; Controls refinement of a reconstruction
;
; SOURCE: refine.pam New ArDean Leith Nov 2000
; Rewritten ArDean Leith Mar 2004
; [] variables ArDean Leith Dec 2005
; Ampenhance fixed ArDean Leith May 2006
; More stacks ArDean Leith Dec 2006
;
; PURPOSE: Controls refinement
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O Registers and files are set in: refine settings refine settings.pam.pam); INPUT REGISTERS:
;
; INPUT REGISTERS:
; [maxspfreq] Maximum spatial freq[a-1] (used in prepare)
; [radius] Radius of structure
; [alignsh] Shift allowed is +- this value
; [prj-radius] Radius of structure for projection
; [iter1] Starting iteration
; [iter-end] Ending iteration
; [lambda] Lambda(angstroms) (used in prepare)
; [small-ang] Small angle refinement flag (1 is true)
; [converg] Convergence criterion percentage
;
; INPUT FILES:
; [params] input/params Parameter doc. file
; [order_select] input/order_select Group selection file
; [start_vol] input/vol01 Initial starting volume
; [sel_particles] input/select_*** Particle selection files
; [start_group_align] input/align_01_*** Alignment parameter input file
; [unaligned_images] input/data*** Unaligned stacked image files
; [start_aligned_images] input/dala01_*** Aligned stacked image files
;
; PROCEDURES CALLED:
; refine_settings refine_settings.pam
; prepare prepare.pam
;
; grploop grploop.pam OR
; smangloop smangloop.pam
;
; mergegroups mergegroups.pam
; ... enhance enhance.pam
; ... saveresp saveresp.pam
; endmerge endmerge.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 all available OMP processors
0
; Input initial parameters & file names
@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
MY FL
; Loop over all iterations
DO LB1 [iter]=[iter1],[iter-end]
RR S [ang-step]
([ang-steps]) ; Angular step for projection angle (varies with iteration)
[iter]
RR S [ang-limit] ; Restriction on angular degree search (varies with iteration)
([ang-limits])
[iter]
RR S [ampenhance] ; Amplitude enhancement flag (varies with iteration)
([amp-enhance-flags])
[iter]
FT ; Fourier on current volume
[current_vol] ; Volume produced by previous iter.
[iter_vft] ; Fourier of volume (used by all groups on this iter. in grploop)
; Create reference 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
IF ([small-ang].EQ.0) THEN ; 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 ; 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
UD N [num-grps] ; Get number of defocus groups
[order_select]
; Process all defocus groups one by one
[num-big] = 0 ; Number of large proj. angle displacements
DO LB3 [i]=1,[num-grps]
UD S [i],[grp] ; Get defocus group number from unsorted list
[order_select]
VM
date '+ TIME: %x %X'
VM
echo " Processing group: {***[grp]}"
MY FL ; Flush results file
; grploop/smangloop returns [stop]
IF([small-ang].EQ.0)THEN ; Runs main refinement smangloop tasks
@grploop([ang-step],[ang-limit],[radius],[alignsh],[prj-radius],[iter],[grp],[stop],[maxspfreq])
ELSE
@smangloop([ang-step],[radius],[alignsh],[prj-radius],[iter],[grp],[stop],[iter1],[maxspfreq])
ENDIF
; Check size of projection angular changes
; [stop] returns % of images whose proj. angle moved by >1.5*[ang-step]
IF([stop].GT.[converg]) [num-big]=[num-big]+1 ; Excessive ang. change for this group
MY FL ; Flush results file
LB3
UD E ; Finished with incore doc file
VM
echo " Iteration: {**[iter]} Excessive proj. ang. changes in: {***[num-big]} groups"
; If projection 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 file
LB1
LB71
VM
echo ' ' ; echo " Alignment halting after iteration: {***[iter]}"
VM
date '+ TIME: %x %X'
VM
echo ' '
DO [i]=1,[num-grps]
UD IC [i], [grp] ; Get defocus group number from list
[order_select]
@endmerge([prj-radius],[grp],[iter])
ENDDO
UD ICE
[order_select]
; Prepare final resolution files
@endrefine([maxspfreq],[iter])
VM
date '+ TIME: %x %X'
VM
echo ' '
VM
echo " SUCCESS, FINISHED REFINEMENT"
EN
;