{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Example joint fit between GBM and Swift BAT\n", "\n", "This demonstrates 3ML's ability to to joint fit between two instruments with different likelihoods. Here, we have GBM data which obey a Poisson-Gaussian profile likelihoog ( PGSTAT in XSPEC lingo) and Swift BAT which data which are the result of a \"fit\" via a coded mask and hence obey a Gaussian ( $\\chi^2$ ) likelihood.\n", "\n", "3ML automatically probes the data and selects the proper likelihood for each data set. Details for the basics of plugin setup can be found in the basic_tests example. Here we concentrate on joint fitting." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Configuration read from /Users/jburgess/.threeML/threeML_config.yml\n" ] } ], "source": [ "%matplotlib inline\n", "%matplotlib notebook\n", "\n", "from threeML import *\n", "import os" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plugin setup\n", "\n", "We have data from the same time interval from Swift BAT and a GBM NAI and BGO detector. We simply read in the files and select the energy range that we want to perform the fit over.\n", "\n" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Auto-probed noise models:\n", "- observation: gaussian\n", "- background: None\n", "Range 15-150 translates to channels 3-62\n", "Now using 60 channels out of 80\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "WARNING RuntimeWarning: Maximum MC energy is smaller than maximum EBOUNDS energy\n", "\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
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ValueUnit
joint_fit.spectrum.main.Band.K(2.90 +/- 0.10) x 10^-21 / (cm2 keV s)
joint_fit.spectrum.main.Band.alpha-1.005 +/- 0.021
joint_fit.spectrum.main.Band.xp(3.47 +/- 0.32) x 10^2keV
joint_fit.spectrum.main.Band.beta-2.42 +/- 0.20
cons_n61.56 +/- 0.04
cons_b01.39 +/- 0.09
\n", "
" ], "text/plain": [ " Value Unit\n", "joint_fit.spectrum.main.Band.K (2.90 +/- 0.10) x 10^-2 1 / (cm2 keV s)\n", "joint_fit.spectrum.main.Band.alpha -1.005 +/- 0.021 \n", "joint_fit.spectrum.main.Band.xp (3.47 +/- 0.32) x 10^2 keV\n", "joint_fit.spectrum.main.Band.beta -2.42 +/- 0.20 \n", "cons_n6 1.56 +/- 0.04 \n", "cons_b0 1.39 +/- 0.09 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "Correlation matrix:\n", "\n" ] }, { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
1.000.96-0.940.370.340.66
0.961.00-0.860.320.300.57
-0.94-0.861.00-0.40-0.45-0.76
0.370.32-0.401.000.05-0.01
0.340.30-0.450.051.000.44
0.660.57-0.76-0.010.441.00
" ], "text/plain": [ " 1.00 0.96 -0.94 0.37 0.34 0.66\n", " 0.96 1.00 -0.86 0.32 0.30 0.57\n", "-0.94 -0.86 1.00 -0.40 -0.45 -0.76\n", " 0.37 0.32 -0.40 1.00 0.05 -0.01\n", " 0.34 0.30 -0.45 0.05 1.00 0.44\n", " 0.66 0.57 -0.76 -0.01 0.44 1.00" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "Values of -log(likelihood) at the minimum:\n", "\n" ] }, { "data": { "text/html": [ "
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
-log(likelihood)
BAT77.963337
b0462.016048
n6645.877605
total1185.856990
\n", "
" ], "text/plain": [ " -log(likelihood)\n", "BAT 77.963337\n", "b0 462.016048\n", "n6 645.877605\n", "total 1185.856990" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# turn on the effective area correction and set it's bounds\n", "\n", "nai6.use_effective_area_correction(.2,1.8)\n", "bgo0.use_effective_area_correction(.2,1.8)\n", "\n", "\n", "# refit the data\n", "\n", "_=jl.fit()\n", "\n", "with_eac_res = jl.results\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we have a much better fit to all data sets" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
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