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197
scripts/extract_tables.pl
Executable file
197
scripts/extract_tables.pl
Executable file
@ -0,0 +1,197 @@
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#!/usr/bin/env perl
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# This extracts the gnuplot-ready tables from a psdlag analysis
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# and saves them to temporary files. propogate_tables.sh uses this
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# script to create the tables it saves to analyses/tables.
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use utf8;
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use Encode qw(encode decode);
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use feature 'say';
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use locale;
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use Switch;
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use constant PI => 4 * atan2(1, 1);
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# Enables various levels of output.
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our $verbose=0;
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our $debug=0;
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if ($debug) { $verbose=1; }
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# This section locates the output data of interest in a
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# psdlab output file.
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if (!${^UTF8LOCALE}) {
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say encode($charset,"You are not using UTF-8 encoding. :(");
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}
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my $charset=$ENV{LANG};
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# @ARGV[0] takes the echo wavelength for use in filename
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$echo_λ = @ARGV[0];
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# This program attempts to fill function_bin with the tabulated
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# PSDs and time lags.
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our %function_bin = ();
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open $freq_file,'<',"freq.out" or die $!;
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open $ref_psd_file,'<',"ref_psd.out" or die $!;
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open $echo_psd_file,'<',"echo_psd.out" or die $!;
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open $crsspctrm_file,'<',"crsspctrm.out" or die $!;
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open $timelag_file,'<',"timelag.out" or die $!;
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=pod
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This section collects the various quantities.
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=cut
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@bin_bounds = split /\s/,<$freq_file>;
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@ref_psd = split /\s/,<$ref_psd_file>;
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@ref_psd_σ = split /\s/,<$ref_psd_file>;
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@echo_psd = split /\s/,<$echo_psd_file>;
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@echo_psd_σ = split /\s/,<$echo_psd_file>;
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@crsspctrm_psd = split /\s/,<$crsspctrm_file>;
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@crsspctrm_psd_σ = split /\s/,<$crsspctrm_file>;
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@timelag = split /\s/,<$timelag_file>;
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@timelag_σ = split /\s/,<$timelag_file>;
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if ($debug) {
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print encode($charset,"Found bin boundaries: ");
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foreach (@bin_bounds) {print encode($charset,"$_ ");}
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say encode($charset," ");
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}
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my $count = 0;
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my $upper_bound = 0;
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my $lower_bound = 0;
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foreach (@bin_bounds) {
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$lower_bound = $upper_bound;
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$upper_bound = $_;
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if ($lower_bound == 0) {next}
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my $μ = ($upper_bound + $lower_bound)/2;
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my $Δ = ($upper_bound - $lower_bound)/2;
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#say ($μ,":",$Δ);
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# push(@freq_coords_mean,$μ);
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# push(@freq_coords_σ,$Δ);
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$function_bin{$μ} = {"Δ" => $Δ,
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"ref_PSD_μ" => $ref_psd[$count],
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"ref_PSD_σ" => $ref_psd_σ[$count],
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"echo_PSD_μ" => $echo_psd[$count],
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"echo_PSD_σ" => $echo_psd_σ[$count],
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"crsspctrm_μ" => $crosssp_psd[$count],
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"crsspctrm_σ" => $crosssp_psd_σ[$count],
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"timelag_μ" => $timelag[$count],
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"timelag_σ" => $timelag_σ[$count]};
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# $function_bin{$μ}{"φdiff_μ"} = $μ;
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# $function_bin{$μ}{"φdiff_σ"} = $σ;
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# $μ = $μ/(2*PI*$μ);
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# $σ = $σ/(2*PI*$μ);
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$count = $count + 1;
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}
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close $freq_file;
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close $ref_psd_file;
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close $echo_psd_file;
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close $crsspctrm_file;
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close $timelag_file;
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$numbins = keys %function_bin;
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if ($debug) { say encode($charset,
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"$numbins frequency bins captured in output.");
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}
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if($verbose) {
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say encode($charset,"freq μ (lin) freq σ ".
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"ref_PSD_μ ref_PSD_σ ".
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"echo_PSD_μ echo_PSD_σ ".
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"timelag_μ timelag_σ");
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foreach (sort { $a <=> $b } keys %function_bin) {
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say encode($charset,
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sprintf("%f %f %f %f %f ".
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"%f %f %f ",
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$_,
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$function_bin{$_}{"Δ"},
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$function_bin{$_}{"ref_PSD_μ"},
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$function_bin{$_}{"ref_PSD_σ"},
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$function_bin{$_}{"echo_PSD_μ"},
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$function_bin{$_}{"echo_PSD_σ"},
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$function_bin{$_}{"timelag_μ"},
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$function_bin{$_}{"timelag_σ"}
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));
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}
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}
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say encode($charset,"");
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if($debug) {
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while (each %function_bin ) {
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print encode($charset,$_ . ": ");
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while ( my ($key,$value) = each %{$function_bin{$_}} ) {
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print encode($charset,$key . " => " . $value . "; ");
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}
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say encode($charset,"");
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}
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}
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close($outputfile);
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open($datafile,'>',"tmp.refPSD") or die $!;
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while( each %function_bin) {
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say $datafile
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$_ . " " .
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$function_bin{$_}{"ref_PSD_μ"} . " " .
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$function_bin{$_}{"Δ"} . " " .
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$function_bin{$_}{"ref_PSD_σ"};
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}
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close($datafile);
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open($datafile,'>',"tmp.echoPSD") or die $!;
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while( each %function_bin) {
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say $datafile
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$_ . " " .
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$function_bin{$_}{"echo_PSD_μ"} . " " .
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$function_bin{$_}{"Δ"} . " " .
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$function_bin{$_}{"echo_PSD_σ"};
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}
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close($datafile);
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open($datafile,'>',"tmp.crsspctrmPSD") or die $!;
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while( each %function_bin) {
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say $datafile
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$_ . " " .
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$function_bin{$_}{"crsspctrm_PSD_μ"} . " " .
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$function_bin{$_}{"Δ"} . " " .
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$function_bin{$_}{"crsspctrm_PSD_σ"};
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}
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close($datafile);
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open($datafile,'>',"tmp.timelag") or die $!;
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while( each %function_bin) {
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say $datafile
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$_ . " " .
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$function_bin{$_}{"timelag_μ"} . " " .
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$function_bin{$_}{"Δ"} . " " .
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$function_bin{$_}{"timelag_σ"};
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}
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close($datafile);
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#open($datafile,'>',"tmp.echoPSD") or die $!;
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open($datafile,'>',"cackett_psdlag_" . $echo_λ . ".tab") or die $!;
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say $datafile encode($charset,
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sprintf("#freqmin freqmax psd ".
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"psd error lag lag error "
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));
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foreach ( sort {$a <=> $b} keys %function_bin ) {
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say $datafile encode($charset,
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sprintf("%e %e %e %e %e %e",
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($_ - $function_bin{$_}{"Δ"}),
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($_ + $function_bin{$_}{"Δ"})
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));
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}
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close($datafile)
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57
scripts/plot.sh
Executable file
57
scripts/plot.sh
Executable file
@ -0,0 +1,57 @@
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#!/usr/bin/env bash
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# This metascript uses the available plotting scripts to produce a list of
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# document-rady plots.
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# Only analyses with this error type will be represented in the atlas
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errtype=$(cat err_type)
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ref_band="1367Å"
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case $1 in
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"PSD"|"psd"|"PSDs"|"PSDS"|"psds")
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gnuplot_file=psd_atlas.gp
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scripts/propagate_tables.sh
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gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n||g')
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for tabfile in analyses/tables/PSD_*${errtype}*.tab;
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do
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echo_band=$(basename $tabfile|
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sed 's|PSD[_ ]\(.\{5\}\)[_ ]{[^_ ]*}.tab|\1|')
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if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
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gnuplot_input_edit=$(echo "$gnuplot_input"|
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sed "s|%FILE%|$tabfile|"|
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sed "s|%LABEL%|$echo_band|")
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gnuplot_input="${gnuplot_input_edit}"
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done
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echo "$gnuplot_input"|perl -pe 's||\n|g' > ${gnuplot_file}
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gnuplot $gnuplot_file
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;;
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"lags"|"lag"|"delay"|"delays")
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gnuplot_file=timelag_atlas.gp
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gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n||g')
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scripts/propagate_tables.sh
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for tabfile in analyses/tables/timelag_*${errtype}*.tab;
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do
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ref_band_extracted=$(basename $tabfile|sed 's|timelag_\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}.tab|\1|')
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echo_band=$(basename $tabfile|sed 's|timelag_[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}.tab|\1|')
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if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
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gnuplot_input_edit=$(echo "$gnuplot_input"|
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sed "s|%FILE%|$tabfile|"|
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sed "s|%LABEL%|$echo_band|")
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gnuplot_input="${gnuplot_input_edit}"
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done
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echo "$gnuplot_input"|perl -pe 's||\n|g' > ${gnuplot_file}
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gnuplot $gnuplot_file
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;;
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"tophat"|"th")
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mkdir -p analyses/tables/
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scripts/tophat_fft.pl
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gnuplot scripts/templates/tophat_freqdomain.gp
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gnuplot scripts/templates/tophat_timedomain.gp
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;;
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*)
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echo "Did not understand plot type."
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;;
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esac
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76
scripts/plot_psdlag_grid.sh
Normal file
76
scripts/plot_psdlag_grid.sh
Normal file
@ -0,0 +1,76 @@
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#!/usr/bin/env bash
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ywindow_of () {
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max=0
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min=-5
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while read line
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# for line in $(cat $1)
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do
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read xval yval xerr yerr <<< $line
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echo $xval $yval
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if (bc <<< "$yval > $max"); then max=$yval; fi
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if (bc <<< "$yval < $min"); then min=$yval; fi
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# done
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done < $1
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echo $(bc <<< "$min - 0.5") $(bc <<< "$max + 0.5")
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}
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mkdir -p analyses/tables
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mkdir -p analyses/plots
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# Restore the proper naming conventions for any files stripped
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# of their unicode characters.
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scripts/fix_thor_names.sh
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# Create tables and plot the power spectra and time lags.
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for table in analyses/*
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do
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# Grab and determine labels of analyses, skip if over the same band.
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ref_band=$(basename $table|sed 's|\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}|\1|')
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echo_band=$(basename $table|sed 's|[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}|\1|')
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err_str=$(basename $table|sed 's|[^≺]*[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*;\(σ∊[CLM][MFC]\)}|\1|')
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# Prepare files
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echo "Plotting PSD and time lags for $echo_band, referred to ${ref_band}."
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echoPSD_tabfile=analyses/tables/PSD_${echo_band}_\{${err_str}\}.tab
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refPSD_tabfile=analyses/tables/PSD_${ref_band}_\{${err_str}\}.tab
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timelag_tabfile=analyses/tables/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.tab
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PSD_plotfile=analyses/plots/PSD_${echo_band}_\{${err_str}\}.pdf
|
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timelag_plotfile=analyses/plots/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.pdf
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# Output curves to temporary files using perl script, move tables to
|
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# permanent location. This just assumes there are no conflicts.
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scripts/extract_tables.pl $table > /dev/null
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mv tmp.echoPSD $echoPSD_tabfile
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mv tmp.refPSD $refPSD_tabfile
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mv tmp.timelag $timelag_tabfile
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# Plot PSD and save using gnuplot
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# read ymin ymax <<< $(ywindow_of $timelag_tabfile)
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# echo $ymin $ymax
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cat scripts/templates/psd.gp|
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sed "s|%TITLE%|Power Spectrum for Lightcurves $echo_band and $ref_band|"|
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sed "s|%SUBTITLE%|as reported by Fausnaugh et. al, STORM III, 2016|"|
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sed "s|%FILE1%|$echoPSD_tabfile|"|
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sed "s|%LABEL1%|${echo_band}|"|
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#sed "s|%FILE2%|$refPSD_tabfile|"|
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#sed "s|%LABEL2%|${ref_band}|"|
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sed "s|%YMIN%|$ymin|"|sed "s|%YMAX|$ymax|"|
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sed "s|%OUTPUTFILE%|$PSD_plotfile|" > tmp.gp
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gnuplot tmp.gp
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# Plot time lags and save using gnuplot
|
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# read ymin ymax <<< $(ywindow_of $timelag_tabfile)
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cat scripts/templates/timelag.gp|
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sed "s|%TITLE%|Time Lag for Lightcurve $echo_band relative to $ref_band|"|
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sed "s|%SUBTITLE%|as reported by Fausnaugh et. al, STORM III, 2016|"|
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sed "s|%FILE1%|$timelag_tabfile|"|
|
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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.*
|
||||
29
scripts/propagate_tables.sh
Executable file
29
scripts/propagate_tables.sh
Executable file
@ -0,0 +1,29 @@
|
||||
#!/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.*
|
||||
104
scripts/psdlag_4bin.py
Normal file
104
scripts/psdlag_4bin.py
Normal file
@ -0,0 +1,104 @@
|
||||
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
|
||||
|
||||
|
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t2, l2, l2e = np.loadtxt(echo_file).T
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# errorbar(t1, l1, yerr=l1e, fmt='o', color="green")
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# errorbar(t2, l2, yerr=l2e, fmt='o', color="black")
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P2 = clag.clag('psd10r', [t2], [l2], [l2e], dt, fqL)
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p2 = np.ones(nfq)
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p2, p2e = clag.optimize(P2, p2)
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p2, p2e = clag.errors(P2, p2, p2e)
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# xscale('log'); ylim(-6,2)
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# errorbar(fqd, p1, yerr=p1e, fmt='o', ms=10, color="green")
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# errorbar(fqd, p2, yerr=p2e, fmt='o', ms=10, color="black")
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echo_psd = p2
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echo_psd_err = p2e
|
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|
||||
|
||||
|
||||
|
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Cx = clag.clag('cxd10r', [[t1,t2]], [[l1,l2]], [[l1e,l2e]], dt, fqL, p1, p2)
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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])
|
||||
Loading…
Reference in New Issue
Block a user