Source code for sknano.core.math._transforms
# -*- coding: utf-8 -*-
"""
===============================================================================
Functions for linear algebra transforms (:mod:`sknano.core.math._transforms`)
===============================================================================
.. currentmodule:: sknano.core.math._transforms
"""
from __future__ import absolute_import, division, print_function, \
unicode_literals
from itertools import combinations
import six
from six.moves import range
__docformat__ = 'restructuredtext en'
import numpy as np
__all__ = ['rotate',
'scale',
'translate',
'Rx', 'Ry', 'Rz',
'reflection_matrix',
'rotation_matrix',
'scaling_matrix',
'transformation_matrix',
'axis_angle_from_rotation_matrix']
I = np.identity(4)
_str2array = {}
for i, axis in enumerate(('x', 'y', 'z')):
_str2array[axis] = I[:3, i]
[docs]def rotate(obj, angle=None, axis=None, rot_axis=None, anchor_point=None,
rot_point=None, from_vector=None, to_vector=None, deg2rad=False,
transform_matrix=None, verbose=False):
"""Rotate object.
.. versionadded:: 0.3.0
Parameters
----------
obj : array_like
angle : float, optional
axis : {array_like, str, :class:`~sknano.core.math.Vector`}
anchor_point : {array_like, :class:`~sknano.core.math.Point`}
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
deg2rad : bool, optional
transform_matrix : array_like, optional
Returns
-------
rotated object : array_like
"""
if axis is None and rot_axis is not None:
axis = rot_axis
if verbose:
print('In rotate\n'
'obj: {}\n'.format(obj) +
'axis: {}\n'.format(axis) +
'anchor_point: {}\n'.format(anchor_point) +
'transform_matrix: {}\n'.format(transform_matrix))
if transform_matrix is not None and \
isinstance(transform_matrix, np.ndarray):
if transform_matrix.shape == (3, 3):
I4x4 = np.eye(4)
I4x4[:3, :3] = transform_matrix
transform_matrix = I4x4
t = np.append(np.asarray(obj), 1)
try:
rot_obj = np.dot(transform_matrix, t)[:-1]
except TypeError:
if axis is None and len(obj) > 2:
raise TypeError('Expected `axis` to be a 3D Vector.')
tmatrix = \
transformation_matrix(angle=angle, axis=axis,
anchor_point=anchor_point,
rot_point=rot_point, from_vector=from_vector,
to_vector=to_vector, deg2rad=deg2rad,
verbose=verbose)
rot_obj = np.dot(tmatrix, t)[:-1]
if rot_obj.__class__ != obj.__class__:
rot_obj = obj.__class__(rot_obj)
return rot_obj
[docs]def Rx(angle, deg2rad=False):
"""Generate the :math:`3\\times3` rotation matrix :math:`R_x(\\theta)` \
for a rotation about the :math:`x` axis by an angle :math:`\\theta`.
Parameters
----------
angle : float
The rotation angle :math:`\\theta` in *radians*. If the angle is
given in *degrees*, then you must set `deg2rad=True` to correctly
calculate the rotation matrix.
deg2rad : bool, optional
if `True`, then `angle` is converted from degrees to radians.
Returns
-------
:class:`~numpy:numpy.ndarray`
:math:`3\\times3` rotation matrix :math:`R_x(\\theta)` for a
rotation about the :math:`x` axis by an angle :math:`\\theta`.
.. math::
R_x = \\begin{pmatrix}
1 & 0 & 0\\\\
0 & \\cos\\theta & -\\sin\\theta\\\\
0 & \\sin\\theta & \\cos\\theta
\\end{pmatrix}
Examples
--------
>>> import numpy as np
>>> from sknano.core.math import Rx
>>> Rx(np.pi/4)
array([[ 1. , 0. , 0. ],
[ 0. , 0.70710678, -0.70710678],
[ 0. , 0.70710678, 0.70710678]])
>>> np.alltrue(Rx(np.pi/4) == Rx(45, deg2rad=True))
True
"""
if deg2rad:
angle = np.radians(angle)
cosa = np.cos(angle)
sina = np.sin(angle)
Rmat = np.array([[1.0, 0.0, 0.0], [0.0, cosa, -sina], [0.0, sina, cosa]])
Rmat[np.where(np.abs(Rmat) <= np.finfo(float).eps)] = 0.0
return Rmat
[docs]def Ry(angle, deg2rad=False):
"""Generate the :math:`3\\times3` rotation matrix :math:`R_y(\\theta)` \
for a rotation about the :math:`y` axis by an angle :math:`\\theta`.
Parameters
----------
angle : float
The rotation angle :math:`\\theta` in *radians*. If the angle is
given in *degrees*, then you must set `deg2rad=True` to correctly
calculate the rotation matrix.
deg2rad : bool, optional
if `True`, then `angle` is converted from degrees to radians.
Returns
-------
:class:`~numpy:numpy.ndarray`
:math:`3\\times3` rotation matrix :math:`R_y(\\theta)` for a
rotation about the :math:`y` axis by an angle :math:`\\theta`:
.. math::
R_y = \\begin{pmatrix}
\\cos\\theta & 0 & \\sin\\theta\\\\
0 & 1 & 0\\\\
-\\sin\\theta & 0 & \\cos\\theta
\\end{pmatrix}
Examples
--------
>>> import numpy as np
>>> from sknano.core.math import Ry
>>> Ry(np.pi/4)
array([[ 0.70710678, 0. , 0.70710678],
[ 0. , 1. , 0. ],
[-0.70710678, 0. , 0.70710678]])
>>> np.alltrue(Ry(np.pi/4) == Ry(45, deg2rad=True))
True
"""
if deg2rad:
angle = np.radians(angle)
cosa = np.cos(angle)
sina = np.sin(angle)
Rmat = np.array([[cosa, 0.0, sina], [0.0, 1.0, 0.0], [-sina, 0.0, cosa]])
Rmat[np.where(np.abs(Rmat) <= np.finfo(float).eps)] = 0.0
return Rmat
[docs]def Rz(angle, deg2rad=False):
"""Generate the :math:`3\\times3` rotation matrix :math:`R_z(\\theta)` \
for a rotation about the :math:`z` axis by an angle :math:`\\theta`.
Parameters
----------
angle : float
The rotation angle :math:`\\theta` in *radians*. If the angle is
given in *degrees*, then you must set `deg2rad=True` to correctly
calculate the rotation matrix.
deg2rad : bool, optional
if `True`, then `angle` is converted from degrees to radians.
Returns
-------
:class:`~numpy:numpy.ndarray`
:math:`3\\times3` rotation matrix :math:`R_z(\\theta)` for a
rotation about the :math:`z` axis by an angle :math:`\\theta`.
.. math::
R_z = \\begin{pmatrix}
\\cos\\theta & -\\sin\\theta & 0\\\\
\\sin\\theta & \\cos\\theta & 0\\\\
0 & 0 & 1
\\end{pmatrix}
Examples
--------
>>> import numpy as np
>>> from sknano.core.math import Rz
>>> Rz(np.pi/4)
array([[ 0.70710678, -0.70710678, 0. ],
[ 0.70710678, 0.70710678, 0. ],
[ 0. , 0. , 1. ]])
>>> np.alltrue(Rz(np.pi/4) == Rz(45, deg2rad=True))
True
"""
if deg2rad:
angle = np.radians(angle)
cosa = np.cos(angle)
sina = np.sin(angle)
Rmat = np.array([[cosa, -sina, 0.0], [sina, cosa, 0.0], [0.0, 0.0, 1.0]])
Rmat[np.where(np.abs(Rmat) <= np.finfo(float).eps)] = 0.0
return Rmat
[docs]def reflection_matrix(v):
"""Generate reflection matrix that represents reflection of points \
in a mirror normal to the vector `v`.
Parameters
----------
v : :class:`~sknano.core.math.Vector`
Returns
-------
:class:`~numpy:numpy.ndarray`
"""
from ._vector import Vector
v = Vector(v)
Rmat = np.zeros((v.nd, v.nd))
for i in range(v.nd):
Rmat[i, i] = 1 - 2 * v[i]**2 / v.norm**2
for i, j in combinations(list(range(v.nd)), 2):
Rmat[i, j] = Rmat[j, i] = -2 * v[i] * v[j] / v.norm**2
Rmat[np.where(np.abs(Rmat) <= np.finfo(float).eps)] = 0.0
return Rmat
[docs]def rotation_matrix(angle=None, axis=None, rot_axis=None, anchor_point=None,
rot_point=None, from_vector=None, to_vector=None,
deg2rad=False, verbose=False):
"""Generate an :math:`n\\times n` rotation matrix.
.. versionadded:: 0.3.0
Parameters
----------
angle : float
Rotation angle in **radians**. If `deg2rad` is `True`, `angle` will be
converted to radians from degrees. The *sense* of the rotation is
defined by the *right hand rule*: If your right-hand's thumb points
along the `axis`, then your fingers wrap around the axis in the
*positive sense* of the rotation angle.
axis : {None, array_like, str}, optional
An :math:`n`-element array_like sequence defining the :math:`n`
components of the rotation axis or the string `x`, `y`, or `z`
representing the :math:`x, y, z` axes of a Cartesian coordinate
system in 3D with unit vectors
:math:`\\mathbf{v}_x=\\mathbf{\\hat{x}}`,
:math:`\\mathbf{v}_y=\\mathbf{\\hat{y}}`, and
:math:`\\mathbf{v}_z=\\mathbf{\\hat{z}}`, respectively.
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
deg2rad : bool, optional
If `True`, convert `angle` from degrees to radians.
Returns
-------
Rmat : :class:`~numpy:numpy.ndarray`
If `axis` is `None` then `Rmat` will be a :math:`2D`
rotation matrix :math:`R(\\theta)` that rotates :math:`2D` vectors
counterclockwise by `angle` :math:`\\theta`.
If `axis` is not `None` then `Rmat` will be a rotation matrix that
gives a rotation around the direction of the vector `axis`.
"""
if axis is None and rot_axis is not None:
axis = rot_axis
Rmat = transformation_matrix(angle=angle, axis=axis,
anchor_point=anchor_point,
rot_point=rot_point, from_vector=from_vector,
to_vector=to_vector, deg2rad=deg2rad,
verbose=verbose)
return Rmat[:-1,:-1]
[docs]def scaling_matrix(s=None, v=None):
"""Return scaling matrix.
Parameters
----------
s : {list, float}
v : {None, :class:`~sknano.core.math.Vector`}, optional
Returns
-------
:class:`~numpy:numpy.ndarray`
"""
if not isinstance(s, (list, float)):
raise TypeError('Expected `s` to be a list or a float.')
if isinstance(s, float) and not isinstance(v, (list, np.ndarray)):
raise TypeError('Expected `v` to be a list or numpy array')
if isinstance(s, list):
return np.diag(s)
else:
from ._vector import Vector
v = Vector(v)
Smat = np.zeros((v.nd, v.nd))
for i in range(v.nd):
Smat[i, i] = 1 + (s - 1) * v[i]**2 / v.norm**2
for i, j in combinations(list(range(v.nd)), 2):
Smat[i, j] = Smat[j, i] = (s - 1) * v[i]**2 * v[j]**2 / v.norm**2
Smat[np.where(np.abs(Smat) <= np.finfo(float).eps)] = 0.0
return Smat
[docs]def transformation_matrix(angle=None, axis=None, rot_axis=None,
anchor_point=None, rot_point=None, from_vector=None,
to_vector=None, deg2rad=False, verbose=False):
"""Generate an :math:`(n+1)\\times(n+1)` transformation matrix for an \
affine transformation in :math:`n` dimensions.
.. versionadded:: 0.3.0
Parameters
----------
angle : float
Rotation angle in **radians**. If `deg2rad` is `True`, `angle` will be
converted to radians from degrees. The *sense* of the rotation is
defined by the *right hand rule*: If your right-hand's thumb points
along the `axis`, then your fingers wrap around the axis in the
*positive sense* of the rotation angle.
axis : {None, array_like, str}, optional
An :math:`n`-element array_like sequence defining the :math:`n`
components of the rotation axis or the string `x`, `y`, or `z`
representing the :math:`x, y, z` axes of a Cartesian coordinate
system in 3D with unit vectors
:math:`\\mathbf{v}_x=\\mathbf{\\hat{x}}`,
:math:`\\mathbf{v}_y=\\mathbf{\\hat{y}}`, and
:math:`\\mathbf{v}_z=\\mathbf{\\hat{z}}`, respectively.
anchor_point : {None, array_like}, optional
An :math:`n`-element list or ndarray or
:class:`~sknano.core.math.Point` defining
the origin of the rotation axis.
If `anchor_point` is not `None` and `axis` is a `Vector` instance,
then the origin of the vector defined by :attr:`Vector.p0` will be
changed to `anchor_point`.
If `anchor_point` is `None`, then it defaults to an
:math:`n`-element array of zeros.
deg2rad : bool, optional
If `True`, convert `angle` from degrees to radians.
Returns
-------
Tmat : ndarray
:math:`n+1\\times n+1` transformation matrix for an affine transform
in :math:`n` dimensions.
If `axis` is `None` and `anchor_point` is `None`,
then `Tmat` will be a :math:`2D` rotation matrix :math:`R(\\theta)`
that rotates :math:`2D` vectors counterclockwise by `angle`
:math:`\\theta`.
If `axis` is `None` and `anchor_point` is a 2-element sequence,
then `Rmat` will be a :math:`2D` rotation matrix :math:`R(\\theta)`
about the :math:`2D` `Point` `anchor_point` by `angle`
:math:`\\theta`.
If `axis` is not `None` and `anchor_point` is `None`,
then `Rmat` will be a rotation matrix that gives a rotation around
the direction of the vector `axis`.
Notes
-----
"""
if angle is None and from_vector is None and to_vector is None:
raise TypeError('Expected `angle` or `from_vector` and `to_vector` '
'set to values with valid types.')
if axis is None and rot_axis is not None:
axis = rot_axis
from . import vector, Vector, Point
if angle is None and not (from_vector is None and to_vector is None):
from_vector = Vector(from_vector)
to_vector = Vector(to_vector)
if from_vector.nd != to_vector.nd:
raise ValueError('`from_vector` and `to_vector` must have same '
'dimensions.')
angle = vector.angle(from_vector, to_vector)
if from_vector.nd == 2:
if not np.allclose(Vector(np.dot(Rz(angle)[:2,:2], from_vector)),
to_vector):
angle = -angle
return transformation_matrix(angle=angle, rot_point=rot_point)
elif from_vector.nd == 3:
axis = vector.cross(from_vector, to_vector)
return transformation_matrix(angle=angle, axis=axis,
anchor_point=anchor_point,
rot_point=rot_point)
else:
raise ValueError('currently, transformation_matrices can only '
'be computed for rotation transformations in '
'2D and 3D.')
else:
if deg2rad:
angle = np.radians(angle)
cosa = np.cos(angle)
sina = np.sin(angle)
if axis is None:
if rot_point is not None and \
isinstance(rot_point, (list, np.ndarray)) and \
len(rot_point) == 2:
p = Point(rot_point)
else:
p = Point(nd=2)
Tmat = Rz(angle)
if not np.allclose(p, np.zeros(2)):
for i in range(2):
j, = list(set(range(2)) - {i})
Tmat[i, 2] = p[i] - p[i] * cosa + (-1)**i * p[j] * sina
else:
# Handle 3D rotation about origin
# Handle 3D rotation around the rotation vector
# Handle N-D rotation about origin
# Handle N-D rotation around the N-D rotation vector anchored at
# an arbitrary N-D point.
if isinstance(axis, (str, six.text_type)):
try:
axis = _str2array[axis]
except KeyError:
raise ValueError(
'Invalid `axis` string: {}'.format(axis))
elif not isinstance(axis, (tuple, list, np.ndarray)):
raise ValueError('`axis` must be a sequence')
if anchor_point is None and rot_point is not None:
anchor_point = rot_point
if anchor_point is not None and \
isinstance(anchor_point, (list, np.ndarray)) and \
len(anchor_point) == 3:
anchor_point = Point(anchor_point)
else:
anchor_point = Point()
v = Vector(np.asarray(axis), p0=anchor_point)
Tmat = np.zeros((4, 4))
if np.allclose(v, I[:3, 0]):
Tmat[:3,:3] = Rx(angle)
elif np.allclose(v, I[:3, 1]):
Tmat[:3,:3] = Ry(angle)
elif np.allclose(v, I[:3, 2]):
Tmat[:3,:3] = Rz(angle)
else:
for i in range(3):
Tmat[i, i] = (v[i]**2 +
(v[(i + 1) % 3]**2 +
v[(i + 2) % 3]**2) * cosa) / v.norm**2
for i, j in combinations(list(range(3)), 2):
k = list(set(range(3)) - {i, j})[0]
Tmat[i, j] = \
(v[i] * v[j] * (1 - cosa) +
(-1)**(i + j) * v[k] * v.norm * sina) / v.norm**2
Tmat[j, i] = \
(v[i] * v[j] * (1 - cosa) -
(-1)**(i + j) * v[k] * v.norm * sina) / v.norm**2
if not np.allclose(v.p0, np.zeros(3)):
p = v.p0
for i in range(3):
j, k = list(set(range(3)) - {i})
Tmat[i, 3] = ((p[i] * (v[j]**2 + v[k]**2) -
v[i] * (p[j] * v[j] + p[k] * v[k])) *
(1 - cosa) + (-1)**i *
(p[j] * v[k] - p[k] * v[j]) *
v.norm * sina) / v.norm**2
Tmat[3, 3] = 1.0
Tmat[np.where(np.abs(Tmat) <= np.finfo(float).eps)] = 0.0
return Tmat
[docs]def axis_angle_from_rotation_matrix(rmatrix):
"""Compute the rotation axis and angle from a rotation matrix.
Parameters
----------
rmatrix : :class:`~numpy:numpy.ndarray`
Returns
-------
axis : :class:`~sknano.core.math.Vector`
angle : :class:`~numpy:numpy.float`
.. todo::
Fix code to compute the correct sense of the rotation or
direction of rotation axis vector.
"""
if not isinstance(rmatrix, np.ndarray):
raise TypeError('Expected matrix to be a 3x3 numpy array.')
from ._vector import Vector
angle = np.arccos((np.trace(rmatrix) - 1) / 2)
# compute random vector
x = Vector(np.random.random(3)).unit_vector
axis = (np.dot(rmatrix, x) +
np.dot(rmatrix.T, x) +
(1 - np.trace(rmatrix)) * x).unit_vector
axis.rezero()
return axis, angle