(x41,x42,x51,x52,x55,x56,x76,x77,x47,x74,x14)
; Main refinement group loop
;
; grploop.pam -- Main refinement group loop al Nov 2000
; stat in operation al Feb 2005
; stack alignment al Mar 2005
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; PURPOSE: Runs for each defocus group on each iteration
;
; CALLED FROM: pub_starter.pam or
; refine.pam
;
; INPUT REGISTERS:
; x41 Angular steps (Varies with iter)
; x42 Restrict angular search (Varies with iter)
; x51 Radius of structure
; x52 Image size
; x55 Max. shift allowed is +-x55
; x56 Radius of structure used in projection
; x74 Starting alignment iteration
; x76 Alignment step iteration counter (Varies with iter)
; x77 Defocus group (Varies with group)
; OUTPUT REGISTERS:
; x47 % of images whose proj. angle moved by > 1.5*x41
;
; INPUT FILES (SET IN: refine_settings refine_settings.pam.pam):
; input/order_select [order_select] Image ID doc. fil
; work/select_{***group} [group_select] (From prepare)
; final/vft{**iter} [iter_vft] (From refine)
; work/ctf{***grp} [temp_ctf_file] (From prepare)
; input/dala{**iter}_{***group}@ [aligned_images] Aligned stacked image files
; final/align{**iter}_{***group} [next_group_align]
; input/data{***grp}@ [unaligned_images] Unaligned stacked image file
; final/angvoea_{**iter} [iter_ang_voea]
; final/selvoea_{**iter} [iter_select_voea]
;
; OUTPUT FILES(SET IN: refine_settings refine_settings.pam.pam):
; work/dala{**iter+1}_{***grp}@ [next_aligned_images]
; final/align{**iter+1}_{***group} [next_group_align]
; work/vol{**iter}_{***group} [next_group_vol]
; work/vol_{**iter+1}_odd_{***group} [next_group_vol]_odd (Deleted in mergegroups)
; work/vol_{**iter+1}_even_{***group} [next_group_vol]_even (Deleted in mergegroups)
; local/refproj{**iter}_{***grp}@ [temp_ref_projs] (Created & deleted)
; local/refproj{**iter+1}_{***group} [temp_ref_projs] (Created & deleted)
; final/dres{**iter+1}_{***group} [next_group_dres]
;
; PROCEDURES CALLED: saveresp
;
; INLINE BUFFERS USED: _1, _4
VM
echo " In grploop, Iteration: {**x76} Group: {***x77}"
VM
date '+ Time: %x %X'
x54=5.0 ; First radius for AP (Can alter this)
x17=1.5*x41 ; Convergence criterion angular distance limit.
x58=int(x52/2)+1 ; Image center
x86=x76+1 ; Next iteration
UD N,x53 ; Get number of ref. projections in use
[iter_select_voea]
MY FL ; Flush results file
UD IC,x77,x79 ; Sets x79 to number of images in this group
[order_select]
UD ICE
[order_select]
; Multiply Fourier of current volume by CTF file for this group
MU ; Multiply
[iter_vft] ; Fourier of current volume (final/vft{iter}
[temp_ctf_file] ; CTF file (work/ctf{grp})
_1 ; _1 created here
*
FT ; Reverse Fourier transform
_1 ; Fourier of CTF corrected current volume
_4 ; CTF corrected current volume created here
DE ; _1 can be deleted here
_1 ; Fourier of CTF corrected current volume
; Create stack holding angular reference projections from input volume.
PJ 3Q ; Create reference projections
_4 ; CTF corrected current volume (input)
x56 ; Radius of object
[iter_select_voea] ; Ref. angles selection doc. file (input) - selvoea
[iter_ang_voea] ; Ref. angles doc. file (input)
[temp_ref_projs]@****** ; Template for ref. projections (output) - refproj
DE ; _4 can be deleted here
_4 ; CTF corrected current volume
DE ; Remove existing next alignment doc output file
[next_group_align] ; Alignment doc file
DE ; Remove existing scratch file
work/SCR_{**x76}_{***x77} ; Reference rings scratch file
MY FL ; Flush results file
; Find reference projection matching current aligned image
AP REF
[temp_ref_projs]@****** ; Template of existing ref. projections
(1-x53) ; Ref. projections file numbers
x55 ; Shift search range
(x54,x51,1) ; First, last ring & skip
[iter_ang_voea] ; Ref. angles file (input)
work/SCR_{**x76}_{***x77} ; No scratch file if fits in-core
[aligned_images]***** ; Template for current exp. aligned images
(1-x79) ; Current exp. images file numbers
[group_align] ; Exp. images alignment doc. file < < < .....
(x42,x17) ; Angular proj search restriction & stop threshold
(1) ; Check mirrored projections
[next_group_align] ; Alignment doc file (output)
; Align experimental images
RT SQ ; Rotate & shift (stack operation)
[unaligned_images] ; Unaligned original images (stack)
[next_aligned_images] ; Current aligned images (output)
(6,0,7,8) ; Rot., scale, & shift registers
[next_group_align] ; Alignment doc file from 'AP REF'
; '%BIG-ANGDIF, AVG-ANGDIF, AVG-CCROT, %WORSE, AVG-WORSE, AVG-BETTER'
UD -2, x47, x92, x93, x94, x95, x96
[next_group_align] ; Next align. doc file
UD E
; Echo size of change in proj. angle, etc.
VM
echo " Iteration: {**x76} Group: {***x77} Excessive changes: {***x47}%"
VM
echo " Degred.%: {%f5.1%x94} Avg. degred.: {%f10.2%x95} Avg. improve: {%f10.2%x96}"
VM ; Echo this for isolating stack overflow
echo " Commencing back projection"
MY FL
; Calculate new, refined volume using centered projections and
; the angles from align doc. file
BP 32F ; Back Projection - 3D Fourier
[next_aligned_images]****** ; Template for aligned images (stacked)
[group_select] ; Selection doc. file - select
[next_group_align] ; Alignment doc file - align
* ; No symmetries
[next_group_vol]tmp ; Reconstructed volume - voltmp
[next_group_vol]_odd ; Reconstructed volume - vol_odd
[next_group_vol]_even ; Reconstructed volume - vol_even
MY FL
CG PH,x11,x11,x11,x21,x22,x23 ; Find center of gravity of new vol.
[next_group_vol]tmp
MY FL
; Center reconstructed volume
SH F ; Shift new vol.
[next_group_vol]tmp ; Input volume
[next_group_vol] ; Output voume
-x21,-x22 ; Shifts
-x23
DE ; Delete temp file - vol{iter}tmp
[next_group_vol]tmp
; Find resolution metric
RF 3 x69,x68 ; Phase Residual & shell correl.
[next_group_vol]_odd ; First volume input file
[next_group_vol]_even ; Second volume input file
(0.5)
(0.2,2.0)
C
(90.0)
(3)
[next_group_dres] ; Output document file - dres
; Record group resolution in resolutiongs doc file
@saveresp(x14,x76,x77,x68)
[grp_resol] ; Output file
VM ; Remove - refproj (no longer needed)
\rm -f [temp_ref_projs]*.$DATEXT
IF (x76 .GT. x74) THEN ; Not first iteration
DE ; Remove previous group vol.
[group_vol] ; work/vol_{**x76}_{***x77}
DE ; Remove previous odd group vol.
[group_vol]_odd ; work/vol_{**x76}_{***x77}_odd
DE ; Remove previous even group vol.
[group_vol]_even ; work/vol_{**x76}_{***x77}_even
DE ; Remove previous current aligned images
[aligned_images] ; work/dala{**x76}_{***x77}
ENDIF
MY FL
RE
;