(x41,x42,x51,x52,x55,x56,x76,x77,x47,x74,x14)
; Small angle refinement group loop
;
; SOURCE: smangloop.pam -- Small angle refinement group loop al Nov. 2002
; al Oct. 2004
; exp images name bug al Jan. 2005
; BP align bug al Feb. 2005
; avg CCROT degredations al Feb. 2005
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs/
;
; PURPOSE: Runs for each defocus group on each iteration
;
; CALLED FROM: refine.pam and
; pub_starter.pam
;
; REGISTERS AND FILES ARE SET IN: refine_settings.pam
;
; INPUT REGISTERS:
; x41 Angular difference stopping limit
; x42 Angular search range
; x47 Iteration ending flag (returned)
; x51 Radius (pixels) of the structure
; x52 Image size
; x55 Shift allowed is +-x55
; x56 Radius (pixels) of structure for projection
; x74 Starting alignment iteration
; x76 Alignment step iteration counter
; x77 Current defocus group
; INPUT FILES:
; input/order_select [order_select] Image ID doc. file
; work/defgrp(***grp}/select [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+1}_{***grp} [group_align] (from inital alignment)
; input/data{***grp}@ [unaligned_images] Unaligned stacked image file
; final/angvoea_{**iter} [iter_ang_voea]
; final/selvoea_{**iter} [iter_select_voea]
;
; OUTPUT FILES:
; work/dala{**iter+1}_{***grp}@ [next_aligned_images]
; final/align{**iter+1}_{***grp} [group_align]
; work/defgrp{***grp}/vol{**iter} [next_group_vol]
; work/defgrp{***grp}/vol_{**iter+1}_odd [next_group_vol]_odd (deleted in mergegroups)
; work/defgrp{***grp}/vol_{**iter+1}_even [next_group_vol]_even (deleted in mergegroups)
; _5@ [temp_ref_projs] (created & deleted)
; final/defgrp{***grp}/dres{**iter+1} [next_group_dres] (created dres output doc. file
; final/angvora_{**iter}_{***iter} [img_ang_vora]
;
; INLINE BUFFERS USED: _1
VM
echo " In smangloop, Iteration: {**x76} Group: {***x77}"
VM
date '+ Time: %x %X'
x54 = 5.0 ; First radius for 'AP REF' (Can alter this)
x16 = 1.5 * x41 ; Angular distance limit for stopping iters.
x86 = x76 + 1 ; Next iteration number
UD N x53 ; Get number of ref. projections for this iteration
[iter_select_voea]
UD IC x77, x79 ; Get number of experimental images in this group
[order_select]
UD ICE
[order_select]
MY FL ; Flush results file
MU ; Multiply Fourier vol by CTF
[iter_vft] ; Fourier'd iteration vol (final/vft{iter} (input)
[temp_ctf_file] ; Group CTF correction file (work/ctf{grp}) (input)
_1 ; Multiplied volume (output)
*
FT ; Back Fourier transform
_1 ; Fourier of CTF corrected current volume (input)
_4 ; CTF corrected current volume created here (output)
DE ; _1 can be deleted here
_1 ; Fourier of CTF corrected current volume
MS ; Make empty inline stack for ref. projections
[temp_ref_projs] ; (output)
(x52,x52,1) ; Image size
x53 ; Number of images allowed in stack
DE ; Remove any existing next group align doc file
[next_group_align]
x91 = 0 ; Number of angular changes above iteration stop limit
x47 = 0 ; Not OK to stop iterating
x93 = 0.0 ; Average CCROT correlation coefficient
x94 = 0 ; CCROT degredation counter
x95 = 0.0 ; Average CCROT degredation
x97 = 0 ; CCROT improvement counter
x96 = 0.0 ; Average CCROT improvement
x92 = 0.0 ; Average angular difference
DO LB1 x50=1,x79 ; Loop over experimental sample images
; Format of the alignment parameters doc. file is:
; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT
UD IC x50, x17,x18,x19, x11,x20, x23,x24,x25, x29,x12,x90
[group_align] ; Alignment parameters doc. file (input)
DE ; Remove existing angvora doc. file
[img_ang_vora] ;
VO RAS ; Create proj. angles file for this image
[iter_ang_voea] ; Relative angles file (input)
-x19,-x18,-x17 ; Offset
(1,0) ; Psi set to zero
[img_ang_vora] ; Doc. file for angles to search (output)
; Create stack holding set of reference projections from input volume.
PJ 3Q ; Create ref. projections
_4 ; CTF corrected current volume (input)
x56 ; Radius of computed object
(1-x53) ; Ref. projection file numbers
[img_ang_vora] ; Angles in search area doc. file (input)
[temp_ref_projs]****** ; Template for ref. projections (output)
; Find reference image matching experimental image, parameters to doc. file
; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT
AP REF x11,x11,x11, x11,x11, x11,x11,x11, x11,x12,x31
[temp_ref_projs]****** ; Template of ref. projection files (input)
(1-x53) ; Ref. projection file numbers
x55 ; Shift search range
(x54,x51,1) ; First, last ring, & skip
[img_ang_vora] ; Ref. angles file (input)
SCR.{******x77} ; No scratch file (usually in-core)
[aligned_images]****** ; Aligned original images - dala (input)
x50 ; Current exp. image file number
[group_align] ; Alignment parameters doc. file (input)
(0) ; Angular projection search restriction
(0) ; Mirrored projection check flag
[next_group_align] ; Next align. doc file (output)
IF (x31 .LT. x90) THEN
x95 = x95 + (x90 - x31) ; Sum average CCROT degredation
x94 = x94 + 1 ; Increment CCROT degredations counter
ELSE
x96 = x96 + (x31 - x90) ; Sum average CCROT improvement
x97 = x97 + 1 ; Increment CCROT improvements counter
ENDIF
IF (x12 .GT. x16) x91 = x91 + 1 ; Increment large displacement counter
x92 = x92 + x92 ; Average CCROT
x93 = x93 + x31 ; Sum rotational CCC (for average).
LB1
UD ICE ; Close previous align. file here
[group_align]
; Apply combined transformations to original experimental image stack (whole stack)
RT SQ ; Rotate & shift
[unaligned_images] ; Unaligned original images stack (input)
[next_aligned_images] ; New aligned experimental images stack (output)
(6,0,7,8) ; Angle, scale, X & Y shift registers
[next_group_align] ; Next align. doc file (input)
; Calculate refined 3D structure using centered projections and new angles.
BP 32F ; Back projection, 3D, Fourier space
[next_aligned_images]****** ; Template for aligned images (input)
[group_select] ; Selection doc. file (input)
[next_group_align] ; Align parameters doc file (input)
* ; No symmetries
[next_group_vol]tmp ; Reconstructed 3D file - voltmp (output)
[next_group_vol]_odd ; Reconstructed 3D file - vol_odd (output)
[next_group_vol]_even ; Reconstructed 3D file - vol_even (output)
CG PH,x11,x11,x11,x21,x22,x23 ; Find center of gravity of new vol.
[next_group_vol]tmp
SH F ; Shift new vol. to center of gravity
[next_group_vol]tmp ; volume file - voltmp (input)
[next_group_vol] ; volume file - vol (output)
-x21,-x22,-x23 ; Shift
DE ; Delete temp vol. file - vol{iter}tmp
[next_group_vol]tmp
DE ; Delete file
[next_group_dres] ; FSC document file - dres
RF 3 x69,x68 ; Phase Residual & shell corr.
[next_group_vol]_odd ; First volume file (input)
[next_group_vol]_even ; Second volume file (input)
(0.5) ; Ring width
(0.2,2.0) ; Lower & upper scale factor
C ; Missing cone
(90.0) ; Max tilt angle
(3) ; Noise ocmparison factor
[next_group_dres] ; FSC document file - dres (output)
@saveresp(x14,x76,x77,x68) ; Record group resolution in grp summary doc file
[grp_resol] ; Output file
; Find % of images showing excessive change in angular displacement
x47 = 100 * x91 / x79 ; % of images with excessive change in angular displacement
x92 = x92 / x79 ; Average angular difference
x93 = x93 / x79 ; Average CCROT
IF (x94 .GT. 0) x95 = x95 / x94 ; Average CCROT degredation
IF (x97 .GT. 0) x96 = x96 / x97 ; Average CCROT improvement
x94 = x94 / x79 ; Percent images with CCROT degredation
; '%BIG-ANGDIF, AVG-ANGDIF, AVG-CCROT, %WORSE, AVG-WORSE, AVG-BETTER'
SD -2, x47, x92, x93, x94, x95, x96
[next_group_align] ; Next align. doc file
SD E
[next_group_align] ; Next align. doc file
VM
echo " Iteration: {**x76} Group: {***x77} Big angular changes: {***x47}%"
VM
echo " Degred.: {%f6.2%x94}% Avg. degred.: {%f10.2%x95} Avg. improve: {%f10.2%x96}"
DE ; Remove - refproj
[temp_ref_projs]
IF (x76 .GT. x74) THEN ; Not first iteration
DE ; Remove previous vol
[group_vol]
DE ; Remove previous vol_odd
[group_vol]_odd
DE ; Remove previous vol_even
[group_vol]_even
ENDIF
MY FL
RE