pwem.convert.transformations module

Homogeneous Transformation Matrices and Quaternions.

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.


Christoph Gohlke


Laboratory for Fluorescence Dynamics, University of California, Irvine





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 np.linalg.inv(M), be concatenated using, M1), or transform homogeneous coordinate arrays (v) using, v) for shape (4, *) column vectors, respectively, M.T) for shape (*, 4) row vectors (“array of points”).

This module follows the “column vectors on the right” and “row major storage” (C contiguous) conventions. The translation components are in the right column of the transformation matrix, i.e. M[:3, 3]. The transpose of the transformation matrices may have to be used to interface with other graphics systems, e.g. with OpenGL’s glMultMatrixd(). See also [16].

Calculations are carried out with np.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.


  1. Matrices and transformations. Ronald Goldman. In “Graphics Gems I”, pp 472-475. Morgan Kaufmann, 1990.

  2. More matrices and transformations: shear and pseudo-perspective. Ronald Goldman. In “Graphics Gems II”, pp 320-323. Morgan Kaufmann, 1991.

  3. Decomposing a matrix into simple transformations. Spencer Thomas. In “Graphics Gems II”, pp 320-323. Morgan Kaufmann, 1991.

  4. Recovering the data from the transformation matrix. Ronald Goldman. In “Graphics Gems II”, pp 324-331. Morgan Kaufmann, 1991.

  5. Euler angle conversion. Ken Shoemake. In “Graphics Gems IV”, pp 222-229. Morgan Kaufmann, 1994.

  6. Arcball rotation control. Ken Shoemake. In “Graphics Gems IV”, pp 175-192. Morgan Kaufmann, 1994.

  7. Representing attitude: Euler angles, unit quaternions, and rotation vectors. James Diebel. 2006.

  8. A discussion of the solution for the best rotation to relate two sets of vectors. W Kabsch. Acta Cryst. 1978. A34, 827-828.

  9. Closed-form solution of absolute orientation using unit quaternions. BKP Horn. J Opt Soc Am A. 1987. 4(4):629-642.

  10. Quaternions. Ken Shoemake.

  11. From quaternion to matrix and back. JMP van Waveren. 2005.

  12. Uniform random rotations. Ken Shoemake. In “Graphics Gems III”, pp 124-132. Morgan Kaufmann, 1992.

  13. Quaternion in molecular modeling. CFF Karney. J Mol Graph Mod, 25(5):595-604

  14. New method for extracting the quaternion from a rotation matrix. Itzhack Y Bar-Itzhack, J Guid Contr Dynam. 2000. 23(6): 1085-1087.

  15. Multiple View Geometry in Computer Vision. Hartley and Zissermann. Cambridge University Press; 2nd Ed. 2004. Chapter 4, Algorithm 4.7, p 130.

  16. Column Vectors vs. Row Vectors.


>>> 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)
>>> Re = euler_matrix(alpha, beta, gamma, 'rxyz')
>>> is_same_transform(R, Re)
>>> al, be, ga = euler_from_matrix(Re, 'rxyz')
>>> is_same_transform(Re, euler_matrix(al, be, ga, 'rxyz'))
>>> 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)
>>> 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)
>>> np.allclose(trans, [1, 2, 3])
>>> np.allclose(shear, [0, math.tan(beta), 0])
>>> is_same_transform(R, euler_matrix(axes='sxyz', *angles))
>>> M1 = compose_matrix(scale, shear, angles, trans, persp)
>>> is_same_transform(M, M1)
>>> v0, v1 = random_vector(3), random_vector(3)
>>> M = rotation_matrix(angle_between_vectors(v0, v1), vector_product(v0, v1))
>>> v2 =, M[:3,:3].T)
>>> np.allclose(unit_vector(v1), unit_vector(v2))