compound_Plots.ipynb 569 KB
 NUNEZ Arturo committed Jul 18, 2018 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 { "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%matplotlib notebook\n", "%load_ext autoreload\n", "%autoreload 2" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "\n", "from scipy.stats import rv_continuous\n", "from scipy.interpolate import interp1d\n", "from matplotlib.patches import Circle\n", "from scipy.special import gamma\n", "import numpy as np\n", "import emcee\n", "from mpl_toolkits.axes_grid1 import make_axes_locatable\n", "from numpy import exp, sqrt\n", "from scipy.integrate import quad, dblquad, nquad\n", "import matplotlib.patches as patches\n", "from itertools import product\n", "from scipy.integrate import quad\n", "import scipy.optimize as optimize\n", "import matplotlib.pyplot as plt\n", "import matplotlib as mpl\n", "from sklearn.neighbors import KDTree\n", "import sys\n", "import lmfit\n", "from py_unsio import *\n", "import pymc\n", "import os\n", "from scipy.integrate import simps\n", "from pymodelfit import FunctionModel1DAuto\n", "import wkbl\n", "from wkbl.astro.halo_info import *\n", "from mpl_toolkits.mplot3d import axes3d\n", "from matplotlib import cm\n", "import wkbl.astro.nbody_essentials as nbe\n", "import cfalcon\n", "CF =cfalcon.CFalcon()\n", "import iminuit\n", "from iminuit import Minuit, describe, Struct\n", "import probfit\n", "from matplotlib.colors import LogNorm\n", "from matplotlib.ticker import FormatStrFormatter\n", "import warnings\n",  NUNEZ Arturo committed Jul 20, 2018 61  "import wkbl.astro.halo_info as h\n",  NUNEZ Arturo committed Jul 18, 2018 62 63 64 65 66 67 68 69 70 71 72 73  "warnings.filterwarnings('ignore')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# S and T" ] }, { "cell_type": "code",  NUNEZ Arturo committed Aug 01, 2018 74  "execution_count": 68,  NUNEZ Arturo committed Jul 18, 2018 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94  "metadata": { "collapsed": false }, "outputs": [], "source": [ "\n", "def readSnT(datafile):\n", " myfile = open(datafile)\n", " r = S = T = np.array([])\n", " for l in myfile:\n", " row = l.split(\" \")\n", " if l[0]==\"#\" and row[1]=='r200':\n", " r200 = np.float(row[3] )\n", " if l[0]==\"#\":continue\n", " r = np.append(r,row[0])\n", " S = np.append(S,row[1])\n", " T = np.append(T,row[2])\n", " return r, S, T,r200\n", "HaloB_r, HaloB_S, HaloB_T,HaloB_r200 = readSnT(\"../../datafiles/HALO_B_S_and_T.txt\")\n", "HaloC_r, HaloC_S, HaloC_T,HaloC_r200 = readSnT(\"../../datafiles/HALO_C_S_and_T.txt\")\n",  NUNEZ Arturo committed Jul 20, 2018 95  "Mochima_r, Mochima_S, Mochima_T, Mochima_r200 = readSnT(\"../../datafiles/Mochima_S_and_T.txt\")\n",  NUNEZ Arturo committed Jul 31, 2018 96 97 98 99 100 101 102  "Adicora_r, Adicora_S, Adicora_T, Adicora_r200 = readSnT(\"../../datafiles/Adicora_S_and_T.txt\")\n", "\n", "\n", "HaloB_r_DMO, HaloB_S_DMO, HaloB_T_DMO,HaloB_r200_DMO = readSnT(\"../../datafiles/HALOB_S_and_T_DMO.txt\")\n", "HaloC_r_DMO, HaloC_S_DMO, HaloC_T_DMO,HaloC_r200_DMO = readSnT(\"../../datafiles/HALOC_S_and_T_DMO.txt\")\n", "Mochima_r_DMO, Mochima_S_DMO, Mochima_T_DMO, Mochima_r200_DMO = readSnT(\"../../datafiles/Mochima_S_and_T_DMO.txt\")\n", "Adicora_r_DMO, Adicora_S_DMO, Adicora_T_DMO, Adicora_r200_DMO = readSnT(\"../../datafiles/Adicora_S_and_T_DMO.txt\")\n"  NUNEZ Arturo committed Jul 18, 2018 103 104 105 106  ] }, { "cell_type": "code",  NUNEZ Arturo committed Aug 01, 2018 107  "execution_count": 69,  NUNEZ Arturo committed Jul 18, 2018 108 109 110 111 112 113 114 115  "metadata": { "collapsed": true }, "outputs": [], "source": [ "HB_color = \"#097220\"\n", "HC_color = \"#4c0972\"\n", "Mo_color = \"#094272\"\n",  NUNEZ Arturo committed Jul 20, 2018 116 117  "Ad_color = \"#C70039\"\n", "\n",  NUNEZ Arturo committed Jul 18, 2018 118 119 120 121 122  "font=15" ] }, { "cell_type": "code",  NUNEZ Arturo committed Aug 01, 2018 123  "execution_count": 70,  NUNEZ Arturo committed Jul 18, 2018 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 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' +\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 = $(' ');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", "$(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " this.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " ' ');\n", " var titletext =$(\n", " '
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');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [  NUNEZ Arturo committed Jul 31, 2018 1795  ""  NUNEZ Arturo committed Jul 18, 2018 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810  ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "fig, ax = plt.subplots()\n", "ax.set_ylabel(r\"$\\beta(r)$\",fontsize=1.5*font)\n", "ax.set_xlabel(r\"$\\rm r[kpc]$\",fontsize=1.5*font)\n", "\n", "ax.set_xscale(\"log\")\n",  NUNEZ Arturo committed Jul 20, 2018 1811  "ax.set_ylim([-1.,1])\n",  NUNEZ Arturo committed Jul 18, 2018 1812 1813 1814  "ax.plot(HaloB_r,HaloB_beta,ls='-',lw=2,color=HB_color,label=r\"$\\rm HALO\\,\\,B$\")\n", "ax.plot(HaloC_r,HaloC_beta,ls='-',lw=2,color=HC_color,label=r\"$\\rm HALO\\,\\,C$\")\n", "ax.plot(Mochima_r,Mochima_beta,ls='-',lw=2,color=Mo_color,label=r\"$\\rm Mochima$\")\n",  NUNEZ Arturo committed Jul 20, 2018 1815  "ax.plot(Adicora_r,Adicora_beta,ls='-',lw=2,color=Ad_color,label=r\"$\\rm Mochima$\")\n",  NUNEZ Arturo committed Jul 18, 2018 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827  "#ax.plot(1,1000,ls='-',lw=2,color=HB_color,label=r\"$\\rm HALO\\,\\,B$\")\n", "#ax.plot(1,1000,ls='-',lw=2,color=HC_color,label=r\"$\\rm HALO\\,\\,C$\")\n", "#ax.plot(1,1000,ls='-',lw=2,color=Mo_color,label=r\"$\\rm Mochima$\")\n", "#ax.set_ylim(0.45,1)\n", "legend = ax.legend(loc='lower left', ncol=1, shadow=False, fontsize=font)\n", "frame = legend.get_frame()\n", "ax.tick_params(axis='both', which='major', labelsize=15, size=5,width=1.2)\n", "ax.tick_params(axis='both', which='minor', labelsize=15, size=3,width=1.2)\n", "\n", "ax.axvline(x=HaloB_r200,lw=2,ls='-.',color=HB_color)\n", "ax.axvline(x=HaloC_r200,lw=2,ls='-.',color=HC_color)\n", "ax.axvline(x=Mochima_r200,lw=2,ls='-.',color=Mo_color)\n",  NUNEZ Arturo committed Jul 20, 2018 1828 1829  "plt.tight_layout()\n", "plt.savefig(\"/home/arturo/Documents/LAM/LAM2LUPM/General_Plots/Beta_r_all.pdf\")"  NUNEZ Arturo committed Jul 18, 2018 1830 1831 1832 1833  ] }, { "cell_type": "code",  NUNEZ Arturo committed Jul 31, 2018 1834  "execution_count": 47,  NUNEZ Arturo committed Jul 18, 2018 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854  "metadata": { "collapsed": true }, "outputs": [], "source": [ "def readMomemts(datafile):\n", " myfile = open(datafile)\n", " r = m1 = m2 = m3 = np.array([])\n", " for l in myfile:\n", " row = l.split(\" \")\n", " if l[0]==\"#\" and row[1]=='r200':\n", " r200 = np.float(row[3] )\n", " if l[0]==\"#\":continue\n", " r = np.append(r,float(row[0]))\n", " m1 = np.append(m1,float(row[1]))\n", " m2 = np.append(m2,float(row[2]))\n", " m3 = np.append(m3,float(row[3]))\n", " return r, m1, m2, m3, r200\n", "HaloB_r, HaloB_m1, HaloB_m2,HaloB_m3,HaloB_r200 = readMomemts(\"../../datafiles/HALO_B_Moments.txt\")\n", "HaloC_r, HaloC_m1, HaloC_m2,HaloC_m3,HaloC_r200 = readMomemts(\"../../datafiles/HALO_C_Moments.txt\")\n",  NUNEZ Arturo committed Jul 20, 2018 1855 1856  "Mochima_r, Mochima_m1, Mochima_m2, Mochima_m3, Mochima_r200 = readMomemts(\"../../datafiles/Mochima_Moments.txt\")\n", "Adicora_r, Adicora_m1, Adicora_m2, Adicora_m3, Adicora_r200 = readMomemts(\"../../datafiles/Adicora_Moments.txt\")"  NUNEZ Arturo committed Jul 18, 2018 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869  ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] }, { "cell_type": "code",  NUNEZ Arturo committed Jul 20, 2018 1870  "execution_count": null,  NUNEZ Arturo committed Jul 18, 2018 1871 1872 1873  "metadata": { "collapsed": false },  NUNEZ Arturo committed Jul 20, 2018 1874 1875  "outputs": [], "source": []  NUNEZ Arturo committed Jul 18, 2018 1876 1877 1878  }, { "cell_type": "code",  NUNEZ Arturo committed Jul 31, 2018 1879  "execution_count": 48,  NUNEZ Arturo committed Jul 18, 2018 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 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