; Controls parallel refinement
;
; SOURCE: spider/docs/techs/recon1a/Procs/pub-refine.spi
;
; New ArDean Leith Nov 2000
; [rn] for endmerge ArDean Leith May 2005
; 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
; For gold standard reconstruction ArDean Leith May 2014
; Reference projections parallelized ArDean Leith Oct 2015
; Added PBS support ArDean Leith Feb 2016
; Removed PubSub support ArDean Leith Jun 2020
;
; PURPOSE: Runs on master node to control parallel refinement using cluster.
; Each data group creates one parallel process.
;
; I/O Registers & files are set in: refine-settings.spi
;
; INPUT FILES: ('***' denotes group here)
; [vol_orig] ../Reconstruction/vol_01 Initial reference volume (one)
; [sel_group_orig] ../Reconstruction/input/sel_group Group selection file (one)
; [sel_parts_orig] ../Reconstruction/input/sel_part_*** Group particle selection files (one/group)
; [unaligned_images_orig] ../Reconstruction/input/data_ctfd_*** Unaligned image stacks (one/group)
;
; PROCEDURES CALLED:
; refine-settings refine-settings.spi
; show-r2 show-r2.spi
; pub-prjrefs pub-prjrefs.spi
; .. pub-submit pub-submit.spi
; .. memforqsub (optional) memforqsub.spi
; .. qsub qsub.pbs
; .... pub-refine-start pub-refine-start
; ...... refine-settings refine-settings.spi
; ...... refine-prjloop refine-prjloop.spi
; pub-submit pub-submit.spi
; .. memforqsub (optional) memforqsub.spi
; .. qsub qsub.pbs
; .. pub-refine-start pub-refine-start
; .... refine-settings refine-settings.spi
; .... refine-loop OR refine-loop.spi
; .... refine-smangloop refine-smangloop.spi
; ...... refine-bp refine-bp.spi
; merge-fsc-filt merge-fsc-filt.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 if using 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],[qsub],[incore-yn],[gold-std],[bp-type])
SYS
echo ; echo -e " Alignment shift: {%I0%[alignsh]} Alignment radius: {%I0%[r2]}"
SYS
echo " Projection radius: {%I0%[prj-radius]}"
SYS ; Create output directories if not present
mkdir -p [out_dir] [work_dir]
SD / ITERATION MASKED-RES RESOLUTION
[iter_resol] ; Resolution doc file (output)
SD E
[iter_resol] ; Resolution doc file (finished)
UD N [num-grps] ; Find number of groups
[sel_group] ; Group selection file (input)
IF ( [iter1] == 1 ) THEN
; Ensure that starting input files exist
[iter] = 1
DO [s] = 1,2
; Create subset volumes from initial model
CP
[vol_orig] ; Starting initial model == reference volume
[vol_s] ; Starting subset reference volume
ENDDO
DO [grp] = 1,[num-grps]
; Must create odd and even particle selection lists for all groups
DE
[sel_parts]_s1 ; Odd particle selection doc file (removed)
DE
[sel_parts]_s2 ; Even particle selection doc file (removed)
DOC SPLIT
[sel_parts] ; Particle selection doc file (input)
[sel_parts]_s1 ; Odd particle selection doc file (output)
[sel_parts]_s2 ; Even particle selection doc file (output)
ENDDO
ENDIF
; Show alignment and projection radii on center slice of a reference volume
[s] = 1
@show-r2([r2],[alignsh],[prj-radius])
[vol_orig] ; Starting initial model == reference volume
IF ( [smallang-yn] == 1 ) THEN
; List desired offset angles for reference projections in a doc file.
@refine-setrefangles([iter],[smallang-yn],[ampenhance],[ang-step],[ang-limit],[num-angs])
ENDIF
DO [iter]=[iter1],[iter-end] ; Loop over all iterations ----------------------------------
IF ( [smallang-yn] == 0 ) THEN
; List desired angles ('VO EA') for reference projections in a doc file.
@refine-setrefangles([iter],[smallang-yn],[ampenhance],[ang-step],[ang-limit],[num-angs])
; Create reference projection ('PJ 3F') stacks from both subset reference volumes
; in parallel. Waits for all nodes to finish their projections.
@pub-prjrefs([iter],[num-grps],[prj-radius],[qsub])
ENDIF
; Process experimental images in parallel by groups of images using PBS.
; Find alignment parameters ('AP SHC' or 'AP REF') which align experimental images
; with the most similar projection image. This is done for the two subsets of images.
; Then align ('RT SF') the images and backproject ('BP 3F') to create two subset volumes.
[task] = [smallang-yn] ; pub-refine-start starts: refine-loop or refine-loop-smang
[script] = './spider $PRJEXT/$DATEXT @pub-refine-start ' ; Script that runs refinement
@pub-submit([iter],[num-grps],[task],[qsub])
[script] ; Script that runs refinement
; Consolidate ('AS S') all parallel group volumes for both subsets into two subset
; output volumes, find resolution ('FSC') by comparing FSC of the two subsets, and
; filter ('FD C') the combined volumes to limit resolution.
@merge-fsc-filt([pixsiz],[iter],[ampenhance],[r2],[sphdecon],[gold-std],[qsub])
; Show center slice of current volume
[next-iter] = [iter] + 1;
@show-r2([r2],[alignsh],[prj-radius])
[next_vol] ; Filtered volume (output)
SYS
echo " Iteration: {%I0%[iter]} Finished" ; echo
MY FL ; Flush results
ENDDO ; End of loop over all iterations ----------------------------
SYS ; Echo current time
echo -n " Refinement finished after iteration: {**[iter]} " ; date '+ Time: %x %X' ; echo
EN
;