; Controls and synchronizes refinement
;
; SOURCE: spider/docs/techs/recon1/Procs/pub-refine.spi
;
; New ArDean Leith Nov 2000
; [rn] for endmerge ArDean Leith May 2005
; [] from publish ArDean Leith Feb 2006
; Ampenhance ArDean Leith May 2006
; More stacks ArDean Leith Dec 2006
; Existing iter_refangs bug ArDean Leith Aug 2010
; COG centering ArDean Leith Sep 2010
; Dala files removed ArDean Leith Jan 2012
; pixsiz, resol headers,... ArDean Leith Aug 2012
; For CTF corrected images ArDean Leith Oct 2013
;
; PURPOSE: Runs on master node to control PubSub refinement. Master procedure for
; multiple iteration refinement on parallel cluster using: PubSub to control
; distribution of parallel jobs. Each data group uses one parallel process.
;
; I/O Registers & files are set in: refine-settings.spi
;
; INPUT REGISTERS:
; [maxspfreq] Maximum spatial freq (1/A) (used in prepare)
; [r2] Radius of object
; [alignsh] Translation shift allowed is +-[alignsh]
; [iter-end] Ending iteration
;
;
; INPUT FILES: ('***' denotes group here)
; [params] ../params Params file (one)
; [vol_orig] ../Reconstruction/vol_01 Initial volume file (one)
; [sel_group_orig] ../Reconstruction/input/bp_sel_group Group selection file (one)
; [sel_parts_orig] ../Reconstruction/input/bp_sel_part_*** Group particle selection files (one/group)
; [unaligned_images_orig] ../Reconstruction/input/bp_data_ctfd_*** Unaligned image stacks (one/group)
;
; PROCEDURES CALLED:
; refine-settings refine-settings.spi
; refine-prepare refine-prepare.spi
; refine-refangles refine-refangles.spi
;
; publish publish.perl
; ... pub-refine-start pub-refine-start
; ....... refine-settings refine-settings.spi
; ....... refine-loop refine-loop.spi
; ....... refine-smangloop refine-smangloop.spi
; ....... refine-bp refine-bp.spi
;
; refine-merge refine-merge.spi
; ... enhance (optional) enhance.spi
;
; ---------------------------------------------------------------------
; -- END BATCH HEADER --
MD
TR OFF ; Loop info turned off
MD
VB OFF ; File info turned off
MD
SET MP ; Use only one or two processors on master node!!
1
; Input initial parameters & file names but not angular steps
@refine-settings([pixsiz],[r2],[alignsh],[prj-radius],[iter1],[iter-end],[sphdecon],[smallang-yn],[winsiz],[incore-yn],[prepare-yn],[bp-type])
UD N [num-grps] ; Find number of groups
[sel_group] ; Group selection file (input)
[iter] = 2
@refine-merge([pixsiz],[iter],[ampenhance],[r2])
SYS
echo " Iteration: {%I0%[iter]} Finished" ; echo
EN
;