; Computes alignment parameters for sample images
;
; SOURCE: apsh.spi ArDean Leith Nov 2004
;
; PURPOSE: Multireference alignment of an image series.
; Sample images are aligned with reference projections via
; shifts (translations) and rotations.
;
; FOR PROJECTS WITH SINGLE OR MULTIPLE GROUPS.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; INSTRUCTIONS: pub_apsh.html
;
;------------ Edit next 7 Input parameters ------------------------------
x12=0 ; If >0 use PubSub
x13=2 ; If >1 do multiple groups
x31 = 8 ; Translation search range (must be divisible by step size)
x32 = 2 ; Translation step size
x20 = 366.47 ; Diameter of object (Angstroms) for alignment search.
; (EDIT as needed!) Used to find radius of last alignment ring.
x21 = 5 ; First rotation alignment ring, only radii > this will be analyzed
x22 = 0 ; Last rotation ring (If zero, compute from object diameter)
; ----------------- Input files --------------------------------------------
FR G
[parameters]../params ; Parameter setting file
FR G
[order]../Power_Spectra/order_defgrps ; List of groups (group selection doc file)
; If file missing, create using: 'DOC CREATE'
IF (x13.GT.1) THEN
FR G
[ref_images_template]df{***x77}/prj**** ; Reference image name template
ELSE
FR G
[ref_images_template]prj**** ; Reference image name template
ENDIF
FR G
[ref_images_selection]projlist ; Reference images selection doc. file
FR G
[ref_images_angles]refangles ; Reference images angles doc. file
FR G
[sample_images_template]../Particles/win/ser****** ; Sample image name template
FR G
[sample_images_selection]part_by_group_{***x77} ; Particle selection doc file
; ----------------- Output files -------------------------------------------------
FR G
[align_parameters]align_01_{***x77} ; Alignment parameters doc. file
; ----------------- END BATCH HEADER -------------------------------------------
IF (x77 .GT. 0) x12 = 0 ; Secondary PubSub run
IF (x13 .LE. 1) x77 = 1 ; Single group only use default output file name
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
IF (x12 .EQ. 0) THEN ; Normal run (Not a primary PubSub run)
IF (x22.LE.0) THEN ; Compute alignment radius from object size
UD 5,x39 ; Get pixel size (A) from [parameters] file
[parameters]
UD 17,x52 ; Get window size (pixels) from [parameters] file
[parameters]
x22 = INT(x20/(2.0*x39)) ; Compute object radius (pixels) for last alignment ring
x46 = x22 + x31 ; Compute last ring + translation range
x45 = INT(x52/2) - 1 ; Compute max. radius of object within window
IF (x46.GE.x45) THEN
x22 = x45 - x31 - 1 ; Reduce radius of last alignment ring to fit window
ENDIF
ENDIF
IF (x77 .LE. 0) THEN ; Group not on command line, get it from selection file
UD N,x70 ; Get number of groups
[order] ; Groups selection file (input)
x70=2 ;;;;;;;;
DO LB2 x11=1,x70 ; Loop over all groups
UD x11,x77 ; Get current group number
[order] ; Group selection file (input)
ENDIF
DE ; Delete existing alignment parameter output doc. files.
[align_parameters]
AP SH ; Align sample images using multiple references
[ref_images_template] ; Reference image name template (input)
[ref_images_selection] ; Reference images selection doc. file (input)
x31,x32 ; Search range, step size
x21,x22 ; First and last ring
[ref_images_angles] ; Ref. angles doc file (input)
[sample_images_template] ; Sample images name template (input)
[sample_images_selection] ; Sample images selection doc. file (input)
* ; No sample images align. doc file
(0) ; NO restriction on Angular proj search
(1) ; Check mirrored positions
[align_parameters] ; Alignment angles doc. file (output)
MY FL ; Flush results file
LB2 ; End loop for multiple groups
ELSE ; Primary PubSub run
UD N,x70 ; Get number of groups
[order] ; Groups selection file (input)
DO LB2 x11=1,x70 ; Loop over all groups
UD x11,x77 ; Get current group number
[order] ; Group selection file (input)
VM ; Use PubSub to create parallel 'AP SH' processes
publish './spider bat/$DATEXT @pub_apshctf {***x77} x77={***x77}'
LB2
ENDIF
EN
;