; Controls serial alignment
;
; SOURCE: spider/docs/techs/recon1/Procs/align.spi
;
; PURPOSE: Multi-reference alignment of an image series.
; Experimental images are aligned with reference projections via
; shifts (translations) and rotations.
;
; USAGE: clean ; ./spider spi/dat @align 0
;
; I/O Registers & files are set in: recon-settings.spi
;
; VARIABLE REGISTERS:
; [r2] Alignment radius of object
; [alignsh] Translation shift allowed is +-[alignsh]
; [incore-yn] Incore images used
;
; INPUT FILES: ([init_dir] denotes input/output directory, '***' denotes group, '%' denotes subset)
; [init_sel_grp] [init_dir]/sel_group Group selection file (one)
; [init_sel_part] [init_dir]/sel_part_*** Group particle selection files (one/group)
; [init_unaligned] [init_dir]/data_*** CTF corrected, unaligned image stacks (one/group) (one/group)
; [ref_projs] [init_dir]/projs_00 Reference projections (one)
;
; OUTPUT FILES: ([init_dir] denotes output directory and '%' denotes subset)
; [out_align_doc] [init_dir]/align_01_***_s% Alignment parameter doc files (one/group)
; [out_aligned] [init_dir]/dala_***@ Rotationally aligned particle stacks (one/group)
;
; PROCEDURES CALLED:
; recon-settings recon-settings.spi
;
; -------------------------------- END BATCH HEADER ----------------------------
MD
TR OFF ; Loop info turned off
MD
VB OFF ; File info turned off
; Get reconstruction parameters & file names
@recon-settings([pixsiz],[ang-step],[r2],[alignsh],[prj-radius],[winsiz],[incore-yn],[bp-type],[qsub],[masterCPUs],[groupCPUs])
SYS
echo -e " Alignment shift: {%I0%[alignsh]} Alignment radius: {%I0%[r2]}"
SYS
echo " Projection radius: {%I0%[prj-radius]}" ; echo
[iter] = 0
[next-iter] = 1
GLO [r2] = [r2]
GLO [alignsh] = [alignsh]
GLO [incore-yn] = 1
; Processes experimental images in series by groups of images.
; Find alignment parameters ('AP SHC') which best align experimental images with
; optimal projection image.
; Rotate ('RT SF') original particle images using these rotational alignment parameters.
UD N [num-grps]
[init_sel_grp]
; ; Create directories for output and scratch files
; SYS
; mkdir -p [init_dir]
DO [grp] = 1,[num-grps] ; Loop over all groups -----------------
@align-loop
[grp]
ENDDO ; End of: Loop over all groups --------
SYS
echo -en ' Alignment completed' ; date '+ TIME: %x %X' ; echo
EN
; Modified 2017-08-03
;