Tomax

Scripts to find the tilt axis from fiducial markers in tilt series

A C-shell script

#!/bin/tcsh -f

# tomax
# A script to find the approximate tilt axis angle in a tomographic series
# Usage:
#       tomax -angles <start,increment,end> <files>
# Example:
#       tomax -angles 40,1.5,60 "c*.star"
# Author: Bernard Heymann
# 20070209 - 20200326

# Defaults
set ANG = "-90,1,90"

# Recreate command line
echo -n tomax
set a = 1
while ( $a <= $#argv )
	echo -n " $argv[$a]"
	@ a++
end
echo " "

if ( $#argv < 1 ) then
	echo "No input!"
	exit
endif

# Interpret options
set a = 1
while ( "x$argv[$a]" =~ x-* )
#	echo $a $argv[$a]
	if ( "x$argv[$a]" =~ x-ang* ) then
		@ a++
		set ANG = $argv[$a]
	endif
	@ a++
end

set PF = $argv[$a]
set A = `echo $ANG | cut -f1 -d","`
set AI = `echo $ANG | cut -f2 -d","`
set AE = `echo $ANG | cut -f3 -d","`

echo "Tilt axis angle determination:"
echo "-----------------------------"
date
echo "File       = $PF"
echo "Angles     = $ANG"
echo ""
echo Angle Residual

set BRES = 1000.0
set BANG = 0.0

@ C = 1
@ NDN = 1
while ( $NDN )
	set LN = `printf "tomax_%03d.log" $C`
	set CMD = "btrack -v 1 -exclude none -reset -update -track 1 -axis $A -resol 20,1000 -recenter -refine markers $PF"
	echo $CMD > $LN
	$CMD >> $LN
	set RES = `awk '$1=="Average" && $2=="residual" { print $4 }' $LN`
	echo $A $RES
	if ( `echo "$BRES > $RES" | bc` ) then
		set BRES = $RES
		set BANG = $A
	endif
	set A = `echo $A + $AI | bc`
	set NDN = `echo "if ($A <= $AE) { print 1 } else { print 0 }" | bc `
	@ C++
end

echo ""
echo "Best tilt axis angle = $BANG"

A Perl script

#!/usr/bin/perl -w

# tomax.pl
# A script to find the approximate tilt axis angle in a tomographic tilt series
# Usage:
#       tomax.pl --start <angle> --end <angle> --inc <angle> --file file
# Example:
#       tomax.pl --start -30 --end 45 --inc 1.5 --file in.star
# Author: Bernard Heymann
# 20200326

use strict;
use Getopt::Long;

my $pf = "";
my $start = -90;
my $end = 90;
my $inc = 1;

GetOptions ("file=s" => \$pf,		# parameter file
			"start=f" => \$start, 	# starting angle
			"end=f"	=> \$end,		# final angle
			"inc=f"	=> \$inc)		# angular increment
or die("Error in command line arguments\n");

if ( ! -f $pf ) {
	print "Error: File $pf not found!\n";
	exit -1;
}

print "Tilt axis angle determination:\n";
print "-----------------------------\n";
print localtime() . "\n";
print "File       = $pf\n";
print "Angles     = $start,$end,$inc\n";
print "\n";
print "Angle Residual\n";

my $best_angle = 0;
my $best_residual = 1000;

for ( my $a = $start; $a <= $end; $a += $inc ) {
	my $result = `btrack -v 1 -exclude none -reset -update -track 1 -axis $a -resol 20,1000 -recenter -refine markers $pf 2>&1`;
	foreach my $line ( split("\n", $result) ) {
		if ( $line =~ /Average residual = ([\d.e]+)/ ) {
			print "$a\t$1\n";
			if ( $best_residual > $1 ) {
				$best_residual = $1;
				$best_angle = $a;
			}
        }
	}
}

print "\nBest tilt axis angle = $best_angle\n";