; Restacks particles and optionally applies CTF correction
;
; PURPOSE: Restacks particles listed in a set of particle selection files
; into specified number of new stacks. Can apply CTF correction
; filter to files while restacking.
;
; SOURCE: spider/docs/techs/recon1/Procs/stackwins-n-ctf.spi
;
; USAGE: spider spi/dat @stackwins-n-ctf
; ------------------- Parameters -------------------
[want-stats-only-yn] = 0 ; Want statistics only and no stacks? (1 == no stacks)
[apply-ctf-yn] = 1 ; Apply ctf correction? (0 == no)
; (Used to restack images that have not been corrected)
[want-align-yn] = 0 ; Want to copy alignment files also? (0 == no)
; (Used to duplicate an existing alignment file set)
[want-global-yn] = 1 ; Want global lookup table? (0 == no)
; ------------------ Input files -----------------------
[old_sel_grp] = '../sel_micrograph' ; Group (or micrograph) selection file (one)
![old_sel_part] = '../Particles/win/sel_part_****' ; Particle selection files (one/micrograph)
[old_sel_part] = '../Particles/win/sel_good_****' ; Particle selection files (one/micrograph)
[old_stack] = '../Particles/win/data_bymic_****' ; Existing particle stacks (one/micrograph)
[ctf_cor] = '../Power_Spectra/power/flipctf_****' ; OPTIONAL CTF correction file (one/micrograph)
![old_align] = 'input/align_01_***' ; OPTIONAL Alignment parameter files (one/group)
[old_align] = '*' ; OPTIONAL Alignment parameter files
; ----------------- Output files -----------------------
;
; Set in: recon-settings according to [steptype]
; OUTPUTS: (Where [win_dir] denotes new input directory, [rec_dir] denotes recon directory, ### denotes view *** denotes group)
; [sel_group] [win_dir]/sel_group' ; New group selection file (one)
; [sel_parts] [win_dir]/sel_part_***' ; New particle selection files (one/group)
; [unaligned_images] [win_dir]/data_***' ; New particle stacks (one/group)
; [part2global] [win_dir]/part2glonum_***' ; OPTIONAL Global particle lookup table (one/group)
; [global2grp_lut] [win_dir]/global2group' ; OPTIONAL Combined global lookup table (one)
; [next_group_align] [rec_dir]/align_01_***' ; OPTIONAL Alignment parameter files (one/group)
;
; -------------- END BATCH HEADER -------------------------------
MD ; Skip unnecessary output
VB OFF
MD ; Skip unnecessary output
TR OFF
; Get reconstruction file names
[steptype] = 0 ; Output is for alignment step
@recon-settings([steptype],[num-grps],[pixsiz],[ang-step],[r2],[alignsh],[prj-radius],[winsiz],[incore-yn],[bp-type],[qsub])
[iter] = 1
SYS ; Create output directory if needed
mkdir -p [win_dir]
UD N [old_num_grps] ; Find number of old groups (usually micrographs)
[old_sel_grp] ; Old group (micrograph) selection file (input)
[ntot] = 0 ; Initialize overall cumulative total
DO ; Loop over all old groups (micrographs) ---------------
UD NEXT [key], [ingrp] ; Get old group (micrograph) number
[old_sel_grp] ; Old group (micrograph) selection file (input)
IF ( [key] <= 0 ) EXIT
; Accumulate total number of particles
UD N [numparts]
[old_sel_part][ingrp] ; Old particle selection file (input)
SYS
echo " Group: {%I4%[ingrp]} has: {%I6%[numparts]} particles."
; Count number of selected particles
[ntot] = [ntot] + [numparts]
ENDDO ; End loop over micrographs -----------------------------
UD NEXT E ; Finished with doc file
[old_sel_grp] ; Finished with doc file (input)
[newnpg] = [ntot]/[num-grps] ; Number of particles in new groups
[newnpg1] = INT([newnpg]) ; Number of particles in new groups
IF ([newnpg] > [newnpg1])[newnpg]=INT([newnpg]+1) ; Number of particles in new groups
SYS
echo ; echo " Restacking: {%I6%[ntot]} particles"
SYS
echo " From: {%I4%[old_num_grps]} groups into: {%I3%[num-grps]} groups, with {%I5%[newnpg]} particles each." ; echo
IF ( [want-stats-only-yn] == 1 ) THEN
EN
ENDIF
DE ; Remove any new group selection file
[sel_group] ; New group selection file (removed)
SD / GROUP NUM_PARTS
[sel_group] ; Group selection doc file (output)
[grp] = 1
DE A
[sel_parts]
DE A
[unaligned_images][grp]
DE A
[part2global][grp]
IF ( [want-global-yn] == 1 ) THEN
DE
[global2grp_lut]
SD / APSHSLICE MIC_SLICE APSHGROUP MIC_NUM
[global2grp_lut]
ENDIF
; Compute number of particles for each new group
[newnpg] = [ntot]/[num-grps] ; Number of particles in new groups
[newnpg1] = INT([newnpg]) ; Number of particles in new groups
IF ([newnpg] > [newnpg1])[newnpg]=INT([newnpg]+1) ; Number of particles in new groups
[grp] = 0 ; Initialize output group number
[outpart] = [newnpg] + 1 ; To force new output group
[needold] = 1 ; To force new input group
[part_counter] = 0 ; Initialize overall counter
DO ; Loop over all old particles ----------------
IF ( [needold] >= 1 ) THEN
; Start another input group (micrograph)
IF ( [want-align-yn] > 0) THEN
UD ICE ; Close doc file
[old_align][ingrp] ; Old alignment doc file (closed)
ENDIF
UD NEXT [key], [ingrp] ; Get next group (micrograph) number
[old_sel_grp] ; Group (micrograph) selection file (input)
IF ([key] <= 0) EXIT ; Finished with all old groups
[needold] = 0 ; Flag to use old group
ENDIF
[calcgrpnum] = int([part_counter]*[num-grps]/[ntot])+1 ; The group number we *should* be on
; IF ( [outpart] > [newnpg] ) THEN ; (OUTPART is incremented after this step, so OUTPART+1 would get included)
IF ( [calcgrpnum] > [grp] ) THEN
[part_counter] ; DIAGNOSTIC outpart newgroup
; Must start another output group
IF ( [grp] > 0) THEN
; Not first output group, give details on last output group
SYS
echo " Filled group: {%I3%[grp]} with: {%I6%[outpart]} particles."
SD E ; Close doc file
[sel_parts] ; Finished with this particle selection file (closed)
SD E ; Close doc file
[next_group_align] ; Finished with this alignment file (closed)
SD E ; Close doc file
[part2global][grp] ; Global number doc file (closed)
SD [grp],[grp],[outpart] ; Place group # in group selection file
[sel_group] ; Group selection file (output)
ENDIF
[grp] = [grp] + 1 ; New output group #
IF ( [grp] <= [num-grps] ) THEN
; Delete pre-existing files and label new doc files
DE ; Remove existing particle selection file
[sel_parts] ; Particle selection file (removed)
SD / # ORIG_MICRO MIC_WIN_# GLOBAL_# GRP
[sel_parts] ; Particle selection file (output)
DE ; Remove existing output stack
[unaligned_images][grp] ; Particle stack file (removed)
IF ( [want-global-yn] > 0) THEN
DE ; Remove existing global lookup file
[part2global][grp] ; Existing global number lookup file (removed)
SD / KEY: WIN-NUM REG: GLOBAL-NUM MICROGRAPH; Label for new global number doc file
[part2global][grp] ; New global number doc file (output)
ENDIF
IF ( [want-align-yn] > 0) THEN
DE ; Remove existing alignment file
[next_group_align] ; Existing global alignment file (removed)
SD / KEY PSI, THE, PHI, REF#, EXP#, CUM.{ROT, SX, SY}, NPROJ, DIFF, CCROT, ROT, SX, SY, MIR-CC
[next_group_align] ; New global number doc file (output)
ENDIF
ENDIF
[outpart] = 0 ; Reset output particle # to zero
ENDIF ; For starting new group
UD NEXT [key], [inpart],[d2],[mic],[glonum] ; Get next input particle number
[old_sel_part][ingrp] ; Old particle selection file (input)
IF ( [key] <= 0) THEN
[needold] = 1 ; Flag for need to start next input group
UD NEXT E ; (Goes into infinite loop without this)
[old_sel_part][ingrp]
CYCLE ; Finished with this input group
ENDIF
; Have old and new particle numbers now
[outpart] = [outpart] + 1 ; New output particle #
[part_counter] = [part_counter] + 1
IF ( [apply-ctf-yn] > 0) THEN
; Apply CTF correction to image and restack
TF COR
[old_stack][ingrp]@******[inpart] ; Existing particle stack (input)
[ctf_cor][mic] ; CTF correction file (input)
[unaligned_images]@******[outpart] ; CTF corrected particle stack (output)
ELSE
; No CTF correction, just restacking
CP
[old_stack][ingrp]@******[inpart] ; Existing particle stack (input)
[unaligned_images]@******[outpart] ; New particle stack (output)
ENDIF
; FI H [mic],[glonum] ; Query image header values
; [old_stack][ingrp]@******[inpart] ; Existing particle stack (input)
; MIC,NUM
;
; FI H [mic] ; Query image header values
; [old_stack][ingrp]@******[inpart] ; Existing particle stack (input)
; MIC
SD [outpart], [outpart],[mic],[inpart],[glonum],[grp] ; Save new particle data
[sel_parts] ; Particle selection file (output)
IF ( [want-global-yn] > 0) THEN
SD [outpart],[glonum],[mic] ; Save lookup table
[part2global][grp] ; New global number doc file (output)
SD [glonum], [outpart],[inpart],[grp],[mic]
[global2grp_lut]
ENDIF
IF ( [want-align-yn] > 0) THEN
; Get image dimension
UD IC [inpart], [r1],[r2],[r3],[r4],[r5],[r6],[r7],[r8],[r9],[r10],[r11],[r12],[r13],[r14],[r15]
[old_align][ingrp] ; Old alignment doc file (input)
SD [outpart],[r1],[r2],[r3],[r4],[outpart],[r6],[r7],[r8],[r9],[r10],[r11],[r12],[r13],[r14],[r15]
[next_group_align] ; New alignment doc file (output)
ENDIF
ENDDO ; End loop over all old particles ----------------
IF ( [outpart] > 0) THEN
SYS
echo " Filled group: {%I3%[grp]} with: {%I6%[outpart]} particles."
SD E ; Close doc file
[sel_parts] ; Output particle selection file (closed)
ENDIF
UD ICE ; Close doc file
[old_align][ingrp] ; Old alignment doc file (closed)
; UD NEXT E ; Close doc file
; [sel_group] ; Group selection doc file (closed)
UD NEXT E ; Close doc file
[old_sel_grp] ; Group selection doc file (closed)
[dummy] = -[num-grps]
SD / PARTSBEFORE PARTS_AFTER
[sel_group]
SD [dummy], [ntot],[part_counter]
[sel_group]
SD E
[sel_group]
IF ( [want-global-yn] == 1 ) THEN
SD E
[global2grp_lut]
ENDIF
SYS
echo
EN
;
; Modified 2016-07-07
; 2016-07-07 (agl) -- From: restack-n-ctf
; 2015-11-18 (agl) -- Use 'TF COR' not 'FD'!!
; 2014-08-13 (trs) -- Added combined global lookup
; 2013-11-29 (trs) -- Bug fix: went into infinite (?) loop if in-core files weren't closed
; 2013-11-28 (trs) -- Bug fix: now gets micrograph# and global particle number from OLD_SEL_PART instead of stack
; 2013-10-16 (agl) -- Modernized
; 2012-07-19 (trs) -- Creates output directory if needed
; 2012-05-01 (trs) -- Optionally writes global particle number to header position 42
; 2012-04-05 (trs) -- Doesn't use output from pnums.spi anymore
; 2012-04-05 (trs) -- Adapted from listallparticles.spi
; 2010-09-02 (trs & ay) -- Trap for >999 micrographs for 'SD [dummy]' line
; 2009-10-16 (trs) -- Removed option for unstacked images
; 2008-10-03 (trs) -- Added output file part2global
; 2008-10-03 (trs) -- Assigns global particle number
; 2007-12-17 (trs) -- Optional parameter for maximum number of particles per micrograph
; 2007-10-10 (trs) -- Gets number of micrographs from sel_micrograph
;