Beautifier: Beautify the ISAC 2D clustering result with the original pixel size.

Usage in command lines:

sxisac_post_processing.py  stack_file  isac_directory  class_file_name_no_dir_info --radius=particle_radius  --CTF  --single_stack_output 

sxisac_post_processing.py exists only in MPI version.

mpirun -np 32 sxisac_post_processing.py bdb:data fisac1 locres.hdf --radius=28

stack_file

Original image stack: Particles required to create the full-sized class averages. The images must be square (nx=ny) and the stack must be bdb format (default required string)

isac_directory

Isac output directory: Name of the directory where isac was run previously. (default required string)

class_file_name_no_dir_info

Isac class file name: Name of the file (no directory info) that contains the class averages. It is located in the Isac directory. (default required string)

radius

Particle radius [Pixels]: There is no default radius. (default required int)

CTF

Phase-flip: If set, the data will be phase-flipped using CTF information included in the image headers. (default False)

single_stack_output

Single stack output: If set, only one stack for all classes will be generated. Otherwise, which is the default, one file per class will be generated. (default False)

The output directory is created in the isac directory and has the format “post_processing_YYYY-MM-DD–HH-MM-SS”. It contains all the output files “original_image_number_in_each_class_average.txt”, “twoD_params_info_list.txt” and “radius_adjusted_class_averages.hdf” (one file or multiple files according to the –single_stack_output option).

Horatiu Voicu and Pawel A. Penczek

sxisac_post_processing.py

alpha:: in development