(x41,x42,x51,x52,x55,x56,x76,x77,x47,x74)
; Main refinement group loop
;
; grploop.pam -- Main refinement group loop al Nov 2000
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; PURPOSE: Runs for each defocus group on each iteration
;
; CALLED FROM: pub_starter.pam
;
; INPUT REGISTERS:
; x41 Angular steps (varies with iter)
; x42 Restrict angular search (varies with iter)
; x51 Radius of the structure
; x52 Image size
; x55 Shift allowed is +-x55
; x56 Radius of the structure used in porjection
; 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)
; final/dres{**iter+1}_{***group} [next_group_dres] (Created dres output doc. file
;
; PROCEDURES CALLED:
;
; INLINE BUFFERS USED: _1, _4, _8
VM
echo "In grploop, Iteration: {**x76} Group: {***x77}"
VM
date
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
x48=0 ; Number of angular changes
x46=0 ; Number of angular changes greater than iteration stop limit
x99=1
UD N,x53
[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 ; 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
CP ; Copy current aligned images to inline stack
[aligned_images] ; Input file needed
_8@ ; Current aligned images stack _8 created here (large)
x79 ; Number of images in stack _8@
DE ; Remove existing next alignment doc output file
[next_group_align] ; Alignment doc 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
_8@****** ; Template for current exp. aligned images
(1-x79) ; Current exp. images file numbers
[group_align] ; Exp. images alignment doc. file < < < .....
x42 ; Angular projection search restriction
(1) ; Check mirrored projections
[next_group_align] ; Alignment doc file (output)
; Close input doc file
UD ICE
[iter_ang_voea] ; Finished with angvoea
; Use cross-correlation to center 2D images
; Use already calculated projections as reference images
x91 = 0.0 ; Average correlation coefficient
x37 = 0.0 ; Average degredataion
x38 = 0.0 ; Average improvement
x39 = 0.0 ; Improvement counter
x40 = 0.0 ; Degredation counter
IQ FI x95 ; See if have previous alignment
[group_align] ; Doc file from previous alignment
x96 = 0
IF (x95.GT. 0) THEN ; Find cols. in previous align. doc file
UD N,x95,x96
[group_align] ; Doc file from previous alignment
ENDIF
DO LB5 x21=1,x79 ; Loop over all sample images
; Retrieve new alignment file data (just created above)
; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT
UD IC,x21, x80,x80,x80, x81,x80, x61,x62,x63, x80,x12,x31
[next_group_align] ; Doc file just created by 'AP REF'
IF (x96 .GT. 0) THEN
; Find changes in CC for this iteration
; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT
UD IC,x21, x80,x80,x80, x93,x80, x80,x80,x80, x80,x94,x90
[group_align] ; Doc file from previous 'AP REF
IF (x31 .LT. x90) THEN
x39 = x39 + (x90-x31) ; Sum average degredation
x40 = x40 + 1 ; Degredations counter
;;VM
;;echo {***x21} DEGRADES - Ref: {******x93} Diff: {%f6.1%x94}
ELSE
x38 = x38+(x31-x90) ; Sum average improvement
x37 = x37+1 ; Improvements counter
;;VM
;;echo {***x21} BETTER --- Ref: {******x93} Diff: {%f6.1%x94} CCROT: {%f6.0%x90}...{%f6.0%x31}"
ENDIF
ENDIF
IF (x81 .NE. 0) THEN
; Reference projection found within restricted search area
x48 = x48 + 1 ; Count successful searches
IF (x12.GT.x17)x46 = x46 + 1 ; Count large angle displacements
x91 = x91+x31 ; Sum rotational CC's (for average).
ENDIF
; Apply combined transformation to original exp. sample image
IF (x81 .GE. 0) THEN ; No mirror
RT SQ ; Rotate & shift
[unaligned_images]{******x21}; Unaligned original images (stack)
_8@{******x21} ; Current aligned images (output)
x61 ; Inplane rotation angle
x62,x63 ; Shifts
ELSE ; Mirrored
RT SQ ; Rotate & shift
[unaligned_images]{******x21}; Unaligned original image
_1 ; Temp. output file
x61 ; Inplane rotation angle
x62,x63 ; Shifts
MR ; Mirror
_1 ; Rotated, unaligned original image
_8@{******x21} ; Current aligned images (output)
Y ; Around Y axis
ENDIF
LB5
; Close doc files
UD ICE
[next_group_align] ; Finished with align. doc file
UD ICE
[group_align] ; Finished with align. doc file
; Check size of change in proj. angle
; Return % of image whose proj. angle moved by > 1.5*x41 criterion
x46 = x46 / x48
x47 = x46 * 100
VM
echo "Iteration: {**x76} Group: {*****x77} Excessive changes: {***x47}%"
x92 = x91 / x48 ; Averaged CCROT
IF (x40 .GT. 0) x39 = x39 / x40 ; Average degredation
x40 = x40 / x79 ; Percent CCROT Degredation
IF (x37 .GT. 0) x38 = x38 / x37 ; Average improvement
SD -1,x92,x40,x39,x38 ; Save avg. CC in doc file
[next_group_align]
SD E
[next_group_align] ; Finished with next group align doc. file
; Remove temp. inline files
DE
_1
; Store aligned projections
CP ; Create hard copy of aligned images
_8@
[next_aligned_images] ; No longer overwrites input files!!
VM ; Echo this for isolating stack overflow
echo "Commencing back projection"
MY FL
; Calculate new, refined volume using centered projections and
; the corrected angles from align doc. file
BP 32F ; Back Projection - 3D Fourier
_8@****** ; Template for current aligned images
[group_select] ; Selection doc. file - select
[next_group_align] ; Alignment doc file - align
* ; No symmetries
[next_group_vol]tmp ; Reconstructed 3D file - voltmp
[next_group_vol]_odd ; Reconstructed 3D file - vol_odd
[next_group_vol]_even ; Reconstructed 3D file - vol_even
DE ; _8 no longer needed
_8
MY FL
; Center 3D
CG PH,x11,x11,x11,x21,x22,x23 ; Center of Gravity of new vol.
[next_group_vol]tmp
MY FL
SH F ; Shift new vol.
[next_group_vol]tmp ; Input file - voltmp
[next_group_vol] ; Output file - vol
-x21,-x22
-x23
DE ; Delete temp file - vol{iter}tmp
[next_group_vol]tmp
RF 3 ; 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
VM ; Remove - refproj (no longer needed)
\rm -f [temp_ref_projs]*.$DATEXT
IF(x76.LT.x75) THEN ; Not last iteration
DE ; Remove group vol. from this iter
[group_vol] ; work/vol_{**x76}_{***x77}
DE ; Remove odd group vol.
[group_vol]_odd ; work/vol_{**x76}_{***x77}_odd
DE ; Remove even group vol.
[group_vol]_even ; work/vol_{**x76}_{***x77}_even
DE ; Remove current aligned images
[aligned_images] ; work/dala{**x76}_{***x77}
ENDIF
MY FL
RE
;