([ang-step],[radius],[alignsh],[prj-radius],[iter],[grp],[toobig],[maxspfreq])
; Small angle refinement group loop
;
; SOURCE: smangloop.pam ArDean Leith Nov. 2002
; rewrite ArDean Leith Oct. 2004
; exp images name bug ArDean Leith Jan. 2005
; BP align bug ArDean Leith Feb. 2005
; avg CCROT degredations ArDean Leith Feb. 2005
; [] ArDean Leith Dec. 2005
; more stacks ArDean Leith Dec. 2006
; removed iter1 parameter ArDean Leith Feb. 2007
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs/
;
; PURPOSE: Small angle refinement group loop. Runs for each defocus
; group on each iteration
;
; CALLED FROM: pub_refine_start or
; refine.pam
;
; REGISTERS AND FILES ARE SET IN: refine settings refine settings.pam.pam); INPUT REGISTERS:
;
; INPUT REGISTERS:
; [ang-step] Angular difference stopping limit
; [toobig] Iteration ending flag (returned)
; [radius] Radius (pixels) of the structure
; [alignsh] Shift allowed is +-[alignsh]
; [prj-radius] Radius (pixels) of structure for projection
; [iter] Alignment step iteration counter
; [grp] Current defocus group
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES (SET IN: refine_settings refine_settings.pam.pam):
; [order_select] input/order_select Image ID doc. file
; [sorted_order_select] input/order_select_sort Image ID doc. fil
; [sel_particles] input/select_*** Particle selection doc. file
; [iter_vft] final/vft## Current filtered volume (from refine)
; [temp_ctf_file] work/ctf*** CTF corrected volume (from prepare)
; [aligned_images] input/dala##_***@ Aligned stacked image files
; [group_align] final/align##+_*** Alignment parameter doc file
; [unaligned_images] input/data***@ Unaligned stacked image file
; [iter_ang_voea] final/angvoea_## Ref. angles doc. file
; [iter_select_voea] final/selvoea_## Ref. angles selection doc. file
;
; OUTPUT FILES(SET IN: refine_settings refine_settings.pam.pam):
; [next_aligned_images] work/dala##+_***@ Aligned stacked image file
; [next_group_align] final/align##+_*** Alignment parameter doc file
; [next_group_vol] work/defgrp***/vol##+ Reconstructed volume
; [next_group_vol]_odd work/defgrp***/vol_##+_odd (created & deleted)
; [next_group_vol]_even work/defgrp***/vol_##+_even (created & deleted)
; [next_group_dres] final/defgrp***/dres##+ Resolution curve doc. file
; [img_ang_vora] final/angvora_##_***
; [temp_ref_projs]_5@ (created & deleted)
;
; PROCEDURES CALLED:
;
; INLINE BUFFERS USED: _1,_4
VM
echo " In smangloop, Iteration: {**[iter]} Group: {***[grp]}"
VM
date '+ Time: %x %X'
[radius1] = 5.0 ; First radius for 'AP REF' (Can alter this)
[converg] = 1.5*[ang-step] ; Angular distance limit for stopping iters.
[next-iter]=[iter]+1
UD N [num-refs] ; Get number of ref. imges
[iter_select_voea] ; Reference image selection file (input)
; Get number of images in current group
UD N,[numgrps] ; Find number of defocus groups
[order_select] ; (input)
DO LB1 [i]=1,[numgrps] ; Loop over defocus groups --------
; GROUP, PART.
UD IC [i], [grpt], [num-imgs] ; Get current number of particles
[order_select] ; Doc file listing groups (input)
IF ([grpt].EQ.[grp])GOTO LB2
LB1
LB2 ; Got number of particles in group
UD ICE
[order_select]
MY FL ; Flush results file
; Multiply Fourier of current volume by CTF file for this group
MU ; Multiply
[iter_vft] ; Fourier of current volume (input}
[temp_ctf_file] ; CTF file (work/ctf{grp}) (input)
_1 ; _1 created here (output)
* ; No more multiplications
FT ; Fourier transform
_1 ; Fourier of CTF corrected volume (input)
_4 ; CTF corrected current volume (output)
DE ; _1 can be deleted here
_1 ; Fourier of CTF corrected current volume
FI [nsam] ; Find image size
_4 ; CTF corrected current volume (input)
(2) ; Location of nsam in header
MS ; Make MT inline stack for ref. projections
[temp_ref_projs] ; MT stack (output)
([nsam],[nsam],1) ; Image size
[num-refs] ; Number of images allowed in stack
DE ; Remove existing align parameter doc file
[next_group_align]
; Make header for next group align doc file
SD /PSI, THE, PHI, REF, EXP, ANG, SX, SY, NPROJ, DIFF, CCROT, ANG, SX, SY, MIR-CC
[next_group_align] ; (output)
[num-big] = 0 ; Number of angular changes above iteration stop limit
[toobig] = 0 ; Not OK to stop iterating
[sum-ccrot] = 0.0 ; Sum of CCROT correlation coefficients
[num-degred] = 0.0 ; Number of CCROT degredations
[sum-degred] = 0.0 ; Sum of CCROT degredations
[num-impr] = 0.0 ; Number of CCROT improvements
[sum-impr] = 0.0 ; Sum of CCROT improvements
[sum-diff] = 0.0
DO LB3 [numpart]=1,[num-imgs] ; Loop over all particles
UD [numpart], [img] ; Get current particle number
[sel_particles] ; Group particle selection file (input)
; Format of alignment parameters doc. file is:
; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT
UD IC [img], [psi],[the],[phi], [d],[exp], [d],[d],[d], [d],[d],[old-ccrot]
[group_align] ; Input alignment parameters doc. file
DE ; Remove existing angvora doc. file
[img_ang_vora] ; angvora
VO RAS
[iter_ang_voea] ; Relative angles file (input)
-[phi],-[the],-[psi] ; 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)
[prj-radius] ; Radius of computed object
(1-[num-refs]) ; Ref. projection file numbers
[img_ang_vora] ; Angles in search area doc. file (input)
[temp_ref_projs]****** ; Template for ref. projections (output)
MY FL ; Flush results file
; Find reference image matching experimental image. Output to registers not doc. file
; PSI,THE,PHI, REF#,EXP#, ANG, SX, SY, NPROJ,DIFF, CCROT, CURRENT_ALIGN
AP REF [psi],[the],[phi], [ref],[exp], [inp],[sx],[sy], [nproj],[diff], [ccrot], x70,x71,x72,x73
[temp_ref_projs]****** ; Template of existing ref. projections (input)
(1-[num-refs]) ; Ref. projection file numbers
[alignsh] ; Shift search range
([radius1],[radius],1) ; First, last ring, & skip
[img_ang_vora] ; Ref. angles file (input)
SCR.{******[grp]} ; No scratch file (usually will fit in-core)
[aligned_images]****** ; Aligned original images (input)
[img] ; Current exp. image file number
[group_align] ; Alignment parameters doc. file (input)
(0) ; Angular projection search restriction
(0) ; Mirrored projection check flag
; PSI,THE,PHI, REF#,EXP#, ANG, SX, SY, NPROJ,DIFF,CCROT
SD [img], [psi],[the],[phi], [ref],[img],[inp],[sx],[sy], [num-refs],[diff],[ccrot], x70,x71,x72,x73
[next_group_align] ; Next align. doc file (output)
IF ([ccrot] .LT. [old-ccrot]) THEN
[sum-degred]=[sum-degred]+([old-ccrot]-[ccrot]) ; Sum average CCROT degredation
[num-degred]=[num-degred]+1 ; Increment CCROT degredations counter
ELSE
[sum-impr]=[sum-impr]+([ccrot]-[old-ccrot]) ; Sum average CCROT improvement
[num-impr]=[num-impr]+1 ; Increment CCROT improvements counter
ENDIF
IF ([diff] .GT.[converg]) [num-big]=[num-big]+1 ; Increment large displacement counter
[sum-ccrot]=[sum-ccrot]+[ccrot] ; Sum rotational CCC (for average).
[sum-diff]=[sum-diff]+[diff] ; Sum of angular differences
; Apply combined transformation to original exp. sample image
RT SQ ; Rotate & shift
[unaligned_images]@{******[img]} ; Unaligned original images stack (input)
[next_aligned_images]{******[img]} ; New aligned exp. images stack (output)
[inp] ; Inplane rotation angle
[sx],[sy] ; X & Y shift
LB3
UD ICE ; Close this file here
[group_align]
; 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)
[sel_particles] ; Particle selection doc. file (input)
[next_group_align] ; Align parameters doc file (input)
* ; No symmetries file
[next_group_vol]tmp ; Reconstructed 3D file (output)
[next_group_vol]_odd ; Reconstructed 3D file (output)
[next_group_vol]_even ; Reconstructed 3D file (output)
CG PH,x11,x11,x11,[xcg],[ycg],[zcg] ; 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)
-[xcg],-[ycg],-[zcg] ; Shift amounts
DE ; Delete temp vol. file - vol{iter}tmp
[next_group_vol]tmp
DE ; Delete file
[next_group_dres] ; FSC document file - dres
RF 3 ; Phase Residual & shell correl.
[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 and upper scale factor
C ; Missing cone
(90.0) ; Maximum tilt angle
(3) ; Factor for noise comparison
[next_group_dres] ; Resolution document file (output)
DE ; Remove - refproj (no longer needed)
[temp_ref_projs]
IF ([iter] .GT. 1) THEN ; Not first iteration
DE ; Remove previous group vol.
[group_vol]
DE ; Remove previous odd group vol.
[group_vol]_odd
DE ; Remove previous even group vol.
[group_vol]_even
ENDIF
; Find % of images showing excessive change in angular displacement
[toobig]=100*[num-big]/[num-imgs] ; % of images with excessive change in ang. displacement
VM
echo "Iteration: {**[iter]} Group: {***[grp]} Excessive changes: {***[toobig]}%"
[avg-ccrot] = [sum-ccrot]/[num-imgs] ; Average CCROT
[avg-degred]=0.0 ; Average CCROT degredation
IF ([num-degred] .GT. 0)[avg-degred]=[sum-degred] /[num-degred] ; Average CCROT degredation
[avg-impr]=0.0 ; Average CCROT improvement
IF ([num-impr] .GT. 0) [avg-impr]=[sum-impr]/[num-impr] ; Average CCROT improvement
[per-degred] = 100*[num-degred]/[num-imgs] ; Percent images with CCROT degredation
[avg-diff]=[sum-diff]/[num-imgs] ; Average angular difference
VM
echo " CCROT degred.: {***[per-degred]}% Avg degred.: {%F8.2%[avg-degred]} Avg improve: {%F8.2%[avg-impr]}"
SD / %Large angles, Avg. Ang-diff, Avg. CCROT, % degred., Avg degred., Avg improv.
[next_group_align] ; Next align. doc file (output)
SD -2, [toobig],[avg-diff],[avg-ccrot],[per-degred],[avg-degred],[avg-impr]
[next_group_align] ; Next align. doc file (output)
SD E ; Close doc file
[next_group_align] ; Next align. doc file
MY FL
RE