WaveOrtOMP

This program is used to find orientation of Icosahedral particle images using Wavelet transform and projection matching, parallelized using OpenMP

WaveOrtOMP raw.img proj.img [ignorerefid] [ignorecen] [tree=<number>] [topnum=<int>] [usemyangle] [angrange=<degree>] [mask=<pixels>] [ctf=<ctf para file>] [minN=<n>] [first=<n0>] [last=<n1>] [frac=<0 to d-1>/<d>] [cpu=<n>] [writeali[=<ali.img>]] [nowave] [verbose] [showlist] [touch=<filename>]

Parameters:


raw.imgthe image file for raw particles
proj.imgthe image file for complete projections in Icosahedral asymmetric unit
[ignorerefid]ignore the best matched projection ID stored in image header, to start from scratch and avoid formal wrong result, default is to honor it and speed up
[ignorecen]ignore the center parameters and assume particles are physically centered
[tree=<number>]if multiscale is employed to speed up processing, default to 1 with no speedup
[topnum=<int>]number of top ranked groups for further exhausted search, should use with "tree" option
[usemyangle]start from the Euler angles stored in the header, only search neighbor angular region, will force "ignorerefid" set
[angrange=<degree>]the minimal angular range in degree around the intermediate best orientation to search for next round, default is 2.5 of the angular step size for Icosahedral projections
[mask=<pixels>]mask radius in pixel, the center of mask will move to particle center if center shift found. default to nx/2
[ctf=<ctf para file>]apply the CTF parameters specified in thefile in EMAN order
[minN=<n>]only process those with NImg<minN, this is just a filter for efficiency
[first=<n0>]the first image to process in the file, default to 0
[last=<n1>] the last image to process in the file, default to the last in the file
[frac=<0 to d-1>/<d>]for runpar parallelization, set this thread to only work on certain fraction of images of all images in the file, default to 0/1 (all images in the file)
[cpu=<n>]number of CPUs to use. parallelized with OpenMP
[writeali[=<ali.img>]]write out to file WaveOrt-aligned.img the alignment pairs of raw image and the corresponding best projection with correct inplane rotation to match the raw image
[nowave]don't do wavelet transform
[verbose]if set, output some intermediate results
[showlist]if set, output the list of projection IDs that corresponding projections searched at each cycle, to reflect the dynamic nature of this algorithm
[touch=<filename>]if set, create an empty file (filename) as a stamp file to signal successful run

Usage:

WaveOrt raw.hed proj.hed outort=res-ort.dat

WaveOrt raw.hed proj.hed outort=res-ort.dat frac=0/1 ignorerefid verbose frac=3/6

Description

This program tries to find the best matched icoshedral projection to set the 3 Euler angles for each raw particle image in the file assuming that particles are already well centered, then store the orientation parameters to image header without any modification of the actual image data to minimize the interpolation errors.

The algorithm is classified as projection matching, but with Wavelet transform of both the raw images and the projection images before the matching search starts. The reference projections would be treated as already Wavelet transformed if the size is half of the raw image size, otherwise it must be the same size as the raw image size and will be Wavelet transformed. Ask Ali Saad for detailed explanation for Wavelet transform.

The 3 Euler parameters are determined


EMAN Manual page, generated Tue Oct 8 21:50:26 2002