; >Create group and particle selection files
;
; SOURCE: dftotals.spi More stacks, merged with sort.pam Dec. 2006 ArDean Leith
;
; PURPOSE: Creates particle selection files by applying cutoff. Creates an
; updated group selection file
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ------------ Input files ---------------------------------------
FR G
[defgrps]sel_group ; Defocus groups selection file
FR G
[docapsh]../Alignment/align_01_{***[grp]} ; Document file from 'AP SH' command
FR G
[thresh]thresh ; [optional] Doc file with CC thresholds
; --------------- Output files -------------------------------------
FR G
[sel_particles]sel_particles_{***[grp]} ; Output file (one for each defocus group)
; ; Contains the particle numbers whose correlation
; ; coefficients are greater than the threshold
FR G
[defgrps_lim]sel_group_cclim ; Defocus groups selection file
FR G
[defgrps_lim_sorted]sel_group_cclim_sorted ; Defocus groups selection file
; -------------- END BATCH HEADER ---------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
DE ; Remove any existing output doc file
[defgrps_lim]
SD / GROUP PARTICLES DEFOCUS
[defgrps_lim] ; Group election file (output)
IQ FI [exists] ; If thresh file exists, use thresh
[thresh] ; Threshold doc file (input)
UD N,[numgrps] ; Get number of groups
[defgrps] ; Group selection doc file (input)
[all] = 0
[saved] = 0
IF ([exists].LE.0) THEN
; ***** No threshold doc file : Keep all particles ********************************
DO LB1 [numgrp]=1,[numgrps] ; Loop over all defocus group(s)
UD [numgrp], [grp],[numparts],[def] ; Get current group number and particles
[defgrps] ; Group selection doc file (input)
; Create particle selection file
DE ; Remove any existing output doc file
[sel_particles] ; Selection file
SD / PARTICLE NUMBER
[sel_particles] ; Selection file (output)
DO LB2 [part]=1,[numparts] ; Loop over particles in this defocus group
; PHI,THE,PSI, REF#,IMG#,INPLANE, SX,SY,NPROJ, DIFF,CCROT,INPLANE,SX,SY
UD IC [part], [d],[d],[d], [d],[d],[d], [d],[d],[d], [d],[cc]
[docapsh]
SD [part], [part] ; Save: Particle #, CC value, Defocus
[sel_particles] ; Selection file (output)
LB2
UD ICE
[docapsh]
SD E ; Free doc file
[sel_particles]
SD [numgrp], [grp],[numparts],[def] ; Save: Group, Particle #, Defocus
[defgrps_lim] ; Selection file (output)
[all] = [all] + [numparts]
LB1
VM
echo ' ' ; echo ' 'Overall particles: {******[all]}
ELSE
; ********* Apply cuttoff threshold **************************************************
DO LB3 [numgrp]=1,[numgrps] ; Loop over all defocus group(s)
UD [numgrp], [grp],[numparts],[def] ; Get current group number and particles
[defgrps] ; Group selection doc file (input)
[all] = [all] + [numparts]
[key] = 0
; Create particle selection file
DE ; Remove any existing output doc file
[sel_particles] ; Selection file
SD / PARTICLE NUMBER
[sel_particles] ; Selection file (output)
DO LB4 [part]=1,[numparts] ; Loop over particles in this defocus group
; PHI,THE,PSI, REF#,IMG#,INPLANE, SX,SY,NPROJ, DIFF,CCROT,INPLANE,SX,SY
UD IC [part], [d],[d],[d], [d],[d],[d], [d],[d],[d], [d],[cc]
[docapsh] ; Alignment doc file (input)
UD [grp],[ccthresh] ; Get CC threshold for this defocus group
[thresh] ; Threshold doc file (input)
IF ([cc].GE.[ccthresh])THEN ; CC above threshold for this particle
[key]=[key]+1 ; Increment new particle counter = key
SD [key], [part] ; Save: Particle #
[sel_particles] ; Selection file (output)
ENDIF
LB4
UD ICE
[docapsh]
SD E ; Free doc file
[sel_particles]
SD [numgrp], [grp],[key],[def] ; Save: Group, Particle #, Defocus
[defgrps_lim] ; Selection file (output)
VM
echo ' 'Group: {***[grp]} Cutoff: {%F8.2%[ccthresh]} Saved: {******[key]} Out of: {******[numparts]}
[saved] = [saved] + [key]
LB3
VM
echo ' '; echo ' 'Overall saved: {******[saved]} Out of: {******[all]}
ENDIF
SD E
[defgrps_lim] ; Selection file (output)
FR L
[tmp1]order_select_jnk1 ; Temp output file (deleted)
; DOC file sorting
DOC SORT
[defgrps_lim] ; Defocus selection doc file (input)
[tmp1] ; Sorted Temp file (output)
2 ; Sort column
Yes ; Renumber keys
DE ; Remove any existing output file
[defgrps_lim_sorted]
UD N, [nkey] ; Get number of keys in sorted
[tmp1] ; Temp file (input)
; Reverse sorting order of output doc file
DO LB5 [i]=1,[nkey] ; Loop over defocus groups
[grp]=[nkey]-[i]+1 ; Reverse order
; GROUP, PARTICLES, DEFOCUS
UD IC [grp], [grp], [part], [def]
[tmp1] ; Doc file (input)
SD [i], [grp], [part], [def]
[defgrps_lim_sorted] ; Reverse sorted doc file (output)
LB5
SD E
[defgrps_lim_sorted]
UD ICE ; Close doc files
[tmp1]
DE ; Destroy temp. doc files
[tmp1]
VM
echo ' '
EN D
;