Create O2 tag

git-svn-id: https://svn.ligo.caltech.edu/svn/bayeswave/tags/O2@609 c56465c9-8126-4a4f-9d7d-ac845eff4865

postprocess/BWBweb.css

+body {
+    font: 90% Lucida Sans;
+    margin: 20px;
+    line-height: 26px;
+}
+
+.container {
+    min-width: 1220px;
+}
+
+.wrapper {
+    position: relative;
+    overflow: auto;
+}
+
+/*#top, #sidebar, #bottom, .menuitem { */
+#top, #bottom, .menuitem {
+    border-radius: 4px;
+    margin: 4px;
+}
+
+#top {
+    background-color: #71B09F;
+    color: #ffffff;
+    border: 1px solid #374040;
+    padding: 15px;
+}
+
+#menubar {
+    width: 200px;
+    float: left
+}
+
+#main {
+    padding: 10px;
+    margin: 0 210px;
+    /*padding-right: 0px;
+    margin-right: 0px;*/
+    min-width: 1010px;
+}
+
+/* #sidebar {
+    background-color: #32a4e7;
+    color: #ffffff;
+    padding: 10px;
+    width: 180px;
+    bottom: 0;
+    top: 0;
+    right: 0;
+    position: absolute;
+} */
+
+#bottom {
+    border: 1px solid #d4d4d4;
+    background-color: #f1f1f1;
+    text-align: center;
+    padding: 10px;
+    font-size: 70%;
+    line-height: 14px;
+}
+
+#top h1, #top p, #menulist {
+    margin: 0;
+    padding: 0;
+}
+
+.menuitem {
+    background-color: #B1C7C7;
+    border: 1px solid #333333;
+    list-style-type: none;
+    padding: 2px;
+    cursor: pointer;
+}
+
+.menuitem:hover {
+  background-color: #7A8787;
+}
+
+a {
+    color: #000000;
+    text-decoration: underline;
+}
+
+a:hover {
+    text-decoration: none;
+}
+
+table {
+    width:100%;
+}
+table, th, td {
+    border: 1px solid #333333;
+    border-collapse: collapse;
+}
+th, td {
+    padding: 5px;
+    text-align: left;
+}
+table#tab1 tr:nth-child(even) {
+    background-color: #d4d4d4;
+}
+table#tab1 tr:nth-child(odd) {
+   background-color:#fff;
+}
+table#tab1 th {
+    background-color: #71B09F;
+    color: white;
+}

postprocess/bayestar_bin_samples

+#!/usr/bin/python
+#
+# Copyright (C) 2011  Leo Singer
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+"""
+Convert a list of posterior samples to a HEALPix FITS image using an adaptively
+refined HEALPix tree, subdividing each node if it contains more than
+--samples-per-bin posterior samples. By default, the resolution is set to the
+deepest resolution of the tree.
+
+If an input filename is specified, then the posterior samples are read from it.
+If no input filename is provided, then input is read from stdin.
+"""
+__author__ = "Leo Singer <leo.singer@ligo.org>"
+
+
+# Command line interface
+
+from optparse import Option, OptionParser
+from lalinference.bayestar import command
+parser = OptionParser(
+    formatter=command.NewlinePreservingHelpFormatter(),
+    description = __doc__,
+    usage = "%prog [options] [INPUT] -o OUTPUT.fits[.gz]",
+    option_list = [
+        Option("--nside", "-n", type=int, default=-1,
+            help="HEALPix lateral resolution [default: auto]"),
+        Option("-o", "--output", metavar="OUTPUT.fits[.gz]",
+            help="name of output FITS file [required]"),
+        Option("--samples-per-bin", type=int, default=30,
+            help="Samples per bin [default: %default]"),
+        Option("--objid",
+            help="Event ID to be stored in FITS header [default: %default]"),
+    ]
+)
+opts, args = parser.parse_args()
+infilename = command.get_input_filename(parser, args)
+
+if opts.output is None:
+    parser.error('--output: missing required argument')
+
+
+# Late imports.
+import matplotlib as mpl
+mpl.use('Agg')
+import numpy as np
+import healpy as hp
+import lalinference.bayestar.fits
+import lalinference.bayestar.postprocess
+import pylal.bayespputils
+
+# --- Read input file
+samples = np.recfromtxt(infilename, names=True)
+
+# -- Undo sin(dec)
+phi = samples['ra']
+dec = np.arcsin(samples['sin_dec'])
+theta = 0.5*np.pi - dec
+
+
+p = lalinference.bayestar.postprocess.adaptive_healpix_histogram(
+    theta, phi, opts.samples_per_bin, nside=opts.nside)
+
+# Write output to FITS file.
+lalinference.bayestar.fits.write_sky_map(opts.output, p,
+    creator=parser.get_prog_name(), objid=opts.objid)

postprocess/bayestar_plot_allsky

+#!/usr/bin/python
+#
+# Copyright (C) 2011  Leo Singer
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+"""
+Plot an all-sky map on a Mollweide projection.
+By default, plot in celestial coordinates (RA, Dec).
+
+To plot in geographic coordinates (longitude, latitude) with major
+coastlines overlaid, provide the --geo flag.
+
+Public-domain cartographic data is courtesy of Natural Earth
+(http://www.naturalearthdata.com) and processed with MapShaper
+(http://www.mapshaper.org).
+"""
+__author__ = "Leo Singer <leo.singer@ligo.org>"
+
+
+# Command line interface
+
+from optparse import Option, OptionParser
+from lalinference.bayestar import command
+from matplotlib import cm
+colormap_choices = sorted(cm.cmap_d.keys())
+parser = OptionParser(
+    description = __doc__,
+    usage = "%prog [options] [INPUT]",
+    option_list = [
+        Option("-o", "--output", metavar="FILE.{pdf,png}",
+            help="name of output file [default: plot to screen]"),
+        Option("--colormap", default="jet", choices=colormap_choices,
+            metavar='|'.join(colormap_choices),
+            help="name of matplotlib colormap [default: %default]"),
+        Option("--figure-width", metavar="INCHES", type=float, default=8.,
+            help="width of figure in inches [default: %default]"),
+        Option("--figure-height", metavar="INCHES", type=float, default=6.,
+            help="height of figure in inches [default: %default]"),
+        Option("--dpi", metavar="PIXELS", type=int, default=300,
+            help="resolution of figure in dots per inch [default: %default]"),
+        Option("--contour", metavar="PERCENT", type=float, action="append",
+            default=[], help="plot contour enclosing this percentage of"
+            + " probability mass [may be specified multiple times, default: none]"),
+        Option("--radec", nargs=2, metavar="RA Dec", type=float, action="append",
+            default=[], help="right ascension (deg) and declination (deg) to mark"
+            + " [may be specified multiple times, default: none]"),
+        Option("--geo", action="store_true", default=False,
+            help="Plot in geographic coordinates, (lat, lon) instead of (RA, Dec) [default: %default]")
+    ]
+)
+opts, args = parser.parse_args()
+infilename = command.get_input_filename(parser, args)
+
+# Late imports
+
+# Choose a matplotlib backend that is suitable for headless
+# rendering if output to file is requested
+import matplotlib
+if opts.output is not None:
+    matplotlib.use('agg')
+
+import os
+import json
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import rcParams
+import healpy as hp
+import lal
+from lalinference.bayestar import fits
+from lalinference.bayestar import plot
+
+fig = plt.figure(figsize=(opts.figure_width, opts.figure_height), frameon=False)
+ax = plt.subplot(111,
+    projection='mollweide' if opts.geo else 'astro mollweide')
+ax.cla()
+ax.grid()
+
+skymap, metadata = fits.read_sky_map(infilename)
+nside = hp.npix2nside(len(skymap))
+
+if opts.geo:
+    dlon = -lal.GreenwichMeanSiderealTime(lal.LIGOTimeGPS(metadata['gps_time'])) % (2*np.pi)
+else:
+    dlon = 0
+
+# Convert sky map from probability to probability per square degree.
+probperdeg2 = skymap / hp.nside2pixarea(nside, degrees=True)
+
+# Plot sky map.
+vmax = probperdeg2.max()
+plot.healpix_heatmap(probperdeg2, dlon=dlon,
+    vmin=0., vmax=vmax, cmap=plt.get_cmap(opts.colormap))
+
+# Plot colorbar.
+cb = plot.colorbar(vmax)
+
+# -- KLUDGE Jonah is trying to clean up junk under color bar
+etick = "{0:.1e}".format(vmax)
+# cb.ax.set_xticklabels(['0','','','','', etick])
+cb.set_ticks([0,vmax])
+cb.set_ticklabels(['0', etick])
+
+ 
+# Set colorbar label.
+cb.set_label(r'prob. per sq. deg')
+
+# Add contours.
+if opts.contour:
+    indices = np.argsort(-skymap)
+    region = np.empty(skymap.shape)
+    region[indices] = 100 * np.cumsum(skymap[indices])
+    cs = plot.healpix_contour(region, dlon=dlon,
+        colors='k', linewidths=0.5, levels=opts.contour)
+    fmt = r'%g\%%' if rcParams['text.usetex'] else '%g%%'
+    plt.clabel(cs, fmt=fmt, fontsize=6, inline=True)
+
+if opts.geo:
+    geojson_filename = os.path.join(os.path.dirname(plot.__file__),
+        'ne_simplified_coastline.json')
+    with open(geojson_filename, 'r') as geojson_file:
+        geojson = json.load(geojson_file)
+    for shape in geojson['geometries']:
+        verts = np.deg2rad(shape['coordinates'])
+        plt.plot(verts[:, 0], verts[:, 1], color='black', linewidth=1, alpha=0.5)
+
+# Add markers (e.g., for injections or external triggers).
+for ra, dec in np.deg2rad(opts.radec):
+    # Convert the right ascension to either a reference angle from -pi to pi
+    # or a wrapped angle from 0 to 2 pi, depending on the version of Matplotlib.
+    # FIXME: Remove this after all Matplotlib monkeypatches are obsolete.
+    if opts.geo or plot.mpl_version < '1.2.0':
+        ra = plot.reference_angle(ra + dlon)
+    else:
+        ra = plot.wrapped_angle(ra + dlon)
+    ax.plot(ra, dec, '*', markerfacecolor='white', markeredgecolor='black', markersize=10)
+
+# If we are using a new enough version of matplotlib, then
+# add a white outline to all text to make it stand out from the background.
+plot.outline_text(ax)
+
+fig.patch.set_alpha(0.)
+ax.patch.set_alpha(0.)
+ax.set_alpha(0.)
+
+if opts.output is None:
+    plt.show()
+else:
+    plt.savefig(opts.output, dpi=opts.dpi)

postprocess/make_pec_webpage.sh

+#!/bin/bash
+
+# Get path of BayesWaveBurst to figure out where the postprocessing scripts are
+pathtoBWB=$(which BayesWaveBurst)
+# The argument for this script is the path to the job we want to analyze
+dirname=$1
+# The user may provide the sky-location (right ascension "ra" and declination "dec") of an injected
+# signal, a request to compute matches between injected and reconsturcted signals, none of the above,
+# or all of the above
+echo
+if [ "$#" -eq 3 ] ; then
+    echo "You requested to display the sky location of the injections"
+    ra=$2
+    dec=$3
+fi
+if [ "$#" -eq 2 ] ; then
+    echo "You provided an MDC log file"
+    mdc=$2
+fi
+
+if [ -s "$pathtoBWB" ] ; then
+    pathtoBWB=${pathtoBWB%src*}
+    echo
+    echo "Entering $dirname ..."
+    cd $dirname
+    MDC="$(grep MDC *bayeswave.run)"
+    inj="$(grep \\.xml *bayeswave.run)"
+    echo
+    echo " * Running skymap..."
+    if [ ${#MDC} -ne "0" -o ${#inj} -ne "0" ] ; then
+    	#$pathtoBWB/postprocess/run_skymap.sh $ra $dec
+        if [ "$#" -eq 3 ] ; then
+    	    python $pathtoBWB/postprocess/skymap/megasky.py --ra=$ra --dec=$dec
+        elif [ "$#" -eq 2 ] ; then
+    	    python $pathtoBWB/postprocess/skymap/megasky.py --mdc=$mdc
+        else
+            echo "   Failed to generate skymap!"
+        fi
+    else
+        python $pathtoBWB/postprocess/skymap/megasky.py
+    fi
+    echo
+    echo " * Running megaplot..."
+    python -W ignore $pathtoBWB/postprocess/megaplot.py
+    #echo
+    #echo " * Running plot_evidence..."
+    #python -W ignore $pathtoBWB/postprocess/plot_evidence.py
+    #echo
+    #echo " * Running skyview..."
+    #export PYTHONPATH=$PYTHONPATH:$pathtoBWB/postprocess/skymap:/home/jkanner/lib64/python:/home/jkanner/lib/python:$pathtoBWB/postprocess/s6
+    #python -W ignore $pathtoBWB/postprocess/skyview.py
+    echo
+    echo " * Compressing analyzed data..."
+    #tar -cf waveforms.tar waveforms
+    #tar -cf chains.tar chains
+    #tar -cf snr.tar *snr
+    cd ..
+    echo
+    echo " * ...DONE!"
+    echo
+    echo
+    echo
+    echo "To move the postprocessing results in order to make them visible. Run:"
+    echo "rsync -av --progress <path to this directory> <path to the desired directory in the public_html> --exclude '*/*snr' --exclude '*/waveforms' --exclude '*/chains' --exclude '*/post' --include='*/' --include='*html' --include '*/html/*'  --include '*/plots/*' --include '*/tables/*' --include condorOut*txt --include *bayeswave.run --exclude='*'"
+    echo
+    echo
+else
+    echo "Make sure the BayesWaveBurst command is in your path before running this script!"
+fi

postprocess/many_plots.sh

+#!/bin/bash
+
+# Get path of BayesWaveBurst to figure out where the postprocessing scripts are
+pathtoBWB=$(which BayesWaveBurst)
+
+if [ -s "$pathtoBWB" ] ; then
+    pathtoBWB=${pathtoBWB%src*}
+    fulldirname="$(pwd)"
+    for dirname in $fulldirname/job*; do
+        echo
+        echo "Entering $dirname ..."
+        cd $dirname
+        MDC="$(grep MDC *bayeswave.run)"
+        if [ ${#MDC} -ne "0" ]
+        then
+            echo
+            echo " * Running plot_waveform..."
+            python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=True
+            #python -W ignore /home/francesco.pannarale/scripts/BayesWaveTools/plot_waveform.py --mdc=True
+            echo
+            echo " * Running plot_evidence..."
+            
+        else
+            echo
+            echo " * Running plot_waveform..."
+            python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=False
+            #python -W ignore /home/francesco.pannarale/scripts/BayesWaveTools/plot_waveform.py --mdc=False
+        fi
+        echo
+        echo " * Running skymap..."
+        $pathtoBWB/postprocess/run_skymap.sh
+        echo
+        echo " * Compressing analyzed data..."
+        tar -cf waveforms.tar waveforms
+        tar -cf chains.tar chains
+        tar -cf snr.tar *snr
+        cd ..
+        echo
+        echo " * ...DONE!"
+        echo
+    done
+    echo
+    echo
+    echo "To move the postprocessing results in order to make them visible. Run:"
+    echo "  rsync -av --progress <path to this directory> <path to the desired directory in the public_html>  --exclude '*/*snr' --exclude '*/waveforms' --exclude '*/chains' --exclude '*/post' --include='*/' --include '*html' --include '*png' --include condorOut_BWB.txt --exclude='*'"
+    echo
+    echo
+else
+    echo "Make sure the BayesWaveBurst command is in your path before running this script!"
+fi

postprocess/many_plots_1job.sh

+#!/bin/bash
+
+# Get path of BayesWaveBurst to figure out where the postprocessing scripts are
+pathtoBWB=$(which BayesWaveBurst)
+# The argument for this script is the path to the job we want to analyze
+dirname=$1
+# The user may provide the sky-location (right ascension "ra" and declination "dec") of an injected
+# signal, a request to compute matches between injected and reconsturcted signals, none of the above,
+# or all of the above
+echo
+if [ "$#" -eq 2 ] ; then
+    echo "You requested to display matches and injected signals"
+    match=$2
+fi
+if [ "$#" -eq 3 ] ; then
+    echo "You requested to display the sky location of the injections"
+    ra=$2
+    dec=$3
+fi
+if [ "$#" -eq 4 ] ; then
+    echo "You requested to display matches, injected signals, and the sky location of the injections"
+    ra=$2
+    dec=$3
+    match=$4
+fi
+
+if [ -s "$pathtoBWB" ] ; then
+    pathtoBWB=${pathtoBWB%src*}
+    echo
+    echo "Entering $dirname ..."
+    cd $dirname
+    MDC="$(grep MDC *bayeswave.run)"
+    if [ ${#MDC} -ne "0" ] ; then
+        echo
+        echo " * Running plot_waveform..."
+	if [ "$match" = "True" ]; then
+            python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=True --match=True
+	else
+	    python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=True
+	fi
+        #echo
+        #echo " * Running plot_evidence..."
+	#python -W ignore $pathtoBWB/postprocess/plot_evidence.py
+    else
+        echo
+        echo " * Running plot_waveform..."
+	if [ "$match" = "True" ]; then
+	    python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=False --match=True
+	else
+            python -W ignore $pathtoBWB/postprocess/plot_waveform.py --mdc=False
+	fi
+        #echo
+        #echo " * Running plot_evidence..."
+	#python -W ignore $pathtoBWB/postprocess/plot_evidence.py
+    fi
+    echo
+    echo " * Running skymap..."
+    $pathtoBWB/postprocess/run_skymap.sh $ra $dec
+    echo
+    echo " * Compressing analyzed data..."
+    tar -cf waveforms.tar waveforms
+    tar -cf chains.tar chains
+    tar -cf snr.tar *snr
+    cd ..
+    echo
+    echo " * ...DONE!"
+    echo
+    echo
+    echo
+    echo "To move the postprocessing results in order to make them visible. Run:"
+    echo "  rsync -av --progress <path to this directory> <path to the desired directory in the public_html>  --exclude '*/*snr' --exclude '*/waveforms' --exclude '*/chains' --exclude '*/post' --include='*/' --include '*html' --include '*png' --include condorOut_BWB.txt --exclude='*'"
+    echo
+    echo
+else
+    echo "Make sure the BayesWaveBurst command is in your path before running this script!"
+fi

postprocess/navigate.js

+$(document).ready(function(){
+    $("#summary").click(function(){
+    $("#main").load("./html/summary.html");
+  });
+});
+$(document).ready(function(){
+  $("#timedomain").click(function(){
+    $("#main").load("./html/timedomain.html");
+  });
+});
+$(document).ready(function(){
+  $("#freqdomain").click(function(){
+    $("#main").load("./html/freqdomain.html");
+  });
+});
+$(document).ready(function(){
+  $("#timefreq").click(function(){
+    $("#main").load("./html/timefreq.html");
+  });
+});
+$(document).ready(function(){
+    $("#overlap").click(function(){
+    $("#main").load("./html/overlap.html");
+  });
+});
+$(document).ready(function(){
+    $("#energy").click(function(){
+    $("#main").load("./html/energy.html");
+  });
+});
+$(document).ready(function(){
+    $("#t0").click(function(){
+    $("#main").load("./html/t0.html");
+  });
+});
+$(document).ready(function(){
+    $("#duration").click(function(){
+    $("#main").load("./html/duration.html");
+  });
+});
+$(document).ready(function(){
+    $("#f0").click(function(){
+    $("#main").load("./html/f0.html");
+  });
+});
+$(document).ready(function(){
+    $("#band").click(function(){
+    $("#main").load("./html/band.html");
+  });
+});
+$(document).ready(function(){
+    $("#hmax").click(function(){
+    $("#main").load("./html/hmax.html");
+  });
+});
+$(document).ready(function(){
+    $("#t_at_hmax").click(function(){
+    $("#main").load("./html/t_at_hmax.html");
+  });