; Applies alignment parameters
;
; SOURCE: Adapted from apshgrp.spi Jan 11, 2009
;
;----------------- Input files --------------------------------------------
FR G
[defgrps]../Reconstruction/sel_group ; List of groups (group selection doc file)
FR G
[unaligned_images]../Alignment/data{***[grp]}@ ; Unaligned particles stacks
FR G
[align_parameters]../Alignment/align_01_{***[grp]} ; Alignment parameters doc. file
; ----------------- Output files ------------------------------------------------
FR G
[aligned_images]../Alignment/dala01_{***[grp]}@ ; Rotated, shifted (aligned) particles
; ----------------- END BATCH HEADER -------------------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
UD N [numgrps] ; Get number of groups
[defgrps] ; Groups selection file (input)
MD
SET MP ; Use all processors (needed here for secondary runs)
0
VM
echo "Realigning particles" ; date
DO LB2 [numgrp]=1,[numgrps] ; Loop over all group(s)
UD [numgrp],[grp] ; Get current group number
[defgrps] ; Group selection file (input)
FI X [numpart] ; Get number of particles
[unaligned_images] ; Unaligned particles name template (input)
(26) ; Max. image number in stack
VM
echo "Working on group #{****[grp]} with {******[numpart]} particles"
; Apply alignment parameters to unaligned particles
; Order in doc file: PHI,THETA,PSI, REF#,IMG#, ROT,SX,SY
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)
MY FL ; Flush results file
LB2 ; End loop for multiple groups
VM
echo "Done" ; date
EN D
;