([sp_pixsiz],[r2],[alignsh],[prj-radius],[iter1],[iter-end],[sphdecon],[smallang-yn],[qsub],[incore-yn],[gold-std],[bp-type])
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; Sets refinement parameters and files
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; SOURCE: spider/docs/techs/recon1/Procs/refine_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
; Dala removal ArDean Leith Jan 2012
; [pixsiz] returned, fsc, ofsc... ArDean Leith Aug 2012
; Skip 3.3,3... ArDean Leith Sep 2012
; For CTF corrected images ArDean Leith Oct 2013
; For gold standard reconstruction ArDean Leith May 2014
; Added spherical deconvolution ArDean Leith Jan 2016
; Inlined params, changed dirs ArDean Leith Mar 2016
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; INPUT REGISTERS: None
;
; OUTPUT REGISTERS:
; [sp_pixsiz] Pixel size (A)
; [r2] Object alignment radius (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prj-radius] Object projection radius (pixels)
; [iter1] Starting iteration
; [iter-end] Ending iteration
; [sphdecon] Spherical deconvolution angle (degrees)
; [smallang-yn] Small angle refinement flag (1 == True)
; [qsub] Specifies que type (1 == use PBS)
; [incore-yn] Incore files (1 == true)
; [gold-std] Use 'gold-standard' work-flow (1 == True)
; [bp-type] Backprojection method (2 == 'BP 3F')
;
;
; ------------- Adjust these parameters for your project --------------- EDIT -----
[qsub] = 1 ; Specifies que (1 == use PBS, 2 == PBS with memory estimate, 0 == use PubSub, <0 == none)
[diam] = 420 ; Diameter of the object (A), used to find radius for alignment.
[sp_pixsiz] = 1.68 ; Pixel size from 'params.spi' file (A)
[sp_winsiz] = 280 ; Window size from 'params.spi' file (pixels)
[win-frac] = 0.95 ; Fraction of window diameter used in projection (0.95 == 95%)
[incore-yn] = 1 ; Load input images into incore stack (>0 == yes we have enough memory)
[alignsh] = 8 ; Alignment shift (pixels) searched is +- this value
[iter1] = 1 ; Starting alignment step (iteration)
[iter-end] = 12 ; Ending alignment step (iteration)
[bp-type] = 2 ; Backprojection method (1=='BP CG', 2=='BP 3F', 3=='BP RP', 4=='BP 3N')
[sphdecon] = 0 ; Spherical deconvolution angle in degreees (0 == Do not deconvolve)
[gold-std] = 1 ; Use 'gold-standard resolution' work-flow (1 == use gold, 0 == use legacy)
; Following two string variables are used during usual refinement (one value / iteration) (Set for up to: 20 iterations)
!GLO [ang-steps] = '15,10,3.3,3,2, 2,2,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5' ; Angular separation (degrees)
GLO [ang-steps] = '15,3.3,3, 2,2, 2,1.5,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5' ; Angular separation (degrees)
!GLO [ang-limits] = '0,0,0, 0,15, 8,6,5,5,5, 5,5,5,5,5, 5,5,5,5,5' ; Angular separation limits (degrees)
GLO [ang-limits] = '0,0,0, 15,8, 6,5,5,5,5, 5,5,5,5,5, 5,5,5,5,5,5' ; Angular separation limits (degrees)
; Following string variable is used to activate OPTIONAL amplitude enhancement (Set for up to: 20 iterations)
GLO [amp-enhance-flags] = '0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0' ; Amplitude enhancement selector
[smallang-yn] = 0 ; Use small angle refinement instead of regular (1 == Yes)
; Following two global register variables are only used during 'small angle refinement'
GLO [ang-step-sm] = 5 ; Angular degree step
GLO [theta-sm] = 2.0 ; Theta range
; ----------------- Original input files --- May have to EDIT these names, These files must exist ------
GLO [in_dir] = '../win_1' ; Dir. for starting selection files
GLO [out_dir] = '../final_1/' ; Dir. for significant output files
GLO [sel_group] = '[in_dir]/sel_group' ; Group selection doc file (one)
GLO [sel_parts] = '[in_dir]/sel_part_{***[grp]}' ; Particle selection doc files (one/group)
GLO [vol_orig] = '[in_dir]/reference_volume_fqnp' ; Initial reference volume (one)
; This variable: [unaligned_images] must be an absolute path to images or a link to an absolute path!
GLO [unaligned_images] = '[in_dir]/data_{***[grp]}' ; Original unaligned images stack (one/group)
; OPTIONAL files needed if using amplitude enhancement
GLO [scattering_doc] = '[in_dir]/scattering' ; OPTIONAL enhancement doc file (one)
GLO [mask] = '[in_dir]/mask' ; OPTIONAL mask for enhancement (one)
; 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)
; OPTIONAL initial alignment parameter doc file if starting from reconstruction
!GLO [group_align_orig] = '[in_dir]/align_{**[iter]}_{***[grp]}' ; OPTIONAL Initial alignment parameter file (one/group)
GLO [group_align_orig] = '*' ; OPTIONAL Initial alignment parameter file (one/group)
; -------------- Output files -- Usually no need to edit for default refinement ---------------------
GLO [work_dir] = 'work/' ; Work dir (one)
GLO [sel_parts_s] = '[sel_parts]_s{*[s]}' ; Particle subset selection doc file (two/group)
GLO [vol] = '[out_dir]/vol_{**[iter]}' ; Current volume
GLO [vol_s] = '[vol]_s{*[s]}' ; Current subset volume (two/iter)
GLO [next_vol] = '[out_dir]/vol_{**[next-iter]}' ; Next volume (one/iter)
GLO [next_vol_s] = '[next_vol]_s{*[s]}' ; Next subset volume (two/iter)
GLO [group_vol_stem] = '[work_dir]/vol_{**[iter]}_{***[grp]}_***' ; Current group volume (one/group/iter)
GLO [group_vol_s] = '[work_dir]/vol_{**[iter]}_{***[grp]}_s{*[s]'; Current group subset volumes (two/group/iter)
GLO [next_group_vol] = '[work_dir]/vol_{**[next-iter]}_{***[grp]}' ; Next group volume (one/group/iter)
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 subset group volume (two/group/iter)
GLO [group_align] = '[out_dir]/align_{**[iter]}_{***[grp]}' ; Group alignment doc file
GLO [group_align_s] = '[group_align]_s{*[s]}' ; Group subset alignment doc files (two/group/iter)
GLO [next_group_align] = '[out_dir]/align_{**[next-iter]}_{***[grp]}' ; Next group alignment doc file
GLO [next_group_align_s] = '[next_group_align]_s{*[s]}' ; Next group subset alignment doc file (one/group/iter)
GLO [iter_refangs] = '[work_dir]/ref_angs_{**[iter]}' ; Reference angle file (one/iter)
GLO [iter_refangs_grp] = '[work_dir]/ref_angs_{**[iter]}_{***[grp]}' ; Reference projection angles doc file (one/group/iter) (deleted)
GLO [ref_projs_s] = '[work_dir]/ref_projs_{**[iter]}_s{*[s]}' ; Subset reference projections (one/iter)
GLO [ref_projs_s_grp] = '[ref_projs_s]_{***[grp]}@' ; Subset group reference projections (two/group/iter) (deleted)
GLO [fsc_mask] = '[out_dir]/fsc_mask' ; Mask for FSC (one)
GLO [next_u_fsc] = '[out_dir]/fscdoc_u_{**[next-iter]}' ; Unmasked FSC curve doc file (one/iter)
GLO [next_m_fsc] = '[out_dir]/fscdoc_m_{**[next-iter]}' ; Masked FSC curve doc file (one/iter)
GLO [m_fsc] = '[out_dir]/fscdoc_m_{**[iter]}' ; Masked FSC curve doc file (one/iter)
GLO [fsc_plots] = 'fsc_iter.gpl' ; Gnuplot script for FSC plotting (one)
GLO [iter_resol] = '[out_dir]/resolutions' ; Overall resolution doc file (one)
GLO [ang_voea] = '[out_dir]/angvoea' ; OPTIONAL, Small angle refinement ref. angles (one/group/iter)
GLO [ang_vora] = '[out_dir]/angvora_{**[iter]}_{***[grp]}' ; OPTIONAL, Small angle refinement ref. angles (one/group/iter)
GLO [temp_ref_projs] = '_5@' ; OPTIONAL, Small angle refinement local scratch file (deleted)
GLO [enhance_doc] = '[work_dir]/enhance_doc_{**[next-iter]}' ; OPTIONAL, Enhancement doc file output (one/iter)
GLO [ref_rings] = '[work_dir]/SCR_{**[iter]}_{***[grp]}' ; OPTIONAL, Reference rings files output (one/group/iter)
GLO [wait_file] = 'jnk_waited_***' ; OPTIONAL, Created when local copy finished (one/group)
GLO [finished_file] = 'jnk_sync_{****[rn]}_' ; OPTIONAL, Created when parallel segment finished (one/group)
GLO [temp_in_images] = '_8@' ; OPTIONAL, Used by alignment & back projection internally
GLO [temp_out_images] = '[work_dir]/dala_{***[grp]}@' ; OPTIONAL, Used if [incore-yn] == 0 or small angle ref. (deleted)
; ----------------- END BATCH HEADER ---------------------------------
; ---- Should not 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
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