; Controls reconstruction
;
; FILE: spider/docs/techs/recon/newprogs/pub_recon.pam
; New ArDean Leith Dec 2009
;
; PURPOSE: Runs on one node to control and reconstrtuction
;
; INPUT
; [params] ../params ; Reconstruction parameter file
; [sel_grp] sel_group_cclim ; Defocus group selection file
; [sel_part] sel_particles_{***[grp]} ; Particle selection files (one / defocus group)
; [ali] ../Alignment/dala01_{***[grp]}@** ; Aligned particle images (one stack / defocus group)
; [angles] ../Alignment/align_01_{***[grp]} ; Alignment parameter doc files (one / defocus group)
;
; OUTPUT:
; [selodd] df{***[grp]}/sel_odd ; Selection files for odd-numbered particles (one / defocus group)
; [seleven] df{***[grp]}/sel_even ; Selection files for even-numbered particles (one / defocus group)
; [volodd] vol01_odd ; Volume created from "odd" particles
; [voleven] vol01_even ; Volume created from "even" particles
; [grpvolodd] df{***[grp]}/vol01_odd ; Volumes for even-numbered particles (one per group)
; [grpvoleven] df{***[grp]}/vol01_even ; Volumes for odd-numbered particles (one per group)
; [grpfsc] df{***[grp]}/fscdoc ; FSC doc files (one per group)
; [ctf] df***/ctffile ; CTF correction files (one per group)
; [vol] vol01 ; CTF-corrected combined volume
; [combfsc] combires ; FSC doc file with FSC curve for combined volume
; [res_file] resolution ; Resolution doc file for combined volume
;
; PROCEDURES CALLED:
; recon recon.spi
; publish publish
;
; -------------------- Inpub files ( From recon.spi) ---------------------------
[sel_grp] = 'sel_group_cclim' ; Defocus group selection file
; -------------------- Output files ( From recon.spi) ---------------------------
[ctf] = 'df{***[grp]}/ctffile' ; CTF correction files (completion flag)
[combfsc] = 'combires' ; FSC doc file with FSC curve for combined volume
; -------------- END BATCH HEADER -------------------------------------------
MD
TR OFF ; Loop info turned off
MD
VB OFF ; File info turned off
MD
() OFF ; No need for () in DO loops
MD
SET MP ; Use single OMP processor
1
DE ; Delete existing file
[combfsc] ; FSC doc file file used as completion flag
DO ; --------------------------- Loop starts group back projections --------------
UD NEXT [key],[grp],[p],[def] ; Get group from group sel. file
[sel_grp] ; Group selection file (input)
IF ([key] .LE. 0) EXIT ; End of groups in selection file
DE ; Delete existing file
[ctf] ; CTF correction file used as completion flag
VM ; Process all defocus groups in parallel
publish './spider spi/$DATEXT @recon {***[grp]} grp={***[grp]}'
ENDDO
UD NEXT END ; Reset group sel. file
[sel_grp] ; Group selection file (ends)
VM ; Echo start time
date '+ TIME: %x %X'
DO ; --------------------------- Loop waits for group back projections ------------
UD NEXT [key],[grp] ; Get group from group sel. file
[sel_grp] ; Group selection file (input)
IF ([key] .LE. 0) EXIT ; End of groups in selection file
VM
echo " Waiting for group: {**[grp]}"
MY FL ; Flush results file
; Wait for all subscribers to finish back projections
IQ SYNC ; Wait for CTF file creation
[ctf]
(10 3600000)
VM
echo " Finished group: {**[grp]}"
VM
date '+ TIME: %x %X'
ENDDO
; --------------------------------- Start volume combination & resolution calc. -----
VM ; Combine group volumes and find resolution
publish './spider spi/$DATEXT @recon 0 grp=-99'
VM
date '+ TIME: %x %X'
IQ SYNC ; Wait for FSC file creation signal
[combfsc] ; Doc file (output)
(10 3600000)
VM
date '+ TIME: %x %X'
VM
echo " RECONSTRUCTION FINISHED"
EN
;