; Controls and synchronizes refinement
;
; FILE: pub_refine.pam ArDean Leith Nov 2000
; ArDean Leith Mar 2004
; [rn] ArDean Leith Feb 2005
; [rn] for endmerge ArDean Leith May 2005
; [] ArDean Leith Dec 2005
; ""on publish line ArDean Leith Jan 2006
; [] from publish ArDean Leith Feb 2006
; Newdala removed ArDean Leith Mar 2006
; Ampenhance fixed ArDean Leith May 2006
; More stacks ArDean Leith Dec 2006
; MP = 1 ArDean Leith Jan 2008
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; PURPOSE: Runs on one node to control and synchronize refinement
;
; I/O Registers & files are set in: refine settings refine settings.pam.pam)
;
; INPUT REGISTERS:
; [maxspfreq] Maximum spatial freq[a-1] (used in prepare)
; [radius] Radius of structure
; [alignsh] Shift allowed is +-[alignsh]
; [iter-end] Ending iteration
; [lambda] Lambda(angstroms) (used in prepare)
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES:
; [order_select] input/order_select Group selection file
; [sorted_order_select] input/order_select_sort Sorted group selection file
; [unaligned_images] input/data*** Unaligned stacked image files
; [aligned_images] input/dala01_*** Aligned stacked image files
; [start_group_align] input/align_01_*** Alignment parameter input file
; [start_vol] input/vol01 Initial starting volume
;
; PROCEDURES CALLED:
; refine_settings refine_settings.pam
; sort sort.pam
; prepare prepare.pam
;
; publish publish
; ... pub_refine_start pub_refine_start
; ....... refine_settings refine_settings.pam
; ....... grploop grploop.pam
; ....... smangloop smangloop.pam
; ....pub_refine_doc_sync pub_refine_doc_sync.pam
; pub_refine_wait pub_refine_wait.pam
;
; mergegroups mergegroups.pam
; ... enhance enhance.pam
; ... saveresp saveresp.pam
; publish publish
; ... pub_refine_start pub_refine_start
; ...... refine_settings refine_settings.pam
; ...... endmerge endmerge.pam
; ....pub_refine_doc_sync pub_refine_doc_sync.pam
; pub_refine_wait pub_refine_wait.pam
;
; endrefine endrefine.pam
; ... saveresp saveresp.pam
;
; ---------------------------------------------------------------------
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
; Input initial parameters & file names but not angular steps
@refine_settings([maxspfreq],[radius],[alignsh],[prj-radius],[iter1],[iter-end],[lambda],[small-ang],[winsize],[converg])
IF([iter1].LE.1)THEN
; Prepare input files (only needs to be done once)
@prepare([maxspfreq],[lambda],[iter1])
ENDIF
[xdum]=0.0
; Loop over all iterations
DO LB1 [iter]=[iter1],[iter-end]
FT ; Fourier on volume
[current_vol] ; Volume produced by previous iter.
[iter_vft] ; Used by all groups on this iter. in xoop - vft
; Create ref. angle & ref. selection doc files for this iteration
DE
[iter_ang_voea] ; Ref. angles doc file
DE
[iter_select_voea] ; Ref. angle selection doc file
RR S [ang-step] ; Angular step (varies with iteration)
([ang-steps])
[iter]
RR S [ang-limit] ; Restriction on ang. search degrees (varies with iteration)
([ang-limits])
[iter]
RR S [ampenhance] ; Amplitude enhancement register setting (varies with iteration)
([amp-enhance-flags])
[iter]
IF ([small-ang].EQ.0) THEN
; For regular angle refinement
VO EA,[num-angles] ; Sets [num-angles] to number of reference projections
[ang-step] ; Angular step (varies with iteration)
(0,90.0) ; Angles
(0,359.9) ; Angles
[iter_ang_voea] ; Create ref. angles doc file (output)
ELSE
; For SMALL angle refinement
VO EA,[num-angles] ; Sets [num-angles] to number of reference projections
[ang-step] ; Angular step
(0,[ang-limit]) ; SMALL Angles
(0,0) ; SMALL Angles
[iter_ang_voea] ; Create ref. angles doc file (output)
ENDIF
DOC CREATE ; Create ref. angle selection doc file
[iter_select_voea] ; Ref. angle selection doc file (output)
(1) ; First register
1-[num-angles] ; Select all angles
; Find number of defocus groups
UD N [num-grps]
[sorted_order_select]
; Generate random number ([rn]) for unique DOC_SYNC files
[rn]=int(ran([xdum])*9999)
; Process all defocus groups in parallel
[task] = [small-ang] ; Pub_starter selector flag
DO LB3 [i]=1,[num-grps]
UD IC [i],[grp] ; Get this defocus group number
[sorted_order_select]
; Use pub_refine_start to create parallel grploop for each defocus group
VM
publish './spider pam/$DATEXT @pub_refine_start {***[grp]} task={*[task]} iter={**[iter]} grp={***[grp]} rn={****[rn]}'
;
LB3
UD ICE ; End doc file UD ICE use
[sorted_order_select]
VM
date '+ TIME: %x %X'
VM
echo " Waiting for iteration: {**[iter]}"
MY FL ; Flush results file
; Wait for all subscribers to finish grploop, returns [num-big]
[task] = 0 ; Pub_starter selector flag
@pub_refine_wait([task],[num-big],[num-grps],[iter],[converg],[rn])
; [num-big] returns number of groups having excessive changes
; (this is summed in: pub_refine_wait)
VM
echo " After pub_refine_wait, Excessive changes in: {***[num-big]} groups"
; If angular changes were small in all groups, can stop now
IF([num-big].EQ.0) GOTO LB71
; Consolidate data for CTF corrections
@mergegroups([maxspfreq],[iter],[ampenhance])
DE ; Delete vft file.
[iter_vft] ; Used by all groups this iter.
DE ; Delete ref. angle selection file
[iter_select_voea] ; Ref. angle selection doc file
MY FL ; flush results
LB1
LB71
VM
date '+ TIME: %x %X'
VM
echo " Alignment halting after iteration: {***[iter]}"
VM
echo " "
; Start up endmerge using PubSub
DO LB11 [i]=1,[num-grps]
UD S [i],[grp] ; Get defocus group number
[sorted_order_select]
;By setting [task]=2 pub_refine_start starts: endmerge
VM
publish './spider pam/$DATEXT @pub_refine_start {***[grp]} task=2 iter={**[iter]} grp={***[grp]} rn={****[rn]}'
LB11
UD E ; End doc file UD use
VM
date '+ TIME: %x %X'
VM
echo " Waiting for endmerge for iteration: {**[iter]}"
MY FL ; Flush results
; Wait for all subscriber group tasks
[task]=2
@pub_refine_wait([task],[num-big],[num-grps],[iter],[converg],[rn])
; Prepare final resolution files
@endrefine([maxspfreq],[iter])
VM
date '+ TIME: %x %X'
VM
echo " SUCCESS, REFINEMENT FINISHED"
EN
;