Name

sxtransform2d - apply orientation parameters stored in files headers to the input stack and write images to the output stack.

Usage

Usage in command lines:

sxtransform2d.py input_stack.hdf output_stack.hdf --shift --method=quadratic

Usage in python programming:

transform2d(input_stack.hdf, output-stack.hdf, shift, method)

Input

input_stack.hdf

input set of 2-D images in a stack file (format hdf). They should have alignment parameters attributes 'alpha', 'sx', 'sy', and 'mirror' set in their headers

shift

if present, the command will apply only translations disregarding the rotation angle, it is useful for centering the data (default False)

ignore_mirror

If centering data with CTF and astigmatism, use option ignore mirror (default False)

method

interpolation method used: linear, quadratic, gridding (default - quadratic). Note for translation only Fourier phase multiplication is used, see fshift.

Output

outputput_stack.hdf

output set of transformed 2-D images in a stack file (any format). The orientation parameters 'alpha', 'sx', 'sy', and 'mirror' in their headers are set to zero.

Description

• For the program to work, attributes 'alpha', 'sx', 'sy', and 'mirror' have to be set in the header of each file.
• If all 'alpha', 'sx', 'sy', and 'mirror' are set to zero, images are copied to the output stack.

Method

Gridding

Reference

Penczek 2002

Author / Maintainer

Pawel A. Penczek

Keywords

category 1

APPLICATIONS

category 3

GRIDDING

Files

sparx/bin/sxtransform2d.py

See also

sxali2d, sxshiftali

Maturity

alpha

perfect.

Bugs

For output stack files other than hdf the attributes may not work.