; Calculate two half-set reconstructions for each group
; SOURCE: spider/docs/techs/recon1/Procs/recon-loop.spi
;
; PURPOSE: Calculate two half-set and one overall reconstructions for each group
;
; INPUT REGISTERS: From command line
; [grp] group
;
; INPUT FILES: ([win_dir] denotes input directory, '***' denotes group, '%' denotes subset)
; ([rec_dir] denotes alignment/reconstruction output directory)
; [sel_parts] [win_dir]/sel_part_*** Group particle selection files (one/group)
; [aligned_images] [rec_dir]/dala_*** Aligned stacked image files (one-stack/group)
; [group_align] [rec_dir]/align_##_*** Alignment parameter doc files (one/group)
;
; OUTPUT FILES:
; [next_group_vol] [rec_dir]/vol_##+_*** Reconstructed group volumes (one/group)
; [next_group_vol]_s1 [rec_dir]/vol_##+_***_s1 Group subset volume (one/group)
; [next_group_vol]_s2 [rec_dir]/vol_##+_***_s2 Group subset volume (one/group)
; [temp_images] _8 If [incore-yn] == 0, Created & deleted
; [finished_file] jnk_sync_$$$$_*** Created & deleted
;
; PARAMETERS: Set seldom altered parameters here
[rp-lam] = 0.2e-7; 0.2e-5 ; BP RP: lambda
[rp-cor] = 0.0 ; BP RP: correction limit
[rp-iter] = 50 ; BP RP: iteration limit
[rp-mode] = 0 ; BP RP: mode
[rp-min] = 0.5 ; BP RP: minimum (not used in mode 0)
[rp-max] = 0.5 ; BP RP: maximum (not used in mode 0)
[rp-smooth] = 0.5 ; BP RP: smoothing (not used in mode 0)
[cg-err] = 1.0E-5 ; BP CG: error limit, chi^2 limit
[cg-chi] = 0.0 ; BP CG: chi^2 limit (none)
[cg-iter] = 25 ; BP CG: iteration limit
[cg-mode] = 1 ; BP CG: mode
[cg-lam] = 2000 ; BP CG: weighting
;
; ------------------------------- END BATCH HEADER -------------------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
[iter] = 0
[next-iter] = 1
IF ( [grp] == 0 ) THEN
; [grp] not sent on command line so this is in series not parallel
RR [grp] ; Input group from caller for inline use
? ENTER GROUP ?
MD
SET MP
4
ELSE
; Get reconstruction parameters & file names
[steptype] = 1 ; Reconstruction step
@recon-settings([steptype],[num-grps],[pixsiz],[ang-step],[r2],[alignsh],[prj-radius],[winsiz],[incore-yn],[bp-type],[qsub])
MD
SET MP
10 ; Edit this!!!
ENDIF
IF ( [incore-yn] == 0 ) THEN
; Use disk image stack
GLO [temp_images] = '[aligned_images]@'
ELSE
; Load input image stack into incore image stack first
GLO [temp_images] = '_8@'
FI H [numparts] ; Get number of particles
[aligned_images]@ ; Image stack (input)
MAXIM ; Max. image number in stack
SYS ; Echo progress
echo ' Copying: [aligned_images] Into: [temp_images] '
MY FL
CP ; Load input images into incore stack
[aligned_images]@ ; Image stack (input)
[temp_images] ; Incore stack (output)
[numparts] ; Stack size
ENDIF
MY FL
; 'Back project' aligned particle images according to angles from alignment doc file
[bp-typet] = [bp-type] ; Hack to overcome global symbol parsing bug
IF ( [bp-typet] == 1 ) THEN
SYS ; Echo progress
echo -n " Back projecting group: {%I3%[grp]} with 'BP CG', On: " ; hostname
MY FL ; Flush results file
; Create group volumes using 'BP CG 3' .
BP CG 3 ; Back Projection - CG
[temp_images]***** ; Template for image files (input)
[sel_parts][grp] ; Group particle selection doc file (input)
[rad-bp] ; Radius of restored object
[next_group_align] ; Alignment parameter doc file (input)
F ; Fourier-based spline interpolation
[next_group_vol] ; Reconstructed group vol - overall (output)
[next_group_vol]_s1 ; Reconstructed group vol - subset 1 (output)
[next_group_vol]_s2 ; Reconstructed group vol - subset 2 (output)
[cg-err],[cg-chi] ; Error limit, chi^2 limit
[cg-iter],[cg-mode] ; Iteration limit, mode
[cg-lam] ; Weighting
ELSEIF ( [bp-typet] == 2 ) THEN
SYS ; Echo progress
echo -n " Back projecting group: {%I3%[grp]} with 'BP 3F', On: " ; hostname
MY FL ; Flush results file
BP 32F ; Back Projection - 3D Fourier
[temp_images]***** ; Template for image files (input)
[sel_parts][grp] ; Particle selection doc file (input)
[next_group_align] ; Alignment parameter doc file (input)
[symmetry_doc] ; Symmetries doc file (* = none) (input)
[next_group_vol] ; Reconstructed group vol - overall (output)
[next_group_vol]_s1 ; Reconstructed group vol - subset 1 (output)
[next_group_vol]_s2 ; Reconstructed group vol - subset 2 (output)
ELSEIF ( [bp-typet] == 3 ) THEN
SYS ; Echo progress
echo -n " Back projecting group: {%I3%[grp]} with 'BP RP', On: " ; hostname
MY FL ; Flush results file
; Compute the group subset reconstructions. --------------------------------
BP RP 3 [niter] ; [niter] returns # iterations used
[temp_images]***** ; Template for image files (input)
[sel_parts][grp] ; Particle selection doc file (input)
[r-bp] ; Radius of restored object
[next_group_align] ; Alignment parameter doc file (input)
[symmetry_doc] ; Symmetries doc file (* = none) (input)
[next_group_vol] ; Reconstructed group vol - overall (output)
[next_group_vol]_s1 ; Reconstructed group vol - subset 1 (output)
[next_group_vol]_s2 ; Reconstructed group vol - subset 2 (output)
[rp-lam],[rp-cor] ; Lambda, correction limit
[rp-iter],0 ; Iteration limit, mode
.5, .5 ; Minimum, maximum
.5 ; Smoothing constant
ELSEIF ( [bp-typet] == 4 ) THEN
SYS ; Echo progress
echo -n " Back projecting group: {%I3%[grp]} with 'BP 3N', On: " ; hostname
MY FL ; Flush results file
; Split into odd and even selection lists
DOC SPLIT
[sel_parts] ; Particle selection doc file (input)
[sel_parts]_s1 ; Odd particle selection doc file (output)
[sel_parts]_s2 ; Even particle selection doc file (output)
; Reconstruct odd volume
BP 3N
[temp_images]****** ; Template for image files (input)
[sel_parts]_s1 ; Odd particle selection doc file (output)
[next_group_align] ; Alignment parameter doc file (input)
[symmetry_doc] ; Symmetries doc file (* = none) (input)
[next_group_vol]_s1 ; Reconstructed group vol - subset 1 (output)
; Reconstruct even volume
BP 3N
[temp_images]***** ; Template for image files (input)
[sel_parts]_s2 ; Even particle selection doc file (output)
[next_group_align] ; Alignment parameter doc file (input)
[symmetry_doc] ; Symmetries doc file (* = none) (input)
[next_group_vol]_s1 ; Reconstructed group vol - subset 2 (output)
; Reconstruct combined volume
BP 3N
[temp_images]***** ; Template for image files (input)
[sel_parts] ; Particle selection doc file (input)
[next_group_align] ; Alignment parameter doc file (input)
[symmetry_doc] ; Symmetries doc file (* = none) (input)
[next_group_vol] ; Reconstructed group vol - overall (output)
ENDIF
MY FL ; Flush results file
IF ( [incore-yn] > 0) THEN
DE ; Delete incore stack (deleted)
[temp_images]
ENDIF
IF ( [qsub] >= 0 ) THEN
SYS ; File created when finished (one/group)
touch [finished_file].$DATEXT
EN
ENDIF
RE
;