([ang-step],[ang-limit],[r2],[alignsh],[prj-radius],[iter],[grp],[n-big],[pixsiz])
; Main refinement group loop
;
; SOURCE: spider/docs/techs/recon/newprogs/grploop.pam
; Original ArDean Leith Nov 2000
; %degredations ArDean Leith Feb 2005
; [] ArDean Leith Dec 2005
; More stacks & 'RT SQ' selection ArDean Leith Dec 2006
; 'AP SH' use ArDean Leith Feb 2007
; Group sel. filename ArDean Leith Dec 2009
; Echo formatting ArDean Leith Aug 2010
; COG centering removed ArDean Leith Sep 2010
; 'AP SH' for 2 iters, Skip=2 ArDean Leith Sep 2010
; 'TF COR' ArDean Leith Nov 2010
; Dala removal ArDean Leith Jan 2012
; 'AP SHC', skip=1, FSC mask ArDean Leith Sep 2012
; Denoise exp images ArDean Leith Dec 2012
; 'AP' selection changed ArDean Leith Apr 2015
; [n-big] ArDean Leith Apr 2015
;
; PURPOSE: Main refinement loop. Runs for each defocus group on each iteration
;
; CALLED FROM: pub_refine_start or
; refine.pam
;
; I/O Registers & files are set in: refine_settings.pam)
;
; INPUT REGISTERS:
; [ang-step] Angular steps (Varies with iter)
; [ang-limit] Restrict angular search (Varies with iter)
; [r2] Radius of object used in alignment (pixels)
; [alignsh] Shift allowed is +-[alignsh]
; [prj-radius] Radius of object used in projection
; [iter] Alignment step iteration counter (Varies with iter)
; [grp] Defocus group (Varies with group)
; [pixsiz] Pixel size
; OUTPUT REGISTERS:
; [n-big] # of images whose proj. angle moved by > 1.5*[ang-step]
;
; '##' denotes iteration, '##+' denotes next iteration, '***' denotes group
; INPUT FILES:
; [sel_particles] input/select_*** Group particle selection files
; [iter_vft] final/vft## Current iteration's filtered volume
; [temp_ctf_file] work/ctf*** CTF corrected group volume from prepare
; [group_align] final/align##_*** Alignment parameter doc files
; [unaligned_images] input/data*** Unaligned stacked image files
; [iter_refangs] work/ang_refs_## Ref. angles doc file for this iteration
;
; OUTPUT FILES:
; [next_group_align] final/align##+_*** Alignment parameter doc file
; [next_group_vol] work/vol##+_*** Reconstructed group volume
; [next_group_fsc] final/fscdoc##+_*** Group FSC curve doc file
;
; [next_group_vol]_sub1 work/vol_##+_***_sub1 (Created & later deleted)
; [next_group_vol]_sub2 work/vol_##+_***_sub2 (Created & later deleted)
; [temp_ref_projs] tmp/refproj##_*** (Created & later deleted)
;
; PROCEDURES CALLED:
;
; INLINE BUFFERS USED: _1, _8
SYS
echo -n " Start grploop for iteration: {**[iter]} Group: {***[grp]} --- " ; date '+ %x %X'
[r1] = 5.0 ; First radius for AP (Can alter this)
[ang-change-thr] = 1.5*[ang-step] ; Convergence criterion ang. distance limit.
[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
[iter_refangs] ; Reference images angles file (input)
; Multiply Fourier of current volume by CTF file for this group
TF COR
[iter_vft] ; Fourier of current volume (input}
[temp_ctf_file] ; CTF file (input)
_1 ; CTF corrected volume (output)
MY FL ; Flush results file
DE ; Remove existing ref projections
[temp_ref_projs]@ ; Template for ref. projections (output)
; Create stack holding angular reference projections from CTF corrected volume.
PJ 3F ; Projection operation
_1 ; CTF corrected volume (input)
[prj-radius] ; Radius of object
1-[num-refs] ; Ref. angles used
[iter_refangs] ; Ref. angles doc file (input)
[temp_ref_projs]@****** ; Template for ref. projections (output)
DE ; _1 can be deleted here
_1 ; CTF corrected current volume (removed)
DE ; Remove existing alignment doc file
[next_group_align] ; Alignment parameter doc file
DE ; Remove existing scratch file (rare)
[ref_rings] ; Reference rings scratch file
MY FL ; Flush results file
; Copy to inline file to increase access speed a little
; Note: If INLN_WRTLIN ARRAY OVERFLOWS, remove: _8@ and just use [unaligned_images]@
CP ; Copy unaligned images to inline stack
[unaligned_images]@ ; Input file needed (input)
_8@ ; Unaligned images stack (output)
[maxim] ; Number of images in stack _8@
; Find reference projection matching current aligned image
; (For large images change 'skip' to 2 or 3 to decrease memory)
; Default for unknown return value
[n-big] = -1
[align-first] = 'N'
[align-doc] = '*'
IF ( [iter] > 1 ) THEN
[align-first] = 'F' ! FBS used for alignment
[align-doc] = [group_align]
ENDIF
IF ( [iter] <= 2 ) THEN
AP SHC ; (Can change this)
[temp_ref_projs]@****** ; Template for ref. projections (input)
1-[num-refs] ; Ref. projection file numbers
[alignsh],1 ; Shift search range, Step size
[r1],[r2],1 ; First, last radial ring, & skip
[iter_refangs] ; Ref. angles file (input)
_8@****** ; Template for unaligned images (input)
[sel_particles] ; Particle selection files (input)
[align-doc] ; No alignment parameter doc file (input)
[ang-limit],[ang-change-thr] ; Angular search restriction
Y, [align-first], Y ; Check mir, Do not align first, denoise
[next_group_align] ; Alignment parameter doc file (output)
; Report some 'AP SHC' alignment statistics
IF ( [iter] == 1 ) THEN
UD N [n-exp] ; Find number of exp. images
[sel_particles] ; Particle selection files (input)
SYS
echo " Iteration: {**[iter]} Group: {*****[grp]} Particles:{%I0%[n-exp]} "
ELSE
UD -2,[per-greater],[avg-angdif],[avg-ccrot],[degred],[avg-degred],[avg-impr],[n-exp]
[next_group_align] ; Alignment parameter doc file (input)
SYS
echo " Iter: {**[iter]} Group: {***[grp]} Large angle changes: {%F6.2%[per-greater]}% "
SYS
echo " CCROT degred.: {***[degred]}% Avg. degred.:{%F6.2%[avg-degred]} Avg. improve.:{%F6.2%[avg-impr]}"
ENDIF
ELSE
AP REF ; Poorer search than 'AP SH' but 4-5x faster
[temp_ref_projs]@****** ; Template for ref. projections (input)
1-[num-refs] ; Ref. projection file numbers
[alignsh] ; Shift search range
[r1],[r2],1 ; First, last radial ring, & skip
[iter_refangs] ; Ref. angles file (input)
[ref_rings] ; No such file if rings fit in-core (rare output)
_8@****** ; Template for unaligned images (input)
[sel_particles] ; Particle selection files (input)
[group_align] ; Alignment parameter doc file (input)
[ang-limit],[ang-change-thr] ; Angular search restriction
Y, Y ; Check mir projections, align first
[next_group_align] ; Alignment parameter doc file (output)
; Report some 'AP REF' alignment statistics
UD -2,[per-greater],[avg-angdif],[avg-cc],[degred],[avg-degred],[avg-impr],[n-exp]
[next_group_align] ; Alignment parameter doc file (input)
SYS
echo " Iter: {**[iter]} Group: {***[grp]} Large angle changes: {%F6.2%[per-greater]}% "
IF ( [iter] > 3 ) THEN
SYS
echo " CC degred.: {***[degred]}% Avg. degred.:{%F6.2%[avg-degred]} Avg. improve.:{%F6.2%[avg-impr]}"
ENDIF
UD E ; Close doc file access
; Return # of images whose projection angle changed by > [ang-change-thr]
[n-big] = [per-greater] * [n-exp]
ENDIF
; Apply new alignments to original particle images
RT SF ; 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)
_8@****** ; Current aligned images (output)
SYS ; Echo for isolating stack overflow
echo " Back projecting group: {****[grp]}"
MY FL
; Calculate new, refined volume using centered projections and
; angles from align doc. file. Creates two additional volumes from
; random half subsets of images for use in resolution calculation.
; (If you have large images which give problems allocating memory in 'BP 32F',
; substitute operation 'BP 3F'. Use that operation three times (with 3
; appropriate selection files for the images to be included) to create
; the three output volumes one by one.)
BP 32F ; Back Projection - 3D Fourier
_8@****** ; Current aligned images template (input)
[sel_particles] ; Particle selection doc file (input)
[next_group_align] ; Alignment parameter doc file (input)
* ; No symmetries
[next_group_vol] ; Reconstructed group vol - overall (output)
[next_group_vol]_sub1 ; Reconstructed group vol - subset 1 (output)
[next_group_vol]_sub2 ; Reconstructed group vol - subset 2 (output)
DE ; _8 no longer needed
_8
MY FL ; Flush results file
FSC [half],[spfreq],[res] ; Find phase residual & shell correl.
[next_group_vol]_sub1 ; Reconstructed group vol - subset 1 (input)
[next_group_vol]_sub2 ; Reconstructed group vol - subset 2 (input)
0.5, [r2] ; Shell width, mask radius
[pixsiz] ; Pixel size
[next_group_fsc] ; FSC group doc file (output)
* ; No Gnuplot file wanted
SD [iter], [iter],[grp],[res] ; Save in doc file
[grp_resol] ; Group resolution summary file (output)
SYS ; Remove ref. projections (no longer needed)
\rm -f [temp_ref_projs]*.$DATEXT
IF ( [iter] > 1 ) THEN ; Not first iteration
DE ; Remove previous group volume
[group_vol] ;
DE ; Remove previous subset 1 group vol.
[group_vol]_sub1 ;
DE ; Remove previous subset 2 group vol.
[group_vol]_sub2 ;
ENDIF
MY FL
RE
;