hogehoge.ipynb

{
 "metadata": {
  "name": "",
  "signature": "sha256:66c933038efcdc036641971319f438b16dfd37871c5ffc3119c7e4a2d989e7aa"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%matplotlib inline"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from ecolisim import *"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "init_ipynb()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<script>\n",
        " if(window['d3'] === undefined ||\n",
        "    window['THREE'] === undefined ||\n",
        "    window['Elegans'] === undefined){\n",
        "      var paths = {\n",
        "\t  d3: 'http://cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min',\n",
        "\t  THREE: 'http://cdnjs.cloudflare.com/ajax/libs/three.js/r66/three.min',\n",
        "          Elegans: 'https://cdn.rawgit.com/domitry/elegans/master/release/elegans'\n",
        "      };\n",
        "\n",
        "      var shim = {\n",
        "\t    'THREE': {exports: 'THREE'}\n",
        "      };\n",
        "      \n",
        "      console.log('Begin loading all JavaScript libs...');\n",
        "      require.config({paths: paths, shim: shim});\n",
        "\n",
        "      require(['d3', 'THREE'], function(d3, THREE){\n",
        "\t    window['d3'] = d3;\n",
        "\t    window['THREE'] = THREE;\n",
        "\t    console.log('Finished loading d3.js and Three.js.');\n",
        "\n",
        "        require(['Elegans'], function(Elegans){\n",
        "          window['Elegans'] = Elegans;\n",
        "\t      console.log('Finished loading Elegans.js ;)');\n",
        "          console.log(\"dispatch events...\");\n",
        "\t      var event = document.createEvent(\"HTMLEvents\");\n",
        "\t      event.initEvent(\"load_elegans\", true, false);\n",
        "\t      window.dispatchEvent(event);\n",
        "        });\n",
        "      });\n",
        "    }\n",
        "</script>\n"
       ],
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "<IPython.core.display.HTML at 0x7f0e97b19450>"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sim = Simulator(switch=True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "state = sim.state"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "m1 = MaterialPoint(pos=[2.4e-6, 2.5e-6,0])\n",
      "m2 = MaterialPoint(pos=[0,0,0])\n",
      "m3 = MaterialPoint(pos=[0,5.0e-6, 0])\n",
      "m4 = MaterialPoint(pos=[0,0,0])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "e1 = Ecoli(m1,m2, state.config, species={A: 100, B: 50})\n",
      "e2 = Ecoli(m4,m3, state.config, species={A: 50, B: 100})"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "state.add(e1)\n",
      "state.add(e2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sim.run(5)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "divide!\n",
        "divided!\n",
        "divide!"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "divided!\n",
        "divide!"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "divided!\n",
        "divide!"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "divided!\n"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sim.plot()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<html>\n",
        "  <head>\n",
        "    <script type=\"text/javascript\">\n",
        "     (function(){\n",
        "       /*\n",
        "       data -> [{df: {x: [0,1,2,..,4], y: , z: , height, x_rad, y_rad, z_rad}, t: 0}, {}]\n",
        "\t*/\n",
        "\n",
        "       function render(){\n",
        "\t console.log(\"Begin rendering...\");\n",
        "\t var options = {\"player\": true, \"switch\": true, \"range\": {\"y\": [0, 5e-05], \"x\": [0, 5e-05], \"z\": [0, 5e-05]}, \"autorange\": false, \"space_mode\": \"wireframe\"};\n",
        "\t var stage = new Elegans.Stage(d3.select(\"#\"+\"viz99de2ae9-c3a3-444b-a734-4aaabe21f220\")[0][0], options);\n",
        "\t var data = [{\"df\": {\"y\": [1.9557049879650612e-06, 1.6851847425784544e-06, 1.4146644971918475e-06, 1.1441442518052409e-06, 8.73624006418634e-07, 6.0310376103202714e-07, 1.5217391304347829e-06, 1.8967391304347829e-06, 2.2717391304347829e-06, 2.6467391304347827e-06, 3.0217391304347829e-06, 3.3967391304347832e-06], \"x\": [1.8774767884464587e-06, 1.6177773528753162e-06, 1.3580779173041736e-06, 1.0983784817330309e-06, 8.3867904616188845e-07, 5.78979610590746e-07, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], \"z\": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], \"fill\": [0.6666666666666666, 0.6666666666666666, 0.6666666666666666, 0.6666666666666666, 0.6666666666666666, 0.6666666666666666, 0.3333333333333333, 0.3333333333333333, 0.3333333333333333, 0.3333333333333333, 0.3333333333333333, 0.3333333333333333]}, \"t\": 0}, {\"df\": {\"y\": [4.5927921366305239e-07, 7.2979945904965925e-07, 1.0003197044362661e-06, 1.270839949822873e-06, 1.5413601952094798e-06, 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        "\n",
        "\t console.log(data);\n",
        "\n",
        "\t var colors = [\"#8dd3c7\",\"#bebada\",\"#fb8072\",\"#80b1d3\",\"#fdb462\",\"#b3de69\",\"#fccde5\",\"#d9d9d9\",\"#bc80bd\",\"#ccebc5\",\"#ffed6f\",\"#ffffb3\"];\n",
        "\n",
        "\t if(options['switch']){\n",
        "\t   Elegans.DataBase.add(\"database-particles\", data, \"df\", \"t\", 0)\n",
        "\t   console.log(\"rendering toggle switch\");\n",
        "\t   stage.add(new Elegans.Particles(\"database-particles\", {\n",
        "\t     color: [\"#d73027\", \"#4575b4\"],\n",
        "\t     fill_by: 'fill',\n",
        "\t     name: \"particles\"\n",
        "\t   }));\n",
        "\t }else{\n",
        "\t   for(var i=0; i< data.length; i++){\n",
        "\t     Elegans.DataBase.add(\"database-particles\"+String(i), data[i], \"df\", \"t\", 0)\n",
        "\t     stage.add(new Elegans.Particles(\"database-particles\"+String(i), {\n",
        "\t       color: colors[i],\n",
        "\t       name: \"particles\"\n",
        "\t     }));\n",
        "\t   }\n",
        "\t }\n",
        "\n",
        "\t stage.render();\n",
        "       }\n",
        "\n",
        "       var before_render = function(){\n",
        "         if(!(['d3', 'THREE', 'Elegans'].some(function(lib_name){\n",
        "           if(window[lib_name] === undefined){\n",
        "             console.log(lib_name + ' is not loaded.');\n",
        "             window.addEventListener(\"load_elegans\", before_render);\n",
        "             return true;\n",
        "           }\n",
        "           return false;\n",
        "         }))){\n",
        "           render();\n",
        "         };\n",
        "       };\n",
        "\n",
        "       before_render();\n",
        "     })();\n",
        "    </script>\n",
        "  </head>\n",
        "  <body>\n",
        "    <div id=\"viz99de2ae9-c3a3-444b-a734-4aaabe21f220\"></div>\n",
        "  </body>\n",
        "</html>"
       ],
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "<IPython.core.display.HTML at 0x7f0e95979ed0>"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sim.state.objects[0].sim.plot()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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Wb/wxcBv+lRw9JOY6E5JkVD0l0jzBLD71PXAUcIrzvAWQ5+yvw9++\n0Rab4fU9rNF9aMBndMfaTERcpaQhEjxvwLahfTi8NODFSh8/xtbq8E2Df6rz+hdYOwdAe6yBfSHw\nOXBXwOeMdI6JiEgKy8K/cuCRtA/iHJGYSHc7AJEUVwUcg7VnFB/hnJux7rqLYhOSiIiIiIiIiIiI\niIiIiIiIiIiIiIiIiITp/wParBMoQ9GlogAAAABJRU5ErkJggg==\n",
       "text": [
        "<matplotlib.figure.Figure at 0x7f0e8e8bc350>"
       ]
      }
     ],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sim.state.objects[1].sim.plot()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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       "text": [
        "<matplotlib.figure.Figure at 0x7f0e8e929cd0>"
       ]
      }
     ],
     "prompt_number": 25
    }
   ],
   "metadata": {}
  }
 ]
}