; Create selection files listing particles by defocus group
;
; PURPOSE: Create particle selection doc files listing particles by defocus group.
; There is one selection file for each defocus groups listing original
; particle numbers which fall in that defocus group. Also creates a defocus
; group selection file with number of particles and avg. defocus for each group.
;
; SOURCE: sel_by_group.spi
;
; --------------------- Input files ----------------------------------
FR G
[sel_micro]../Power_Spectra/def_avg ; Micrograph selection file (with defocus, group, avg. defocus)
FR G
[defgrps]../Power_Spectra/order_defgrps ; Defocus group selection file (with defocus)
FR G
[sel_particles_bymic]../Particles/good/ngood{****[mic]} ; Particle selection files (by micrograph)
; --------------------- Output files -------------------------------
FR G
[sel_particles_bygrp]sel_particles_{***[grp]} ; Particle selection files (by defocus group)
FR G
[sel_group]../Reconstruction/sel_group ; Defocus group selection file (with particles, avg defocus)
; -------------- END BATCH HEADER ---------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
VM
mkdir -p ../Reconstruction
UD N [mcgraphs] ; Get number of micrographs from defocus file
[sel_micro] ; Micrograph selection doc file (input)
; / MICROGRAPH DEFOCUS DEF.GROUP DEF.GRP.AVG
UD N [numgrps] ; Get number of defocus groups
[defgrps] ; Defocus group selection file (input)
; / DEF.GROUP DEFOCUS
VM
echo ' 'Number of micrographs: {****[mcgraphs]} Defocus groups: {****[numgrps]}
DE ; Remove existing output file.
[sel_group]
; Title for defocus group selection output doc file
SD / GROUP #PARTICLES AVG.DEFOCUS
[sel_group] ; Defocus group selection file (output)
[tot] = 0 ; Total particle counter
DO [key]=1,[numgrps] ; Loop over all defocus groups ----------------------
; Get current defocus group number from defocus group selection file
UD IC [key], [grp],[defocus] ; Get current group number & avg. CTF
[defgrps] ; Defocus group selection file (input)
VM
echo ' '
DE ; Remove any existing output file.
[sel_particles_bygrp] ; Particle selection file
[parts] = 0 ; Zero particle key number for this defocus group
DO [key]=1,[mcgraphs] ; Loop over all micrographs (key not micrograph #) ------
;Regs: MICROGRAPH DEFOCUS DEF.GROUP DEF.GRP.AVG
UD IC [key] ,[mic], [d], [thisgrp] ; Get defocus group number for this micrograph
[sel_micro] ; Micrograph selection doc file (input)
IF ([thisgrp].EQ.[grp]) THEN
; Current micrograph's group is in the current defocus group
IQ FI [exist]
[sel_particles_bymic] ; Images by micrograph selection doc file
IF ([exist].GT.0) THEN
UD N [numparts] ; Get number of images from micrograph's image selection file
[sel_particles_bymic] ; Image selection doc file (input)
; Title for particle selection output doc file
SD / STACKED_PARTICLE_NO. OLD_PARTICLE_NO. GROUP MICROGRAPH
[sel_particles_bygrp]
VM
echo ' 'Group: {****[grp]} Particles: {*****[numparts]} from Micrograph: {****[mic]}
; Loop over all images in this micrograph -----------------------------------
DO [key1]=1,[numparts]
; Key image
UD IC [key1], [img]
[sel_particles_bymic] ; Image selection doc file (input)
[parts] = [parts] + 1
SD [parts], [parts],[img],[grp],[mic]
[sel_particles_bygrp] ; Image selection doc file (output)
ENDDO
UD ICE ; Finished with particles for this micrograph
[sel_particles_bymic] ; Image selection doc file (input)
[tot] = [tot] + [numparts] ; Increment cumulative total particles counter
ELSE
VM
echo ' 'Group: {****[grp]} Particles: 00000 from micrograph: {****[mic]}
ENDIF
ENDIF
ENDDO
SD E ; Finished with doc file output
[sel_particles_bygrp]
UD ICE ; Finished with doc file input
[sel_micro]
; GROUP #PARTICLES AVG.DEFOCUS
SD [key], [grp], [parts], [defocus]
[sel_group] ; Summary file (output)
ENDDO
SD E ; Finished with doc file output
[sel_group]
VM
echo ' ' ; echo ' 'Groups: {****[numgrps]} Total particles: {******[tot]}
VM
echo ' '
EN
;