([sp_pixsiz],[angStep],[r2],[alignsh],[prjRadius],[sp_winsiz],[incoreYN],[bpType],[qsub],[masterCPUs],[groupCPUs])
;([steptype],[sp_pixsiz],[angStep],[r2],[alignsh],[prjRadius],[sp_winsiz],[incoreYN],[bpType],[qsub],[masterCPUs],[groupCPUs])
;
; Sets reconstruction parameters and files
;
; SOURCE: spider/docs/techs/recon1/Procs/recon_settings.spi
; New ArDean Leith Jul 2002
; [] variables ArDean Leith Dec 2005
; Rewritten, more stacks ArDean Leith Dec 2006
; Variable assignment ArDean Leith Jan 2010
; Even-odd replaced ArDean Leith Jan 2011
; pixsiz returned, fsc ArDean Leith Aug 2012
; For CTF corrected images ArDean Leith Oct 2013
; For gold standard reconstruction ArDean Leith May 2014
; Inlined params, changed dirs ArDean Leith Mar 2016
;
; INPUT REGISTERS: [steptype] (0==align, 1==reconstruct, 3==restack, <1==none)
;
; OUTPUT REGISTERS (SET BELOW):
; [numGrps] Number of groups used
; [sp_pixsiz] Pixel size (A)
; [angStep] Angular step for ref. projections (degrees)
; [r2] Object alignment radius (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prjRadius] Object projection radius (pixels)
; [sp_winsiz] Image/window size = volume size (pixels)
; [incoreYN] Use incore files (1 == true)
; [bpType] Backprojection method (1=='BP CG', 2=='BP 3F', 3=='BP RP', 4=='BP 3N')
; [qsub] Specifies que type (1 == use PBS, 0 == use PubSub, <0 == none)
;
; ---------Set Refinement parameters from parameter file ----------
; ---- Adjust these parameters for your project --------------- EDIT -----
[qsub] = 3 ; Specifies queue (1 == use PBS, 2 == PBS with memory estimate, 0 == use PubSub, 3 == PBSPro, <0 == none)
GLO [pbsFlags] = '-l nodes=1:ppn=8 -q ceitecmu -l walltime=47:59:00' ; Additional user-defined flags for old PBS
GLO [proFlags] = '-l select=1:ncpus=8:mem={%i0%[memMb]}mb -l walltime=47:59:00' ; Additional user-defined flags for PBSPro
[masterCPUs] = 1 ; Number of CPUs to use for master process
[groupCPUs] = 8 ; Number of CPUs to use for group processes
[diam] = -1 ; Diameter of the structure (A) used in alignment search (<0 == from 'params.spi')
[sp_pixsiz] = -1 ; Pixel size (A, <0 == from 'params.spi'))
[sp_winsiz] = -1 ; Window size (pixels, <0 == from 'params.spi')
[winFrac] = 0.95 ; Fraction of window diameter used in projection (0.95 == 95%)
[alignsh] = 8 ; Alignment shift (pixels) searched is +- this value
[angStep] = 15 ; Angular separation for reference projections
[bpType] = 2 ; Backprojection method (1==BP CG, 2==BP 32F, 3==BP RP, 4==BP 3N)
[incoreYN] = 1 ; Load input images into incore stack (>0 == Yes, we have enough memory)
[maxWait] = 600 ; Maximum delay in seconds for copying stacks before next group starts
; ----------------- Original input files --- EDIT names as needed, These files must exist ------
GLO [params] = '../params' ; Parameter doc file (one)
GLO [mic_sel_grp] = '../sel_micrograph' ; Group (or micrograph) selection file (one)
GLO [mic_sel_part] = '../Particles/good/sel_part_****' ; Particle selection files (one/micrograph)
GLO [mic_parts] = '../Particles/win/data_bymic_****' ; Existing particle stacks (one/micrograph)
GLO [mic_align] = 'input/align_01_****' ; Pre-existing alignment parameter files (one/group) (OPTIONAL)
GLO [ref_vol_unfilt] = '../ref_vol_unfilt' ; Initial unfiltered reference volume or reference volume (one)
; OPTIONAL doc file needed if using symmetry
GLO [symmetry_doc] = '*' ; OPTIONAL symmetry doc file for 'back projection' (one)
; -------------- Output files -- Usually no need to edit for default refinement ----------
; filter-refvol.spi
GLO [ref_vol] = '../ref_vol_filt' ; Initial filtered reference volume (one)
; align-regroup.spi
;;; GLO [init_dir] = '../iter_0' ; Dir. used for alignment
GLO [init_dir] = 'iter_0' ; Dir. used for alignment
GLO [init_sel_grp] = '[init_dir]/sel_group' ; Group selection file (one)
GLO [init_sel_part] = '[init_dir]/sel_part_***' ; Particle selection files (one/group)
GLO [init_unaligned] = '[init_dir]/data_***' ; Unaligned particle stacks (one/group)
GLO [init_part2global] = '[init_dir]/part2glonum_***' ; OPTIONAL Global particle lookup table (one/group) (OPTIONAL)
GLO [init_combined_parts] = '[init_dir]/global2group' ; OPTIONAL Combined global lookup table (one) (OPTIONAL)
GLO [init_align_doc] = '[init_dir]/align_00_***' ; OPTIONAL Alignment parameter files (one/group) (OPTIONAL)
; make-ref-views.spi
GLO [iter_refangs] = '[init_dir]/ref_angs_00' ; Reference projection angle file (one)
GLO [ref_projs] = '[init_dir]/ref_projs_00' ; Reference projections (one)
GLO [ref_view_list] = '[init_dir]/sel_proj' ; List of reference views (one)
; align.spi, pub-align.spi, align-loop.spi
GLO [work_dir] = 'work' ; Dir. for scratch files
GLO [out_align_doc] = '[init_dir]/align_01_{***[grp]}' ; Next group alignment doc file stem
GLO [out_aligned] = '[init_dir]/dala_01_***' ; Aligned image data (one/group)
; recon-regroup.spi
;;; GLO [rec_dir] = '../iter_1' ; Dir. for files from reconstruction
GLO [rec_dir] = 'iter_1' ; Dir. for files from reconstruction
GLO [rec_unaligned] = '[rec_dir]/data_***' ; New particle stacks (one/group)
GLO [sel_group] = '[rec_dir]/sel_group' ; New group selection file (one)
; (not naming [sel_group] [rec_sel_grp] so that merge-fsc-filt.spi can be reused from Refinement/)
GLO [rec_sel_part] = '[rec_dir]/sel_part_***' ; New particle selection files (one/group)
GLO [rec_part2global] = '[rec_dir]/part2glonum_***' ; New global particle lookup table (one/group) (OPTIONAL)
GLO [rec_aligned] = '[rec_dir]/dala_01_***' ; New aligned image data (one/group)
GLO [rec_align_doc] = '[rec_dir]/align_01_***' ; Alignment parameter files (one/group) (OPTIONAL)
; recon.spi, pub-recon.spi, recon-loop.spi
GLO [next_group_vol_stem] = '[work_dir]/vol_{**[next-iter]}_***_s{*[s]}' ; Next subset group volume stem
GLO [next_group_vol] = '[work_dir]/vol_01_{***[grp]}' ; Next group volume (one/group)
GLO [next_group_vol_s] = '[next_group_vol]_s{*[s]}' ; Next group halfset volume (two/group)
GLO [group_vol_stem] = '[work_dir]/vol_00_{***[grp]}_***' ; Current group volumes (two/group)
GLO [next_vol_s] = '[next_vol]_s{*[s]}' ; Filtered, shifted volumes (two)
GLO [fsc_mask] = '[rec_dir]/fsc_mask' ; Mask for FSC (one)
GLO [next_u_fsc] = '[rec_dir]/fscdoc_u_01' ; Unmasked FSC curve doc file (one)
GLO [next_m_fsc] = '[rec_dir]/fscdoc_m_01' ; Masked FSC curve doc file (one)
GLO [iter_resol] = '[rec_dir]/resolutions' ; Overall resolution doc file (one)
GLO [next_vol] = '[rec_dir]/vol_01' ; Next volume stem
GLO [wait_file] = 'jnk_waited_***' ; OPTIONAL Created when local copy finished (one/group)
GLO [finished_file] = 'jnk_sync_{****[rn]}_{***[grp]}' ; Created when parallel segment finished (one/group)
; plot-fsc-curve.spi
GLO [fscplots] = 'fsc_iter.gnu' ; Gnuplot script for FSC plotting (one)
; ----------------- END BATCH HEADER -------------------------------------------
; ---- Usually no need to adjust following parameters
; Get values from params
IF ([sp_pixsiz] .LE. 0) THEN
UD IC 5, [sp_pixsiz]
[params]
ENDIF
IF ([sp_winsiz] .LE. 0) THEN
UD IC 17, [sp_winsiz]
[params]
ENDIF
IF ([diam] .LE. 0) THEN
UD IC 18, [sp_partsiz]
[params]
ELSE
[sp_partsiz] = [diam]/[sp_pixsiz]
ENDIF
UD ICE
[params]
[r2] = INT([sp_partsiz]/2.0) ; Alignment radius (pixels) used in alignment search
; Ensure that sum of alignment radius + translation is within window dimensions
[ringsh] = [r2] + [alignsh] ; Last ring + translation step
[maxrad] = INT([sp_winsiz]/2) - 1 ; Max radius of object in window
IF ( [ringsh] >= [maxrad] ) THEN
; Must reduce radius of outer ring, not translation step
[r2] = [maxrad] - [alignsh] - 2 ; Reduces rotational search radius
ENDIF
[prjRadius] = INT(([winFrac]*[sp_winsiz])/2.0 ) ; Convert fraction to pixel radius
RE
; Modified 2017-08-04
; 2017-07-26 (trs) -- now used for align-regroup.spi
; 2017-07-20 (trs) -- specifies #CPUs here
; 2016-10-12 (trs) -- removed numGrps
; 2016-05-26 (trs) -- can get pixel size, window size, and particle size from PARAMS
;