; Prepare files for input to refinement
;
; SOURCE: copyin.pam Merged with sel_align.spi Feb 2005 al
; Rewritten from stack.spi Dec 2006 al
;
; PURPOSE: Prepare files for input to refinement.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; -------------------- Input files -----------------------------------
FR G
[initial_params]../params ; Parameter doc. file
FR G
[defgrps]../Reconstruction/sel_group_cclim ; Group selection file
FR G
[defgrps_sorted]../Reconstruction/sel_group_cclim_sorted ; Sorted group selection file
FR G
[initial_vol]../Reconstruction/vol001 ; Initial starting volume
FR G
[initial_sel_particles]../Reconstruction/sel_particles_{***[grp]} ; Particle selection files
FR G
[initial_group_align]../Alignment/align_01_{***[grp]} ; Initial group alignment parameter files
FR G
[initial_unaligned_images]../Alignment/data{***[grp]} ; Unaligned stacked image files
FR G
[initial_aligned_images]../Alignment/dala01_{***[grp]} ; Aligned stacked image files
; -------------------------- Output files ---------------------------
FR G
[input_dir]input ; Directory
FR G
[order_select]input/order_select ; Group selection file
FR G
[sorted_order_select]input/order_select_sort ; Sorted group selection file
FR G
[start_vol]input/vol01 ; Initial starting volume
FR G
[sel_particles]input/select_{***[grp]} ; Particle selection files
FR G
[start_group_align]input/align_01_{***[grp]} ; Alignment parameter input file
FR G
[unaligned_images]input/data{***[grp]} ; Unaligned stacked image files
FR G
[start_aligned_images]input/dala01_{***[grp]} ; Aligned 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 ; Crete 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].$DATEXT
UD N [num-grp] ; Get total number of defocus groups
[defgrps]
DO LB1 [i]=1,[num-grp] ; Loop over defocus groups ---------------------
UD IC [i], [grp] ; Get number of group
[defgrps] ; Doc file listing groups (input)
VM ; Put particle selection files in input dir
cp [initial_sel_particles].$DATEXT [sel_particles].$DATEXT
VM ; Copy starting alignment parameter files to input dir.
cp [initial_group_align].$DATEXT [start_group_align].$DATEXT
; Copy or link the original unaligned images to input dir
VM ; Link from original dir. to input dir. (very large files)
ln -sf ../[initial_unaligned_images].$DATEXT [unaligned_images].$DATEXT
;VM ; Copy from original dir. to input dir. (very large files)
;cp [initial_unaligned_images].$DATEXT [unaligned_images].$DATEXT
; Copy or link the original aligned images to input dir
VM ; Link from original dir. to input dir. (large files)
ln -sf ../[initial_aligned_images].$DATEXT [start_aligned_images].$DATEXT
;VM ; Copy from original dir. to input dir. (large files)
;cp [initial_aligned_images].$DATEXT [start_aligned_images].$DATEXT
VM
echo " Accumulated group: {***[grp]}"
LB1
UD ICE ; Close doc file access
[defgrps]
VM
echo ' '
EN
;