([sp_pixsiz],[r2],[alignsh],[prjRadius],[iter1],[iterEnd],[sphdecon],[smallangYN],[qsub],[incoreYN],[goldStd],[bpType])
;
; Sets refinement parameters and files
;
; 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
;
; INPUT REGISTERS: None
;
; OUTPUT REGISTERS:
; [sp_pixsiz] Pixel size (A)
; [r2] Object alignment radius (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prjRadius] Object projection radius (pixels)
; [iter1] Starting iteration
; [iterEnd] Ending iteration
; [sphdecon] Spherical deconvolution angle (degrees)
; [smallangYN] Small angle refinement flag (1 == True)
; [qsub] Specifies que type (1 == use PBS)
; [incoreYN] Incore files (1 == true)
; [goldStd] Use 'gold-standard' work-flow (1 == True)
; [bpType] Backprojection method (2 == 'BP 3F')
;
;
; ------------- 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:mem={%i0%[memMb]}mb -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 -q ceitecmu -l walltime=47:59:00' ; Additional user-defined flags for PBSPro
[iter1] = 1 ; Starting alignment step (iteration)
[iterEnd] = 15 ; Ending alignment step (iteration)
[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
[bpType] = 2 ; Backprojection method (1=='BP CG', 2=='BP 3F', 3=='BP RP', 4=='BP 3N')
[goldStd] = 1 ; Use 'gold-standard resolution' work-flow (1 == use gold, 0 == use legacy)
[incoreYN] = 1 ; Load input images into incore stack (>0 == yes we have enough memory)
GLO [userMem] = 5000 ; Memory (MB) required for normal refinement (-1 == Automatic)
GLO [smAngMem] = 3611 ; Memory (MB) required for small-angle refinement (-1 == Automatic)
GLO [spdMem] = 7271 ; Memory (MB) required for spherical deconvolution (-1 == Automatic)
; Following two string variables are used during usual refinement (one value / iteration) (Set for up to: 20 iterations)
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, 15,8, 6,5,5,5,5, 5,5,5,5,5, 5,5,5,5,5,5' ; Angular separation limits (degrees)
[smallangYN] = 0 ; Use small angle refinement instead of regular (1 == Yes)
; Following three 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
[sphdecon] = 4.5 ; Spherical deconvolution angle in degreees (0 == Do not deconvolve)
GLO [spdFlags] = '-l select=8:ncpus=2:mem={%i0%[memMb]}mb -q ceitecmu -l walltime=143:59:00' ; Additional user-defined flags for spherical deconvolution
; 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
; ----------------- Original input files --- May have to EDIT these names, These files must exist ------
GLO [in_dir] = '../win_1' ; Dir. for starting selection files
GLO [params] = '../params' ; Parameter doc file (one)
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)
GLO [vol_orig] = '../rec_1/vol_01_s{*[s]}' ; Initial reference volumes (two)
; 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)
GLO [local_work_dir] = 'scratch{***[grp]}' ; OPTIONAL local scratch dir for parallel use (one/group)
; 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 -----------------------------------------------------------------------
GLO [out_dir] = 'final_1' ; Dir. for significant 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 [incoreYN] == 0 or small angle ref. (deleted)
; ----------------- END BATCH HEADER ---------------------------------
; ---- Should not 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
; Get particle size (pixels) from PARAMS, or calculate
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
;