([radius],[alignsh],[prj-radius],[iter],[grp],[toobig])
; Small angle refinement group loop
;
; SOURCE: spider/docs/techs/recon/newprogs/smangloop.pam
; New 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
; Filenames & UD NEXT ArDean Leith Dec 2009
; COG centering removed ArDean Leith Sep 2010
; TF COR ArDean Leith Nov 2010
; UD NEXT E ArDean Leith Sep 2011
; Dala removal ArDean Leith Jan 2012
;
; 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.pam
;
; INPUT REGISTERS:
; [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
; [toobig] Iteration ending flag (returned)
; [ang-step] Angular difference stopping limit (String)
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES:
; [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)
; [group_align] final/align##+_*** Alignment parameter doc file
; [unaligned_images] input/data***@ Unaligned stacked image file
; [iter_refangs] work/ang_refs_## Reference angles doc file
;
; OUTPUT FILES:
; [img_ang_vora] final/angvora_##_*** Projection angles doc file
; [next_group_vol] work/defgrp***/vol##+ Reconstructed group volume
; [next_group_align] final/align##+_*** Alignment parameter doc file
; [next_group_dres] final/defgrp***/dres##+ FSC resolution curve doc file
;
; [next_group_vol]_sub1 work/defgrp***/vol_##+_sub1 (Created & deleted)
; [next_group_vol]_sub2 work/defgrp***/vol_##+_sub2 (Created & deleted)
; [temp_ref_projs] (Created & deleted)
;
; INLINE BUFFERS USED: _1
VM
echo -n " In smangloop, Iteration: {**[iter]} Group: {***[grp]} " ; date '+ Time: %x %X'
[radius1] = 5.0 ; First radius for 'AP REF' (Can alter this)
[converg] = 10000 ; Dummy angular distance limit for stopping iters.
[next-iter] = [iter]+1
UD N [num-refs] ; Get number of reference images used
[iter_refangs] ; Reference images angles doc. file (input)
MY FL ; Flush results file
; Multiply Fourier of current vol. by CTF file for this group
TF COR ; CTF correction
[iter_vft] ; Fourier of current volume (input}
[temp_ctf_file] ; CTF file (input)
_1 ; _1 created here (output)
FI H [nx] ; Find image size
_1 ; CTF corrected current volume (input)
NX ; Get NX from header
MS ; Make MT inline stack for ref. projections
[temp_ref_projs] ; Empty stack (output)
([nx],[nx],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 iter. 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
[num-imgs] = 0 ; Number of images in current group
DO ; Loop over all particles
UD NEXT [key],[img] ; Get particle image number from sel. file
[sel_particles] ; Group particle selection file (input)
IF ([key] .LE. 0) EXIT ; End of images in selection doc file
[num-imgs] = [num-imgs] + 1 ; # of images in current group
; 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 angles doc file
[img_ang_vora] ; (removed)
VO RAS ; Rotate projection dir.
[iter_refangs] ; 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
_1 ; 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 ref. image matching exp. 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)
[ref_rings].{******[grp]} ; No scratch file (usually will fit in-core)
[unaligned_images]@****** ; Aligned original image stack (input)
[img] ; Current exp. image file number
[group_align] ; Alignment parameters doc file (input)
0, 0 ; Angular projection search restriction
N,Y ; Check mir projections, align first
; 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
ENDDO
UD ICE ; Close this file here
[group_align] ; Doc file (closed)
UD NEXT E ; Close this file here
[sel_particles] ; Group particle selection file (closed)
FI H [maxim] ; Find total number of images (not [numparts])
[unaligned_images]@; ; Input file needed (input)
MAXIM ; Max. image number header position
; Note: If 'INLN_WRTLIN ARRAY OVERFLOW', replace: _2 with disk based stack file
MS ; Make empty inline stack
_2 ; Empty stack (output)
[nx],[nx],1 ; Image size
[maxim] ; Number of images allowed in stack
; Apply new alignments to original particle images
RT SQ ; Rotate & shift operation
[unaligned_images]@****** ; Unaligned original stacked images
[sel_particles] ; Particle selection file (input)
6,0,7,8 ; Reg. #s for angle, scale, & shift
[next_group_align] ; Alignment parameter doc file (input)
_2@****** ; Current aligned images (output)
; Calculate refined 3D structure using centered projections and new angles.
BP 32F ; Back projection, Fourier space
_2@****** ; Aligned stacked images (input)
[sel_particles] ; Particle selection doc file (input)
[next_group_align] ; Align parameters doc file (input)
* ; No symmetries file
[next_group_vol] ; Reconstructed vol - overall (output)
[next_group_vol]_sub1 ; Reconstructed vol - subset 1 (output)
[next_group_vol]_sub2 ; Reconstructed vol - subset 2 (output)
DE ; Delete file
[next_group_dres] ; FSC doc file (removed)
DE ; Delete file
_2@ ; Image file (removed)
RF 3 ; Phase Residual & shell correl.
[next_group_vol]_sub1 ; Volume file - subset 1 (input)
[next_group_vol]_sub2 ; Volume file - subset 2 (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] ; FSC doc file (output)
DE ; Remove ref. projections file (removed)
[temp_ref_projs]
IF ([iter] .GT. 1) THEN ; Not first iteration
DE ; Remove previous group vol.
[group_vol]
DE ; Remove previous subset 1 group vol.
[group_vol]_sub1
DE ; Remove previous subset 2 group vol.
[group_vol]_sub2
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 (output)
MY FL
RE