; Computes and optionally applys alignment parameters
;
; SOURCE: apshgrp.spi New Nov 2004 ArDean Leith
; Rewritten Feb 2005 ArDean Leith
; Added alignment option & stack op Nov 2006 ArDean Leith
; SET MP location Feb 2008 ArDean Leith
;
; PURPOSE: Multi-reference alignment of an image series.
; Sample images are aligned with reference projections via
; shifts (translations) and rotations.
; FOR PROJECTS WITH MULTIPLE GROUPS- WITH OR WITHOUT PUBSUB.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
;------------ Edit next 6 Input parameters ------------------------------
[pubsub] = 0 ; If >0 use PubSub
[doalign] = 1 ; If >0 apply alignment to images
[range] = 8 ; Translation search range (must be divisible by step size)
[step] = 2 ; Translation step size
[diam] = 276 ; Diameter of object (Angstroms) for alignment search.
; (EDIT as needed!) Used to find last alignment radius.
[r1] = 5 ; First rotation alignment ring, only radii > this will be analyzed
[r2] = 0 ; Last rotation ring (If zero, compute from object diameter)
; ----------------- Input files --------------------------------------------
FR G
[parameters]../params ; Parameter setting file
FR G
[defgrps]../Reconstruction/sel_group ; List of groups (group selection doc file)
FR G
[ref_images]projs/prj_{***[grp]}@ ; Reference image name
FR G
[ref_images_angles]refangles ; Reference images angles doc. file
FR G
[unaligned_images]data{***[grp]}@ ; Unaligned particles stacks
; ----------------- Output files ------------------------------------------------
FR G
[align_parameters]align_01_{***[grp]} ; Alignment parameters doc. file
FR G
[aligned_images]dala01_{***[grp]}@ ; Rotated, shifted (aligned) particles
; ----------------- END BATCH HEADER -------------------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
; DO NOT WORRY IF [grp] IS UNDEFINED HERE, IT IS TAKEN CARE OF BY PUBSUB
IF ([grp] .GT. 0) [pubsub] = 0 ; Secondary PubSub run
UD N [numgrps] ; Get number of groups
[defgrps] ; Groups selection file (input)
IF ([pubsub] .EQ. 0) THEN ; Main loop runs 'AP SH'
; Used for Non-PubSub and PubSub runs
MD
SET MP ; Use all processors (needed here for secondary runs)
0
IF ([r2].LE.0) THEN ; Compute alignment radius from object size
UD 5,[pxsz] ; Get pixel size (A) from this file
[parameters]
UD 17,[winsz] ; Get window size (pixels) from this file
[parameters]
[r2] = INT([diam]/(2.0*[pxsz])) ; Compute object radius (pixels) for last alignment ring
[tp] = [r2] + [range] ; Compute last ring + translation range
[t] = INT([winsz]/2) - 1 ; Compute max. radius of object within window
IF ([tp] .GE. [t]) THEN
[r2] = [t] - [range] - 1 ; Reduce radius of last alignment ring to fit window
ENDIF
ENDIF
IF ([grp] .GT. 0) [numgrps] = 1 ; Group listed on command line, overides list
DO LB2 [numgrp]=1,[numgrps] ; Loop over all group(s)
IF ([grp] .LT. 1) THEN ; Group not on command line, use list from selection file
UD [numgrp],[grp] ; Get current group number
[defgrps] ; Group selection file (input)
ENDIF
DE ; Delete existing output doc. files.
[align_parameters]
FI X [numpart] ; Get number of particles
[unaligned_images] ; Unaligned particles name template (input)
(26) ; Max. image number in stack
FI X [numproj] ; Get number of projections
[ref_images] ; Unaligned particles name template (input)
(26) ; Max. image number in stack
VM
echo ' 'Aligning group: {****[grp]} with: {******[numpart]} particles
AP SH ; Find Alignment using multiple references
[ref_images]***** ; Reference image file name template (input)
(1-[numproj]) ; List of reference images
[range],[step] ; Search range, step size
[r1],[r2] ; First and last ring
[ref_images_angles] ; Ref. angles doc file (input)
[unaligned_images]***** ; Unaligned particles file name template (input)
(1-[numpart]) ; Number of particles
* ; No unaligned particles align. doc file
(0) ; No restriction on angular proj. search
(1) ; Check mirrored positions
[align_parameters] ; Alignment angles doc. file (output)
IF ([doalign] .GT. 0) THEN
; Apply alignment parameters to unaligned particles
; Order in doc file: PHI,THETA,PSI, REF#,IMG#, ROT,SX,SY
RT SQ ; Rotate & shift whole stack operation
[unaligned_images] ; Unaligned particles stack (input)
[aligned_images] ; Aligned particles stack (output)
(6,0,7,8) ; Reg. numbers for angle, scale,& shifts
[align_parameters] ; Alignment angles doc. file (input)
ENDIF
MY FL ; Flush results file
[grp] = 0 ; Reset default group for next group
LB2 ; End loop for multiple groups
ELSE ; Used only to intiate master PubSub run
DO LB3 [numgrp]=1,[numgrps] ; Loop over all groups
UD [numgrp],[grp] ; Get current group number
[defgrps] ; Group selection file (input)
; Create parallel PubSub run for each group
VM ; Use PubSub to create parallel processes
publish './spider spi/$DATEXT @apshgrp {***[grp]} grp={***[grp]}'
LB3
ENDIF
EN
;