; Prepare files for input to refinement
;
; Adapted from copyin.pam
; NOTE: can combine data sets by using input register, by appending to defocus-group list
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ------------------------- Parameter -------------------------
[firstgrp] = 1 ; first defocus group (can be used to append to data set)
[dala-yn] = 1 ; write aligned images? (0==no)
; ------------------------ Input files ------------------------
FR G
[defgrps]sel_group_cclim ; Group selection file
; DF_GROUP NUMPARTS AVGDEFOCUS
; used used
FR G
[initial_sel_particles]sel_particles_{***[oldgrp]} ; Particle selection files
; DF_SLICE
FR G
[initial_unaligned_images]../Alignment/data*** ; Unaligned stacked image files
FR G
[initial_aligned_images]../Alignment/dala01_*** ; Aligned stacked image files
; ----------------------- Output files -----------------------
FR G
[good_dir]../Reconstruction ; Output directory
FR G
[order_select][good_dir]/good-sel_group_cclim ; Group selection file
; ; (may contain appended groups)
FR G
[sel_particles][good_dir]/good-sel_particles_*** ; Particle selection files
; NEWSLICE OLDSLICE
FR G
[unaligned_images]../Alignment/good-data*** ; Unaligned stacked image files
FR G
[start_aligned_images]../Alignment/good-dala01_*** ; 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
if([dala-yn].ge.1) then
vm
echo "Writing aligned images"
else
vm
echo "Writing unaligned but not aligned images"
endif
vm
echo ; echo "Preparing refinement files"; date
VM ; Crete refinement input directory
mkdir -p [good_dir]
; initialize combined particle-counter
[global-counter] = 0
UD N [num-grp] ; Get total number of defocus groups
[defgrps]
DO LB1 [i]=1,[num-grp] ; Loop over defocus groups ---------------------
UD IC [i], [oldgrp],x99,[defocus-value]
[defgrps] ; Doc file listing groups (input)
[newgrp] = [oldgrp] + [firstgrp] - 1
; clean up pre-existing files
de
[unaligned_images][newgrp]@
de
[sel_particles][newgrp]
if([dala-yn].ge.1) then
de
[start_aligned_images][newgrp]@
endif
ud n [num-particles]
[initial_sel_particles]
sd [i],[newgrp],[num-particles],[defocus-value]
[order_select]
; loop though particles
do lb2 [slice-counter]=1,[num-particles]
; get slice#
ud ic [slice-counter], [old-slice] ; , [particle-num]
[initial_sel_particles] ; WAS [df_dir][oldgrp]/[initial_sel_particles]
; write to selection doc
sd [slice-counter], [slice-counter], [old-slice] ; , [particle-num]
[sel_particles][newgrp]
; increment global particle-counter
[global-counter] = [global-counter] + 1
; copy from total-particle stacks to good-particle stacks
cp
[initial_unaligned_images][oldgrp]@{******[old-slice]}
[unaligned_images][newgrp]@{******[slice-counter]}
if([dala-yn].ge.1) then
cp
[initial_aligned_images][oldgrp]@{******[old-slice]}
[start_aligned_images][newgrp]@{******[slice-counter]}
endif
lb2
; end particle-loop
ud ice
[initial_sel_particles]
sd e
[sel_particles][newgrp]
VM
echo " Accumulated {*****[num-particles]} particles in group: {***[newgrp]}"
LB1
UD ICE ; Close doc file access
[defgrps]
sd e
[order_select]
; renumber
at it
[order_select]
[order_select]
SD / GROUP PARTICLES DEFOCUS
[order_select]
[dummy] = -[num-grp]
sd [dummy], [num-grp],[global-counter]
[order_select]
SD / NUMGROUPS TOT_PARTICLES
[order_select]
sd e
[order_select]
VM
echo ; echo 'Done -- Wrote {*******[global-counter]} particles'; date
EN D
;
; Modified 2012-08-15
; 2012-06-04 (trs) -- added option to write aligned-image stacks (no longer used in refinement)
; 2011-01-07 (trs) -- refinement batch files using fewer and different inputs
; 2011-01-05 (trs) -- using more general SEL_PARTICLES as input
; 2009-01-12 (trs) -- can combine data sets by starting from defocus-group >1
; 2007-03-21 (trs) -- bug fix
; 2007-01-30 (trs) -- adapted from copyin.pam