Angular_refinement

Angular refinement

Purpose

This program is a wrapper to the Spider alignment refinement operationrm orfsf orap mq.

Therm orfsf does a search in the Radon space to look for the best angular and shift position of a given image with respect to the given volume. You may apply these results to the real space images or not, and even to a second set of images. During the Spider call several files are created (although they are removed later):b01.ext, peak?????.ext (whereext stands for the input Fourier-Radon extension).

Thap mq compares the matching between projections of the reference volume and the experimental projections. The set of reference projections is generated via spider. These files are calledideal????.ext (ext is the extension of the input volume) and are deleted at the end of the process. Many files are generated during the alignment process. Particularly,b01.ext,refangles.ext,projlist.ext,assigned_angles,experimentalsel,apmq,kk?????.ext,intersel?????.ext. All these files are deleted at the end of the process.

Many output files are generated by both wrappers, assuming that the input real space selfile isg3ta.sel org3ta_iter_00.sel, then

g3ta_iter_01_orfsf.txt Output document file with the resulting angles, shifts and correlations
g3ta_iter_01_rot_histogram.txt Histogram of the rotational angle displacement
g3ta_iter_01_tilt_histogram.txt Histogram of the tilting angle displacement
g3ta_iter_01_psi_histogram.txt Histogram of the in-plane rotational angle displacement
g3ta_iter_01_shift_histogram.txt Histogram of the shift displacement
g3ta_iter_01_summary.txt Document file with the initial angles, final angles and shifts and the corresponding displacement for each particle
g3ta_iter_01_?????.xmp Set of images corresponding to the real space images where the apropriate shifts and angles are applied. This happens only if the-apply flag is chosen

Usage

1. Radon routines wrapper


$ angular_refinement ...

Paramters

`` Input Fourier-Radon volume (see Radon transform). All images are realigned with respect to this volume
`` Selfile with all Fourier-Radon projections to be aligned
`` Selfile with all projections to be aligned. Thefrt and the`img` selfiles must match
-rot [rot00] [rotF=360] [step rot=10] = Search space for the rotational angle
-tilt [tilt00] [tiltF=90] [step tilt=10] = Search space for the tilting angle
-psi [psi00] [psiF=360] [step psi=10] = Search space for the in-plane rotation angle
-max_shift [shift2] = Search space for the shift

2. Projection Matching routines wrapper


$ angular_refinement ...

Parameters

`` Flag to set this wrapper mode. TheAP MQ Spider routine is used
`` Input reference volume in Spider format
`` Selfile with all projections to be aligned. Thefrt and the`img` selfiles must match
-tilt_step [step tilt10] = Search space for the tilting angle. Projections will be evenly distributed in the projection sphere with this separation. TheVO EA routine is used for this. Projections will be calledideal????.vol
=
= Search space for the shift. max_shift value must be a multiple of shift_step
=
= First and last rings to evaluate

3. Common options

`` Normally, it is checked that the output angles meet the inputrot,`tilt` and`psi` maximum limits. If this option is selected, then this check is not perfomed
`` If this option is chosen, input real space images are shifted and their angles set to the new found ones. The resulting images are written with a different name so that the real space images are not rewritten
`` If this option is chosen, the original real space images are shifted and their angles set to the new found ones. The resulting images are written with the same name as the originals. This is used for combining with IDR_ART

Examples and notes

Common alignment process using the Radon Routines


$ xmipp_angular_refinement -i ART_idr_iter_01_filter_sym.frt -fr g3ta_iter_02.selfrt -img g3ta_iter_02.sel \
-rot -20 20 5 -tilt -15 15 5 -psi -30 30 5 -max_shift 6 -apply -apply_to_original g2ta.sel

--Main.AlfredoSolano - 31 Jan 2007

Angular_refinement