; Determine and apply threshold for the cross correlation
;
; SOURCE: ccthresh.spi
; Merged with dftotals.spi Nov 2006 ArDean Leith
; Selection bugs Feb 2008 Magali
;
; PURPOSE: Creates selection files by applying cutoff
; Determines a threshold for the cross correlation value by
; specifying a percentage of particles to eliminate.
;
; NOTE: Particle totals are approximate due to binning of data in histograms.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ------------ Parameters ---------------------------------------
[cutoff] = 0.15 ; Percentage of particles to eliminate
[make_select] = 0 ; >0 uses cutoff to create selection files
; ------------ Input files ---------------------------------------
FR G
[defgrps]sel_group ; Defocus groups selection file
FR G
[docapsh]../Alignment/align_01_{***[grp]} ; Document file created by 'AP SH'
FR G
[cchist]hist/cchist{***[grp]} ; Histogram doc files (IF: [make_select]>0)
; --------------- Output files -------------------------------------
FR G
[thresh]thresh ; Doc file with CC thresholds
FR G
[sel_particles]sel_particles_{***[grp]} ; Output file (one for each defocus group)
; ; Contains the particle numbers whose
; ; correlation coeffs. are greater than threshold
; -------------- END BATCH HEADER ---------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
UD N,[numgrps] ; Get number of groups
[defgrps] ; Group selection doc file (input)
DE ; Remove any existing output doc file
[thresh]
SD / CC_THRESH N_ABOVE_THR N_BELOW_THR N_TOTAL
[thresh]
IF ([cutoff].LE.0) THEN
; ***** The threshold = 0 case : keep using all particles *************
[zero] = 0.0
DO LB1 [numgrp]=1,[numgrps] ; Loop over all defocus group(s)
UD [numgrp],[grp],[numparts] ; Get current group number and particles
[defgrps] ; Group selection doc file (input)
SD [grp],[zero],[numparts],[zero],[numparts] ; Make threshold file entry
[thresh] ; Threshold file (output)
IF ([make_select].GT.0) THEN
; Create selection file
DE ; Remove any existing output doc file
[sel_particles] ; Selection file
SD/ PARTICLE # CC VALUE
[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],[cc] ; Save: Particle #, CC value
[sel_particles] ; Selection file (output)
LB2
SD E ; Free doc file pointer
[sel_particles]
ENDIF
LB1
SD E ; Free doc file pointer
[thresh]
ELSE
; ********* Apply cuttoff threshold **********************************
VM
echo ' 'Cutoff: {%f5.2%[cutoff]}
[all] = 0
[saved]=0
DO LB3 [numgrp]=1,[numgrps] ; Loop over all defocus group(s)
UD [numgrp],[grp],[numparts] ; Get current group number and particles
[defgrps] ; Group selection doc file (input)
; Determines the number of particles below the percent cutoff ([cutoff]),
; [cutoff] = Percent cutoff
; [grp] = Defocus group
; Gets the total number of particles (from column 2 in histogram),
; Determines the number of particles below the percent cutoff,
; Finds the corresponding CC value (column 1 in histogram).
[ncum] = 0 ; Cumulative no. of particles
[Nbelow] = 0
[nbad] = [cutoff]*[numparts] ; Number of particles to eliminate
UD N,[nbins] ; Find number of bins in histogram
[cchist] ; Histogram doc file (input)
DO LB4 [key] = 1,[nbins] ; Loop over all bins
UD [key],[CC_threshold],[parts]
[cchist] ; Histogram doc file (input)
[ncum] = [ncum] + [parts] ; Number of particles below cuttof
IF ([ncum].GT.[nbad]) THEN
[cuttoffbin] = [key]-1 ; Last bin to discard
UD [cuttoffbin],[CC_threshold] ; Get the cuttoff
[cchist] ; Histogram doc file (input)
GOTO LB5 ; Leave the loop now
ENDIF
[Nbelow] = [ncum] ; No. of particles from previous bins
LB4
LB5
[Nabove] = [numparts] - [Nbelow] ; Number above threshold
; Save [CC_threshold], N_above_threshold, N_below_threshold, total_N
SD [grp],[CC_threshold],[Nabove],[Nbelow],[numparts]
[thresh]
VM
echo ' 'Group: {****[grp]} Saved: {******[Nabove]} Out of: {******[numparts]}
[all] = [all] + [numparts]
[saved] = [saved] + [Nabove]]
IF ([make_select].GT.0) THEN
; Create selection file
[key]=0
DE ; Remove any existing output doc file
[sel_particles] ; Selection file
DO LB6 [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],[img],[d], [d],[d],[d], [d],[cc]
[docapsh]
IF ([cc].GE.[CC_threshold])THEN ; CC above threshold for this particle
[key]=[key]+1 ; Increment new particle counter = key
SD [key],[img],[cc] ; Save: Particle #, CC value
[sel_particles] ; Selection file (output)
ENDIF
LB6
UD ICE
[docapsh]
SD E ; Free doc file pointer
[sel_particles]
ENDIF
LB3
VM
echo ' '; echo ' 'Overall saved: {******[saved]} Out of: {******[all]}
ENDIF
VM
echo ' '
EN D
;