infMagSim_analysis.ipynb

{
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  "signature": "sha256:df35964d79d27e81a0ad76b9942bd898dee7d4493a277a0777405ac4c443f4d8"
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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from math import *\n",
      "import numpy as np\n",
      "import matplotlib\n",
      "import bisect\n",
      "import sys\n",
      "import glob\n",
      "#matplotlib.use('Qt4Agg') # GUI backend\n",
      "import matplotlib.pyplot as plt\n",
      "import matplotlib.gridspec as gridspec\n",
      "from matplotlib.widgets import Slider\n",
      "from matplotlib import cm\n",
      "from mpl_toolkits.mplot3d import Axes3D\n",
      "from functools import partial\n",
      "import IPython.core.display as IPdisp\n",
      "from scipy.fftpack import fft\n",
      "import scipy.signal as signal\n",
      "import matplotlib.animation as animation"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 143
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "folder = \"/home/ctzhou/tmp/\"\n",
      "file_names = glob.glob(folder+'*ions_acc.npz')\n",
      "file_names.sort()\n",
      "i=0\n",
      "for file_name in file_names:\n",
      "    print i, file_name\n",
      "    i += 1"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "0 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+00_nsteps2.0e+03_ions_acc.npz\n",
        "1 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+00_nsteps5.0e+03_ions_acc.npz\n",
        "2 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+00_nsteps7.5e+03_ions_acc.npz\n",
        "3 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+00_nsteps8.0e+03_ions_acc.npz\n",
        "4 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+01_nsteps6.0e+03_ions_acc.npz\n",
        "5 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma1.0e+02_nsteps5.0e+03_ions_acc.npz\n",
        "6 /home/ctzhou/tmp/l0.1250_Vd0.000_np5.0e+02_ni1.0e+06_dt2.9e-04_sigma2.0e+01_nsteps8.0e+03_ions_acc.npz\n",
        "7 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni2.0e+06_dt8.8e-04_sigma1.0e+01_nsteps1.5e+04_ions_acc.npz\n",
        "8 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni2.0e+06_dt8.8e-04_sigma1.0e+01_nsteps2.0e+04_ions_acc.npz\n",
        "9 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni2.0e+06_dt8.8e-04_sigma4.0e+01_nsteps1.0e+04_ions_acc.npz\n",
        "10 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni4.0e+06_dt8.8e-04_sigma1.0e+00_nsteps2.0e+04_ions_acc.npz\n",
        "11 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni4.0e+06_dt8.8e-04_sigma1.0e+01_nsteps1.5e+04_ions_acc.npz\n",
        "12 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni4.0e+06_dt8.8e-04_sigma1.0e+01_nsteps2.0e+04_ions_acc.npz\n",
        "13 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni4.0e+06_dt8.8e-04_sigma1.0e+01_nsteps2.2e+04_ions_acc.npz\n",
        "14 /home/ctzhou/tmp/l0.1250_Vd1.000_np5.0e+02_ni4.0e+06_dt8.8e-04_sigma4.0e+01_nsteps2.0e+04_ions_acc.npz\n"
       ]
      }
     ],
     "prompt_number": 166
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "file_index = 9\n",
      "\n",
      "#plot_dist_func = False\n",
      "plot_dist_func = True\n",
      "file_name = file_names[file_index]\n",
      "data_file = np.load(file_name)\n",
      "print data_file.files\n",
      "grid = data_file['grid']\n",
      "times = data_file['times']\n",
      "ion_densities = data_file['ion_densities']\n",
      "electron_densities = data_file['electron_densities']\n",
      "#charge_derivatives = data_file['charge_derivatives']\n",
      "potentials = data_file['potentials']\n",
      "#potentials_electrons = data_file['potentials_electrons']\n",
      "if file_index>82:\n",
      "    electric_fields = data_file['electric_fields']\n",
      "else:\n",
      "    electric_fields = potentials\n",
      "object_masks = data_file['object_masks']\n",
      "if plot_dist_func:\n",
      "    ion_hist_n_centers = data_file['ion_hist_n_centers']\n",
      "    ion_hist_v_centers = data_file['ion_hist_v_centers']\n",
      "    ion_distribution_functions = data_file['ion_distribution_functions']\n",
      "    electron_hist_n_centers = data_file['electron_hist_n_centers']\n",
      "    electron_hist_v_centers = data_file['electron_hist_v_centers']\n",
      "    electron_distribution_functions = data_file['electron_distribution_functions']\n",
      "    background_ion_density = data_file['background_ion_density']\n",
      "    background_electron_density = data_file['background_electron_density']\n",
      "    box_velocities = data_file['box_velocities']\n",
      "    hole_relative_positions = data_file['hole_relative_positions']\n",
      "    hole_velocities = data_file['hole_velocities']\n",
      "    trapped_electron_distribution_functions = data_file['trapped_electron_distribution_functions']\n",
      "    ions_velocity = data_file['ions_vel']"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "['ions_vel', 'ion_hist_n_centers', 'potentials_electrons', 'background_ion_density', 'electric_fields', 'box_velocities', 'background_electron_density', 'electron_hist_v_centers', 'object_masks', 'ion_distribution_functions', 'trapped_electron_distribution_functions', 'electron_densities', 'hole_velocities', 'grid', 'electron_distribution_functions', 'potentials', 'ion_densities', 'ion_hist_v_centers', 'charge_derivatives', 'times', 'electron_hist_n_centers', 'hole_relative_positions']\n"
       ]
      }
     ],
     "prompt_number": 167
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "file_index = 6\n",
      "\n",
      "#plot_dist_func = False\n",
      "plot_dist_func = True\n",
      "file_name = file_names[file_index]\n",
      "data_file_1 = np.load(file_name)\n",
      "print data_file_1.files\n",
      "grid_1 = data_file_1['grid']\n",
      "times_1 = data_file_1['times']\n",
      "ion_densities_1 = data_file_1['ion_densities']\n",
      "electron_densities_1 = data_file_1['electron_densities']\n",
      "#charge_derivatives = data_file['charge_derivatives']\n",
      "potentials_1 = data_file_1['potentials']\n",
      "#potentials_electrons = data_file['potentials_electrons']\n",
      "if file_index>82:\n",
      "    electric_fields_1 = data_file_1['electric_fields']\n",
      "else:\n",
      "    electric_fields_1 = potentials\n",
      "object_masks_1 = data_file_1['object_masks']\n",
      "if plot_dist_func:\n",
      "    ion_hist_n_centers_1 = data_file_1['ion_hist_n_centers']\n",
      "    ion_hist_v_centers_1 = data_file_1['ion_hist_v_centers']\n",
      "    ion_distribution_functions_1 = data_file_1['ion_distribution_functions']\n",
      "    electron_hist_n_centers_1 = data_file_1['electron_hist_n_centers']\n",
      "    electron_hist_v_centers_1 = data_file_1['electron_hist_v_centers']\n",
      "    electron_distribution_functions_1 = data_file_1['electron_distribution_functions']\n",
      "    background_ion_density_1 = data_file_1['background_ion_density']\n",
      "    background_electron_density_1 = data_file_1['background_electron_density']\n",
      "    box_velocities_1 = data_file_1['box_velocities']\n",
      "    hole_relative_positions_1 = data_file_1['hole_relative_positions']\n",
      "    hole_velocities_1 = data_file_1['hole_velocities']\n",
      "    trapped_electron_distribution_functions_1 = data_file_1['trapped_electron_distribution_functions']\n",
      "    ions_velocity_1 = data_file_1['ions_vel']"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "['box_velocities', 'ion_hist_v_centers', 'charge_derivatives', 'electric_fields', 'electron_densities', 'ion_hist_n_centers', 'hole_velocities', 'times', 'potentials_electrons', 'background_ion_density', 'hole_relative_positions', 'grid', 'electron_hist_v_centers', 'electron_hist_n_centers', 'potentials', 'background_electron_density', 'ion_distribution_functions', 'electron_distribution_functions', 'ion_densities', 'object_masks']\n"
       ]
      },
      {
       "ename": "KeyError",
       "evalue": "'trapped_electron_distribution_functions is not a file in the archive'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-6-a6f8e25bd713>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m     30\u001b[0m     \u001b[0mhole_relative_positions_1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_1\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'hole_relative_positions'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     31\u001b[0m     \u001b[0mhole_velocities_1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_1\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'hole_velocities'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 32\u001b[1;33m     \u001b[0mtrapped_electron_distribution_functions_1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_1\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'trapped_electron_distribution_functions'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     33\u001b[0m     \u001b[0mions_velocity_1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_1\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ions_vel'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;32m/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/numpy/lib/npyio.pyc\u001b[0m in \u001b[0;36m__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m    207\u001b[0m                 \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mzip\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    208\u001b[0m         \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 209\u001b[1;33m             \u001b[1;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"%s is not a file in the archive\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    210\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    211\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m__iter__\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;31mKeyError\u001b[0m: 'trapped_electron_distribution_functions is not a file in the archive'"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "file_index = 4\n",
      "\n",
      "#plot_dist_func = False\n",
      "plot_dist_func = True\n",
      "file_name = file_names[file_index]\n",
      "data_file_2 = np.load(file_name)\n",
      "print data_file_2.files\n",
      "grid_2 = data_file_2['grid']\n",
      "times_2 = data_file_2['times']\n",
      "ion_densities_2 = data_file_2['ion_densities']\n",
      "electron_densities_2 = data_file_2['electron_densities']\n",
      "#charge_derivatives = data_file['charge_derivatives']\n",
      "potentials_2 = data_file_2['potentials']\n",
      "#potentials_electrons = data_file['potentials_electrons']\n",
      "if file_index>82:\n",
      "    electric_fields_2 = data_file_2['electric_fields']\n",
      "else:\n",
      "    electric_fields_2 = potentials\n",
      "object_masks_2 = data_file_2['object_masks']\n",
      "if plot_dist_func:\n",
      "    ion_hist_n_centers_2 = data_file_2['ion_hist_n_centers']\n",
      "    ion_hist_v_centers_2 = data_file_2['ion_hist_v_centers']\n",
      "    ion_distribution_functions_2 = data_file_2['ion_distribution_functions']\n",
      "    electron_hist_n_centers_2 = data_file_2['electron_hist_n_centers']\n",
      "    electron_hist_v_centers_2 = data_file_2['electron_hist_v_centers']\n",
      "    electron_distribution_functions_2 = data_file_2['electron_distribution_functions']\n",
      "    background_ion_density_2 = data_file_2['background_ion_density']\n",
      "    background_electron_density_2 = data_file_2['background_electron_density']\n",
      "    box_velocities_2 = data_file_2['box_velocities']\n",
      "    hole_relative_positions_2 = data_file_2['hole_relative_positions']\n",
      "    hole_velocities_2 = data_file_2['hole_velocities']\n",
      "    trapped_electron_distribution_functions_2 = data_file_2['trapped_electron_distribution_functions']\n",
      "    ions_velocity_2 = data_file_2['ions_vel']"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "['box_velocities', 'ion_hist_v_centers', 'charge_derivatives', 'electric_fields', 'electron_densities', 'ion_hist_n_centers', 'hole_velocities', 'times', 'potentials_electrons', 'background_ion_density', 'hole_relative_positions', 'grid', 'electron_hist_v_centers', 'electron_hist_n_centers', 'potentials', 'background_electron_density', 'ion_distribution_functions', 'electron_distribution_functions', 'ion_densities', 'object_masks']\n"
       ]
      },
      {
       "ename": "KeyError",
       "evalue": "'trapped_electron_distribution_functions is not a file in the archive'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-7-00f41bb3b903>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m     30\u001b[0m     \u001b[0mhole_relative_positions_2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_2\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'hole_relative_positions'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     31\u001b[0m     \u001b[0mhole_velocities_2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_2\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'hole_velocities'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 32\u001b[1;33m     \u001b[0mtrapped_electron_distribution_functions_2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_2\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'trapped_electron_distribution_functions'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     33\u001b[0m     \u001b[0mions_velocity_2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata_file_2\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ions_vel'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;32m/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/numpy/lib/npyio.pyc\u001b[0m in \u001b[0;36m__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m    207\u001b[0m                 \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mzip\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    208\u001b[0m         \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 209\u001b[1;33m             \u001b[1;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"%s is not a file in the archive\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    210\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    211\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m__iter__\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;31mKeyError\u001b[0m: 'trapped_electron_distribution_functions is not a file in the archive'"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def hole_potential(potentials):\n",
      "    real_t =[]\n",
      "    hole_potential_peak = []\n",
      "    for t in np.arange(np.shape(potentials)[0]):\n",
      "        real_t.append(max((t-10)*10+11,t+1))\n",
      "        hole_potential_peak.append(np.amax(potentials[t]))\n",
      "    return np.asarray(real_t[151:]),np.asarray(hole_potential_peak[151:])\n",
      "(real_t_1,hole_potential_peak_1) = hole_potential(potentials_1)\n",
      "(real_t,hole_potential_peak) = hole_potential(potentials)\n",
      "#plt.plot(real_t,hole_potential_peak)\n",
      "#plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "delta_v_box = box_velocities[1:]-box_velocities[:-1]\n",
      "print np.amax(abs(delta_v_box)[100:])\n",
      "print np.argmax(abs(delta_v_box)[100:])\n",
      "dt = 0.3*0.125/np.sqrt(1836)\n",
      "# First, design the Buterworth filter\n",
      "N  = 2    # Filter order\n",
      "Wn1 = .002 # Cutoff frequency\n",
      "Wn2 = .01\n",
      "scaling_fac = 60.\n",
      "B1, A1 = signal.butter(N, Wn1, output='ba') \n",
      "B2, A2 = signal.butter(N, Wn2, output='ba') \n",
      "# Second, apply the filter\n",
      "fig = plt.figure(figsize=(12,12))\n",
      "gs = gridspec.GridSpec(1, 1, height_ratios=[16])\n",
      "gs.update(hspace=0.2)\n",
      "ax1 = plt.subplot(gs[0,0])\n",
      "#ax2 = plt.subplot(gs[0,1])\n",
      "hole_velocities_f = signal.filtfilt(B1,A1, hole_velocities,padlen=0)\n",
      "hole_velocities_1_f = signal.filtfilt(B1,A1, hole_velocities_1,padlen=0)\n",
      "hole_velocities_2_f = signal.filtfilt(B1,A1, hole_velocities_2,padlen=0)\n",
      "box_velocities_f = signal.filtfilt(B1,A1, box_velocities)\n",
      "hole_relative_positions_f = signal.filtfilt(B1,A1, hole_relative_positions)\n",
      "#hole_potential_peak_f = signal.filtfilt(B2,A2, hole_potential_peak)\n",
      "#hole_potential_peak_1_f = signal.filtfilt(B2,A2, hole_potential_peak_1)\n",
      "#hole_potential_peak_scaled = hole_potential_peak_f*scaling_fac\n",
      "#hole_potential_peak_1_scaled = hole_potential_peak_1_f*scaling_fac\n",
      "#ax.plot(real_t,hole_potential_peak_scaled,'r',linewidth=2,label='scaled $\\psi_h$ for $T_e/T_i\\,=\\,10$')\n",
      "#ax.plot(real_t_1,hole_potential_peak_1_scaled,'k',linewidth=2,label='scaled $\\psi_h$ for $T_e/T_i\\,=\\,1$')\n",
      "ax1.plot(box_velocities,'r',linewidth=1,label='Box velocity')\n",
      "ax1.axhline(5., color='k',linewidth=3,label='Counter streaming ion beams')\n",
      "ax1.axhline(-5., color='k',linewidth=3)\n",
      "ax1.plot(-ions_velocity[0][0:-1],'b',linestyle='--',linewidth=4,label='Ion drift velocity,case 1')\n",
      "#plt.plot(hole_relative_positions_f)\n",
      "#ax.plot(box_velocities_1,'g',label='$dt=0.3$')\n",
      "#ax2.plot(-ions_velocity_1[0][0:-1],'g')\n",
      "#ax1.plot(-ions_velocity_2[0][0:-1],'g',linestyle='--',linewidth=4,label='Ion drift velocity,case 2')\n",
      "#plt.plot(box_velocities_f)\n",
      "ax1.plot(hole_velocities_f,'b',linewidth=3,label='Electron hole velocity')\n",
      "#ax.plot(hole_velocities_1_f,'g',linewidth=3)\n",
      "#ax1.plot(hole_velocities_2_f,'g',linewidth=4,label='Electron hole velocity,case 2')\n",
      "plt.title(\"Hole tracking\",fontsize=24)\n",
      "#plt.title(\"hole relative positions,computation domain extends from -1.5 to 1.5\")\n",
      "ax1.set_xlabel(\"time steps\",fontsize=24)\n",
      "ax1.set_ylabel(\"lab frame velocity in $C_s$\",fontsize=24)\n",
      "legend = ax1.legend(loc='upper left', shadow=True,fontsize=24)\n",
      "#plt.ylabel(\"Positions of hole\")\n",
      "#plt.xlim(xmin=0.,xmax=4000.)\n",
      "#plt.ylim(ymin=-7.,ymax=7.)\n",
      "#plt.plot(hole_relative_positions_f)\n",
      "ax1.tick_params(labelsize=24)\n",
      "#ax2.tick_params(labelsize=28)\n",
      "#plt.tight_layout()\n",
      "fig.subplots_adjust(left=0.08, bottom=0.08, right=.96, top=.95, wspace=None, hspace=None)\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "0.0217037\n",
        "9412\n"
       ]
      }
     ],
     "prompt_number": 168
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "left_boundary_escaping_particles = []\n",
      "right_boundary_escaping_particles = []\n",
      "for k in np.arange(np.shape(trapped_electron_distribution_functions)[0]):\n",
      "    right_boundary_escaping_particles.append(np.sum(trapped_electron_distribution_functions[k,85:100,50:100]))\n",
      "    left_boundary_escaping_particles.append(np.sum(trapped_electron_distribution_functions[k,0:15,0:50]))\n",
      "left_boundary_escaping_particles_1 = []\n",
      "right_boundary_escaping_particles_1 = []\n",
      "for k in np.arange(np.shape(trapped_electron_distribution_functions_1)[0]):\n",
      "    right_boundary_escaping_particles_1.append(np.sum(trapped_electron_distribution_functions_1[k,85:100,50:100]))\n",
      "    left_boundary_escaping_particles_1.append(np.sum(trapped_electron_distribution_functions_1[k,0:15,0:50]))\n",
      "plt.figure()\n",
      "plt.plot(np.log(left_boundary_escaping_particles),'r')\n",
      "plt.plot(np.log(right_boundary_escaping_particles))\n",
      "plt.figure()\n",
      "plt.plot(np.log(left_boundary_escaping_particles_1),'r')\n",
      "plt.plot(np.log(right_boundary_escaping_particles_1))\n",
      "#plt.ylim(ymin=0.,ymax=2000)\n",
      "#plt.xlim(xmin=200,xmax=2000)\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 88
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Total_trapped_electrons=[]\n",
      "for k in np.arange(np.shape(trapped_electron_distribution_functions)[0]):\n",
      "    Total_trapped_electrons.append(np.sum(trapped_electron_distribution_functions[k]))\n",
      "Total_trapped_electrons_1=[]\n",
      "for k in np.arange(np.shape(trapped_electron_distribution_functions_1)[0]):\n",
      "    Total_trapped_electrons_1.append(np.sum(trapped_electron_distribution_functions_1[k]))\n",
      "plt.figure()\n",
      "#plt.plot(Total_trapped_electrons,'r')\n",
      "plt.plot(Total_trapped_electrons_1)\n",
      "#plt.plot(np.array(Total_trapped_electrons_1)[0:2009]-np.array(Total_trapped_electrons))\n",
      "plt.ylim(ymin=100000,ymax=200000)\n",
      "plt.xlim(xmin=500,xmax=2050)\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 605
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "L_debye = 0.125\n",
      "dz = (grid[-1]-grid[0])/(np.shape(grid)[0]-1)\n",
      "N_here  = 2    # Filter order\n",
      "Wn_here = .0018 # Cutoff frequency\n",
      "B, A = signal.butter(N_here, Wn_here, output='ba') \n",
      "n_hole_half_width = np.floor(2*L_debye/dze_half_width+1:hole_relative_positions_grid[t]+n_hole_half_width+51]))/50.\n",
      "delta_potential_across_hole_f = signal.filtfilt(B,A, delta_potential_across_hole)\n",
      "plt.plot(delta_potential_across_hole_f)\n",
      "plt.title(\"Potential difference across the hole, $\\phi(x_0-L)-\\phi(x_0+L)$\")\n",
      "plt.xlabel(\"time steps\")\n",
      "plt.ylabel(\"Potential in $T_e/e$')\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "SyntaxError",
       "evalue": "invalid syntax (<ipython-input-121-6478282db251>, line 6)",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;36m  File \u001b[1;32m\"<ipython-input-121-6478282db251>\"\u001b[1;36m, line \u001b[1;32m6\u001b[0m\n\u001b[1;33m    n_hole_half_width = np.floor(2*L_debye/dze_half_width+1:hole_relative_positions_grid[t]+n_hole_half_width+51]))/50.\u001b[0m\n\u001b[1;37m                                                           ^\u001b[0m\n\u001b[1;31mSyntaxError\u001b[0m\u001b[1;31m:\u001b[0m invalid syntax\n"
       ]
      }
     ],
     "prompt_number": 121
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def slider_changed(new_value, data_arrays, plots, fig, times=[], texts=[]):\n",
      "    k = int(new_value)\n",
      "    for plot, data in zip(plots,data_arrays):\n",
      "\tplot.set_ydata(data[k])\n",
      "    for txt in texts:\n",
      "        txt.set_text(\"t = {0}\".format(times[k]))\n",
      "    fig.canvas.draw()\n",
      "\n",
      "def arrow_pressed(event, data_arrays, plots, fig, slider, times=[], texts=[]):\n",
      "    value = slider.val\n",
      "    if (event.key=='left' or event.key=='4'):\n",
      "\tvalue -= 1\n",
      "    elif (event.key=='right' or event.key=='6'):\n",
      "\tvalue += 1\n",
      "    elif (event.key=='down' or event.key=='5'):\n",
      "\tvalue -= 1\n",
      "    elif (event.key=='up' or event.key=='8'):\n",
      "\tvalue += 1\n",
      "    slider.set_val(value)\n",
      "    slider_changed(value, data_arrays, plots, fig, times, texts)\n",
      "\n",
      "k = len(times)-1\n",
      "print times[k]\n",
      "fig = plt.figure(figsize=(18,8))\n",
      "gs = gridspec.GridSpec(4, 3, height_ratios=[16,16,1,1])\n",
      "axes = []\n",
      "plots = []\n",
      "if plot_dist_func:\n",
      "    if len(electron_distribution_functions)>0:\n",
      "\tx_axes = [grid, ion_hist_v_centers, electron_hist_v_centers, grid, grid, grid, grid]\n",
      "    else:\n",
      "\tx_axes = [grid, ion_hist_v_centers, ion_hist_v_centers, grid, grid, grid, grid]\n",
      "else:\n",
      "    x_axes = [grid, grid, grid, grid, grid, grid, grid]\n",
      "if plot_dist_func:\n",
      "    if len(electron_distribution_functions)>0:\n",
      "\tdata_arrays = [potentials, \\\n",
      "\t\t\t   np.squeeze(ion_distribution_functions[:,(ion_distribution_functions.shape[1]-1)*4./8.,:]), \\\n",
      "\t\t\t   np.squeeze(electron_distribution_functions[:,(electron_distribution_functions.shape[1]-1)*4./8.,:]), \\\n",
      "#\t\t\t   electric_fields, ion_densities, electron_densities]\n",
      "\t\t\t   ion_densities-electron_densities, ion_densities, electron_densities]\n",
      "\t#offset = 47\n",
      "\t#offset = 160\n",
      "\t#offset = 280\n",
      "\t#data_arrays = [potentials, \\\n",
      "\t#\t\t   np.squeeze(ion_distribution_functions[:,(len(grid)/2+offset)/10,:]), \\\n",
      "\t#\t\t   (np.squeeze(electron_distribution_functions[:,(len(grid)/2+offset)/10,:])).copy(), \\\n",
      "\t#\t\t   ion_densities-electron_densities, ion_densities, electron_densities]\n",
      "\t#electron_distribution_functions[:,(len(grid)/2+offset)/10,:] = 0\n",
      "    else:\n",
      "\tdata_arrays = [potentials, \\\n",
      "\t\t\t   np.squeeze(ion_distribution_functions[:,(ion_distribution_functions.shape[1]-1)*8./8.,:]), \\\n",
      "\t\t\t   np.squeeze(ion_distribution_functions[:,(ion_distribution_functions.shape[1]-1)*8./8.,:]), \\\n",
      "\t\t\t   electric_fields, ion_densities, electron_densities]\n",
      "#\t\t\t   ion_densities-electron_densities, ion_densities, electron_densities]\n",
      "else:\n",
      "    data_arrays = [potentials, \\\n",
      "\t\t       object_masks, object_masks, \\\n",
      "\t\t       electric_fields, ion_densities, electron_densities]\n",
      "#\t\t       ion_densities-electron_densities, ion_densities, electron_densities]\n",
      "#data_arrays = [potentials, ion_densities-electron_densities, object_masks, charge_derivatives, ion_densities, electron_densities]\n",
      "ranges = []\n",
      "for data in data_arrays:\n",
      "    this_range = [np.nanmin(data[np.fabs(data)<np.inf]),np.nanmax(data[np.fabs(data)<np.inf])]\n",
      "    #print this_range\n",
      "    ranges.append(this_range)\n",
      "for spec, data, this_range, x in zip(gs, data_arrays, ranges, x_axes):\n",
      "    ax = plt.subplot(spec)\n",
      "    ax.set_ylim(this_range)\n",
      "    #ax.set_ylim([-5.1,5.1])\n",
      "    axes.append(ax)\n",
      "    if data.shape[1]==len(x):\n",
      "\tplot, = ax.plot(x,data[k])\n",
      "    else:\n",
      "\tplot, = ax.plot(data[k])\n",
      "    plots.append(plot)\n",
      "\n",
      "texts = []\n",
      "ax = plt.subplot(gs[2,:])\n",
      "ax.axis('off')\n",
      "txt = ax.text(0,0,\"t = {0}\".format(times[k]))\n",
      "texts.append(txt)\n",
      "\n",
      "ax = plt.subplot(gs[3,:])\n",
      "slider = Slider(ax, 'k', 0, k, valinit=len(times)-1, color='#AAAAAA')\n",
      "changed_function = partial(slider_changed, data_arrays=data_arrays, plots=plots, fig=fig, times=times, texts=texts)\n",
      "slider.on_changed(changed_function)\n",
      "\n",
      "arrow_pressed_function = partial(arrow_pressed, data_arrays=data_arrays, plots=plots, fig=fig, slider=slider, times=times, texts=texts)\n",
      "fig.canvas.mpl_connect('key_press_event',arrow_pressed_function)\n",
      "\n",
      "plt.tight_layout()\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "8.743\n"
       ]
      }
     ],
     "prompt_number": 169
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "grid_scaled = grid/L_Debye\n",
      "fig = plt.figure(figsize=(12,12))\n",
      "gs = gridspec.GridSpec(3, 1, height_ratios=[16,16,16])\n",
      "gs.update(hspace=0.2)\n",
      "ax1 = plt.subplot(gs[0,0])\n",
      "ax2 = plt.subplot(gs[1,0])\n",
      "ax3 = plt.subplot(gs[2,0])\n",
      "k = 26\n",
      "ax1.plot(grid_scaled,potentials[k],'b',label='Potential',linewidth=2)\n",
      "ax2.plot(grid_scaled,ion_densities[k],'b',label='Normalized ion density',linewidth=2)\n",
      "ax3.plot(grid_scaled,electron_densities[k],'b',label='Normalized electron density',linewidth=2)\n",
      "legend = ax1.legend(loc='upper left', shadow=True,fontsize=26)\n",
      "legend = ax2.legend(loc='upper left', shadow=True,fontsize=26)\n",
      "legend = ax3.legend(loc='bottom left', shadow=True,fontsize=26)\n",
      "#ax1.set_xlabel(\"time $[1/\\omega_\\mathrm{pe}]$\",fontsize=20)\n",
      "ax1.set_ylabel('$\\phi[T_e/e]$',fontsize=26)\n",
      "ax2.set_ylabel(r'$\\frac{n_i}{n_{\\infty}}$',fontsize=28)\n",
      "ax3.set_ylabel(r'$\\frac{n_e}{n_{\\infty}}$',fontsize=28)\n",
      "ax3.set_xlabel('$x\\ [\\lambda_\\mathrm{De}]$', fontsize=28)\n",
      "ax1.set_xlim(xmin = -10., xmax=10.)\n",
      "ax2.set_xlim(xmin = -10., xmax=10.)\n",
      "ax3.set_xlim(xmin = -10., xmax=10.)\n",
      "ax2.set_ylim(ymin = 0.95, ymax=1.05)\n",
      "ax3.set_ylim(ymin=0.5,ymax =1.2)\n",
      "#ax1.set_aspect('auto')\n",
      "#ax2.set_aspect('auto')\n",
      "#ax3.set_aspect('auto')\n",
      "ax1.tick_params(labelsize=26)\n",
      "ax2.tick_params(labelsize=26)\n",
      "ax3.tick_params(labelsize=26)\n",
      "fig.subplots_adjust(left=0.14, bottom=0.08, right=.94, top=.98, wspace=None, hspace=None)\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 106
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def slider_changed(new_value, data_arrays, plots, fig, times, texts):\n",
      "    k = int(new_value)\n",
      "    for plot, data in zip(plots,data_arrays):\n",
      "\tplot.set_data(data[k].T)\n",
      "    for txt in texts:\n",
      "        txt.set_text(\"t = {0}\".format(times[k]))\n",
      "    fig.canvas.draw()\n",
      "\n",
      "#k=len(times)-1\n",
      "k=0\n",
      "fig = plt.figure(figsize=(18,8))\n",
      "gs = gridspec.GridSpec(4, 1, height_ratios=[16,16,1,1])\n",
      "if len(electron_distribution_functions)>0:\n",
      "    v_th_e = electron_hist_v_centers[-1]/4. # TODO: do this in less hacky way\n",
      "    electron_bin_velocities = electron_hist_v_centers\n",
      "    electron_maxwellian = []\n",
      "    for v_box in box_velocities[:-1]:\n",
      "        this_electron_maxwellian = np.ones_like(electron_distribution_functions[0])\n",
      "        this_electron_maxwellian *= np.exp(-(electron_bin_velocities+v_box)*(electron_bin_velocities+v_box)/2./v_th_e/v_th_e)\n",
      "        electron_maxwellian.append(this_electron_maxwellian)\n",
      "    electron_maxwellian /= v_th_e*np.sqrt(2.*np.pi)\n",
      "    electron_maxwellian *= np.sum(electron_distribution_functions,axis=2)[:,:,None]\n",
      "    electron_maxwellian *= (electron_hist_v_centers[-1]-electron_hist_v_centers[0])/electron_hist_v_centers.shape[0]\n",
      "    #data_arrays = [ion_distribution_functions, electron_distribution_functions]\n",
      "    data_arrays = [ion_distribution_functions, electron_distribution_functions-electron_maxwellian]\n",
      "else:\n",
      "    data_arrays = [ion_distribution_functions, ion_distribution_functions]\n",
      "plots = []\n",
      "ax = plt.subplot(gs[0,0])\n",
      "extent = [ion_hist_n_centers[0], ion_hist_n_centers[-1], ion_hist_v_centers[0], ion_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[0][k].T,origin='lower',extent=extent,cmap='copper')\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "ax.set_xlabel('$y\\ [R_\\mathrm{M}]$', fontsize=16)\n",
      "ax.set_ylabel(r'$v_y\\ [\\frac{R_\\mathrm{M}}{v_\\mathrm{T\\,i}}]$', fontsize=16)\n",
      "cbar = fig.colorbar(im)\n",
      "cbar.set_label(r'$\\frac{f_\\mathrm{e}}{f_\\mathrm{e\\,\\infty}(0)}$', fontsize=16)\n",
      "ax = plt.subplot(gs[1,0])\n",
      "extent = [electron_hist_n_centers[0], electron_hist_n_centers[-1], electron_hist_v_centers[0], electron_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[1][k].T,origin='lower',extent=extent,cmap='pink',vmin=np.amin(data_arrays[1])/8.,vmax=np.amax(data_arrays[1])/8.)\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "fig.colorbar(im)\n",
      "\n",
      "texts = []\n",
      "ax = plt.subplot(gs[2,:])\n",
      "ax.axis('off')\n",
      "txt = ax.text(0,0,\"t = {0}\".format(times[k]))\n",
      "texts.append(txt)\n",
      "\n",
      "ax = plt.subplot(gs[3,:])\n",
      "slider = Slider(ax, 'k', 0, len(times)-1, valinit=k, color='#AAAAAA')\n",
      "changed_function = partial(slider_changed, data_arrays=data_arrays, plots=plots, fig=fig, times=times, texts=texts)\n",
      "slider.on_changed(changed_function)\n",
      "\n",
      "arrow_pressed_function = partial(arrow_pressed, data_arrays=data_arrays, plots=plots, fig=fig, slider=slider, times=times, texts=texts)\n",
      "fig.canvas.mpl_connect('key_press_event',arrow_pressed_function)\n",
      "\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "ValueError",
       "evalue": "operands could not be broadcast together with shapes (500,100,100) (59,100,1) (500,100,100) ",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-82-a45c043d23f7>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m     21\u001b[0m         \u001b[0melectron_maxwellian\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mthis_electron_maxwellian\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     22\u001b[0m     \u001b[0melectron_maxwellian\u001b[0m \u001b[1;33m/=\u001b[0m \u001b[0mv_th_e\u001b[0m\u001b[1;33m*\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msqrt\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m2.\u001b[0m\u001b[1;33m*\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpi\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 23\u001b[1;33m     \u001b[0melectron_maxwellian\u001b[0m \u001b[1;33m*=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msum\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0melectron_distribution_functions\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0maxis\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mNone\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     24\u001b[0m     \u001b[0melectron_maxwellian\u001b[0m \u001b[1;33m*=\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0melectron_hist_v_centers\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m-\u001b[0m\u001b[0melectron_hist_v_centers\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m/\u001b[0m\u001b[0melectron_hist_v_centers\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     25\u001b[0m     \u001b[1;31m#data_arrays = [ion_distribution_functions, electron_distribution_functions]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;31mValueError\u001b[0m: operands could not be broadcast together with shapes (500,100,100) (59,100,1) (500,100,100) "
       ]
      }
     ],
     "prompt_number": 82
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Density of trapped particles\n",
      "def slider_changed(new_value, data_arrays, plots, fig, times, texts):\n",
      "    k = int(new_value)\n",
      "    for plot, data in zip(plots,data_arrays):\n",
      "\tplot.set_data(data[k].T)\n",
      "    for txt in texts:\n",
      "        txt.set_text(\"t = {0}\".format(times[k]))\n",
      "    fig.canvas.draw()\n",
      "\n",
      "#k=len(times)-1\n",
      "k=0\n",
      "fig = plt.figure(figsize=(18,8))\n",
      "gs = gridspec.GridSpec(4, 1, height_ratios=[16,16,1,1])\n",
      "if len(trapped_electron_distribution_functions)>0:\n",
      "    v_th_e = electron_hist_v_centers[-1]/4. # TODO: do this in less hacky way\n",
      "    electron_bin_velocities = electron_hist_v_centers\n",
      "    #electron_maxwellian = []\n",
      "    #for v_box in box_velocities[:-1]:\n",
      "        #this_electron_maxwellian = np.ones_like(trapped_electron_distribution_functions[0])\n",
      "        #this_electron_maxwellian *= np.exp(-(electron_bin_velocities+v_box)*(electron_bin_velocities+v_box)/2./v_th_e/v_th_e)\n",
      "        #electron_maxwellian.append(this_electron_maxwellian)\n",
      "    #electron_maxwellian /= v_th_e*np.sqrt(2.*np.pi)\n",
      "    #electron_maxwellian *= np.sum(trapped_electron_distribution_functions,axis=2)[:,:,None]\n",
      "    #electron_maxwellian *= (electron_hist_v_centers[-1]-electron_hist_v_centers[0])/electron_hist_v_centers.shape[0]\n",
      "    data_arrays = [ion_distribution_functions, trapped_electron_distribution_functions]\n",
      "    #data_arrays = [ion_distribution_functions, electron_distribution_functions]\n",
      "else:\n",
      "    data_arrays = [ion_distribution_functions, ion_distribution_functions]\n",
      "plots = []\n",
      "ax = plt.subplot(gs[0,0])\n",
      "extent = [ion_hist_n_centers[0], ion_hist_n_centers[-1], ion_hist_v_centers[0], ion_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[0][k].T,origin='lower',extent=extent,cmap='copper')\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "ax.set_xlabel('$y\\ [R_\\mathrm{M}]$', fontsize=16)\n",
      "ax.set_ylabel(r'$v_y\\ [\\frac{R_\\mathrm{M}}{v_\\mathrm{T\\,i}}]$', fontsize=16)\n",
      "cbar = fig.colorbar(im)\n",
      "cbar.set_label(r'$\\frac{f_\\mathrm{e}}{f_\\mathrm{e\\,\\infty}(0)}$', fontsize=16)\n",
      "ax = plt.subplot(gs[1,0])\n",
      "extent = [electron_hist_n_centers[0], electron_hist_n_centers[-1], electron_hist_v_centers[0], electron_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[1][k].T,origin='lower',extent=extent,cmap='copper',vmin=np.amin(data_arrays[1])*200,vmax=np.amax(data_arrays[1]))\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "fig.colorbar(im)\n",
      "\n",
      "texts = []\n",
      "ax = plt.subplot(gs[2,:])\n",
      "ax.axis('off')\n",
      "txt = ax.text(0,0,\"t = {0}\".format(times[k]))\n",
      "texts.append(txt)\n",
      "\n",
      "ax = plt.subplot(gs[3,:])\n",
      "slider = Slider(ax, 'k', 0, len(times)-1, valinit=k, color='#AAAAAA')\n",
      "changed_function = partial(slider_changed, data_arrays=data_arrays, plots=plots, fig=fig, times=times, texts=texts)\n",
      "slider.on_changed(changed_function)\n",
      "\n",
      "arrow_pressed_function = partial(arrow_pressed, data_arrays=data_arrays, plots=plots, fig=fig, slider=slider, times=times, texts=texts)\n",
      "fig.canvas.mpl_connect('key_press_event',arrow_pressed_function)\n",
      "\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 171
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Relative density of trapped electrons\n",
      "A = trapped_electron_distribution_functions.astype(np.float32)\n",
      "B = electron_distribution_functions.astype(np.float32)+0.001\n",
      "trapped_relative_density=np.divide(A,B)\n",
      "k=0\n",
      "fig = plt.figure(figsize=(18,8))\n",
      "gs = gridspec.GridSpec(4, 1, height_ratios=[16,16,1,1])\n",
      "if len(trapped_electron_distribution_functions)>0:\n",
      "    electron_bin_velocities = electron_hist_v_centers\n",
      "    data_arrays = [ion_distribution_functions, trapped_relative_density]\n",
      "else:\n",
      "    data_arrays = [ion_distribution_functions, ion_distribution_functions]\n",
      "plots = []\n",
      "ax = plt.subplot(gs[0,0])\n",
      "extent = [ion_hist_n_centers[0], ion_hist_n_centers[-1], ion_hist_v_centers[0], ion_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[0][k].T,origin='lower',extent=extent,cmap='copper')\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "ax.set_xlabel('$y\\ [R_\\mathrm{M}]$', fontsize=16)\n",
      "ax.set_ylabel(r'$v_y\\ [\\frac{R_\\mathrm{M}}{v_\\mathrm{T\\,i}}]$', fontsize=16)\n",
      "cbar = fig.colorbar(im)\n",
      "cbar.set_label(r'$\\frac{f_\\mathrm{e}}{f_\\mathrm{e\\,\\infty}(0)}$', fontsize=16)\n",
      "ax = plt.subplot(gs[1,0])\n",
      "extent = [electron_hist_n_centers[0], electron_hist_n_centers[-1], electron_hist_v_centers[0], electron_hist_v_centers[-1] ]\n",
      "im = ax.imshow(data_arrays[1][k].T,origin='lower',extent=extent,cmap='copper',vmin=np.amin(data_arrays[1]),vmax=np.amax(data_arrays[1]))\n",
      "plots.append(im)\n",
      "ax.set_aspect('auto')\n",
      "fig.colorbar(im)\n",
      "\n",
      "texts = []\n",
      "ax = plt.subplot(gs[2,:])\n",
      "ax.axis('off')\n",
      "txt = ax.text(0,0,\"t = {0}\".format(times[k]))\n",
      "texts.append(txt)\n",
      "\n",
      "ax = plt.subplot(gs[3,:])\n",
      "slider = Slider(ax, 'k', 0, len(times)-1, valinit=k, color='#AAAAAA')\n",
      "changed_function = partial(slider_changed, data_arrays=data_arrays, plots=plots, fig=fig, times=times, texts=texts)\n",
      "slider.on_changed(changed_function)\n",
      "\n",
      "arrow_pressed_function = partial(arrow_pressed, data_arrays=data_arrays, plots=plots, fig=fig, slider=slider, times=times, texts=texts)\n",
      "fig.canvas.mpl_connect('key_press_event',arrow_pressed_function)\n",
      "\n",
      "plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Exception in Tkinter callback\n",
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 398, in button_press_event\n",
        "    FigureCanvasBase.button_press_event(self, x, y, num, dblclick=dblclick, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1887, in button_press_event\n",
        "    self.callbacks.process(s, mouseevent)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n",
        "Exception in Tkinter callback\n",
        "Traceback (most recent call last):\n",
        "  File \"/usr/local/lib/python2.7/lib-tk/Tkinter.py\", line 1470, in __call__\n",
        "    return self.func(*args)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py\", line 383, in motion_notify_event\n",
        "    FigureCanvasBase.motion_notify_event(self, x, y, guiEvent=event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/backend_bases.py\", line 1936, in motion_notify_event\n",
        "    self.callbacks.process(s, event)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 540, in process\n",
        "    proxy(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/cbook.py\", line 415, in __call__\n",
        "    return mtd(*args, **kwargs)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 419, in _update\n",
        "    self.set_val(val)\n",
        "  File \"/home/ctzhou/virtualenvs/ESPIC/lib/python2.7/site-packages/matplotlib/widgets.py\", line 433, in set_val\n",
        "    func(val)\n",
        "  File \"<ipython-input-169-11b5e88310ec>\", line 4, in slider_changed\n",
        "    plot.set_ydata(data[k])\n",
        "AttributeError: 'AxesImage' object has no attribute 'set_ydata'\n"
       ]
      }
     ],
     "prompt_number": 170
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "L_Debye = 0.125\n",
      "mass_ratio = 1836.\n",
      "dt = 0.3\n",
      "time_simulation = np.arange(len(box_velocities))\n",
      "time_simulation_1 = np.arange(len(hole_velocities))\n",
      "time_simulation = time_simulation*dt\n",
      "time_simulation_1 = time_simulation_1*dt\n",
      "hole_velocities_f = signal.filtfilt(B1,A1, hole_velocities,padlen=0)\n",
      "v_th_e = np.sqrt(mass_ratio)\n",
      "inverse_Wp_e = L_Debye/v_th_e\n",
      "times_scaled = times/inverse_Wp_e\n",
      "A = trapped_electron_distribution_functions.astype(np.float32)\n",
      "B = electron_distribution_functions.astype(np.float32)+0.001\n",
      "trapped_relative_density=np.divide(A,B)\n",
      "\n",
      "fig = plt.figure(figsize=(20,12))\n",
      "gs = gridspec.GridSpec(3, 2, height_ratios=[16,16,1,1])\n",
      "gs.update(hspace=0.2)\n",
      "\n",
      "if len(trapped_electron_distribution_functions)>0:\n",
      "    electron_bin_velocities = electron_hist_v_centers\n",
      "    data_arrays = [electron_distribution_functions, trapped_electron_distribution_functions, ion_distribution_functions]\n",
      "else:\n",
      "    data_arrays = [ion_distribution_functions, ion_distribution_functions]\n",
      "plots = []\n",
      "ax1 = plt.subplot(gs[0,0])\n",
      "extent1 = [electron_hist_n_centers[0]/L_Debye, electron_hist_n_centers[-1]/L_Debye, electron_hist_v_centers[0], electron_hist_v_centers[-1] ]\n",
      "ax2 = plt.subplot(gs[1,0])\n",
      "extent2 = [electron_hist_n_centers[0]/L_Debye, electron_hist_n_centers[-1]/L_Debye, electron_hist_v_centers[0], electron_hist_v_centers[-1] ]\n",
      "ax3 = plt.subplot(gs[0,1])\n",
      "extent3 = [ion_hist_n_centers[0]/L_Debye, ion_hist_n_centers[-1]/L_Debye, ion_hist_v_centers[0], ion_hist_v_centers[-1] ]\n",
      "ax4 = plt.subplot(gs[1,1])\n",
      "#extent3 = [ion_hist_n_centers[0]/L_Debye, ion_hist_n_centers[-1]/L_Debye, ion_hist_v_centers[0], ion_hist_v_centers[-1] ]\n",
      "texts = []\n",
      "ax = plt.subplot(gs[2,:])\n",
      "ax.axis('off')\n",
      "ax4.plot(time_simulation,box_velocities,'b',label='Box velocity')\n",
      "ax4.plot(time_simulation_1,hole_velocities_f,'r',linewidth=3,label='Electron hole velocity')\n",
      "legend = ax4.legend(loc='upper right', shadow=True,fontsize=20)\n",
      "ax4.set_xlabel(\"time $[1/\\omega_\\mathrm{pe}]$\",fontsize=26)\n",
      "#ax4.set_ylabel(\"lab frame velocity in $C_s$\",fontsize=20)\n",
      "ax1.tick_params(labelsize=24)\n",
      "ax2.tick_params(labelsize=24)\n",
      "ax3.tick_params(labelsize=24)\n",
      "ax4.tick_params(labelsize=24)\n",
      "for k in np.arange(210):\n",
      "    im1 = ax1.imshow(data_arrays[0][k].T,origin='lower',extent=extent1,cmap='copper')\n",
      "    im2 = ax2.imshow(data_arrays[1][k].T,origin='lower',extent=extent2,cmap='copper',vmin=np.amin(data_arrays[1]),vmax=np.amax(data_arrays[1]))\n",
      "    im3 = ax3.imshow(data_arrays[2][k].T,origin='lower',extent=extent3,cmap='copper')\n",
      "    t = ax.annotate(\"time $[1/\\omega_p]$ = {0}\".format(times_scaled[k]),(0,0),fontsize=24)\n",
      "    im4 = ax4.axvline(times_scaled[k], color='k',linewidth=4)\n",
      "    plots.append([im1,im2,im3,t,im4])\n",
      "    ax1.set_ylabel('$v\\ [\\mathrm{C}_\\mathrm{s}]$', fontsize=28,rotation='horizontal')\n",
      "    ax2.set_xlabel('$x\\ [\\lambda_\\mathrm{De}]$', fontsize=28)\n",
      "    ax2.set_ylabel('$v\\ [\\mathrm{C}_\\mathrm{s}]$', fontsize=28,rotation='horizontal')\n",
      "    ax1.set_aspect('auto')\n",
      "    ax2.set_aspect('auto')\n",
      "    ax3.set_aspect('auto')\n",
      "cbaxes1 = fig.add_axes([.47, 0.63, 0.015, 0.35])\n",
      "cbaxes2 = fig.add_axes([.47, 0.15, 0.015, 0.35])\n",
      "cbaxes3 = fig.add_axes([.911, 0.63, 0.015, 0.35])\n",
      "cbar1 = fig.colorbar(im1,cax = cbaxes1)\n",
      "cbar2 = fig.colorbar(im2,cax = cbaxes2)\n",
      "cbar3 = fig.colorbar(im3,cax = cbaxes3)\n",
      "cbar1.ax.tick_params(labelsize=18)\n",
      "cbar2.ax.tick_params(labelsize=18) \n",
      "cbar3.ax.tick_params(labelsize=18) \n",
      "#cbar1.set_label('$f_\\mathrm{tagged}$', fontsize=20,rotation='horizontal',labelpad=4.)\n",
      "#cbar2.set_label(r'$\\frac{f_\\mathrm{tagged}}{f_\\mathrm{e}}$', fontsize=20,rotation='horizontal')\n",
      "Writer = animation.writers['imagemagick']\n",
      "writer = Writer(fps=10, metadata=dict(artist='Zhou'))\n",
      "im_ani = animation.ArtistAnimation(fig, plots,interval=20, repeat_delay=3000,blit=True)\n",
      "plot_margin = 0.25\n",
      "fig.subplots_adjust(left=0.1, bottom=0., right=.9, top=1, wspace=None, hspace=None)\n",
      "\n",
      "#ax = plt.subplot(gs[3,:])\n",
      "#slider = Slider(ax, 'k', 0, len(times)-1, valinit=k, color='#AAAAAA')\n",
      "#changed_function = partial(slider_changed, data_arrays=data_arrays, plots=plots, fig=fig, times=times, texts=texts)\n",
      "#slider.on_changed(changed_function)\n",
      "\n",
      "#arrow_pressed_function = partial(arrow_pressed, data_arrays=data_arrays, plots=plots, fig=fig, slider=slider, times=times, texts=texts)\n",
      "#fig.canvas.mpl_connect('key_press_event',arrow_pressed_function)\n",
      "im_ani.save('hole_tracking.gif',writer=writer)\n",
      "#plt.show()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print(animation.writers.list())"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "['imagemagick_file', 'imagemagick']\n"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "0.2**0.5"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 132,
       "text": [
        "0.4472135954999579"
       ]
      }
     ],
     "prompt_number": 132
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}