; Parameters and file names for particle verification
;
; SOURCE: spider/docs/techs/recon1/Procs/verify-settings.spi
;
; PURPOSE: Parameters and file names for particle verification procedures
;
; USAGE: Called by particle verification procedures
; ----------------------- Parameters -----------------------
GLO [view-progress] = 1 ; Prints progress message every Nth reference view
; ------------------------- Inputs -------------------------
GLO [params] = '../params' ; Parameter doc file (one)
GLO [win_dir] = '../win_0' ; Master window directory (one)
GLO [rec_dir] = '../rec_1' ; Master reconstruction output directory (one)
GLO [sel_group] = '[win_dir]/sel_group' ; Group selection doc file (one)
GLO [sel_part] = '[win_dir]/sel_part_***' ; Particle selection doc file (one/group)
GLO [ref_view_list] = '[rec_dir]/sel_proj' ; List of reference views (one)
GLO [iter_refangs] = '[rec_dir]/ref_angs_{**[iter]}' ; Reference projection angle file (one)
GLO [aligned_images] = '[rec_dir]/dala_01_***@*****' ; Aligned images (one-stack/group)
GLO [align_doc] = '[rec_dir]/align_01_***' ; Particle alignment doc files (one/group)
GLO [ref_projs] = '[rec_dir]/ref_projs_{**[iter]}' ; Reference projections (one/iter)
; ------------------------ Output ------------------------
GLO [view_dir] = 'views' ; Master view directory (one)
GLO [prj_dir] = '[view_dir]/prj***' ; View sub-directories (one/view)
GLO [filtered_stack] = '[prj_dir]/filtavg' ; Filtered view average stacks (one/view)
GLO [total_view_avg] = '[prj_dir]/allavg' ; OPTIONAL view average stacks (one/view)
GLO [class_avg] = '[prj_dir]/classavg***' ; Class-average files (one/class/view)
GLO [class_var] = '[prj_dir]/classvar***' ; OPTIONAL class-average variance file(one/class/view)
GLO [class_stats_doc] = '[prj_dir]/listclasses' ; CCC for each class-average (one/view)
GLO [cas_prefix] = '[prj_dir]/verify' ; 'CA S' output prefix
GLO [eigenvalue_doc] = '[prj_dir]/listeigenvalues' ; List of eigenvalues (one/view)
GLO [eigen_img] = '[prj_dir]/eigenimg***' ; Eigenimage template (one/view)
GLO [first_good_part_doc] = '[prj_dir]/first_good_part' ; OPTIONAL for reference views (one/view)
GLO [good_classes_list] = '[prj_dir]/sel_class_good' ; Selected classes (one/view)
GLO [class_doc] = '[prj_dir]/sel_part_byclass_***' ; Particle selection by class (one/class/view)
GLO [view_list] = '[prj_dir]/sel_part_byv' ; By-view particle list (one/view)
GLO [sorted_particles] = '[prj_dir]/sel_part_byv_sort' ; Particle list sorted by CCROT (one/view)
GLO [byhand_list] = '[prj_dir]/sel_part_byhand' ; OPTIONAL hand-picked particle list (one/class)
GLO [good_particles] = '[prj_dir]/sel_part_byv_good' ; Good-particle list (one/view)
GLO [not_good_particles] = '[prj_dir]/sel_part_byv_notgood' ; OPTIONAL new bad-particle list (one/view)
GLO [bad_particles] = '[prj_dir]/sel_part_byv_bad' ; Sorted bad-particle list (one/view)
GLO [not_bad_particles] = '[prj_dir]/sel_part_byv_notbad' ; OPTIONAL new good-particle list (one/view)
GLO [new_good_particles] = '[prj_dir]/sel_part_byv_goodB' ; New good particle list (one/view)
GLO [new_bad_particles] = '[prj_dir]/sel_part_byv_badB' ; New bad particle list (one/view)
GLO [best_particles] = '[prj_dir]/sel_part_byv_best' ; Selection & CCC files (one/view)
GLO [sel_part_best] = 'sel_part_best_***' ; Particle selection doc file (one/group)
GLO [sel_group_best] = 'sel_group_best' ; New group selection file (one)
GLO [good_particle_copy] = '../Particles/good/sel_part_***' ; Archive of good particle list (one/view)
GLO [new_good_part_copy] = '../Particles/good/sel_partB_***' ; Archive of good particle list (one/view)
GLO [summary_doc] = 'summary_classify' ; Classification summary doc file (one)
GLO [summary_doc_sorted] = '[summary_doc]_sorted' ; Summary doc file (one)
GLO [good_parts_bymic] = 'summary_good_parts_bymic' ; Summary doc file (one)
GLO [summary_recheckB] = 'summary_recheckB' ; Summary doc file (one)
GLO [sd_vsview] = '[view_dir]/sd_vsview_all' ; Total # all particles by view (one)
GLO [parts_vsview] = '[view_dir]/parts_vsview_all' ; Total # all particles by view (one)
GLO [parts_vsview_good] = '[view_dir]/parts_vsview_good' ; Total # good particles by view (one)
GLO [parts_vsview_best] = '[view_dir]/parts_vsview_best' ; Total # best particles by view (one)
; ----------- END BATCH HEADER ----------------
RE
;