; Prepare selected alignment paramaters file
;
; SOURCE: sel_align.bat
;
; PURPOSE: Prepare alignment pararameter files for refinement
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ------------ Input files ---------------------------------------
FR G
[defocus_group_sel]../Power_Spectra/order_defgrps ; Defocus groups selection file
FR G
[part_by_group]../Reconstruction/df{***x77}/seltotal ; Particle selection file by defocus group
FR G
[ser]../Particles/win/ser{******x55} ; Particle images
FR G
[ali]../Alignment/ali/sar{******x55} ; Aligned particle images
FR G
[align_parameters]../Alignment/align_01_{***x77} ; Alignment file template
; --------------- Output files -------------------------------------
FR G
[data]input/data{***x77}@{******x56} ; Stack files with original images
FR G
[dala]input/dala01_{***x77}@{******x56} ; Stack files with aligned images
FR G
[new_align_parameters]input/align_01_{***x77} ; Alignment file template
; -------------- END BATCH HEADER ------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF
UD N,x20 ; Get number of defocus groups
[defocus_group_sel]
DO LB2 x11=1,x20 ; Loop over all defocus groups
; Get current group number
UD x11,x77 ; Current defocus group number = x77
[defocus_group_sel] ; Defocus group selection file
UD N,X71 ; Get number of particles for this group
[part_by_group]
DO LB1 x56=1,x71 ; Loop over all particles (x56=new number)
UD IC,x56,x55 ; Get particle number=x55
[part_by_group]
UD IC x55, x31,x32,x33,x34,x35,x36,x37,x38,x39,x40,x41,x42,x43,x44,x45 ; Get alignment parameters for this particle
[align_parameters] ; Old alignment file template
SD x56, x31,x32,x33,x34,x35,x36,x37,x38,x39,x40,x41,x42,x43,x44,x45 ; Get alignment parameters for this particle
[new_align_parameters] ; New alignment file template
LB1
UD ICE ; Finished with this defocus group
[part_by_group]
LB2
EN
;