; Prepare files for input to refinement
;
; SOURCE: copyin.pam Merged with sel_align.spi ArDean Leith Feb 2005
; Rewritten from stack.spi ArDean Leith Dec 2006
; Dala removal ArDean Leith Jan 2012
;
; PURPOSE: Prepare files for input to refinement.
;
; MASTER COPY: spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; -------------------- Input files -----------------------------------
[initial_params] = '../params' ; Parameter doc. file
[defgrps] = '../Reconstruction/sel_group_cclim' ; Group selection file
[initial_vol] = '../Reconstruction/vol001' ; Initial starting volume
[initial_sel_particles] = '../Reconstruction/sel_particles_{***[grp]}' ; Particle selection files
[initial_group_align] = '../Alignment/align_01_{***[grp]}' ; Initial group alignment parameter files
[initial_unaligned_images] = '../Alignment/data{***[grp]}' ; Unaligned stacked image files
; -------------------------- Output files ---------------------------
[input_dir] = 'input' ; Directory
[order_select] = 'input/sel_group' ; Group selection file
[start_vol] = 'input/vol01' ; Initial starting volume
[sel_particles] = 'input/select_{***[grp]}' ; Particle selection files
[start_group_align] = 'input/align_01_{***[grp]}' ; Alignment parameter file
[unaligned_images] = 'input/data{***[grp]}' ; Unaligned stacked image files
; -------------- END BATCH HEADER ------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
MD
SET MP
0
VM ; Create refinement input directory
mkdir -p [input_dir]
VM ; Put params file in input dir
cp [initial_params].$DATEXT [input_dir]
VM ; Put group selection file in input dir
cp [defgrps].$DATEXT [order_select].$DATEXT
VM ; Put sorted group selection file in input dir
cp [defgrps_sorted].$DATEXT [sorted_order_select].$DATEXT
VM ; Put initial volume in input directory
cp [initial_vol].$DATEXT [start_vol].$DATEXT
UD N [num-grp] ; Get total number of defocus groups
[defgrps]
DO [i]=1,[num-grp] ; Loop over defocus groups ---------------------
UD IC [i], [grp] ; Get number of group
[defgrps] ; Doc file listing groups (input)
VM ; Put particle selection files in input dir
cp [initial_sel_particles].$DATEXT [sel_particles].$DATEXT
VM ; Copy starting alignment parameter doc files to input dir.
cp [initial_group_align].$DATEXT [start_group_align].$DATEXT
VM
echo " Accumulated group: {***[grp]}"
ENDDO
UD ICE ; Close doc file access
[defgrps]
VM
echo ' '
EN
;