Name

sxave_ali.py - calculate average with or without alignment parameters stored in the headers of 2D EM images

Usage

Usage in command lines:

sxave_ali.py stackname <outname> --ali --set_size=name_of_param_with_size --set_members=name_of_param_with_id

Usage in python programming:

aves_ali(stackname, name_out = None, ali = False, param_to_save_size = None, set_as_member_id = None)

Typical usage

sxave_ali.py mydata.hdf --ali

returns file ave_mydata.hdf (in this case the alignment parameters are applied)

sxave_ali.py mydata.hdf newname.hdf --start=10 --end=19 --ali

returns file newname.hdf, the average is computed for 10 images (index image 10 to 19)

Input

stackname

the input stack of 2D images

Output

• return file:

• average <outname> or ave_stackname according if the user define <outname>

Options

<outname>

name of the average image, if given the function return file <outname>, otherwise the name of file is ave_<stack>

ali

if set, alignment information stored in file headers will be used to compute the average and the variance (default no ali)

set_size=name_of_param_with_size

if set, number of input images is saved to header's parameter with name given in this option

set_members=name_of_param_with_id

if set, list of id of input images is saved to header's parameter named "members", ids of input images are taken from parameters with name given in this option

Description

Compute the average of the 2D images stack with or without considering the alignment parameters (alpha, sx, sy and mirror) stored in the headers. This function return stack with one 2D image, contains the average calculated from given images.

Author / Maintainer

Julien

Keywords

category 1

APPLICATIONS

Files

statistics.py

Maturity

beta

works for author, often works for others.

Bugs

None. It is perfect.