Name

• rot_shift3D - rotate, shift, and scale a 3D image

Usage

• output = rot_shift3D(image, phi=0, theta = 0, psi = 0, sx = 0, sy = 0, sz = 0, scale = 1, mode="background")

Input

image

3D image to be rotated

phi, theta, psi

Euler angles ( in SPIDER convention ) describing rotation

sx, sy, sz

x, y and z shifts, respectively

scale

rescaling factor. scale > 1 will magnify the input volume.

Attention: scale cannot be set as 0.

Example:

image = get_im("FN.spi");

f = rot_shift3D(omage,30); # rotates FN.spi by 30 degrees around the z axis

Output

. output

The rotated, shifted, and scaled output 3D volume.

Description

• 1. Purpose: to apply rotation/shift/scaling to a 3D image via a variety of methods.
• 2. The rotation, shift, and scaling are achieved through the following procedures:
  • Construct a transformation matrix (a class objection of C++ or python)from three Eulerian angles through Transform3D.
  • set translation attribute of the object.
  • set scale attribute of the object.
  • apply the class object to input image.

• Refere to the reference by P. R. Baldwin et al to find out how to construct transformation class.

Author & Maintainer

P. R. Baldwin/zhong Huang

Keywords

category 1

FUNDAMENTALS

category 2

SPATIAL

Files

• (sparx) fundamentals.py
• (libEM/sparx) emdata_sparx.cpp (rot_scale_trans )

See also

• rot_shift2D

Reference

.1. P R Baldwin , Pawel A Penczek, The Transform Class in SPARX and EMAN2. J. Struct. Biol. 157 (2007), pp. 251-261.

Maturity

• alpha

Bugs

• only using quadratic interpolation right now 8/9/2006