([ang-step],[r2],[alignsh],[prj-radius],[iter],[grp],[pixsiz],[bp-type],[iter-end])
; Small angle refinement group loop
;
; SOURCE: spider/docs/techs/recon1/Procs/smangloop.spi
; New ArDean Leith Nov 2002
; Rewrite ArDean Leith Oct 2004
; 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
; For CTF corrected images ArDean Leith Oct 2013
; For gold standard reconstruction ArDean Leith May 2014
;
; PURPOSE: Small angle refinement group loop. Runs for each group on each iteration.
; Finds parameters ('AP REF') which align experimental images with
; projections from current reference volume,
; rotationally aligns ('RT SF') images , and
; backprojects ('BP **') images into new volume.
; CALLED FROM: pub_refine_start OR
; refine.spi
;
; REGISTERS AND FILES ARE SET IN: refine settings.spi
;
; INPUT REGISTERS:
; [ang-step] Angular step
; [r2] Pixel radius of object used in alignment
; [alignsh] Shift allowed is +-[alignsh]
; [prj-radius] Radius (pixels) of structure for projection
; [iter] Alignment step iteration counter
; [grp] Current defocus group
; [pixsiz] Pixel size
; [bp-type] Type of 'back projection'
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES:
; [sel_parts_s] input/select_*** Group particle selection files (one/group)
; [iter_refangs] work/ref_angs_## Ref. angles doc file (one/iteration)
; [unaligned_images] input/data_*** Unaligned stacked image files (one-stack/group)
; [ref_projs_s] work/ref_projs_##_s@ Reference projections (two/iteration)
; [group_align_s] final/align##_***_s@ Alignment parameter doc files (two/iteration/group)
;
; OUTPUT FILES:
; [next_group_align_s] final/align##+_***s@ Alignment parameter doc files (two/iteration/group)
; [next_group_vol_s] work/vol_##+_***_s@ Group subset volumes (two/iteration/group)
; [next_group_vol] work/vol##+_*** Reconstructed group volumes (one/iteration/group)
;
; [temp_out_images] work/dala##+_*** Aligned stacked image file (one/group)
; [ang_vora] final/angvora_##_*** Projection angles doc file (one/group)
; [temp_ref_projs] _5@ Reference projections (created & deleted)
;
; INLINE BUFFERS USED: _5@
;
; ----------------- END BATCH HEADER -------------------------------------
SYS
echo -n " Starting: small-angle refine loop Iteration: {%I0%[iter]} Group:{%I3%[grp]} --- " ; date '+ %x %X'
[r1] = 5.0 ; First radius for 'AP REF' (Can alter this)
[big_move] = 1.5 * [ang-step] ; Angular distance for big moves.
[next-iter] = [iter]+1
FI H [maxim],[nx],[ny] ; Find total number of images (not [numparts])
[unaligned_images]@ ; Input file needed (input)
MAXIM, NX, NY ; Max. image number, image size
UD N [num-refs] ; Get number of reference images used
[ang_voea] ; Reference images angles doc file (input)
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
MY FL ; Flush results file
DE ; Delete existing files
[next_group_align]_s1 ; Alignment parameter doc file (deleted)
DE ; Delete existing files
[next_group_align]_s2 ; Alignment parameter doc file (deleted)
; Make header for next group align doc files
SD /PSI, THE, PHI, REF, EXP, ANG, SX, SY, NPROJ, DIFF, CCROT, ANG, SX, SY, MIR-CC
[next_group_align]_s1 ; Alignment parameter doc file (output)
SD /PSI, THE, PHI, REF, EXP, ANG, SX, SY, NPROJ, DIFF, CCROT, ANG, SX, SY, MIR-CC
[next_group_align]_s2 ; Alignment parameter doc file (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 [s] = 1,2 ; Loop over resolution subsets ---------------
DO ; Loop over all particles
UD NEXT [key],[img] ; Get particle number
[sel_parts_s] ; Group particle selection file (input)
IF ( [key] <= 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_s] ; Input alignment parameters doc file
DE ; Delete
[ang_vora] ; angvora doc file (removed)
VO RAS ; Rotate projection dir.
[ang_voea] ; Relative angles file (input)
-[phi],-[the],-[psi] ; Offset
1, 0 ; Psi set to zero
[ang_vora] ; Doc file for angles to search (output)
; Create stack holding set of reference projections from input volume.
PJ 3Q ; Create ref. projections
[vol] ; Current volume (input)
[prj-radius] ; Radius of computed object
1-[num-refs] ; Ref. projection file numbers
[ang_vora] ; Angles in search area doc file (input)
[temp_ref_projs]****** ; Template for ref. projections (output)
; 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], [t0],[t1],[t2],[t3]
[temp_ref_projs]****** ; Template of existing ref. projections (input)
1-[num-refs]) ; Ref. projection file numbers
[alignsh] ; Shift search range
[r1], [r2], 1 ; First, last ring, & skip
[ang_vora] ; Ref. angles file (input)
SCR.{******[grp]} ; No scratch file (usually will fit in-core)
[unaligned_images]@****** ; Original unaligned image stack (input)
[img] ; Current exp. image file number
[group_align_s] ; Alignment parameters doc file (input)
0 ; Angular projection restriction
N, Y ; No mirrored projection check, 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], [t0],[t1],[t2],[t3]
[next_group_align_s] ; Next align. doc file (output)
IF ( [ccrot] < [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] > [big_move]) [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 particle image
RT SF ; Rotate & shift
[unaligned_images]@{******[img]} ; Unaligned original images stack (input)
[temp_out_images]{******[img]} ; Temp aligned exp. images stack (output)
[inp] ; Inplane rotation angle
[sx],[sy] ; X & Y shift
ENDDO ; End of loop over all particles --------------------
; Calculate new, refined subset volume using centered projections and
; angles from align doc. file.
@refine-bp([iter],[iter-end],[grp],[s], [bp-type],[prj-radius])
UD ICE ; Close this file here
[group_align_s] ; Doc file (closed)
ENDDO ; End of loop over resolution subsets ----------------------------
DE
[ang_vora] ; Doc file (removed)
DE ; Delete
[temp_ref_projs] ; Ref. projections file (removed)
DE ; Delete
[temp_out_images]@ ; Aligned image stack (removed)
; Find % of images showing excessive change in angular displacement
[toobig]=100*[num-big]/[num-imgs] ; % of images with excessive change in ang. displacement
SYS
echo " Iteration: {%I2%[iter]} Group: {%I3%[grp]} Excessive changes: {%I3%[toobig]}%"
[avg-ccrot] = [sum-ccrot]/[num-imgs] ; Average CCROT
[avg-degred] = 0.0 ; Average CCROT degredation
IF ( [num-degred] > 0)[avg-degred]=[sum-degred]/[num-degred] ; Average CCROT degredation
[avg-impr] = 0.0 ; Average CCROT improvement
IF ([num-impr] > 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
SYS
echo " CCROT degred.: {%I3%[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] ; Alignment doc file (output)
SD -2, [toobig],[avg-diff],[avg-ccrot],[per-degred],[avg-degred],[avg-impr]
[next_group_align] ; Alignment doc file (output)
SD E ; Close doc file
[next_group_align] ; Alignment doc file (closed)
RE
;