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      "\"\"\"\n",
      "Matplotlib Animation Example\n",
      "\n",
      "author: Jake Vanderplas\n",
      "email: vanderplas@astro.washington.edu\n",
      "website: http://jakevdp.github.com\n",
      "license: BSD\n",
      "Please feel free to use and modify this, but keep the above information. Thanks!\n",
      "\"\"\"\n",
      "# reference: http://matplotlib.sourceforge.net/api/animation_api.html\n",
      "from brian2 import *\n",
      "import numpy as np\n",
      "import mpl_toolkits.mplot3d.axes3d as p3\n",
      "from matplotlib import pyplot as plt\n",
      "from matplotlib import animation\n",
      "import h5py\n",
      "\n",
      "class Anim3dScatterPlot:\n",
      "    plottingTimeRange = 300# ms to show at a time\n",
      "    def openHdf5(self, hdf5name , permision = \"w\"):\n",
      "        self.hdf = h5py.File(hdf5name, permision)\n",
      "\n",
      "    def closeHdf5(self):\n",
      "        self.hdf.close()\n",
      "\n",
      "    def getData(self, group,  level ):\n",
      "\n",
      "        return self.hdf['/'+group+'/'+str(level)]\n",
      "\n",
      "    def getDownsampleData(self, group, start, end , screenSize = 1024):\n",
      "        bestLevel = 1\n",
      "        data = self.getData(group,bestLevel)\n",
      "        print group + \" has been downsampled \"+ str(bestLevel) + \" times\"\n",
      "        start = int(start/bestLevel)\n",
      "        end = int(end/bestLevel)\n",
      "        if (end > data.shape[0]):\n",
      "            print data.shape\n",
      "            print \"WARNING: you requested end = \"+str(float(end))+\" seconds but data length is \"+str(float(data.shape[0] *bestLevel/10000))+\" seconds\"\n",
      "            end=data.shape[0] -1\n",
      "\n",
      "        return data[start:end]\n",
      "\n",
      "    def incorperateData(self, group, start, end):\n",
      "\n",
      "        #because timestep is 0.1 mseconds, and start and end is expressed in seconds.\n",
      "        start = int(start * 10000)\n",
      "        end = int(end * 10000)\n",
      "\n",
      "        voltage = self.getDownsampleData('voltage', start, end)\n",
      "        spikes = self.getDownsampleData('spikes', start, end)            \n",
      "\n",
      "        return voltage, spikes\n",
      "\n",
      "    def create3dAnim(self):\n",
      "        plottingTimeRange = self.plottingTimeRange\n",
      "        self.openHdf5('simulation.hdf5',permision = \"r\")\n",
      "        start = .001 #seconds\n",
      "        end = .3#.13\n",
      "        voltage, spikes = self.incorperateData('voltage',start,end)\n",
      "        times = np.array(range(0,len(voltage)))*.001\n",
      "\n",
      "        # Attaching 3D axis to the figure\n",
      "        fig = plt.figure()\n",
      "        ax = p3.Axes3D(fig)\n",
      "\n",
      "        # Setting the axes properties\n",
      "        ax.set_xlim3d([0.0, 3.0])\n",
      "        ax.set_xlabel('Neuron')\n",
      "        ax.set_ylim3d([-0.03, 0.3])\n",
      "        ax.set_ylabel('Time in ms*10')\n",
      "        ax.set_zlim3d([-70.0, 15.0])\n",
      "        ax.set_zlabel('Voltage')\n",
      "        ax.set_title('Neuron voltage')\n",
      "        ax.view_init(elev=15.0, azim=-10)\n",
      "\n",
      "        c = np.array([[0],[0],[0],[0]])\n",
      "        line = ax.plot(c[0, 0:1],c[1, 0:1],c[2, 0:1], lw=4)[0]\n",
      "        line2 = ax.plot(c[0, 0:1],c[1, 0:1],c[2, 0:1], lw=4)[0]\n",
      "        line3 = ax.plot(c[0, 0:1],c[1, 0:1],c[2, 0:1], lw=4)[0]\n",
      "        line4 = ax.plot(c[0, 0:1],c[1, 0:1],c[2, 0:1], lw=4)[0]\n",
      "        xVals = np.array([[0.0]*plottingTimeRange,[1]*plottingTimeRange,[2]*plottingTimeRange,[3]*plottingTimeRange])\n",
      "\n",
      "        def generateLine(timePoint):\n",
      "            timePointEnd = timePoint+plottingTimeRange\n",
      "            line.set_data(xVals[0],times[0:plottingTimeRange])\n",
      "            line.set_3d_properties(transpose(voltage)[0][timePoint:timePointEnd])\n",
      "            line2.set_data(xVals[1],times[0:plottingTimeRange])\n",
      "            line2.set_3d_properties(transpose(voltage)[1][timePoint:timePointEnd])\n",
      "            line3.set_data(xVals[2],times[0:plottingTimeRange])\n",
      "            line3.set_3d_properties(transpose(voltage)[2][timePoint:timePointEnd])\n",
      "            line4.set_data(xVals[3],times[0:plottingTimeRange])\n",
      "            line4.set_3d_properties(transpose(voltage)[3][timePoint:timePointEnd])\n",
      "\n",
      "            if timePoint == 100 or timePoint == 200 or timePoint == 400 or timePoint == 600 or timePoint == 800:\n",
      "                print 'rendering timePoint:\\t',timePoint\n",
      "\n",
      "        line_ani = animation.FuncAnimation(fig, generateLine, frames=1000, interval=.01, blit=False)\n",
      "        ext = 'mp4'\n",
      "        fps = 30\n",
      "        codec = {'mp4': 'libx264', 'webm': 'libvpx'}.get(ext, 'mpeg4')\n",
      "        line_ani.save('testVoltage.mp4', fps=30, extra_args=['-vcodec', 'libx264'])\n",
      "\n",
      "        plt.show()\n",
      "\n",
      "    def __init__(self):\n",
      "        self.create3dAnim()\n",
      "        self.closeHdf5\n",
      "\n",
      "def main():\n",
      "    run3dAnim = Anim3dScatterPlot()\n",
      "\n",
      "if  __name__ =='__main__':main()\n",
      "\n",
      "print 'done'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}