; Computes alignment parameters for sample images
;
; SOURCE: apsh.spi Nov 2004 ArDean Leith
; Added alignment option & stack op Nov 2006 ArDean Leith
;
; PURPOSE: Multi-reference alignment of an image series.
; Sample images are aligned with reference projections via
; shifts (translations) and rotations.
; THIS PROCEDURE IS FOR PROJECTS WITH A SINGLE GROUP.
; USE: apshgrp.spi FOR ALIGNING MULTIPLE GROUPS
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
;------------ Edit next 7 Input parameters ------------------------------
[grp] = 1 ; Group number (If used in your file name)
[doalign] = 1 ; If >0 apply alignment to images
[range] = 8 ; Translation search range (must be divisible by step size)
[step] = 2 ; Translation step size
[diam] = 366 ; Diameter of object (Angstroms) for alignment search.
; (EDIT as needed!) Used to find last alignment radius.
[r1] = 5 ; First rotation alignment ring, only radii > this will be analyzed
[r2] = 0 ; Last rotation ring (If zero, compute from object diameter)
; ----------------- Input files --------------------------------------------
FR G
[parameters]../params ; Parameter setting file
FR G
[ref_images]projs/prj_{***[grp]}@ ; Reference image
FR G
[ref_images_angles]refangles ; Reference images angles doc. file
FR G
[unaligned_images]data{***[grp]}@ ; Unaligned particles name template
; ----------------- Output files -------------------------------------------------
FR G
[align_parameters]align_01_{***[grp]} ; Alignment parameters doc. file
FR G
[aligned_images]dala01_{***[grp]}@ ; Rotated, shifted (aligned) particles
; ----------------- END BATCH HEADER -------------------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
IF ([r2] .LE. 0) THEN ; Compute alignment radius from object size
UD 5,[pxsz] ; Get pixel size (A) from this file
[parameters]
UD 17,[winsz] ; Get window size (pixels) from this file
[parameters]
[r2] = INT([diam]/(2.0*[pxsz])) ; Compute object radius (pixels) for last alignment ring
[tp] = [r2] + [range] ; Compute last ring + translation range
[t] = INT([winsz]/2) - 1 ; Compute max. radius of object within window
IF ([tp] .GE. [t]) THEN
[r2] = [t] - [range] - 1 ; Reduce radius of last alignment ring to fit window
ENDIF
ENDIF
DE ; Delete existing alignment parameter output doc. files.
[align_parameters]
FI X [numpart] ; Get number of particles
[unaligned_images] ; Unaligned particles name template (input)
(26) ; Max. image number in stack
FI X [numproj] ; Get number of projections
[ref_images] ; Unaligned particles name template (input)
(26) ; Max. image number in stack
VM
echo ' 'Finding alignment for: {******[numpart]} particles
AP SH ; Align sample images using multiple references
[ref_images]**** ; Reference image name template (input)
(1-[numproj]) ; List of reference images
[range],[step] ; Search range, step size
[r1],[r2] ; First and last ring
[ref_images_angles] ; Ref. angles doc file (input)
[unaligned_images]***** ; Unaligned particles name template (input)
(1-[numpart]) ; Number of particles
* ; No unaligned images align. doc file
(0) ; No restriction on angular proj. search
(1) ; Check mirrored positions
[align_parameters] ; Alignment angles doc. file (output)
IF ([doalign] .GT. 0) THEN
; Apply alignment parameters to unaligned images
; Order in doc file: PHI,THETA,PSI, REF#,IMG#, ROT,SX,SY
VM
echo " Applying alignment parameters"
RT SQ ; Rotate & shift whole stack operation
[unaligned_images] ; Unaligned particles stack (input)
[aligned_images] ; Aligned particles stack (output)
(6,0,7,8) ; Reg. numbers for angle, scale,& shifts
[align_parameters] ; Alignment angles doc. file (input)
ENDIF
VM
echo " "
EN
;