0.5
>>> direct = np.random.random(3) - 0.5
>>> S = scale_matrix(factor, origin)
>>> S = scale_matrix(factor, origin, direct)
"""
if direction is None:
# uniform scaling
M = np.array(
((factor, 0.0, 0.0, 0.0),
(0.0, factor, 0.0, 0.0),
(0.0, 0.0, factor, 0.0),
(0.0, 0.0, 0.0, 1.0)), dtype=np.float64)
if origin is not None:
M[:3, 3] = origin[:3]
M[:3, 3] *= 1.0 - factor
else:
# nonuniform scaling
direction = unit_vector(direction[:3])
factor = 1.0 - factor
M = np.identity(4)
M[:3, :3] -= factor * np.outer(direction, direction)
if origin is not None:
M[:3, 3] = (factor * np.dot(origin[:3], direction)) * direction
return M
[docs]
def scale_from_matrix(matrix):
"""Return scaling factor, origin and direction from scaling matrix.
>>> from MDAnalysis.lib.transformations import (scale_matrix,
... scale_from_matrix, is_same_transform)
>>> import random
>>> import numpy as np
>>> factor = random.random() * 10 - 5
>>> origin = np.random.random(3) - 0.5
>>> direct = np.random.random(3) - 0.5
>>> S0 = scale_matrix(factor, origin)
>>> factor, origin, direction = scale_from_matrix(S0)
>>> S1 = scale_matrix(factor, origin, direction)
>>> is_same_transform(S0, S1)
True
>>> S0 = scale_matrix(factor, origin, direct)
>>> factor, origin, direction = scale_from_matrix(S0)
>>> S1 = scale_matrix(factor, origin, direction)
>>> is_same_transform(S0, S1)
True
"""
M = np.array(matrix, dtype=np.float64, copy=False)
M33 = M[:3, :3]
factor = np.trace(M33) - 2.0
try:
# direction: unit eigenvector corresponding to eigenvalue factor
l, V = np.linalg.eig(M33)
i = np.where(abs(np.real(l) - factor) < 1e-8)[0][0]
direction = np.real(V[:, i]).squeeze()
direction /= vector_norm(direction)
except IndexError:
# uniform scaling
factor = (factor + 2.0) / 3.0
direction = None
# origin: any eigenvector corresponding to eigenvalue 1
l, V = np.linalg.eig(M)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no eigenvector corresponding to eigenvalue 1")
origin = np.real(V[:, i[-1]]).squeeze()
origin /= origin[3]
return factor, origin, direction
def projection_matrix(point, normal, direction=None,
perspective=None, pseudo=False):
"""Return matrix to project onto plane defined by point and normal.
Using either perspective point, projection direction, or none of both.
If pseudo is True, perspective projections will preserve relative depth
such that Perspective = dot(Orthogonal, PseudoPerspective).
>>> from MDAnalysis.lib.transformations import (projection_matrix,
... is_same_transform)
>>> import numpy as np
>>> P = projection_matrix((0, 0, 0), (1, 0, 0))
>>> np.allclose(P[1:, 1:], np.identity(4)[1:, 1:])
True
>>> point = np.random.random(3) - 0.5
>>> normal = np.random.random(3) - 0.5
>>> direct = np.random.random(3) - 0.5
>>> persp = np.random.random(3) - 0.5
>>> P0 = projection_matrix(point, normal)
>>> P1 = projection_matrix(point, normal, direction=direct)
>>> P2 = projection_matrix(point, normal, perspective=persp)
>>> P3 = projection_matrix(point, normal, perspective=persp, pseudo=True)
>>> is_same_transform(P2, np.dot(P0, P3))
True
>>> P = projection_matrix((3, 0, 0), (1, 1, 0), (1, 0, 0))
>>> v0 = (np.random.rand(4, 5) - 0.5) * 20.0
>>> v0[3] = 1.0
>>> v1 = np.dot(P, v0)
>>> np.allclose(v1[1], v0[1])
True
>>> np.allclose(v1[0], 3.0-v1[1])
True
"""
M = np.identity(4)
point = np.array(point[:3], dtype=np.float64, copy=no_copy_shim)
normal = unit_vector(normal[:3])
if perspective is not None:
# perspective projection
perspective = np.array(perspective[:3], dtype=np.float64,
copy=False)
M[0, 0] = M[1, 1] = M[2, 2] = np.dot(perspective - point, normal)
M[:3, :3] -= np.outer(perspective, normal)
if pseudo:
# preserve relative depth
M[:3, :3] -= np.outer(normal, normal)
M[:3, 3] = np.dot(point, normal) * (perspective + normal)
else:
M[:3, 3] = np.dot(point, normal) * perspective
M[3, :3] = -normal
M[3, 3] = np.dot(perspective, normal)
elif direction is not None:
# parallel projection
direction = np.array(direction[:3], dtype=np.float64, copy=no_copy_shim)
scale = np.dot(direction, normal)
M[:3, :3] -= np.outer(direction, normal) / scale
M[:3, 3] = direction * (np.dot(point, normal) / scale)
else:
# orthogonal projection
M[:3, :3] -= np.outer(normal, normal)
M[:3, 3] = np.dot(point, normal) * normal
return M
[docs]
def projection_from_matrix(matrix, pseudo=False):
"""Return projection plane and perspective point from projection matrix.
Return values are same as arguments for projection_matrix function:
point, normal, direction, perspective, and pseudo.
>>> from MDAnalysis.lib.transformations import (projection_matrix,
... projection_from_matrix, is_same_transform)
>>> import numpy as np
>>> point = np.random.random(3) - 0.5
>>> normal = np.random.random(3) - 0.5
>>> direct = np.random.random(3) - 0.5
>>> persp = np.random.random(3) - 0.5
>>> P0 = projection_matrix(point, normal)
>>> result = projection_from_matrix(P0)
>>> P1 = projection_matrix(*result)
>>> is_same_transform(P0, P1)
True
>>> P0 = projection_matrix(point, normal, direct)
>>> result = projection_from_matrix(P0)
>>> P1 = projection_matrix(*result)
>>> is_same_transform(P0, P1)
True
>>> P0 = projection_matrix(point, normal, perspective=persp, pseudo=False)
>>> result = projection_from_matrix(P0, pseudo=False)
>>> P1 = projection_matrix(*result)
>>> is_same_transform(P0, P1)
True
>>> P0 = projection_matrix(point, normal, perspective=persp, pseudo=True)
>>> result = projection_from_matrix(P0, pseudo=True)
>>> P1 = projection_matrix(*result)
>>> is_same_transform(P0, P1)
True
"""
M = np.array(matrix, dtype=np.float64, copy=False)
M33 = M[:3, :3]
l, V = np.linalg.eig(M)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not pseudo and len(i):
# point: any eigenvector corresponding to eigenvalue 1
point = np.real(V[:, i[-1]]).squeeze()
point /= point[3]
# direction: unit eigenvector corresponding to eigenvalue 0
l, V = np.linalg.eig(M33)
i = np.where(abs(np.real(l)) < 1e-8)[0]
if not len(i):
raise ValueError("no eigenvector corresponding to eigenvalue 0")
direction = np.real(V[:, i[0]]).squeeze()
direction /= vector_norm(direction)
# normal: unit eigenvector of M33.T corresponding to eigenvalue 0
l, V = np.linalg.eig(M33.T)
i = np.where(abs(np.real(l)) < 1e-8)[0]
if len(i):
# parallel projection
normal = np.real(V[:, i[0]]).squeeze()
normal /= vector_norm(normal)
return point, normal, direction, None, False
else:
# orthogonal projection, where normal equals direction vector
return point, direction, None, None, False
else:
# perspective projection
i = np.where(abs(np.real(l)) > 1e-8)[0]
if not len(i):
raise ValueError(
"no eigenvector not corresponding to eigenvalue 0")
point = np.real(V[:, i[-1]]).squeeze()
point /= point[3]
normal = - M[3, :3]
perspective = M[:3, 3] / np.dot(point[:3], normal)
if pseudo:
perspective -= normal
return point, normal, None, perspective, pseudo
def clip_matrix(left, right, bottom, top, near, far, perspective=False):
"""Return matrix to obtain normalized device coordinates from frustrum.
The frustrum bounds are axis-aligned along x (left, right),
y (bottom, top) and z (near, far).
Normalized device coordinates are in range [-1, 1] if coordinates are
inside the frustrum.
If perspective is True the frustrum is a truncated pyramid with the
perspective point at origin and direction along z axis, otherwise an
orthographic canonical view volume (a box).
Homogeneous coordinates transformed by the perspective clip matrix
need to be dehomogenized (devided by w coordinate).
>>> from MDAnalysis.lib.transformations import clip_matrix
>>> import numpy as np
>>> frustrum = np.random.rand(6)
>>> frustrum[1] += frustrum[0]
>>> frustrum[3] += frustrum[2]
>>> frustrum[5] += frustrum[4]
>>> M = clip_matrix(perspective=False, *frustrum)
>>> np.dot(M, [frustrum[0], frustrum[2], frustrum[4], 1.0])
array([-1., -1., -1., 1.])
>>> np.dot(M, [frustrum[1], frustrum[3], frustrum[5], 1.0])
array([1., 1., 1., 1.])
>>> M = clip_matrix(perspective=True, *frustrum)
>>> v = np.dot(M, [frustrum[0], frustrum[2], frustrum[4], 1.0])
>>> v / v[3]
array([-1., -1., -1., 1.])
>>> v = np.dot(M, [frustrum[1], frustrum[3], frustrum[4], 1.0])
>>> v / v[3]
array([ 1., 1., -1., 1.])
"""
if left >= right or bottom >= top or near >= far:
raise ValueError("invalid frustrum")
if perspective:
if near <= _EPS:
raise ValueError("invalid frustrum: near <= 0")
t = 2.0 * near
M = (
(-t / (right - left), 0.0, (right + left) / (right - left), 0.0),
(0.0, -t / (top - bottom), (top + bottom) / (top - bottom), 0.0),
(0.0, 0.0, -(far + near) / (far - near), t * far / (far - near)),
(0.0, 0.0, -1.0, 0.0))
else:
M = (
(2.0 / (right - left), 0.0, 0.0, (right + left) / (left - right)),
(0.0, 2.0 / (top - bottom), 0.0, (top + bottom) / (bottom - top)),
(0.0, 0.0, 2.0 / (far - near), (far + near) / (near - far)),
(0.0, 0.0, 0.0, 1.0))
return np.array(M, dtype=np.float64)
def shear_matrix(angle, direction, point, normal):
"""Return matrix to shear by angle along direction vector on shear plane.
The shear plane is defined by a point and normal vector. The direction
vector must be orthogonal to the plane's normal vector.
A point P is transformed by the shear matrix into P" such that
the vector P-P" is parallel to the direction vector and its extent is
given by the angle of P-P'-P", where P' is the orthogonal projection
of P onto the shear plane.
>>> from MDAnalysis.lib.transformations import shear_matrix
>>> import random, math
>>> import numpy as np
>>> angle = (random.random() - 0.5) * 4*math.pi
>>> direct = np.random.random(3) - 0.5
>>> point = np.random.random(3) - 0.5
>>> normal = np.cross(direct, np.random.random(3))
>>> S = shear_matrix(angle, direct, point, normal)
>>> np.allclose(1.0, np.linalg.det(S))
True
"""
normal = unit_vector(normal[:3])
direction = unit_vector(direction[:3])
if abs(np.dot(normal, direction)) > 1e-6:
raise ValueError("direction and normal vectors are not orthogonal")
angle = math.tan(angle)
M = np.identity(4)
M[:3, :3] += angle * np.outer(direction, normal)
M[:3, 3] = -angle * np.dot(point[:3], normal) * direction
return M
[docs]
def shear_from_matrix(matrix):
"""Return shear angle, direction and plane from shear matrix.
>>> from MDAnalysis.lib.transformations import (shear_matrix,
... shear_from_matrix, is_same_transform)
>>> import random, math
>>> import numpy as np
>>> angle = (random.random() - 0.5) * 4*math.pi
>>> direct = np.random.random(3) - 0.5
>>> point = np.random.random(3) - 0.5
>>> normal = np.cross(direct, np.random.random(3))
>>> S0 = shear_matrix(angle, direct, point, normal)
>>> angle, direct, point, normal = shear_from_matrix(S0)
>>> S1 = shear_matrix(angle, direct, point, normal)
>>> is_same_transform(S0, S1)
True
"""
M = np.array(matrix, dtype=np.float64, copy=False)
M33 = M[:3, :3]
# normal: cross independent eigenvectors corresponding to the eigenvalue 1
l, V = np.linalg.eig(M33)
i = np.where(abs(np.real(l) - 1.0) < 1e-4)[0]
if len(i) < 2:
raise ValueError("no two linear independent eigenvectors found {0!s}".format(l))
V = np.real(V[:, i]).squeeze().T
lenorm = -1.0
for i0, i1 in ((0, 1), (0, 2), (1, 2)):
n = np.cross(V[i0], V[i1])
l = vector_norm(n)
if l > lenorm:
lenorm = l
normal = n
normal /= lenorm
# direction and angle
direction = np.dot(M33 - np.identity(3), normal)
angle = vector_norm(direction)
direction /= angle
angle = math.atan(angle)
# point: eigenvector corresponding to eigenvalue 1
l, V = np.linalg.eig(M)
i = np.where(abs(np.real(l) - 1.0) < 1e-8)[0]
if not len(i):
raise ValueError("no eigenvector corresponding to eigenvalue 1")
point = np.real(V[:, i[-1]]).squeeze()
point /= point[3]
return angle, direction, point, normal
[docs]
def decompose_matrix(matrix):
"""Return sequence of transformations from transformation matrix.
matrix : array_like
Non-degenerative homogeneous transformation matrix
Return tuple of:
scale : vector of 3 scaling factors
shear : list of shear factors for x-y, x-z, y-z axes
angles : list of Euler angles about static x, y, z axes
translate : translation vector along x, y, z axes
perspective : perspective partition of matrix
Raise ValueError if matrix is of wrong type or degenerative.
>>> from MDAnalysis.lib.transformations import (translation_matrix,
... decompose_matrix, scale_matrix, euler_matrix)
>>> import numpy as np
>>> T0 = translation_matrix((1, 2, 3))
>>> scale, shear, angles, trans, persp = decompose_matrix(T0)
>>> T1 = translation_matrix(trans)
>>> np.allclose(T0, T1)
True
>>> S = scale_matrix(0.123)
>>> scale, shear, angles, trans, persp = decompose_matrix(S)
>>> scale[0]
0.123
>>> R0 = euler_matrix(1, 2, 3)
>>> scale, shear, angles, trans, persp = decompose_matrix(R0)
>>> R1 = euler_matrix(*angles)
>>> np.allclose(R0, R1)
True
"""
# pylint: disable=unsubscriptable-object
M = np.array(matrix, dtype=np.float64, copy=True).T
if abs(M[3, 3]) < _EPS:
raise ValueError("M[3, 3] is zero")
M /= M[3, 3]
P = M.copy()
P[:, 3] = 0, 0, 0, 1
if not np.linalg.det(P):
raise ValueError("matrix is singular")
scale = np.zeros((3, ), dtype=np.float64)
shear = [0, 0, 0]
angles = [0, 0, 0]
if any(abs(M[:3, 3]) > _EPS):
perspective = np.dot(M[:, 3], np.linalg.inv(P.T))
M[:, 3] = 0, 0, 0, 1
else:
perspective = np.array((0, 0, 0, 1), dtype=np.float64)
translate = M[3, :3].copy()
M[3, :3] = 0
row = M[:3, :3].copy()
scale[0] = vector_norm(row[0])
row[0] /= scale[0]
shear[0] = np.dot(row[0], row[1])
row[1] -= row[0] * shear[0]
scale[1] = vector_norm(row[1])
row[1] /= scale[1]
shear[0] /= scale[1]
shear[1] = np.dot(row[0], row[2])
row[2] -= row[0] * shear[1]
shear[2] = np.dot(row[1], row[2])
row[2] -= row[1] * shear[2]
scale[2] = vector_norm(row[2])
row[2] /= scale[2]
shear[1:] /= scale[2]
if np.dot(row[0], np.cross(row[1], row[2])) < 0:
scale *= -1
row *= -1
angles[1] = math.asin(-row[0, 2])
if math.cos(angles[1]):
angles[0] = math.atan2(row[1, 2], row[2, 2])
angles[2] = math.atan2(row[0, 1], row[0, 0])
else:
#angles[0] = math.atan2(row[1, 0], row[1, 1])
angles[0] = math.atan2(-row[2, 1], row[1, 1])
angles[2] = 0.0
return scale, shear, angles, translate, perspective
[docs]
def compose_matrix(scale=None, shear=None, angles=None, translate=None,
perspective=None):
"""Return transformation matrix from sequence of transformations.
This is the inverse of the decompose_matrix function.
Sequence of transformations:
scale : vector of 3 scaling factors
shear : list of shear factors for x-y, x-z, y-z axes
angles : list of Euler angles about static x, y, z axes
translate : translation vector along x, y, z axes
perspective : perspective partition of matrix
>>> from MDAnalysis.lib.transformations import (compose_matrix,
... decompose_matrix, is_same_transform)
>>> import math
>>> import numpy as np
>>> scale = np.random.random(3) - 0.5
>>> shear = np.random.random(3) - 0.5
>>> angles = (np.random.random(3) - 0.5) * (2*math.pi)
>>> trans = np.random.random(3) - 0.5
>>> persp = np.random.random(4) - 0.5
>>> M0 = compose_matrix(scale, shear, angles, trans, persp)
>>> result = decompose_matrix(M0)
>>> M1 = compose_matrix(*result)
>>> is_same_transform(M0, M1)
True
"""
M = np.identity(4)
if perspective is not None:
P = np.identity(4)
P[3, :] = perspective[:4]
M = np.dot(M, P)
if translate is not None:
T = np.identity(4)
T[:3, 3] = translate[:3]
M = np.dot(M, T)
if angles is not None:
R = euler_matrix(angles[0], angles[1], angles[2], 'sxyz')
M = np.dot(M, R)
if shear is not None:
Z = np.identity(4)
Z[1, 2] = shear[2]
Z[0, 2] = shear[1]
Z[0, 1] = shear[0]
M = np.dot(M, Z)
if scale is not None:
S = np.identity(4)
S[0, 0] = scale[0]
S[1, 1] = scale[1]
S[2, 2] = scale[2]
M = np.dot(M, S)
M /= M[3, 3]
return M
def orthogonalization_matrix(lengths, angles):
"""Return orthogonalization matrix for crystallographic cell coordinates.
Angles are expected in degrees.
The de-orthogonalization matrix is the inverse.
>>> from MDAnalysis.lib.transformations import orthogonalization_matrix
>>> import numpy as np
>>> O = orthogonalization_matrix((10., 10., 10.), (90., 90., 90.))
>>> np.allclose(O[:3, :3], np.identity(3, float) * 10)
True
>>> O = orthogonalization_matrix([9.8, 12.0, 15.5], [87.2, 80.7, 69.7])
>>> np.allclose(np.sum(O), 43.063229)
True
"""
a, b, c = lengths
angles = np.radians(angles)
sina, sinb, _ = np.sin(angles)
cosa, cosb, cosg = np.cos(angles)
co = (cosa * cosb - cosg) / (sina * sinb)
return np.array(
(
(a * sinb * math.sqrt(1.0 - co * co), 0.0, 0.0, 0.0),
(-a * sinb * co, b * sina, 0.0, 0.0),
(a * cosb, b * cosa, c, 0.0),
(0.0, 0.0, 0.0, 1.0)),
dtype=np.float64)
def superimposition_matrix(v0, v1, scaling=False, usesvd=True):
"""Return matrix to transform given vector set into second vector set.
`v0` and `v1` are shape `(3, *)` or `(4, *)` arrays of at least 3 vectors.
If `usesvd` is ``True``, the weighted sum of squared deviations (RMSD) is
minimized according to the algorithm by W. Kabsch [8]. Otherwise the
quaternion based algorithm by B. Horn [9] is used (slower when using
this Python implementation).
The returned matrix performs rotation, translation and uniform scaling
(if specified).
>>> from MDAnalysis.lib.transformations import (superimposition_matrix,
... random_rotation_matrix, scale_matrix, translation_matrix,
... concatenate_matrices)
>>> import random
>>> import numpy as np
>>> v0 = np.random.rand(3, 10)
>>> M = superimposition_matrix(v0, v0)
>>> np.allclose(M, np.identity(4))
True
>>> R = random_rotation_matrix(np.random.random(3))
>>> v0 = ((1,0,0), (0,1,0), (0,0,1), (1,1,1))
>>> v1 = np.dot(R, v0)
>>> M = superimposition_matrix(v0, v1)
>>> np.allclose(v1, np.dot(M, v0))
True
>>> v0 = (np.random.rand(4, 100) - 0.5) * 20.0
>>> v0[3] = 1.0
>>> v1 = np.dot(R, v0)
>>> M = superimposition_matrix(v0, v1)
>>> np.allclose(v1, np.dot(M, v0))
True
>>> S = scale_matrix(random.random())
>>> T = translation_matrix(np.random.random(3)-0.5)
>>> M = concatenate_matrices(T, R, S)
>>> v1 = np.dot(M, v0)
>>> v0[:3] += np.random.normal(0.0, 1e-9, 300).reshape(3, -1)
>>> M = superimposition_matrix(v0, v1, scaling=True)
>>> np.allclose(v1, np.dot(M, v0))
True
>>> M = superimposition_matrix(v0, v1, scaling=True, usesvd=False)
>>> np.allclose(v1, np.dot(M, v0))
True
>>> v = np.empty((4, 100, 3), dtype=np.float64)
>>> v[:, :, 0] = v0
>>> M = superimposition_matrix(v0, v1, scaling=True, usesvd=False)
>>> np.allclose(v1, np.dot(M, v[:, :, 0]))
True
"""
v0 = np.array(v0, dtype=np.float64, copy=no_copy_shim)[:3]
v1 = np.array(v1, dtype=np.float64, copy=no_copy_shim)[:3]
if v0.shape != v1.shape or v0.shape[1] < 3:
raise ValueError("vector sets are of wrong shape or type")
# move centroids to origin
t0 = np.mean(v0, axis=1)
t1 = np.mean(v1, axis=1)
v0 = v0 - t0.reshape(3, 1)
v1 = v1 - t1.reshape(3, 1)
if usesvd:
# Singular Value Decomposition of covariance matrix
u, s, vh = np.linalg.svd(np.dot(v1, v0.T))
# rotation matrix from SVD orthonormal bases
R = np.dot(u, vh)
if np.linalg.det(R) < 0.0:
# R does not constitute right handed system
R -= np.outer(u[:, 2], vh[2, :] * 2.0)
s[-1] *= -1.0
# homogeneous transformation matrix
M = np.identity(4)
M[:3, :3] = R
else:
# compute symmetric matrix N
xx, yy, zz = np.einsum('ij,ij->i', v0 , v1)
xy, yz, zx = np.einsum('ij,ij->i', v0, np.roll(v1, -1, axis=0))
xz, yx, zy = np.einsum('ij,ij->i', v0, np.roll(v1, -2, axis=0))
N = (
(xx + yy + zz, 0.0, 0.0, 0.0),
(yz - zy, xx - yy - zz, 0.0, 0.0),
(zx - xz, xy + yx, -xx + yy - zz, 0.0),
(xy - yx, zx + xz, yz + zy, -xx - yy + zz))
# quaternion: eigenvector corresponding to most positive eigenvalue
l, V = np.linalg.eigh(N)
q = V[:, np.argmax(l)]
q /= vector_norm(q) # unit quaternion
# homogeneous transformation matrix
M = quaternion_matrix(q)
# scale: ratio of rms deviations from centroid
if scaling:
M[:3, :3] *= math.sqrt(np.einsum('ij,ij->',v1,v1) /
np.einsum('ij,ij->',v0,v0))
# translation
M[:3, 3] = t1
T = np.identity(4)
T[:3, 3] = -t0
M = np.dot(M, T)
return M
def euler_matrix(ai, aj, ak, axes='sxyz'):
"""Return homogeneous rotation matrix from Euler angles and axis sequence.
ai, aj, ak : Euler's roll, pitch and yaw angles
axes : One of 24 axis sequences as string or encoded tuple
>>> from MDAnalysis.lib.transformations import (euler_matrix,
... _AXES2TUPLE, _TUPLE2AXES)
>>> import math
>>> import numpy as np
>>> R = euler_matrix(1, 2, 3, 'syxz')
>>> np.allclose(np.sum(R[0]), -1.34786452)
True
>>> R = euler_matrix(1, 2, 3, (0, 1, 0, 1))
>>> np.allclose(np.sum(R[0]), -0.383436184)
True
>>> ai, aj, ak = (4.0*math.pi) * (np.random.random(3) - 0.5)
>>> for axes in _AXES2TUPLE.keys():
... R = euler_matrix(ai, aj, ak, axes)
>>> for axes in _TUPLE2AXES.keys():
... R = euler_matrix(ai, aj, ak, axes)
"""
try:
firstaxis, parity, repetition, frame = _AXES2TUPLE[axes]
except (AttributeError, KeyError):
_ = _TUPLE2AXES[axes]
firstaxis, parity, repetition, frame = axes
i = firstaxis
j = _NEXT_AXIS[i + parity]
k = _NEXT_AXIS[i - parity + 1]
if frame:
ai, ak = ak, ai
if parity:
ai, aj, ak = -ai, -aj, -ak
si, sj, sk = math.sin(ai), math.sin(aj), math.sin(ak)
ci, cj, ck = math.cos(ai), math.cos(aj), math.cos(ak)
cc, cs = ci * ck, ci * sk
sc, ss = si * ck, si * sk
M = np.identity(4)
if repetition:
M[i, i] = cj
M[i, j] = sj * si
M[i, k] = sj * ci
M[j, i] = sj * sk
M[j, j] = -cj * ss + cc
M[j, k] = -cj * cs - sc
M[k, i] = -sj * ck
M[k, j] = cj * sc + cs
M[k, k] = cj * cc - ss
else:
M[i, i] = cj * ck
M[i, j] = sj * sc - cs
M[i, k] = sj * cc + ss
M[j, i] = cj * sk
M[j, j] = sj * ss + cc
M[j, k] = sj * cs - sc
M[k, i] = -sj
M[k, j] = cj * si
M[k, k] = cj * ci
return M
def euler_from_matrix(matrix, axes='sxyz'):
"""Return Euler angles from rotation matrix for specified axis sequence.
axes : One of 24 axis sequences as string or encoded tuple
Note that many Euler angle triplets can describe one matrix.
>>> from MDAnalysis.lib.transformations import (euler_matrix,
... euler_from_matrix, _AXES2TUPLE)
>>> import math
>>> import numpy as np
>>> R0 = euler_matrix(1, 2, 3, 'syxz')
>>> al, be, ga = euler_from_matrix(R0, 'syxz')
>>> R1 = euler_matrix(al, be, ga, 'syxz')
>>> np.allclose(R0, R1)
True
>>> angles = (4.0*math.pi) * (np.random.random(3) - 0.5)
>>> for axes in _AXES2TUPLE.keys():
... R0 = euler_matrix(axes=axes, *angles)
... R1 = euler_matrix(axes=axes, *euler_from_matrix(R0, axes))
... if not np.allclose(R0, R1): print(axes, "failed")
"""
try:
firstaxis, parity, repetition, frame = _AXES2TUPLE[axes.lower()]
except (AttributeError, KeyError):
_ = _TUPLE2AXES[axes]
firstaxis, parity, repetition, frame = axes
i = firstaxis
j = _NEXT_AXIS[i + parity]
k = _NEXT_AXIS[i - parity + 1]
M = np.array(matrix, dtype=np.float64, copy=False)[:3, :3]
if repetition:
sy = math.sqrt(M[i, j] * M[i, j] + M[i, k] * M[i, k])
if sy > _EPS:
ax = math.atan2(M[i, j], M[i, k])
ay = math.atan2(sy, M[i, i])
az = math.atan2(M[j, i], -M[k, i])
else:
ax = math.atan2(-M[j, k], M[j, j])
ay = math.atan2(sy, M[i, i])
az = 0.0
else:
cy = math.sqrt(M[i, i] * M[i, i] + M[j, i] * M[j, i])
if cy > _EPS:
ax = math.atan2(M[k, j], M[k, k])
ay = math.atan2(-M[k, i], cy)
az = math.atan2(M[j, i], M[i, i])
else:
ax = math.atan2(-M[j, k], M[j, j])
ay = math.atan2(-M[k, i], cy)
az = 0.0
if parity:
ax, ay, az = -ax, -ay, -az
if frame:
ax, az = az, ax
return ax, ay, az
[docs]
def euler_from_quaternion(quaternion, axes='sxyz'):
"""Return Euler angles from quaternion for specified axis sequence.
>>> from MDAnalysis.lib.transformations import euler_from_quaternion
>>> import numpy as np
>>> angles = euler_from_quaternion([0.99810947, 0.06146124, 0, 0])
>>> np.allclose(angles, [0.123, 0, 0])
True
"""
return euler_from_matrix(quaternion_matrix(quaternion), axes)
def quaternion_from_euler(ai, aj, ak, axes='sxyz'):
"""Return quaternion from Euler angles and axis sequence.
ai, aj, ak : Euler's roll, pitch and yaw angles
axes : One of 24 axis sequences as string or encoded tuple
>>> from MDAnalysis.lib.transformations import quaternion_from_euler
>>> q = quaternion_from_euler(1, 2, 3, 'ryxz')
>>> np.allclose(q, [0.435953, 0.310622, -0.718287, 0.444435])
True
"""
try:
firstaxis, parity, repetition, frame = _AXES2TUPLE[axes.lower()]
except (AttributeError, KeyError):
_ = _TUPLE2AXES[axes]
firstaxis, parity, repetition, frame = axes
i = firstaxis + 1
j = _NEXT_AXIS[i + parity - 1] + 1
k = _NEXT_AXIS[i - parity] + 1
if frame:
ai, ak = ak, ai
if parity:
aj = -aj
ai /= 2.0
aj /= 2.0
ak /= 2.0
ci = math.cos(ai)
si = math.sin(ai)
cj = math.cos(aj)
sj = math.sin(aj)
ck = math.cos(ak)
sk = math.sin(ak)
cc = ci * ck
cs = ci * sk
sc = si * ck
ss = si * sk
quaternion = np.empty((4, ), dtype=np.float64)
if repetition:
quaternion[0] = cj * (cc - ss)
quaternion[i] = cj * (cs + sc)
quaternion[j] = sj * (cc + ss)
quaternion[k] = sj * (cs - sc)
else:
quaternion[0] = cj * cc + sj * ss
quaternion[i] = cj * sc - sj * cs
quaternion[j] = cj * ss + sj * cc
quaternion[k] = cj * cs - sj * sc
if parity:
quaternion[j] *= -1
return quaternion
def quaternion_about_axis(angle, axis):
"""Return quaternion for rotation about axis.
>>> from MDAnalysis.lib.transformations import quaternion_about_axis
>>> import numpy as np
>>> q = quaternion_about_axis(0.123, (1, 0, 0))
>>> np.allclose(q, [0.99810947, 0.06146124, 0, 0])
True
"""
quaternion = np.zeros((4, ), dtype=np.float64)
quaternion[1] = axis[0]
quaternion[2] = axis[1]
quaternion[3] = axis[2]
qlen = vector_norm(quaternion)
if qlen > _EPS:
quaternion *= math.sin(angle / 2.0) / qlen
quaternion[0] = math.cos(angle / 2.0)
return quaternion
def quaternion_matrix(quaternion):
"""Return homogeneous rotation matrix from quaternion.
>>> from MDAnalysis.lib.transformations import (identity_matrix,
... quaternion_matrix, rotation_matrix)
>>> import numpy as np
>>> M = quaternion_matrix([0.99810947, 0.06146124, 0, 0])
>>> np.allclose(M, rotation_matrix(0.123, (1, 0, 0)))
True
>>> M = quaternion_matrix([1, 0, 0, 0])
>>> np.allclose(M, identity_matrix())
True
>>> M = quaternion_matrix([0, 1, 0, 0])
>>> np.allclose(M, np.diag([1, -1, -1, 1]))
True
"""
q = np.array(quaternion[:4], dtype=np.float64, copy=True)
nq = np.dot(q, q)
if nq < _EPS:
return np.identity(4)
q *= math.sqrt(2.0 / nq)
q = np.outer(q, q)
return np.array(
(
(1.0 - q[2, 2] - q[3, 3], q[1, 2] - q[3, 0], q[1, 3] + q[2, 0], 0.0),
(q[1, 2] + q[3, 0], 1.0 - q[1, 1] - q[3, 3], q[2, 3] - q[1, 0], 0.0),
(q[1, 3] - q[2, 0], q[2, 3] + q[1, 0], 1.0 - q[1, 1] - q[2, 2], 0.0),
(0.0, 0.0, 0.0, 1.0)
), dtype=np.float64)
def quaternion_from_matrix(matrix, isprecise=False):
"""Return quaternion from rotation matrix.
If isprecise=True, the input matrix is assumed to be a precise rotation
matrix and a faster algorithm is used.
>>> from MDAnalysis.lib.transformations import (identity_matrix,
... quaternion_from_matrix, rotation_matrix, random_rotation_matrix,
... is_same_transform, quaternion_matrix)
>>> import numpy as np
>>> q = quaternion_from_matrix(identity_matrix(), True)
>>> np.allclose(q, [1., 0., 0., 0.])
True
>>> q = quaternion_from_matrix(np.diag([1., -1., -1., 1.]))
>>> np.allclose(q, [0, 1, 0, 0]) or np.allclose(q, [0, -1, 0, 0])
True
>>> R = rotation_matrix(0.123, (1, 2, 3))
>>> q = quaternion_from_matrix(R, True)
>>> np.allclose(q, [0.9981095, 0.0164262, 0.0328524, 0.0492786])
True
>>> R = [[-0.545, 0.797, 0.260, 0], [0.733, 0.603, -0.313, 0],
... [-0.407, 0.021, -0.913, 0], [0, 0, 0, 1]]
>>> q = quaternion_from_matrix(R)
>>> np.allclose(q, [0.19069, 0.43736, 0.87485, -0.083611])
True
>>> R = [[0.395, 0.362, 0.843, 0], [-0.626, 0.796, -0.056, 0],
... [-0.677, -0.498, 0.529, 0], [0, 0, 0, 1]]
>>> q = quaternion_from_matrix(R)
>>> np.allclose(q, [0.82336615, -0.13610694, 0.46344705, -0.29792603])
True
>>> R = random_rotation_matrix()
>>> q = quaternion_from_matrix(R)
>>> is_same_transform(R, quaternion_matrix(q))
True
"""
M = np.array(matrix, dtype=np.float64, copy=no_copy_shim)[:4, :4]
if isprecise:
q = np.empty((4, ), dtype=np.float64)
t = np.trace(M)
if t > M[3, 3]:
q[0] = t
q[3] = M[1, 0] - M[0, 1]
q[2] = M[0, 2] - M[2, 0]
q[1] = M[2, 1] - M[1, 2]
else:
i, j, k = 1, 2, 3
if M[1, 1] > M[0, 0]:
i, j, k = 2, 3, 1
if M[2, 2] > M[i, i]:
i, j, k = 3, 1, 2
t = M[i, i] - (M[j, j] + M[k, k]) + M[3, 3]
q[i] = t
q[j] = M[i, j] + M[j, i]
q[k] = M[k, i] + M[i, k]
q[3] = M[k, j] - M[j, k]
q *= 0.5 / math.sqrt(t * M[3, 3])
else:
m00 = M[0, 0]
m01 = M[0, 1]
m02 = M[0, 2]
m10 = M[1, 0]
m11 = M[1, 1]
m12 = M[1, 2]
m20 = M[2, 0]
m21 = M[2, 1]
m22 = M[2, 2]
# symmetric matrix K
K = np.array((
(m00 - m11 - m22, 0.0, 0.0, 0.0),
(m01 + m10, m11 - m00 - m22, 0.0, 0.0),
(m02 + m20, m12 + m21, m22 - m00 - m11, 0.0),
(m21 - m12, m02 - m20, m10 - m01, m00 + m11 + m22)))
K /= 3.0
# quaternion is eigenvector of K that corresponds to largest eigenvalue
l, V = np.linalg.eigh(K)
q = V[[3, 0, 1, 2], np.argmax(l)]
if q[0] < 0.0:
q *= -1.0
return q
def quaternion_multiply(quaternion1, quaternion0):
"""Return multiplication of two quaternions.
>>> from MDAnalysis.lib.transformations import quaternion_multiply
>>> import numpy as np
>>> q = quaternion_multiply([4, 1, -2, 3], [8, -5, 6, 7])
>>> np.allclose(q, [28, -44, -14, 48])
True
"""
w0, x0, y0, z0 = quaternion0
w1, x1, y1, z1 = quaternion1
return np.array(
(
-x1 * x0 - y1 * y0 - z1 * z0 + w1 * w0,
x1 * w0 + y1 * z0 - z1 * y0 + w1 * x0,
-x1 * z0 + y1 * w0 + z1 * x0 + w1 * y0,
x1 * y0 - y1 * x0 + z1 * w0 + w1 * z0), dtype=np.float64)
def quaternion_conjugate(quaternion):
"""Return conjugate of quaternion.
>>> from MDAnalysis.lib.transformations import (random_quaternion,
... quaternion_conjugate)
>>> import numpy as np
>>> q0 = random_quaternion()
>>> q1 = quaternion_conjugate(q0)
>>> q1[0] == q0[0] and all(q1[1:] == -q0[1:])
True
"""
return np.array(
(
quaternion[0], -quaternion[1],
-quaternion[2], -quaternion[3]), dtype=np.float64)
def quaternion_inverse(quaternion):
"""Return inverse of quaternion.
>>> from MDAnalysis.lib.transformations import (random_quaternion,
... quaternion_inverse)
>>> import numpy as np
>>> q0 = random_quaternion()
>>> q1 = quaternion_inverse(q0)
>>> np.allclose(quaternion_multiply(q0, q1), [1, 0, 0, 0])
True
"""
return quaternion_conjugate(quaternion) / np.dot(quaternion, quaternion)
[docs]
def quaternion_real(quaternion):
"""Return real part of quaternion.
>>> from MDAnalysis.lib.transformations import quaternion_real
>>> quaternion_real([3.0, 0.0, 1.0, 2.0])
3.0
"""
return quaternion[0]
[docs]
def quaternion_imag(quaternion):
"""Return imaginary part of quaternion.
>>> from MDAnalysis.lib.transformations import quaternion_imag
>>> quaternion_imag([3.0, 0.0, 1.0, 2.0])
[0.0, 1.0, 2.0]
"""
return quaternion[1:4]
def quaternion_slerp(quat0, quat1, fraction, spin=0, shortestpath=True):
r"""Return spherical linear interpolation between two quaternions.
>>> from MDAnalysis.lib.transformations import (random_quaternion,
... quaternion_slerp)
>>> import math
>>> import numpy as np
>>> q0 = random_quaternion()
>>> q1 = random_quaternion()
>>> q = quaternion_slerp(q0, q1, 0.0)
>>> np.allclose(q, q0)
True
>>> q = quaternion_slerp(q0, q1, 1.0, 1)
>>> np.allclose(q, q1)
True
>>> q = quaternion_slerp(q0, q1, 0.5)
>>> angle = math.acos(np.dot(q0, q))
>>> np.allclose(2.0, math.acos(np.dot(q0, q1)) / angle) or \
... np.allclose(2.0, math.acos(-np.dot(q0, q1)) / angle)
True
"""
q0 = unit_vector(quat0[:4])
q1 = unit_vector(quat1[:4])
if fraction == 0.0:
return q0
elif fraction == 1.0:
return q1
d = np.dot(q0, q1)
if abs(abs(d) - 1.0) < _EPS:
return q0
if shortestpath and d < 0.0:
# invert rotation
d = -d
q1 *= -1.0
angle = math.acos(d) + spin * math.pi
if abs(angle) < _EPS:
return q0
isin = 1.0 / math.sin(angle)
q0 *= math.sin((1.0 - fraction) * angle) * isin
q1 *= math.sin(fraction * angle) * isin
q0 += q1
return q0
def random_quaternion(rand=None):
"""Return uniform random unit quaternion.
rand: array like or None
Three independent random variables that are uniformly distributed
between 0 and 1.
>>> from MDAnalysis.lib.transformations import (random_quaternion,
... vector_norm)
>>> import numpy as np
>>> q = random_quaternion()
>>> np.allclose(1.0, vector_norm(q))
True
>>> q = random_quaternion(np.random.random(3))
>>> len(q.shape), q.shape[0]==4
(1, True)
"""
if rand is None:
rand = np.random.rand(3)
else:
assert len(rand) == 3
r1 = np.sqrt(1.0 - rand[0])
r2 = np.sqrt(rand[0])
pi2 = math.pi * 2.0
t1 = pi2 * rand[1]
t2 = pi2 * rand[2]
return np.array(
(
np.cos(t2) * r2,
np.sin(t1) * r1,
np.cos(t1) * r1,
np.sin(t2) * r2), dtype=np.float64)
def random_rotation_matrix(rand=None):
"""Return uniform random rotation matrix.
rnd: array like
Three independent random variables that are uniformly distributed
between 0 and 1 for each returned quaternion.
>>> from MDAnalysis.lib.transformations import random_rotation_matrix
>>> import numpy as np
>>> R = random_rotation_matrix()
>>> np.allclose(np.dot(R.T, R), np.identity(4))
True
"""
return quaternion_matrix(random_quaternion(rand))
[docs]
class Arcball(object):
"""Virtual Trackball Control.
>>> from MDAnalysis.lib.transformations import Arcball
>>> import numpy as np
>>> ball = Arcball()
>>> ball = Arcball(initial=np.identity(4))
>>> ball.place([320, 320], 320)
>>> ball.down([500, 250])
>>> ball.drag([475, 275])
>>> R = ball.matrix()
>>> np.allclose(np.sum(R), 3.90583455)
True
>>> ball = Arcball(initial=[1, 0, 0, 0])
>>> ball.place([320, 320], 320)
>>> ball.setaxes([1,1,0], [-1, 1, 0])
>>> ball.setconstrain(True)
>>> ball.down([400, 200])
>>> ball.drag([200, 400])
>>> R = ball.matrix()
>>> np.allclose(np.sum(R), 0.2055924)
True
>>> ball.next()
"""
def __init__(self, initial=None):
"""Initialize virtual trackball control.
initial : quaternion or rotation matrix
"""
self._axis = None
self._axes = None
self._radius = 1.0
self._center = [0.0, 0.0]
self._vdown = np.array([0, 0, 1], dtype=np.float64)
self._constrain = False
if initial is None:
self._qdown = np.array([1, 0, 0, 0], dtype=np.float64)
else:
initial = np.array(initial, dtype=np.float64)
if initial.shape == (4, 4):
self._qdown = quaternion_from_matrix(initial)
elif initial.shape == (4, ):
initial /= vector_norm(initial)
self._qdown = initial
else:
raise ValueError("initial not a quaternion or matrix")
self._qnow = self._qpre = self._qdown
[docs]
def place(self, center, radius):
"""Place Arcball, e.g. when window size changes.
center : sequence[2]
Window coordinates of trackball center.
radius : float
Radius of trackball in window coordinates.
"""
self._radius = float(radius)
self._center[0] = center[0]
self._center[1] = center[1]
[docs]
def setaxes(self, *axes):
"""Set axes to constrain rotations."""
if axes is None:
self._axes = None
else:
self._axes = [unit_vector(axis) for axis in axes]
[docs]
def setconstrain(self, constrain):
"""Set state of constrain to axis mode."""
self._constrain = constrain is True
[docs]
def getconstrain(self):
"""Return state of constrain to axis mode."""
return self._constrain
[docs]
def down(self, point):
"""Set initial cursor window coordinates and pick constrain-axis."""
self._vdown = arcball_map_to_sphere(point, self._center, self._radius)
self._qdown = self._qpre = self._qnow
if self._constrain and self._axes is not None:
self._axis = arcball_nearest_axis(self._vdown, self._axes)
self._vdown = arcball_constrain_to_axis(self._vdown, self._axis)
else:
self._axis = None
[docs]
def drag(self, point):
"""Update current cursor window coordinates."""
vnow = arcball_map_to_sphere(point, self._center, self._radius)
if self._axis is not None:
vnow = arcball_constrain_to_axis(vnow, self._axis)
self._qpre = self._qnow
t = np.cross(self._vdown, vnow)
if np.dot(t, t) < _EPS:
self._qnow = self._qdown
else:
q = [np.dot(self._vdown, vnow), t[0], t[1], t[2]]
self._qnow = quaternion_multiply(q, self._qdown)
[docs]
def next(self, acceleration=0.0):
"""Continue rotation in direction of last drag."""
q = quaternion_slerp(self._qpre, self._qnow, 2.0 + acceleration, False)
self._qpre, self._qnow = self._qnow, q
[docs]
def matrix(self):
"""Return homogeneous rotation matrix."""
return quaternion_matrix(self._qnow)
def arcball_map_to_sphere(point, center, radius):
"""Return unit sphere coordinates from window coordinates."""
v = np.array(
(
(point[0] - center[0]) / radius,
(center[1] - point[1]) / radius,
0.0
), dtype=np.float64
)
n = v[0] * v[0] + v[1] * v[1]
if n > 1.0:
v /= math.sqrt(n) # position outside of sphere
else:
v[2] = math.sqrt(1.0 - n)
return v
def arcball_constrain_to_axis(point, axis):
"""Return sphere point perpendicular to axis."""
v = np.array(point, dtype=np.float64, copy=True)
a = np.array(axis, dtype=np.float64, copy=True)
v -= a * np.dot(a, v) # on plane
n = vector_norm(v)
if n > _EPS:
if v[2] < 0.0:
v *= -1.0
v /= n
return v
if a[2] == 1.0:
return np.array([1, 0, 0], dtype=np.float64)
return unit_vector([-a[1], a[0], 0])
[docs]
def arcball_nearest_axis(point, axes):
"""Return axis, which arc is nearest to point."""
point = np.array(point, dtype=np.float64, copy=False)
nearest = None
mx = -1.0
for axis in axes:
t = np.dot(arcball_constrain_to_axis(point, axis), point)
if t > mx:
nearest = axis
mx = t
return nearest
# epsilon for testing whether a number is close to zero
_EPS = np.finfo(float).eps * 4.0
# axis sequences for Euler angles
_NEXT_AXIS = [1, 2, 0, 1]
# map axes strings to/from tuples of inner axis, parity, repetition, frame
_AXES2TUPLE = {
'sxyz': (0, 0, 0, 0), 'sxyx': (0, 0, 1, 0), 'sxzy': (0, 1, 0, 0),
'sxzx': (0, 1, 1, 0), 'syzx': (1, 0, 0, 0), 'syzy': (1, 0, 1, 0),
'syxz': (1, 1, 0, 0), 'syxy': (1, 1, 1, 0), 'szxy': (2, 0, 0, 0),
'szxz': (2, 0, 1, 0), 'szyx': (2, 1, 0, 0), 'szyz': (2, 1, 1, 0),
'rzyx': (0, 0, 0, 1), 'rxyx': (0, 0, 1, 1), 'ryzx': (0, 1, 0, 1),
'rxzx': (0, 1, 1, 1), 'rxzy': (1, 0, 0, 1), 'ryzy': (1, 0, 1, 1),
'rzxy': (1, 1, 0, 1), 'ryxy': (1, 1, 1, 1), 'ryxz': (2, 0, 0, 1),
'rzxz': (2, 0, 1, 1), 'rxyz': (2, 1, 0, 1), 'rzyz': (2, 1, 1, 1)}
_TUPLE2AXES = dict((v, k) for k, v in _AXES2TUPLE.items())
def vector_norm(data, axis=None, out=None):
"""Return length, i.e. eucledian norm, of ndarray along axis.
>>> from MDAnalysis.lib.transformations import vector_norm
>>> import numpy as np
>>> v = np.random.random(3)
>>> n = vector_norm(v)
>>> np.allclose(n, np.linalg.norm(v))
True
>>> v = np.random.rand(6, 5, 3)
>>> n = vector_norm(v, axis=-1)
>>> np.allclose(n, np.sqrt(np.sum(v*v, axis=2)))
True
>>> n = vector_norm(v, axis=1)
>>> np.allclose(n, np.sqrt(np.sum(v*v, axis=1)))
True
>>> v = np.random.rand(5, 4, 3)
>>> n = np.empty((5, 3), dtype=np.float64)
>>> vector_norm(v, axis=1, out=n)
>>> np.allclose(n, np.sqrt(np.sum(v*v, axis=1)))
True
>>> vector_norm([])
0.0
>>> vector_norm([1.0])
1.0
"""
data = np.array(data, dtype=np.float64, copy=True)
if out is None:
if data.ndim == 1:
return math.sqrt(np.dot(data, data))
data *= data
out = np.atleast_1d(np.sum(data, axis=axis))
np.sqrt(out, out)
return out
else:
data *= data
np.sum(data, axis=axis, out=out)
np.sqrt(out, out)
def unit_vector(data, axis=None, out=None):
"""Return ndarray normalized by length, i.e. eucledian norm, along axis.
>>> from MDAnalysis.lib.transformations import unit_vector
>>> import numpy as np
>>> v0 = np.random.random(3)
>>> v1 = unit_vector(v0)
>>> np.allclose(v1, v0 / np.linalg.norm(v0))
True
>>> v0 = np.random.rand(5, 4, 3)
>>> v1 = unit_vector(v0, axis=-1)
>>> v2 = v0 / np.expand_dims(np.sqrt(np.sum(v0*v0, axis=2)), 2)
>>> np.allclose(v1, v2)
True
>>> v1 = unit_vector(v0, axis=1)
>>> v2 = v0 / np.expand_dims(np.sqrt(np.sum(v0*v0, axis=1)), 1)
>>> np.allclose(v1, v2)
True
>>> v1 = np.empty((5, 4, 3), dtype=np.float64)
>>> unit_vector(v0, axis=1, out=v1)
>>> np.allclose(v1, v2)
True
>>> list(unit_vector([]))
[]
>>> list(unit_vector([1.0]))
[1.0]
"""
if out is None:
data = np.array(data, dtype=np.float64, copy=True)
if data.ndim == 1:
data /= math.sqrt(np.dot(data, data))
return data
else:
if out is not data:
out[:] = np.array(data, copy=False)
data = out
length = np.atleast_1d(np.sum(data * data, axis))
np.sqrt(length, length)
if axis is not None:
length = np.expand_dims(length, axis)
data /= length
if out is None:
return data
def random_vector(size):
"""Return array of random doubles in the half-open interval [0.0, 1.0).
>>> from MDAnalysis.lib.transformations import random_vector
>>> import numpy as np
>>> v = random_vector(10000)
>>> np.all(v >= 0.0) and np.all(v < 1.0)
True
>>> v0 = random_vector(10)
>>> v1 = random_vector(10)
>>> np.any(v0 == v1)
False
"""
return np.random.random(size)
def inverse_matrix(matrix):
"""Return inverse of square transformation matrix.
>>> from MDAnalysis.lib.transformations import (random_rotation_matrix,
... inverse_matrix)
>>> import numpy as np
>>> M0 = random_rotation_matrix()
>>> M1 = inverse_matrix(M0.T)
>>> np.allclose(M1, np.linalg.inv(M0.T))
True
>>> for size in range(1, 7):
... M0 = np.random.rand(size, size)
... M1 = inverse_matrix(M0)
... if not np.allclose(M1, np.linalg.inv(M0)): print(size)
"""
return np.linalg.inv(matrix)
[docs]
def concatenate_matrices(*matrices):
"""Return concatenation of series of transformation matrices.
>>> from MDAnalysis.lib.transformations import concatenate_matrices
>>> import numpy as np
>>> M = np.random.rand(16).reshape((4, 4)) - 0.5
>>> np.allclose(M, concatenate_matrices(M))
True
>>> np.allclose(np.dot(M, M.T), concatenate_matrices(M, M.T))
True
"""
M = np.identity(4)
for i in matrices:
M = np.dot(M, i)
return M
def is_same_transform(matrix0, matrix1):
"""Return True if two matrices perform same transformation.
>>> from MDAnalysis.lib.transformations import (is_same_transform,
... random_rotation_matrix)
>>> import numpy as np
>>> is_same_transform(np.identity(4), np.identity(4))
True
>>> is_same_transform(np.identity(4), random_rotation_matrix())
False
"""
matrix0 = np.array(matrix0, dtype=np.float64, copy=True)
matrix0 /= matrix0[3, 3]
matrix1 = np.array(matrix1, dtype=np.float64, copy=True)
matrix1 /= matrix1[3, 3]
return np.allclose(matrix0, matrix1)
def _import_module(module_name, warn=True, prefix='_py_', ignore='_'):
"""Try import all public attributes from module into global namespace.
Existing attributes with name clashes are renamed with prefix.
Attributes starting with underscore are ignored by default.
Return True on successful import.
"""
sys.path.append(os.path.dirname(__file__))
try:
module = __import__(module_name)
except ImportError:
sys.path.pop()
if warn:
warnings.warn("failed to import module " + module_name)
else:
sys.path.pop()
for attr in dir(module):
if ignore and attr.startswith(ignore):
continue
if prefix:
if attr in globals():
globals()[prefix + attr] = globals()[attr]
elif warn:
warnings.warn("no Python implementation of " + attr)
globals()[attr] = getattr(module, attr)
return True
# orbeckst --- some simple geometry
[docs]
def rotaxis(a, b):
"""Return the rotation axis to rotate vector a into b.
Parameters
----------
a, b : array_like
two vectors
Returns
-------
c : np.ndarray
vector to rotate a into b
Note
----
If a == b this will always return [1, 0, 0]
"""
if np.allclose(a, b):
return np.array([1, 0, 0])
c = np.cross(a, b)
return c / np.linalg.norm(c)
_import_module('_transformations')
# Documentation in HTML format can be generated with Epydoc
__docformat__ = "restructuredtext en"