; Rotate and shift images for Alignment
;
; SOURCE: alignsh.spi
; Added alignment stack op Nov 2006 ArDean Leith
;
; PURPOSE: Rotate and shift images according to parameters
; determined earlier by 'AP SH'.
; (Not needed if already done in: apshgrp.spi)
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; --------------- Input files ----------------------------------------
FR G
[defgrps]../Power_Spectra/order_defgrps ; Defocus groups selection file
FR G
[align_parameters]align_01_*** ; Alignment parameter files
FR G
[img]jnk/jnk_{******[part]} ; Unaligned image stack file
; --------------- Output file ----------------------------------
FR G
[aligned_images]jnk/jnkali_dala01_{******[part]} ; Rotated, shifted (aligned) images
; -------------- END BATCH HEADER ---------------------------------
UD N,[numgrps] ; Get number of defocus groups
[defgrps]
[grp]=1
DO LB1 [part]=1,1917 ; Loop over all particles
; Parameter order in doc file: PHI,THETA,PSI, REF#,IMG#, ROT,SX,SY
UD IC [part], x11,x12,x13, x14,x14, x15,x16,x17
[align_parameters][grp] ; Alignment angles doc. file
RT SQ ; Rotate & shift the images
[img] ; Input image stack
[aligned_images] ; Output image stack
(x15) ; angle, scale
(x16,x17) ; x, & y shift
LB1
; Finished with incore group selection doc. file
UD ICE
[defgrps] ; Defocus group selection file
EN
;