([doalign],[shrange],[step],[diam],[r1],[r2],[max-wait])
; Compute alignment parameters and optionally apply them
;
; SOURCE: spider/docs/techs/recon/newprogs/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
; VAR name Feb 2010 ArDean Leith
; VAR names changed Dec 2010 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.
;
;------------ Edit next 7 Input parameters ------------------------------
[doalign] = 1 ; If >0 apply alignment to images
[shrange] = 8 ; Translation search range (must be divisible by step size)
[step] = 2 ; Translation step size
[diam] = 348 ; Diameter of object (Angstroms) for alignment search.
; (EDIT as needed!) Used to find last rotational 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)
[max-wait] = 600 ; maximum headstart in seconds for copying stacks before next group starts
; ----------------- Input files --------------------------------------------
GLOBAL [params] = '../params' ; Parameter setting file
GLOBAL [group_list] = 'sel_group' ; List of defocus groups (doc. file)
GLOBAL [ref_images] = 'projs/prj_{***[grp]}@' ; Reference images
GLOBAL [ref_images_angles] = 'refangles' ; Reference images angles doc. file
GLOBAL [unaligned_images] = 'data{***[grp]}@' ; Unaligned particles images
GLOBAL [group_particle_list] = 'sel_particles_***' ; Group particle list
GLOBAL [mic2global_lut] = '../Particles/coords/mic2global****' ; Micrograph-to-particle lookup-table
; ----------------- Output files ------------------------------------------------
GLOBAL [temp_images] = '_8@' ; Local stacks (if fits in memory)
;GLOBAL [temp_images] = '/var/tmp/data{***[grp]}@' ; Local stacks (if doesn't fit in memory)
GLOBAL [align_parameters] = 'align_01_***' ; Alignment parameters doc. file
GLOBAL [align_params_all] = 'align_01_all' ; Combined alignment parameters
GLOBAL [aligned_images] = 'dala01_{***[grp]}@' ; Rotated, shifted (aligned) particles
GLOBAL [dummy_wait_file] = 'jnk_apshwait***' ; Dummy file created when finished copying
GLOBAL [finished_flag] = 'flag-apsh-done_{***[grp]}' ; Dummy file created when finished
; ----------------- END BATCH HEADER -------------------------------------------
RE
;