; Controls parallel alignment
;
; SOURCE: spider/docs/techs/recon1/Procs/pub-align.spi
;
; PURPOSE: Multi-reference alignment of an image series.
; Experimental images are aligned with reference projections via
; shifts (translations) and rotations.
; FOR PROJECTS WITH MORE THAN ONE GROUP
;
; USAGE: clean ; ./spider spi/dat @pub-align 0
;
; I/O Registers & files are set in: recon-settings.spi
;
; INPUT FILES: ([win_dir] denotes input directory, '***' denotes group, '%' denotes subset)
; [sel_group] [win_dir]/sel_group Group selection file (one)
; [sel_parts] [win_dir]/sel_part_*** Group particle selection files (one/group)
; [unaligned_images] [win_dir]/data_*** Unaligned image stacks (one/group)
; [ref_projs] [rec_dir]/projs_00 Reference projections (one)
;
; OUTPUT FILES: ('[rec_dir] denotes reconstruction output directory)
; [next_group_align_s] [rec_dir]/align_01_***_s% Alignment parameter doc files (two/group)
; [aligned_images] [rec_dir]/dala_***@ Rotationally aligned particle stacks (two/group)
; [finished_file] jnk_sync_$$$$_*** Created when this parallel task is finished (one)
;
; PROCEDURES CALLED:
; recon-settings recon-settings.spi
; memforqsub (optional) memforqsub.spi
; pub_submit pub_submit.spi
; .. qsub qsub.pbs
; .... align-loop align-loop
; ...... recon-settings recon-settings.spi
;
; -------------------------------- END BATCH HEADER ----------------------------
MD
TR OFF ; Loop info turned off
MD
VB OFF ; File info turned off
MD
SET MP ; Use only a few processors on master node!!
1
SYS
echo
; Get reconstruction parameters & file names
[steptype] = 0 ; Alignment step
@recon-settings([steptype],[num-grps],[pixsiz],[ang-step],[r2],[alignsh],[prj-radius],[winsiz],[incore-yn],[bp-type],[qsub])
[iter] = 0
; Create directories for output and scratch files
SYS
mkdir -p [rec_dir] [work_dir]
; Processes experimental images in parallel by groups of images.
; Find alignment parameters ('AP SHC') which best align experimental images with
; projection images.
; Rotate ('RT SF') original particle images using these rotational alignment parameters.
[task] = 4 ; Starts: spider @align-loop for each group
[script] = './spider $PRJEXT/$DATEXT @align-loop '
@pub-submit([iter],[num-grps],[task],[qsub])
[script] ; Script that runs alignment parallel job
SYS
echo -en ' Alignment completed' ; date '+ TIME: %x %X' ; echo
EN
;