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caes 2017-06-22 06:10:46 -04:00
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197
scripts/extract_tables.pl Executable file
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#!/usr/bin/env perl
# This extracts the gnuplot-ready tables from a psdlag analysis
# and saves them to temporary files. propogate_tables.sh uses this
# script to create the tables it saves to analyses/tables.
use utf8;
use Encode qw(encode decode);
use feature 'say';
use locale;
use Switch;
use constant PI => 4 * atan2(1, 1);
# Enables various levels of output.
our $verbose=0;
our $debug=0;
if ($debug) { $verbose=1; }
# This section locates the output data of interest in a
# psdlab output file.
if (!${^UTF8LOCALE}) {
say encode($charset,"You are not using UTF-8 encoding. :(");
}
my $charset=$ENV{LANG};
# @ARGV[0] takes the echo wavelength for use in filename
$echo_λ = @ARGV[0];
# This program attempts to fill function_bin with the tabulated
# PSDs and time lags.
our %function_bin = ();
open $freq_file,'<',"freq.out" or die $!;
open $ref_psd_file,'<',"ref_psd.out" or die $!;
open $echo_psd_file,'<',"echo_psd.out" or die $!;
open $crsspctrm_file,'<',"crsspctrm.out" or die $!;
open $timelag_file,'<',"timelag.out" or die $!;
=pod
This section collects the various quantities.
=cut
@bin_bounds = split /\s/,<$freq_file>;
@ref_psd = split /\s/,<$ref_psd_file>;
@ref_psd_σ = split /\s/,<$ref_psd_file>;
@echo_psd = split /\s/,<$echo_psd_file>;
@echo_psd_σ = split /\s/,<$echo_psd_file>;
@crsspctrm_psd = split /\s/,<$crsspctrm_file>;
@crsspctrm_psd_σ = split /\s/,<$crsspctrm_file>;
@timelag = split /\s/,<$timelag_file>;
@timelag_σ = split /\s/,<$timelag_file>;
if ($debug) {
print encode($charset,"Found bin boundaries: ");
foreach (@bin_bounds) {print encode($charset,"$_ ");}
say encode($charset," ");
}
my $count = 0;
my $upper_bound = 0;
my $lower_bound = 0;
foreach (@bin_bounds) {
$lower_bound = $upper_bound;
$upper_bound = $_;
if ($lower_bound == 0) {next}
my $μ = ($upper_bound + $lower_bound)/2;
my $Δ = ($upper_bound - $lower_bound)/2;
#say ($μ,":",$Δ);
# push(@freq_coords_mean,$μ);
# push(@freq_coords_σ,$Δ);
$function_bin{$μ} = {"Δ" => $Δ,
"ref_PSD_μ" => $ref_psd[$count],
"ref_PSD_σ" => $ref_psd_σ[$count],
"echo_PSD_μ" => $echo_psd[$count],
"echo_PSD_σ" => $echo_psd_σ[$count],
"crsspctrm_μ" => $crosssp_psd[$count],
"crsspctrm_σ" => $crosssp_psd_σ[$count],
"timelag_μ" => $timelag[$count],
"timelag_σ" => $timelag_σ[$count]};
# $function_bin{$μ}{"φdiff_μ"} = $μ;
# $function_bin{$μ}{"φdiff_σ"} = $σ;
# $μ = $μ/(2*PI*$μ);
# $σ = $σ/(2*PI*$μ);
$count = $count + 1;
}
close $freq_file;
close $ref_psd_file;
close $echo_psd_file;
close $crsspctrm_file;
close $timelag_file;
$numbins = keys %function_bin;
if ($debug) { say encode($charset,
"$numbins frequency bins captured in output.");
}
if($verbose) {
say encode($charset,"freq μ (lin) freq σ ".
"ref_PSD_μ ref_PSD_σ ".
"echo_PSD_μ echo_PSD_σ ".
"timelag_μ timelag_σ");
foreach (sort { $a <=> $b } keys %function_bin) {
say encode($charset,
sprintf("%f %f %f %f %f ".
"%f %f %f ",
$_,
$function_bin{$_}{"Δ"},
$function_bin{$_}{"ref_PSD_μ"},
$function_bin{$_}{"ref_PSD_σ"},
$function_bin{$_}{"echo_PSD_μ"},
$function_bin{$_}{"echo_PSD_σ"},
$function_bin{$_}{"timelag_μ"},
$function_bin{$_}{"timelag_σ"}
));
}
}
say encode($charset,"");
if($debug) {
while (each %function_bin ) {
print encode($charset,$_ . ": ");
while ( my ($key,$value) = each %{$function_bin{$_}} ) {
print encode($charset,$key . " => " . $value . "; ");
}
say encode($charset,"");
}
}
close($outputfile);
open($datafile,'>',"tmp.refPSD") or die $!;
while( each %function_bin) {
say $datafile
$_ . " " .
$function_bin{$_}{"ref_PSD_μ"} . " " .
$function_bin{$_}{"Δ"} . " " .
$function_bin{$_}{"ref_PSD_σ"};
}
close($datafile);
open($datafile,'>',"tmp.echoPSD") or die $!;
while( each %function_bin) {
say $datafile
$_ . " " .
$function_bin{$_}{"echo_PSD_μ"} . " " .
$function_bin{$_}{"Δ"} . " " .
$function_bin{$_}{"echo_PSD_σ"};
}
close($datafile);
open($datafile,'>',"tmp.crsspctrmPSD") or die $!;
while( each %function_bin) {
say $datafile
$_ . " " .
$function_bin{$_}{"crsspctrm_PSD_μ"} . " " .
$function_bin{$_}{"Δ"} . " " .
$function_bin{$_}{"crsspctrm_PSD_σ"};
}
close($datafile);
open($datafile,'>',"tmp.timelag") or die $!;
while( each %function_bin) {
say $datafile
$_ . " " .
$function_bin{$_}{"timelag_μ"} . " " .
$function_bin{$_}{"Δ"} . " " .
$function_bin{$_}{"timelag_σ"};
}
close($datafile);
#open($datafile,'>',"tmp.echoPSD") or die $!;
open($datafile,'>',"cackett_psdlag_" . $echo_λ . ".tab") or die $!;
say $datafile encode($charset,
sprintf("#freqmin freqmax psd ".
"psd error lag lag error "
));
foreach ( sort {$a <=> $b} keys %function_bin ) {
say $datafile encode($charset,
sprintf("%e %e %e %e %e %e",
($_ - $function_bin{$_}{"Δ"}),
($_ + $function_bin{$_}{"Δ"})
));
}
close($datafile)

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scripts/plot.sh Executable file
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#!/usr/bin/env bash
# This metascript uses the available plotting scripts to produce a list of
# document-rady plots.
# Only analyses with this error type will be represented in the atlas
errtype=$(cat err_type)
ref_band="1367Å"
case $1 in
"PSD"|"psd"|"PSDs"|"PSDS"|"psds")
gnuplot_file=psd_atlas.gp
scripts/propagate_tables.sh
gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
for tabfile in analyses/tables/PSD_*${errtype}*.tab;
do
echo_band=$(basename $tabfile|
sed 's|PSD[_ ]\(.\{5\}\)[_ ]{[^_ ]*}.tab|\1|')
if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
gnuplot_input_edit=$(echo "$gnuplot_input"|
sed "s|%FILE%|$tabfile|"|
sed "s|%LABEL%|$echo_band|")
gnuplot_input="${gnuplot_input_edit}"
done
echo "$gnuplot_input"|perl -pe 's|␤|\n|g' > ${gnuplot_file}
gnuplot $gnuplot_file
;;
"lags"|"lag"|"delay"|"delays")
gnuplot_file=timelag_atlas.gp
gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
scripts/propagate_tables.sh
for tabfile in analyses/tables/timelag_*${errtype}*.tab;
do
ref_band_extracted=$(basename $tabfile|sed 's|timelag_\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}.tab|\1|')
echo_band=$(basename $tabfile|sed 's|timelag_[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}.tab|\1|')
if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
gnuplot_input_edit=$(echo "$gnuplot_input"|
sed "s|%FILE%|$tabfile|"|
sed "s|%LABEL%|$echo_band|")
gnuplot_input="${gnuplot_input_edit}"
done
echo "$gnuplot_input"|perl -pe 's|␤|\n|g' > ${gnuplot_file}
gnuplot $gnuplot_file
;;
"tophat"|"th")
mkdir -p analyses/tables/
scripts/tophat_fft.pl
gnuplot scripts/templates/tophat_freqdomain.gp
gnuplot scripts/templates/tophat_timedomain.gp
;;
*)
echo "Did not understand plot type."
;;
esac

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scripts/plot_psdlag_grid.sh Normal file
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#!/usr/bin/env bash
ywindow_of () {
max=0
min=-5
while read line
# for line in $(cat $1)
do
read xval yval xerr yerr <<< $line
echo $xval $yval
if (bc <<< "$yval > $max"); then max=$yval; fi
if (bc <<< "$yval < $min"); then min=$yval; fi
# done
done < $1
echo $(bc <<< "$min - 0.5") $(bc <<< "$max + 0.5")
}
mkdir -p analyses/tables
mkdir -p analyses/plots
# Restore the proper naming conventions for any files stripped
# of their unicode characters.
scripts/fix_thor_names.sh
# Create tables and plot the power spectra and time lags.
for table in analyses/*
do
# Grab and determine labels of analyses, skip if over the same band.
ref_band=$(basename $table|sed 's|\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}|\1|')
echo_band=$(basename $table|sed 's|[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}|\1|')
err_str=$(basename $table|sed 's|[^≺]*[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*;\(σ∊[CLM][MFC]\)}|\1|')
# Prepare files
echo "Plotting PSD and time lags for $echo_band, referred to ${ref_band}."
echoPSD_tabfile=analyses/tables/PSD_${echo_band}_\{${err_str}\}.tab
refPSD_tabfile=analyses/tables/PSD_${ref_band}_\{${err_str}\}.tab
timelag_tabfile=analyses/tables/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.tab
PSD_plotfile=analyses/plots/PSD_${echo_band}_\{${err_str}\}.pdf
timelag_plotfile=analyses/plots/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.pdf
# Output curves to temporary files using perl script, move tables to
# permanent location. This just assumes there are no conflicts.
scripts/extract_tables.pl $table > /dev/null
mv tmp.echoPSD $echoPSD_tabfile
mv tmp.refPSD $refPSD_tabfile
mv tmp.timelag $timelag_tabfile
# Plot PSD and save using gnuplot
# read ymin ymax <<< $(ywindow_of $timelag_tabfile)
# echo $ymin $ymax
cat scripts/templates/psd.gp|
sed "s|%TITLE%|Power Spectrum for Lightcurves $echo_band and $ref_band|"|
sed "s|%SUBTITLE%|as reported by Fausnaugh et. al, STORM III, 2016|"|
sed "s|%FILE1%|$echoPSD_tabfile|"|
sed "s|%LABEL1%|${echo_band}|"|
#sed "s|%FILE2%|$refPSD_tabfile|"|
#sed "s|%LABEL2%|${ref_band}|"|
sed "s|%YMIN%|$ymin|"|sed "s|%YMAX|$ymax|"|
sed "s|%OUTPUTFILE%|$PSD_plotfile|" > tmp.gp
gnuplot tmp.gp
# Plot time lags and save using gnuplot
# read ymin ymax <<< $(ywindow_of $timelag_tabfile)
cat scripts/templates/timelag.gp|
sed "s|%TITLE%|Time Lag for Lightcurve $echo_band relative to $ref_band|"|
sed "s|%SUBTITLE%|as reported by Fausnaugh et. al, STORM III, 2016|"|
sed "s|%FILE1%|$timelag_tabfile|"|
sed "s|%LABEL1%|${echo_band}|"|
sed "s|%YMIN%|$ymin|"|sed "s|%YMAX|$ymax|"|
sed "s|%OUTPUTFILE%|$timelag_plotfile|" > tmp.gp
gnuplot tmp.gp
done
rm tmp.*

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scripts/propagate_tables.sh Executable file
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#!/usr/bin/env bash
mkdir -p data
ref_band="1367A"
for lightcurve in data/lc/*.lc
do
echo_band=$(basename $lightcurve|sed 's|[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}|\1|')
if [[ $ref_band == $echo_band ]]; then continue; fi
err_str=$(basename $lightcurve|sed 's|[^≺]*[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*;\(σ∊[CLM][MFC]\)}|\1|')
echo "Tabling PSD and time lags referred to ${ref_band} for $echo_band{${err_str}}."
# Propagate tables into analyses/tables
echoPSD_tabfile=analyses/tables/PSD_${echo_band}_\{${err_str}\}.tab
refPSD_tabfile=analyses/tables/PSD_${ref_band}_\{${err_str}\}.tab
timelag_tabfile=analyses/tables/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.tab
# Output curves to temporary files using perl script, move tables to
# permanent location. This just assumes there are no conflicts.
scripts/extract_tables.pl $lightcurve > /dev/null
mv tmp.echoPSD $echoPSD_tabfile
mv tmp.refPSD $refPSD_tabfile
mv tmp.timelag $timelag_tabfile
done
rm tmp.*

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scripts/psdlag_4bin.py Normal file
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import numpy as np
from scipy.stats import norm
from scipy.stats import lognorm
import sys
import getopt
sys.path.insert(1,"/usr/local/science/clag-agn/data/")
import clag
import matplotlib
# %pylab inline
ref_file="data/lc/1367A.lc"
echo_file="data/lc/2246A.lc"
#ref_file = str(sys.argv[1])
#echo_file = str(sys.argv[2])
dt = 0.01
t1, l1, l1e = np.loadtxt(ref_file).T
# errorbar(t1, l1, yerr=l1e, fmt='o')
fqL = np.array([0.0049999999, 0.018619375, 0.044733049, 0.069336227, 0.10747115, 0.16658029,
0.25819945, 0.40020915, 0.62032418])
fqL = np.array([0.0049999999, 0.044733049, 0.10747115,
0.25819945, 0.62032418])
fqL = np.array([0.0049999999, 0.018619375, 0.069336227, 0.10747115, 0.62032418])
fqL = np.logspace(np.log10(0.005),np.log10(0.6),5)
nfq = len(fqL) - 1
fqd = 10**(np.log10( (fqL[:-1]*fqL[1:]) )/2.)
P1 = clag.clag('psd10r', [t1], [l1], [l1e], dt, fqL)
p1 = np.ones(nfq)
p1, p1e = clag.optimize(P1, p1)
p1, p1e = clag.errors(P1, p1, p1e)
# xscale('log'); ylim(-4,2)
# errorbar(fqd, p1, yerr=p1e, fmt='o', ms=10, color="black")
ref_psd = p1
ref_psd_err = p1e
t2, l2, l2e = np.loadtxt(echo_file).T
# errorbar(t1, l1, yerr=l1e, fmt='o', color="green")
# errorbar(t2, l2, yerr=l2e, fmt='o', color="black")
P2 = clag.clag('psd10r', [t2], [l2], [l2e], dt, fqL)
p2 = np.ones(nfq)
p2, p2e = clag.optimize(P2, p2)
p2, p2e = clag.errors(P2, p2, p2e)
# xscale('log'); ylim(-6,2)
# errorbar(fqd, p1, yerr=p1e, fmt='o', ms=10, color="green")
# errorbar(fqd, p2, yerr=p2e, fmt='o', ms=10, color="black")
echo_psd = p2
echo_psd_err = p2e
Cx = clag.clag('cxd10r', [[t1,t2]], [[l1,l2]], [[l1e,l2e]], dt, fqL, p1, p2)
p = np.concatenate( ((p1+p2)*0.5-0.3,p1*0+0.1) ) # a good starting point generally
p, pe = clag.optimize(Cx, p)
phi, phie = p[nfq:], pe[nfq:]
lag, lage = phi/(2*np.pi*fqd), phie/(2*np.pi*fqd)
cx, cxe = p[:nfq], pe[:nfq]
cross_spectrm = cx
cross_spectrm_err = cxe
# xscale('log'); ylim(-2,1)
# errorbar(fqd, lag, yerr=lage, fmt='o', ms=10,color="black")
s, loc, scale = lognorm.fit(lag,loc=.01)
# xscale('log'); ylim(-4,1.5)
# errorbar(fqd, lag, yerr=lage, fmt='o', ms=10,color="black")
##plot(fqd,norm.pdf(fqd,mu,sigma))
#plot(fqd,lognorm.pdf(fqd,s,loc,scale))
# mu,sigma
#plot(ifft(lag))
np.savetxt("freq.out",fqL.reshape((-1,len(fqL))))
np.savetxt("ref_psd.out",[ref_psd,ref_psd_err])
np.savetxt("echo_psd.out",[echo_psd,echo_psd_err])
np.savetxt("crsspctrm.out",[cross_spectrm,cross_spectrm_err])
np.savetxt("timelag.out",[lag,lage])