; Controls and synchronizes alignment
;
; SOURCE pub_apsh.bat 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 MULTIPLE DEFOCUS GROUPs. IF YOU HAVE ONLY
; SINGLE GROUP USE:
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs/
;
; INSTRUCTIONS: pub_apsh.html
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
;------------ Edit next 4 Alignment parameters ---------------------
x20 = 366.47 ; Diameter of object (Angstroms) used in alignment search.
; (EDIT as needed!)
; Diameter is used to find radius of last alignment ring.
x31 = 8 ; Translation search range (must be divisible by step size)
x32 = 2 ; Translation step size
x21 = 5 ; First rotation alignment ring, only radii > this will be analyzed
; ----------------- Input files --------------------------------------------
FR G
[params]../params ; Parameter setting file
FR G
[order]../Power_Spectra/order_defgrps ; Defocus groups selection file
FR G
[ref_images_template]prj/prj**** ; Reference image name template
FR G
[ref_images_selection]projlist ; List of reference image numbers
FR G
[ref_images_angles]refangles ; Ref. angles doc file
FR G
[sample_images_template]../Particles/win/ser****** ; Particle images
FR G
[sample_images_selection]part_by_group_{***x77} ; Particle selection doc file
; ----------------- Output files -----------------------------------------
FR G
[align_parameters]align_{***x77} ; Alignment parameters doc. file
;
; -------------------------------------------------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
IF (x14 .NE. 1) THEN ; Primary PubSub run
UD N,x70 ; Get number of defocus groups
[order] ; Defocus groups selection file (input)
DO LB1 x11=1,x70 ; Loop over all groups
UD x11,x77 ; Get current defocus group number
[order] ; Defocus group selection file (input)
VM ; Use PubSub to create parallel processes
publish './spider bat/$DATEXT @pub_apsh {***x77} x14=1 x77={***x77}'
MY FL ; Flush results file
LB1
ELSE ; Secondary PubSub run
UD 5,x39 ; Get pixel size (A) from [params] file
[parameters]
UD 17,x52 ; Get window size (pixels) from [params] 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
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)
* ; Sample images align. doc file (input)
(0) ; NO restriction on Angular proj search
(1) ; Check mirrored positions
[align_parameters] ; Alignment angles doc. file (output)
ENDIF
EN ; This SPIDER ends now
;