([steptype],[num-grps],[sp_pixsiz],[ang-step],[r2],[alignsh],[prj-radius],[sp_winsiz],[incore-yn],[bp-type],[qsub])
;
; Sets reconstruction parameters and files
;
; SOURCE: spider/docs/techs/recon1a/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):
; [num-grps] Number of groups used
; [sp_pixsiz] Pixel size (A)
; [ang-step] Angular step for ref. projections (degrees)
; [r2] Object alignment radius (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prj-radius] Object projection radius (pixels)
; [sp_winsiz] Image/window size = volume size (pixels)
; [incore-yn] Use incore files (1 == true)
; [bp-type] Backprojection method (1=='BP CG', 2=='BP 3F', 3=='BP RP', 4=='BP 3N')
; [qsub] Specifies que type (1 == use PBS, <0 == none)
;
; ---------Set Refinement parameters from parameter file ----------
; ---- Adjust these parameters for your project --------------- EDIT -----
[num-grps] = 10 ; Number of groups
[qsub] = 1 ; Specifies que (1 == use PBS, <0 == none)
[diam] = 414 ; Diameter of the structure (A) used in alignment search. EDIT as needed.
[sp_pixsiz] = 1.1 ; Pixel size from 'params.spi' file (A)
[sp_winsiz] = 400 ; Window size from 'params.spi' file (pixels)
[win-frac] = 0.95 ; Fraction of window diameter used in projection (0.95 == 95%)
[alignsh] = 8 ; Alignment shift (pixels) searched is +- this value
[ang-step] = 15 ; Angular separation for reference projections
[bp-type] = 2 ; Backprojection method (1==BP CG, 2==BP 3F, 3==BP RP, 4==BP 3N)
[rad-bp] = -1 ; Radius of reconstructed object, pixels (<0 will use: 95% winsize / 2)
[incore-yn] = 1 ; Load input images into incore stack (>0 == Yes, we have enough memory)
[max-wait] = 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 [ref_vol_unfilt] = '../ref_vol_unfilt' ; Initial unfiltered reference volume or reference volume (one)
GLO [ref_vol] = '../ref_vol' ; Initial filtered reference volume or reference volume (one)
GLO [vol] = '../ref_vol' ; Initial starting volume (== ref vol) (one)
IF ( [steptype] <= 0) THEN
GLO [win_dir] = '../win_0' ; Dir. used for alignment
ELSE
GLO [win_dir] = '../win_1' ; Dir. used for reconstruction or refinement
ENDIF
GLO [sel_group] = '[win_dir]/sel_group' ; Group selection doc file (one)
GLO [sel_parts] = '[win_dir]/sel_part_{***[grp]}' ; Particle selection doc files (one/group)
; The variable: [unaligned_images] must be an absolute path to images or a link to an absolute path!
GLO [unaligned_images] = '[win_dir]/data_{***[grp]}' ; Original unaligned images stack (one/group)
; OPTIONAL local dir for speeding up parallel use
GLO [local_work_dir] = '/scratch' ; OPTIONAL local scratch dir for parallel use (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 reconstruction ----------
IF ( [steptype] <= 0) THEN
GLO [rec_dir] = '../rec_0/' ; Dir. for files from alignment
ELSE
GLO [rec_dir] = '../rec_1' ; Dir. for files from reconstruction
ENDIF
GLO [work_dir] = 'work/' ; Dir. for scratch files
GLO [aligned_images] = '[rec_dir]/dala_01_{***[grp]}' ; Aligned image data (one/group)
GLO [vol] = '[rec_dir]/vol_00' ; Current volume == ref. volume (one)
GLO [next_vol] = '[rec_dir]/vol_01' ; Next volume stem
GLO [next_vol_s] = '[next_vol]_s{*[s]}' ; Filtered, shifted volumes (two)
GLO [group_vol_stem] = '[work_dir]/vol_00_{***[grp]}_***' ; Current group volumes (two/group)
GLO [next_group_vol] = '[work_dir]/vol_01_{***[grp]}' ; Next group volume (one/group)
!GLO [next_group_vol_stem] = '[work_dir]/vol_01_***_s{*[s]}' ; Next group volume stem
GLO [next_group_vol_stem] = '[work_dir]/vol_{**[next-iter]}_***_s{*[s]}' ; Next subset group volume stem
GLO [next_group_vol_s] = '[next_group_vol]_s{*[s]}' ; Next group volume (two/group)
GLO [next_group_align] = '[rec_dir]/align_01_{***[grp]}' ; Next group alignment doc file stem
GLO [iter_refangs] = '[rec_dir]/ref_angs_00' ; Reference projection angle file (one)
GLO [iter_refangs_grp] = '[work_dir]/ref_angs_00_{***[grp]}' ; Reference projection angles doc file (one/group) (deleted)
GLO [ref_projs] = '[rec_dir]/ref_projs_00' ; Reference projections (one)
GLO [ref_view_list] = '[rec_dir]/sel_proj' ; List of reference views (one)
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 [next_gm_fsc] = '[rec_dir]/fscdoc_gm_01' ; Masked gold-standard FSC curve doc file (one only if legacy)
GLO [fscplots] = 'fsc_iter.gnu' ; Gnuplot script for FSC plotting (one)
GLO [iter_resol] = '[rec_dir]/resolutions' ; Overall resolution doc file (one)
GLO [ref_rings] = '[work_dir]/SCR_00_{***[grp]}' ; OPTIONAL Reference rings files output (one/group)
GLO [wait_file] = 'jnk_waited_***' ; OPTIONAL Created when local copy finished (one/group)
GLO [part2global] = '[win_dir]/part2glonum_***' ; OPTIONAL Global particle lookup table (one/group)
GLO [global2grp_lut] = '[win_dir]/global2group' ; OPTIONAL Combined global lookup table (one)
GLO [finished_file] = 'jnk_sync_{****[rn]}_{***[grp]}' ; Created when parallel segment finished (one/group)
; ----------------- END BATCH HEADER -------------------------------------------
; ---- Usually no need to adjust following parameters
[r2] = INT([diam]/(2.0*[sp_pixsiz])) ; Alignment radius (pixels) used in alignment search
; Ensure that sum of alignment radius + translation is within window dimensions
[ring-sh] = [r2] + [alignsh] ; Last ring + translation step
[maxrad] = INT([sp_winsiz]/2) - 1 ; Max radius of object in window
IF ( [ring-sh] >= [maxrad] ) THEN
; Must reduce radius of outer ring, not translation step
[r2] = [maxrad] - [alignsh] - 2 ; Reduces rotational search radius
ENDIF
[prj-radius] = INT(([win-frac]*[sp_winsiz])/2.0 ) ; Convert fraction to pixel radius
RE
;