TimeLapseData3d.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "No module named PyQt4",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-1d9e0f4598c5>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'matplotlib qt'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2156\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2157\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2158\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2160\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2077\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2078\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2079\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2080\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2081\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/magics/pylab.pyc\u001b[0m in \u001b[0;36mmatplotlib\u001b[0;34m(self, line)\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/magics/pylab.pyc\u001b[0m in \u001b[0;36mmatplotlib\u001b[0;34m(self, line)\u001b[0m\n\u001b[1;32m     98\u001b[0m             \u001b[0;32mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Available matplotlib backends: %s\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mbackends_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     99\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 100\u001b[0;31m             \u001b[0mgui\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbackend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0menable_matplotlib\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgui\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    101\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_show_matplotlib_backend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgui\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbackend\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    102\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36menable_matplotlib\u001b[0;34m(self, gui)\u001b[0m\n\u001b[1;32m   2947\u001b[0m                 \u001b[0mgui\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbackend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfind_gui_and_backend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpylab_gui_select\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2948\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2949\u001b[0;31m         \u001b[0mpt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mactivate_matplotlib\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbackend\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2950\u001b[0m         \u001b[0mpt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfigure_inline_support\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbackend\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2951\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/IPython/core/pylabtools.pyc\u001b[0m in \u001b[0;36mactivate_matplotlib\u001b[0;34m(backend)\u001b[0m\n\u001b[1;32m    305\u001b[0m     \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrcParams\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'backend'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbackend\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    306\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 307\u001b[0;31m     \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpyplot\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    308\u001b[0m     \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpyplot\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mswitch_backend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbackend\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    309\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/pyplot.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m    113\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    114\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbackends\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpylab_setup\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 115\u001b[0;31m \u001b[0m_backend_mod\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew_figure_manager\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdraw_if_interactive\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_show\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpylab_setup\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    116\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    117\u001b[0m \u001b[0m_IP_REGISTERED\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/__init__.pyc\u001b[0m in \u001b[0;36mpylab_setup\u001b[0;34m()\u001b[0m\n\u001b[1;32m     30\u001b[0m     \u001b[0;31m# imports. 0 means only perform absolute imports.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     31\u001b[0m     backend_mod = __import__(backend_name,\n\u001b[0;32m---> 32\u001b[0;31m                              globals(),locals(),[backend_name],0)\n\u001b[0m\u001b[1;32m     33\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     34\u001b[0m     \u001b[0;31m# Things we pull in from all backends\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     16\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     17\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 18\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_qt5agg\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mFigureCanvasQTAggBase\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0m_FigureCanvasQTAggBase\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     19\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     20\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_agg\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mFigureCanvasAgg\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_qt5agg.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_agg\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mFigureCanvasAgg\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 16\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_qt5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mQtCore\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     17\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_qt5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mQtGui\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     18\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mbackend_qt5\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mFigureManagerQT\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     24\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     25\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwidgets\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mSubplotTool\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 26\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbackends\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mqt_editor\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfigureoptions\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mfigureoptions\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     27\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     28\u001b[0m from .qt_compat import (QtCore, QtGui, QtWidgets, _getSaveFileName,\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/qt_editor/figureoptions.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     18\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     19\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcm\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmarkers\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolors\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mmcolors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 20\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbackends\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mqt_editor\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformlayout\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mformlayout\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     21\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbackends\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mqt_compat\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mQtGui\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     22\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/qt_editor/formlayout.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     54\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     55\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcolors\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mmcolors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 56\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbackends\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mqt_compat\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mQtGui\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mQtWidgets\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mQtCore\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     57\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     58\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python2.7/site-packages/matplotlib/backends/qt_compat.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m    135\u001b[0m     \u001b[0;31m# have been changed in the above if block\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    136\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mQT_API\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mQT_API_PYQT\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mQT_API_PYQTv2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m  \u001b[0;31m# PyQt4 API\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 137\u001b[0;31m         \u001b[0;32mfrom\u001b[0m \u001b[0mPyQt4\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mQtCore\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mQtGui\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    138\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    139\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mImportError\u001b[0m: No module named PyQt4"
     ]
    }
   ],
   "source": [
    "%matplotlib qt\n",
    "\n",
    "import time\n",
    "import copy\n",
    "import numpy as np\n",
    "from skimage.filters import gaussian_filter\n",
    "\n",
    "from tifffile import imread, imsave\n",
    "import cPickle as pickle\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from spimagine import volfig, volshow\n",
    "from spimagine import EllipsoidMesh, Mesh\n",
    "\n",
    "%reload_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "from netsurface3d import NetSurf3d\n",
    "from data4d import Data4d"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load time-lapse data..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "filenames = ['/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t1.TIF'] #,\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t2.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t3.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t4.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t5.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t6.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t7.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t8.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t9.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t10.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t11.TIF',\n",
    "#             '/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry_t12.TIF']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dimensions of frame 0 :  (31, 512, 512)\n"
     ]
    }
   ],
   "source": [
    "data = Data4d( filenames, pixelsize=(1.,1.,5.), silent=False )\n",
    "data.set_seg_params(K=30,max_delta_k=4)\n",
    "objects = []\n",
    "ecells = []"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Min radius and max radius at which to look for cells (around center points (seed points))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "max_rs = (data.images[0].shape[2] / 8,\n",
    "          data.images[0].shape[1] / 8,\n",
    "          data.images[0].shape[0] / 2)\n",
    "\n",
    "min_rs = (5,5,1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## adding E cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "Ea = data.init_object(\"Ea\")\n",
    "objects.append(Ea)\n",
    "ecells.append(Ea)\n",
    "\n",
    "Ep = data.init_object(\"Ep\")\n",
    "objects.append(Ep)\n",
    "ecells.append(Ep)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added appearance for \"Ea\" in frame 0 with seed coordinates [ 110.  300.   12.]\n",
      "      Optimum energy:  95253.0\n",
      "      Nodes in/out:  7349 8011\n"
     ]
    }
   ],
   "source": [
    "# data.add_object_at( Ea, min_rs, max_rs, frame=0, seed=(110,300,12), frame_to=11, seed_to=(105,310,16), segment_it=True )\n",
    "data.add_object_at( Ea, min_rs, max_rs, frame=0, seed=(110,300,12), segment_it=True )\n",
    "data.track(Ea, seed_frame=0, target_frames=range(1,len(data.images)), recenter_iterations=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added appearance for \"Ep\" in frame 0 with seed coordinates [ 110.  350.   12.]\n",
      "      Optimum energy:  87730.0\n",
      "      Nodes in/out:  7060 8300\n",
      "Added appearance for \"Ep\" in frame 1 with seed coordinates [ 112.  351.   12.]\n",
      "      Optimum energy:  85070.0\n",
      "      Nodes in/out:  7123 8237\n",
      "Added appearance for \"Ep\" in frame 2 with seed coordinates [ 115.  352.   13.]\n",
      "      Optimum energy:  83739.0\n",
      "      Nodes in/out:  7540 7820\n",
      "Added appearance for \"Ep\" in frame 3 with seed coordinates [ 118.  352.   13.]\n",
      "      Optimum energy:  84401.0\n",
      "      Nodes in/out:  7321 8039\n",
      "Added appearance for \"Ep\" in frame 4 with seed coordinates [ 120.  353.   13.]\n",
      "      Optimum energy:  81773.0\n",
      "      Nodes in/out:  7064 8296\n",
      "Added appearance for \"Ep\" in frame 5 with seed coordinates [ 122.  354.   14.]\n",
      "      Optimum energy:  77667.0\n",
      "      Nodes in/out:  7152 8208\n",
      "Added appearance for \"Ep\" in frame 6 with seed coordinates [ 125.  355.   14.]\n",
      "      Optimum energy:  77966.0\n",
      "      Nodes in/out:  6948 8412\n",
      "Added appearance for \"Ep\" in frame 7 with seed coordinates [ 128.  356.   14.]\n",
      "      Optimum energy:  76400.0\n",
      "      Nodes in/out:  6888 8472\n",
      "Added appearance for \"Ep\" in frame 8 with seed coordinates [ 130.  357.   15.]\n",
      "      Optimum energy:  73514.0\n",
      "      Nodes in/out:  7570 7790\n",
      "Added appearance for \"Ep\" in frame 9 with seed coordinates [ 132.  358.   15.]\n",
      "      Optimum energy:  73070.0\n",
      "      Nodes in/out:  7895 7465\n",
      "Added appearance for \"Ep\" in frame 10 with seed coordinates [ 135.  358.   15.]\n",
      "      Optimum energy:  72557.0\n",
      "      Nodes in/out:  7793 7567\n",
      "Added appearance for \"Ep\" in frame 11 with seed coordinates [ 138.  359.   16.]\n",
      "      Optimum energy:  73558.0\n",
      "      Nodes in/out:  8091 7269\n"
     ]
    }
   ],
   "source": [
    "data.add_object_at( Ep, min_rs, max_rs, frame=0, seed=(110,350,12), frame_to=11, seed_to=(140,360,16), segment_it=True )\n",
    "# data.add_object_at( Ep, min_rs, max_rs, frame=0, seed=(110,350,12), segment_it=True )\n",
    "# data.track(Ep, seed_frame=0, target_frames=range(1,len(data.images)), recenter_iterations=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## adding direct neighbors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "neighbors = []\n",
    "for i in range(12):\n",
    "    n = data.init_object(\"n\"+str(i))\n",
    "    objects.append(n)\n",
    "    neighbors.append(n)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added appearance for \"n0\" in frame 0 with seed coordinates [  90.  390.   12.]\n",
      "      Optimum energy:  75930.0\n",
      "      Nodes in/out:  4803 10557\n",
      "Added appearance for \"n0\" in frame 1 with seed coordinates [  90.  390.   12.]\n",
      "      Optimum energy:  74323.0\n",
      "      Nodes in/out:  4958 10402\n",
      "    Updated center to [ 91 387  12]\n",
      "Added appearance for \"n0\" in frame 2 with seed coordinates [  91.  387.   12.]\n",
      "      Optimum energy:  73773.0\n",
      "      Nodes in/out:  5196 10164\n",
      "    Updated center to [ 90 384  12]\n",
      "Added appearance for \"n0\" in frame 3 with seed coordinates [  90.  384.   12.]\n",
      "      Optimum energy:  74514.0\n",
      "      Nodes in/out:  5173 10187\n",
      "    Updated center to [ 89 381  11]\n",
      "Added appearance for \"n0\" in frame 4 with seed coordinates [  89.  381.   11.]\n",
      "      Optimum energy:  72659.0\n",
      "      Nodes in/out:  5013 10347\n",
      "    Updated center to [ 89 378  11]\n",
      "Added appearance for \"n0\" in frame 5 with seed coordinates [  89.  378.   11.]\n",
      "      Optimum energy:  72933.0\n",
      "      Nodes in/out:  5167 10193\n",
      "    Updated center to [ 89 376  11]\n",
      "Added appearance for \"n0\" in frame 6 with seed coordinates [  89.  376.   11.]\n",
      "      Optimum energy:  71406.0\n",
      "      Nodes in/out:  5220 10140\n",
      "    Updated center to [ 90 374  11]\n",
      "Added appearance for \"n0\" in frame 7 with seed coordinates [  90.  374.   11.]\n",
      "      Optimum energy:  73036.0\n",
      "      Nodes in/out:  4990 10370\n",
      "    Updated center to [ 91 374  11]\n",
      "Added appearance for \"n0\" in frame 8 with seed coordinates [  91.  374.   11.]\n",
      "      Optimum energy:  70742.0\n",
      "      Nodes in/out:  4933 10427\n",
      "    Updated center to [ 93 374  11]\n",
      "Added appearance for \"n0\" in frame 9 with seed coordinates [  93.  374.   11.]\n",
      "      Optimum energy:  70880.0\n",
      "      Nodes in/out:  5207 10153\n",
      "    Updated center to [ 94 374  11]\n",
      "Added appearance for \"n0\" in frame 10 with seed coordinates [  94.  374.   11.]\n",
      "      Optimum energy:  70732.0\n",
      "      Nodes in/out:  5233 10127\n",
      "    Updated center to [ 95 373  11]\n",
      "Added appearance for \"n0\" in frame 11 with seed coordinates [  95.  373.   11.]\n",
      "      Optimum energy:  70788.0\n",
      "      Nodes in/out:  5282 10078\n",
      "    Updated center to [ 96 371  11]\n",
      "Added appearance for \"n1\" in frame 0 with seed coordinates [ 150.  410.   12.]\n",
      "      Optimum energy:  76298.0\n",
      "      Nodes in/out:  5767 9593\n",
      "Added appearance for \"n1\" in frame 1 with seed coordinates [ 150.  410.   12.]\n",
      "      Optimum energy:  77784.0\n",
      "      Nodes in/out:  5588 9772\n",
      "    Updated center to [147 410  12]\n",
      "Added appearance for \"n1\" in frame 2 with seed coordinates [ 147.  410.   12.]\n",
      "      Optimum energy:  76435.0\n",
      "      Nodes in/out:  5694 9666\n",
      "    Updated center to [143 410  12]\n",
      "Added appearance for \"n1\" in frame 3 with seed coordinates [ 143.  410.   12.]\n",
      "      Optimum energy:  75318.0\n",
      "      Nodes in/out:  5709 9651\n",
      "    Updated center to [141 410  11]\n",
      "Added appearance for \"n1\" in frame 4 with seed coordinates [ 141.  410.   11.]\n",
      "      Optimum energy:  72662.0\n",
      "      Nodes in/out:  5791 9569\n",
      "    Updated center to [140 409  11]\n",
      "Added appearance for \"n1\" in frame 5 with seed coordinates [ 140.  409.   11.]\n",
      "      Optimum energy:  72107.0\n",
      "      Nodes in/out:  5734 9626\n",
      "    Updated center to [139 408  11]\n",
      "Added appearance for \"n1\" in frame 6 with seed coordinates [ 139.  408.   11.]\n",
      "      Optimum energy:  72192.0\n",
      "      Nodes in/out:  6132 9228\n",
      "    Updated center to [138 407  11]\n",
      "Added appearance for \"n1\" in frame 7 with seed coordinates [ 138.  407.   11.]\n",
      "      Optimum energy:  71963.0\n",
      "      Nodes in/out:  6091 9269\n",
      "    Updated center to [137 406  11]\n",
      "Added appearance for \"n1\" in frame 8 with seed coordinates [ 137.  406.   11.]\n",
      "      Optimum energy:  72070.0\n",
      "      Nodes in/out:  6047 9313\n",
      "    Updated center to [137 405  12]\n",
      "Added appearance for \"n1\" in frame 9 with seed coordinates [ 137.  405.   12.]\n",
      "      Optimum energy:  69897.0\n",
      "      Nodes in/out:  6949 8411\n",
      "    Updated center to [136 404  12]\n",
      "Added appearance for \"n1\" in frame 10 with seed coordinates [ 136.  404.   12.]\n",
      "      Optimum energy:  70040.0\n",
      "      Nodes in/out:  7141 8219\n",
      "    Updated center to [135 403  12]\n",
      "Added appearance for \"n1\" in frame 11 with seed coordinates [ 135.  403.   12.]\n",
      "      Optimum energy:  69486.0\n",
      "      Nodes in/out:  6901 8459\n",
      "    Updated center to [134 402  12]\n",
      "Added appearance for \"n2\" in frame 0 with seed coordinates [ 200.  390.   12.]\n",
      "      Optimum energy:  76861.0\n",
      "      Nodes in/out:  6539 8821\n",
      "Added appearance for \"n2\" in frame 1 with seed coordinates [ 200.  390.   12.]\n",
      "      Optimum energy:  75820.0\n",
      "      Nodes in/out:  6512 8848\n",
      "    Updated center to [198 387  11]\n",
      "Added appearance for \"n2\" in frame 2 with seed coordinates [ 198.  387.   11.]\n",
      "      Optimum energy:  73204.0\n",
      "      Nodes in/out:  6595 8765\n",
      "    Updated center to [196 386  11]\n",
      "Added appearance for \"n2\" in frame 3 with seed coordinates [ 196.  386.   11.]\n",
      "      Optimum energy:  73119.0\n",
      "      Nodes in/out:  6584 8776\n",
      "    Updated center to [195 385  11]\n",
      "Added appearance for \"n2\" in frame 4 with seed coordinates [ 195.  385.   11.]\n",
      "      Optimum energy:  70811.0\n",
      "      Nodes in/out:  6596 8764\n",
      "    Updated center to [195 384  11]\n",
      "Added appearance for \"n2\" in frame 5 with seed coordinates [ 195.  384.   11.]\n",
      "      Optimum energy:  70308.0\n",
      "      Nodes in/out:  6569 8791\n",
      "    Updated center to [195 383  11]\n",
      "Added appearance for \"n2\" in frame 6 with seed coordinates [ 195.  383.   11.]\n",
      "      Optimum energy:  68590.0\n",
      "      Nodes in/out:  6557 8803\n",
      "    Updated center to [195 382  11]\n",
      "Added appearance for \"n2\" in frame 7 with seed coordinates [ 195.  382.   11.]\n",
      "      Optimum energy:  72727.0\n",
      "      Nodes in/out:  6010 9350\n",
      "    Updated center to [194 382  11]\n",
      "Added appearance for \"n2\" in frame 8 with seed coordinates [ 194.  382.   11.]\n",
      "      Optimum energy:  72645.0\n",
      "      Nodes in/out:  4880 10480\n",
      "    Updated center to [190 384  11]\n",
      "Added appearance for \"n2\" in frame 9 with seed coordinates [ 190.  384.   11.]\n",
      "      Optimum energy:  71134.0\n",
      "      Nodes in/out:  5201 10159\n",
      "    Updated center to [187 385  10]\n",
      "Added appearance for \"n2\" in frame 10 with seed coordinates [ 187.  385.   10.]\n",
      "      Optimum energy:  71343.0\n",
      "      Nodes in/out:  4877 10483\n",
      "    Updated center to [185 385  10]\n",
      "Added appearance for \"n2\" in frame 11 with seed coordinates [ 185.  385.   10.]\n",
      "      Optimum energy:  72546.0\n",
      "      Nodes in/out:  4862 10498\n",
      "    Updated center to [182 385  10]\n",
      "Added appearance for \"n3\" in frame 0 with seed coordinates [ 190.  315.   12.]\n",
      "      Optimum energy:  87278.0\n",
      "      Nodes in/out:  6706 8654\n",
      "Added appearance for \"n3\" in frame 1 with seed coordinates [ 190.  315.   12.]\n",
      "      Optimum energy:  83345.0\n",
      "      Nodes in/out:  6679 8681\n",
      "    Updated center to [187 315  11]\n",
      "Added appearance for \"n3\" in frame 2 with seed coordinates [ 187.  315.   11.]\n",
      "      Optimum energy:  79440.0\n",
      "      Nodes in/out:  6526 8834\n",
      "    Updated center to [186 316  11]\n",
      "Added appearance for \"n3\" in frame 3 with seed coordinates [ 186.  316.   11.]\n",
      "      Optimum energy:  78802.0\n",
      "      Nodes in/out:  6518 8842\n",
      "    Updated center to [186 317  11]\n",
      "Added appearance for \"n3\" in frame 4 with seed coordinates [ 186.  317.   11.]\n",
      "      Optimum energy:  77854.0\n",
      "      Nodes in/out:  6682 8678\n",
      "    Updated center to [186 317  11]\n",
      "Added appearance for \"n3\" in frame 5 with seed coordinates [ 186.  317.   11.]\n",
      "      Optimum energy:  75215.0\n",
      "      Nodes in/out:  6672 8688\n",
      "    Updated center to [186 318  11]\n",
      "Added appearance for \"n3\" in frame 6 with seed coordinates [ 186.  318.   11.]\n",
      "      Optimum energy:  73093.0\n",
      "      Nodes in/out:  6505 8855\n",
      "    Updated center to [187 319  11]\n",
      "Added appearance for \"n3\" in frame 7 with seed coordinates [ 187.  319.   11.]\n",
      "      Optimum energy:  80143.0\n",
      "      Nodes in/out:  5742 9618\n",
      "    Updated center to [188 320  11]\n",
      "Added appearance for \"n3\" in frame 8 with seed coordinates [ 188.  320.   11.]\n",
      "      Optimum energy:  80641.0\n",
      "      Nodes in/out:  3638 11722\n",
      "    Updated center to [186 325  10]\n",
      "Added appearance for \"n3\" in frame 9 with seed coordinates [ 186.  325.   10.]\n",
      "      Optimum energy:  78576.0\n",
      "      Nodes in/out:  4028 11332\n",
      "    Updated center to [185 329  10]\n",
      "Added appearance for \"n3\" in frame 10 with seed coordinates [ 185.  329.   10.]\n",
      "      Optimum energy:  75774.0\n",
      "      Nodes in/out:  4422 10938\n",
      "    Updated center to [185 332  10]\n",
      "Added appearance for \"n3\" in frame 11 with seed coordinates [ 185.  332.   10.]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Optimum energy:  73995.0\n",
      "      Nodes in/out:  4689 10671\n",
      "    Updated center to [185 333  10]\n",
      "Added appearance for \"n4\" in frame 0 with seed coordinates [ 145.  265.   12.]\n",
      "      Optimum energy:  88657.0\n",
      "      Nodes in/out:  6504 8856\n",
      "Added appearance for \"n4\" in frame 1 with seed coordinates [ 145.  265.   12.]\n",
      "      Optimum energy:  86819.0\n",
      "      Nodes in/out:  6692 8668\n",
      "    Updated center to [144 265  12]\n",
      "Added appearance for \"n4\" in frame 2 with seed coordinates [ 144.  265.   12.]\n",
      "      Optimum energy:  83175.0\n",
      "      Nodes in/out:  6568 8792\n",
      "    Updated center to [145 265  11]\n",
      "Added appearance for \"n4\" in frame 3 with seed coordinates [ 145.  265.   11.]\n",
      "      Optimum energy:  81557.0\n",
      "      Nodes in/out:  6192 9168\n",
      "    Updated center to [146 265  11]\n",
      "Added appearance for \"n4\" in frame 4 with seed coordinates [ 146.  265.   11.]\n",
      "      Optimum energy:  80481.0\n",
      "      Nodes in/out:  6182 9178\n",
      "    Updated center to [147 264  11]\n",
      "Added appearance for \"n4\" in frame 5 with seed coordinates [ 147.  264.   11.]\n",
      "      Optimum energy:  79805.0\n",
      "      Nodes in/out:  6039 9321\n",
      "    Updated center to [149 263  11]\n",
      "Added appearance for \"n4\" in frame 6 with seed coordinates [ 149.  263.   11.]\n",
      "      Optimum energy:  79073.0\n",
      "      Nodes in/out:  5664 9696\n",
      "    Updated center to [151 264  11]\n",
      "Added appearance for \"n4\" in frame 7 with seed coordinates [ 151.  264.   11.]\n",
      "      Optimum energy:  78921.0\n",
      "      Nodes in/out:  5572 9788\n",
      "    Updated center to [152 263  11]\n",
      "Added appearance for \"n4\" in frame 8 with seed coordinates [ 152.  263.   11.]\n",
      "      Optimum energy:  76092.0\n",
      "      Nodes in/out:  5418 9942\n",
      "    Updated center to [152 263  10]\n",
      "Added appearance for \"n4\" in frame 9 with seed coordinates [ 152.  263.   10.]\n",
      "      Optimum energy:  76489.0\n",
      "      Nodes in/out:  4651 10709\n",
      "    Updated center to [152 263  10]\n",
      "Added appearance for \"n4\" in frame 10 with seed coordinates [ 152.  263.   10.]\n",
      "      Optimum energy:  76757.0\n",
      "      Nodes in/out:  4264 11096\n",
      "    Updated center to [153 264  10]\n",
      "Added appearance for \"n4\" in frame 11 with seed coordinates [ 153.  264.   10.]\n",
      "      Optimum energy:  75057.0\n",
      "      Nodes in/out:  4280 11080\n",
      "    Updated center to [153 265  10]\n",
      "Added appearance for \"n5\" in frame 0 with seed coordinates [ 110.  230.   12.]\n",
      "      Optimum energy:  90461.0\n",
      "      Nodes in/out:  7426 7934\n",
      "Added appearance for \"n5\" in frame 1 with seed coordinates [ 110.  230.   12.]\n",
      "      Optimum energy:  85976.0\n",
      "      Nodes in/out:  7346 8014\n",
      "    Updated center to [109 231  12]\n",
      "Added appearance for \"n5\" in frame 2 with seed coordinates [ 109.  231.   12.]\n",
      "      Optimum energy:  84079.0\n",
      "      Nodes in/out:  7261 8099\n",
      "    Updated center to [109 232  12]\n",
      "Added appearance for \"n5\" in frame 3 with seed coordinates [ 109.  232.   12.]\n",
      "      Optimum energy:  80634.0\n",
      "      Nodes in/out:  7261 8099\n",
      "    Updated center to [110 233  12]\n",
      "Added appearance for \"n5\" in frame 4 with seed coordinates [ 110.  233.   12.]\n",
      "      Optimum energy:  80625.0\n",
      "      Nodes in/out:  7240 8120\n",
      "    Updated center to [111 233  12]\n",
      "Added appearance for \"n5\" in frame 5 with seed coordinates [ 111.  233.   12.]\n",
      "      Optimum energy:  79525.0\n",
      "      Nodes in/out:  7717 7643\n",
      "    Updated center to [112 232  12]\n",
      "Added appearance for \"n5\" in frame 6 with seed coordinates [ 112.  232.   12.]\n",
      "      Optimum energy:  77053.0\n",
      "      Nodes in/out:  7663 7697\n",
      "    Updated center to [112 233  12]\n",
      "Added appearance for \"n5\" in frame 7 with seed coordinates [ 112.  233.   12.]\n",
      "      Optimum energy:  78043.0\n",
      "      Nodes in/out:  7740 7620\n",
      "    Updated center to [110 234  12]\n",
      "Added appearance for \"n5\" in frame 8 with seed coordinates [ 110.  234.   12.]\n",
      "      Optimum energy:  75664.0\n",
      "      Nodes in/out:  7760 7600\n",
      "    Updated center to [108 235  12]\n",
      "Added appearance for \"n5\" in frame 9 with seed coordinates [ 108.  235.   12.]\n",
      "      Optimum energy:  73949.0\n",
      "      Nodes in/out:  7719 7641\n",
      "    Updated center to [107 236  12]\n",
      "Added appearance for \"n5\" in frame 10 with seed coordinates [ 107.  236.   12.]\n",
      "      Optimum energy:  74460.0\n",
      "      Nodes in/out:  7560 7800\n",
      "    Updated center to [107 239  12]\n",
      "Added appearance for \"n5\" in frame 11 with seed coordinates [ 107.  239.   12.]\n",
      "      Optimum energy:  75476.0\n",
      "      Nodes in/out:  7588 7772\n",
      "    Updated center to [108 241  12]\n",
      "Added appearance for \"n6\" in frame 0 with seed coordinates [  40.  255.   12.]\n",
      "      Optimum energy:  76191.0\n",
      "      Nodes in/out:  6272 9088\n",
      "Added appearance for \"n6\" in frame 1 with seed coordinates [  40.  255.   12.]\n",
      "      Optimum energy:  77355.0\n",
      "      Nodes in/out:  6119 9241\n",
      "    Updated center to [ 41 256  12]\n",
      "Added appearance for \"n6\" in frame 2 with seed coordinates [  41.  256.   12.]\n",
      "      Optimum energy:  77671.0\n",
      "      Nodes in/out:  6074 9286\n",
      "    Updated center to [ 41 257  12]\n",
      "Added appearance for \"n6\" in frame 3 with seed coordinates [  41.  257.   12.]\n",
      "      Optimum energy:  74868.0\n",
      "      Nodes in/out:  6162 9198\n",
      "    Updated center to [ 42 257  11]\n",
      "Added appearance for \"n6\" in frame 4 with seed coordinates [  42.  257.   11.]\n",
      "      Optimum energy:  73580.0\n",
      "      Nodes in/out:  5827 9533\n",
      "    Updated center to [ 43 257  11]\n",
      "Added appearance for \"n6\" in frame 5 with seed coordinates [  43.  257.   11.]\n",
      "      Optimum energy:  73157.0\n",
      "      Nodes in/out:  5932 9428\n",
      "    Updated center to [ 44 256  11]\n",
      "Added appearance for \"n6\" in frame 6 with seed coordinates [  44.  256.   11.]\n",
      "      Optimum energy:  73975.0\n",
      "      Nodes in/out:  6031 9329\n",
      "    Updated center to [ 46 257  11]\n",
      "Added appearance for \"n6\" in frame 7 with seed coordinates [  46.  257.   11.]\n",
      "      Optimum energy:  73316.0\n",
      "      Nodes in/out:  5374 9986\n",
      "    Updated center to [ 47 259  10]\n",
      "Added appearance for \"n6\" in frame 8 with seed coordinates [  47.  259.   10.]\n",
      "      Optimum energy:  72940.0\n",
      "      Nodes in/out:  4987 10373\n",
      "    Updated center to [ 47 261  10]\n",
      "Added appearance for \"n6\" in frame 9 with seed coordinates [  47.  261.   10.]\n",
      "      Optimum energy:  71571.0\n",
      "      Nodes in/out:  5051 10309\n",
      "    Updated center to [ 48 263  10]\n",
      "Added appearance for \"n6\" in frame 10 with seed coordinates [  48.  263.   10.]\n",
      "      Optimum energy:  72550.0\n",
      "      Nodes in/out:  4859 10501\n",
      "    Updated center to [ 49 265  10]\n",
      "Added appearance for \"n6\" in frame 11 with seed coordinates [  49.  265.   10.]\n",
      "      Optimum energy:  71587.0\n",
      "      Nodes in/out:  5362 9998\n",
      "    Updated center to [ 49 266  10]\n",
      "Added appearance for \"n7\" in frame 0 with seed coordinates [  45.  300.   18.]\n",
      "      Optimum energy:  80891.0\n",
      "      Nodes in/out:  8110 7250\n",
      "Added appearance for \"n7\" in frame 1 with seed coordinates [  45.  300.   18.]\n",
      "      Optimum energy:  78659.0\n",
      "      Nodes in/out:  8018 7342\n",
      "    Updated center to [ 47 295  17]\n",
      "Added appearance for \"n7\" in frame 2 with seed coordinates [  47.  295.   17.]\n",
      "      Optimum energy:  78558.0\n",
      "      Nodes in/out:  8690 6670\n",
      "    Updated center to [ 49 291  16]\n",
      "Added appearance for \"n7\" in frame 3 with seed coordinates [  49.  291.   16.]\n",
      "      Optimum energy:  80910.0\n",
      "      Nodes in/out:  8816 6544\n",
      "    Updated center to [ 50 288  15]\n",
      "Added appearance for \"n7\" in frame 4 with seed coordinates [  50.  288.   15.]\n",
      "      Optimum energy:  79640.0\n",
      "      Nodes in/out:  8639 6721\n",
      "    Updated center to [ 51 286  14]\n",
      "Added appearance for \"n7\" in frame 5 with seed coordinates [  51.  286.   14.]\n",
      "      Optimum energy:  81076.0\n",
      "      Nodes in/out:  8229 7131\n",
      "    Updated center to [ 51 286  13]\n",
      "Added appearance for \"n7\" in frame 6 with seed coordinates [  51.  286.   13.]\n",
      "      Optimum energy:  76212.0\n",
      "      Nodes in/out:  5271 10089\n",
      "    Updated center to [ 52 281  11]\n",
      "Added appearance for \"n7\" in frame 7 with seed coordinates [  52.  281.   11.]\n",
      "      Optimum energy:  71735.0\n",
      "      Nodes in/out:  6091 9269\n",
      "    Updated center to [ 53 279  11]\n",
      "Added appearance for \"n7\" in frame 8 with seed coordinates [  53.  279.   11.]\n",
      "      Optimum energy:  72856.0\n",
      "      Nodes in/out:  6208 9152\n",
      "    Updated center to [ 53 277  11]\n",
      "Added appearance for \"n7\" in frame 9 with seed coordinates [  53.  277.   11.]\n",
      "      Optimum energy:  70774.0\n",
      "      Nodes in/out:  6336 9024\n",
      "    Updated center to [ 53 276  11]\n",
      "Added appearance for \"n7\" in frame 10 with seed coordinates [  53.  276.   11.]\n",
      "      Optimum energy:  72951.0\n",
      "      Nodes in/out:  6287 9073\n",
      "    Updated center to [ 53 276  11]\n",
      "Added appearance for \"n7\" in frame 11 with seed coordinates [  53.  276.   11.]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Optimum energy:  70790.0\n",
      "      Nodes in/out:  6281 9079\n",
      "    Updated center to [ 53 275  11]\n",
      "Added appearance for \"n8\" in frame 0 with seed coordinates [  67.  355.   18.]\n",
      "      Optimum energy:  82851.0\n",
      "      Nodes in/out:  4854 10506\n",
      "Added appearance for \"n8\" in frame 1 with seed coordinates [  67.  355.   18.]\n",
      "      Optimum energy:  81880.0\n",
      "      Nodes in/out:  5408 9952\n",
      "    Updated center to [ 70 350  18]\n",
      "Added appearance for \"n8\" in frame 2 with seed coordinates [  70.  350.   18.]\n",
      "      Optimum energy:  81806.0\n",
      "      Nodes in/out:  5564 9796\n",
      "    Updated center to [ 72 346  18]\n",
      "Added appearance for \"n8\" in frame 3 with seed coordinates [  72.  346.   18.]\n",
      "      Optimum energy:  79917.0\n",
      "      Nodes in/out:  6517 8843\n",
      "    Updated center to [ 71 344  18]\n",
      "Added appearance for \"n8\" in frame 4 with seed coordinates [  71.  344.   18.]\n",
      "      Optimum energy:  79496.0\n",
      "      Nodes in/out:  6440 8920\n",
      "    Updated center to [ 71 342  18]\n",
      "Added appearance for \"n8\" in frame 5 with seed coordinates [  71.  342.   18.]\n",
      "      Optimum energy:  77620.0\n",
      "      Nodes in/out:  6763 8597\n",
      "    Updated center to [ 72 342  18]\n",
      "Added appearance for \"n8\" in frame 6 with seed coordinates [  72.  342.   18.]\n",
      "      Optimum energy:  77800.0\n",
      "      Nodes in/out:  7978 7382\n",
      "    Updated center to [ 71 339  17]\n",
      "Added appearance for \"n8\" in frame 7 with seed coordinates [  71.  339.   17.]\n",
      "      Optimum energy:  79378.0\n",
      "      Nodes in/out:  6461 8899\n",
      "    Updated center to [ 73 335  16]\n",
      "Added appearance for \"n8\" in frame 8 with seed coordinates [  73.  335.   16.]\n",
      "      Optimum energy:  74796.0\n",
      "      Nodes in/out:  5828 9532\n",
      "    Updated center to [ 70 332  15]\n",
      "Added appearance for \"n8\" in frame 9 with seed coordinates [  70.  332.   15.]\n",
      "      Optimum energy:  73007.0\n",
      "      Nodes in/out:  6080 9280\n",
      "    Updated center to [ 68 330  14]\n",
      "Added appearance for \"n8\" in frame 10 with seed coordinates [  68.  330.   14.]\n",
      "      Optimum energy:  73183.0\n",
      "      Nodes in/out:  5688 9672\n",
      "    Updated center to [ 66 330  13]\n",
      "Added appearance for \"n8\" in frame 11 with seed coordinates [  66.  330.   13.]\n",
      "      Optimum energy:  72204.0\n",
      "      Nodes in/out:  5850 9510\n",
      "    Updated center to [ 64 330  13]\n",
      "Added appearance for \"n9\" in frame 0 with seed coordinates [ 110.  275.   24.]\n",
      "      Optimum energy:  85146.0\n",
      "      Nodes in/out:  6414 8946\n",
      "Added appearance for \"n9\" in frame 1 with seed coordinates [ 110.  275.   24.]\n",
      "      Optimum energy:  83328.0\n",
      "      Nodes in/out:  7067 8293\n",
      "    Updated center to [110 269  23]\n",
      "Added appearance for \"n9\" in frame 2 with seed coordinates [ 110.  269.   23.]\n",
      "      Optimum energy:  84384.0\n",
      "      Nodes in/out:  7497 7863\n",
      "    Updated center to [110 266  23]\n",
      "Added appearance for \"n9\" in frame 3 with seed coordinates [ 110.  266.   23.]\n",
      "      Optimum energy:  79127.0\n",
      "      Nodes in/out:  7821 7539\n",
      "    Updated center to [109 265  23]\n",
      "Added appearance for \"n9\" in frame 4 with seed coordinates [ 109.  265.   23.]\n",
      "      Optimum energy:  80409.0\n",
      "      Nodes in/out:  7224 8136\n",
      "    Updated center to [108 266  22]\n",
      "Added appearance for \"n9\" in frame 5 with seed coordinates [ 108.  266.   22.]\n",
      "      Optimum energy:  80390.0\n",
      "      Nodes in/out:  5123 10237\n",
      "    Updated center to [104 269  21]\n",
      "Added appearance for \"n9\" in frame 6 with seed coordinates [ 104.  269.   21.]\n",
      "      Optimum energy:  82632.0\n",
      "      Nodes in/out:  4150 11210\n",
      "    Updated center to [102 269  20]\n",
      "Added appearance for \"n9\" in frame 7 with seed coordinates [ 102.  269.   20.]\n",
      "      Optimum energy:  82054.0\n",
      "      Nodes in/out:  4062 11298\n",
      "    Updated center to [101 268  19]\n",
      "Added appearance for \"n9\" in frame 8 with seed coordinates [ 101.  268.   19.]\n",
      "      Optimum energy:  81515.0\n",
      "      Nodes in/out:  3155 12205\n",
      "    Updated center to [101 266  19]\n",
      "Added appearance for \"n9\" in frame 9 with seed coordinates [ 101.  266.   19.]\n",
      "      Optimum energy:  84366.0\n",
      "      Nodes in/out:  6449 8911\n",
      "    Updated center to [101 273  19]\n",
      "Added appearance for \"n9\" in frame 10 with seed coordinates [ 101.  273.   19.]\n",
      "      Optimum energy:  82427.0\n",
      "      Nodes in/out:  11498 3862\n",
      "    Updated center to [103 272  18]\n",
      "Added appearance for \"n9\" in frame 11 with seed coordinates [ 103.  272.   18.]\n",
      "      Optimum energy:  80714.0\n",
      "      Nodes in/out:  11498 3862\n",
      "    Updated center to [104 271  17]\n",
      "Added appearance for \"n10\" in frame 0 with seed coordinates [ 130.  315.   24.]\n",
      "      Optimum energy:  85946.0\n",
      "      Nodes in/out:  7840 7520\n",
      "Added appearance for \"n10\" in frame 1 with seed coordinates [ 130.  315.   24.]\n",
      "      Optimum energy:  78537.0\n",
      "      Nodes in/out:  8795 6565\n",
      "    Updated center to [130 311  22]\n",
      "Added appearance for \"n10\" in frame 2 with seed coordinates [ 130.  311.   22.]\n",
      "      Optimum energy:  81891.0\n",
      "      Nodes in/out:  9420 5940\n",
      "    Updated center to [129 309  20]\n",
      "Added appearance for \"n10\" in frame 3 with seed coordinates [ 129.  309.   20.]\n",
      "      Optimum energy:  82350.0\n",
      "      Nodes in/out:  9512 5848\n",
      "    Updated center to [127 309  18]\n",
      "Added appearance for \"n10\" in frame 4 with seed coordinates [ 127.  309.   18.]\n",
      "      Optimum energy:  78812.0\n",
      "      Nodes in/out:  9151 6209\n",
      "    Updated center to [126 308  17]\n",
      "Added appearance for \"n10\" in frame 5 with seed coordinates [ 126.  308.   17.]\n",
      "      Optimum energy:  77004.0\n",
      "      Nodes in/out:  9215 6145\n",
      "    Updated center to [125 307  16]\n",
      "Added appearance for \"n10\" in frame 6 with seed coordinates [ 125.  307.   16.]\n",
      "      Optimum energy:  78548.0\n",
      "      Nodes in/out:  9430 5930\n",
      "    Updated center to [124 306  16]\n",
      "Added appearance for \"n10\" in frame 7 with seed coordinates [ 124.  306.   16.]\n",
      "      Optimum energy:  74925.0\n",
      "      Nodes in/out:  9223 6137\n",
      "    Updated center to [124 305  16]\n",
      "Added appearance for \"n10\" in frame 8 with seed coordinates [ 124.  305.   16.]\n",
      "      Optimum energy:  76012.0\n",
      "      Nodes in/out:  8873 6487\n",
      "    Updated center to [123 304  16]\n",
      "Added appearance for \"n10\" in frame 9 with seed coordinates [ 123.  304.   16.]\n",
      "      Optimum energy:  73953.0\n",
      "      Nodes in/out:  9022 6338\n",
      "    Updated center to [122 301  16]\n",
      "Added appearance for \"n10\" in frame 10 with seed coordinates [ 122.  301.   16.]\n",
      "      Optimum energy:  76533.0\n",
      "      Nodes in/out:  8831 6529\n",
      "    Updated center to [120 298  16]\n",
      "Added appearance for \"n10\" in frame 11 with seed coordinates [ 120.  298.   16.]\n",
      "      Optimum energy:  79440.0\n",
      "      Nodes in/out:  9264 6096\n",
      "    Updated center to [117 292  16]\n",
      "Added appearance for \"n11\" in frame 0 with seed coordinates [ 125.  360.   24.]\n",
      "      Optimum energy:  78131.0\n",
      "      Nodes in/out:  9254 6106\n",
      "Added appearance for \"n11\" in frame 1 with seed coordinates [ 125.  360.   24.]\n",
      "      Optimum energy:  76691.0\n",
      "      Nodes in/out:  9322 6038\n",
      "    Updated center to [126 358  22]\n",
      "Added appearance for \"n11\" in frame 2 with seed coordinates [ 126.  358.   22.]\n",
      "      Optimum energy:  82059.0\n",
      "      Nodes in/out:  9783 5577\n",
      "    Updated center to [127 358  20]\n",
      "Added appearance for \"n11\" in frame 3 with seed coordinates [ 127.  358.   20.]\n",
      "      Optimum energy:  81012.0\n",
      "      Nodes in/out:  9249 6111\n",
      "    Updated center to [127 360  18]\n",
      "Added appearance for \"n11\" in frame 4 with seed coordinates [ 127.  360.   18.]\n",
      "      Optimum energy:  79684.0\n",
      "      Nodes in/out:  8979 6381\n",
      "    Updated center to [128 362  17]\n",
      "Added appearance for \"n11\" in frame 5 with seed coordinates [ 128.  362.   17.]\n",
      "      Optimum energy:  79197.0\n",
      "      Nodes in/out:  8972 6388\n",
      "    Updated center to [130 363  16]\n",
      "Added appearance for \"n11\" in frame 6 with seed coordinates [ 130.  363.   16.]\n",
      "      Optimum energy:  76492.0\n",
      "      Nodes in/out:  8640 6720\n",
      "    Updated center to [132 364  16]\n",
      "Added appearance for \"n11\" in frame 7 with seed coordinates [ 132.  364.   16.]\n",
      "      Optimum energy:  74672.0\n",
      "      Nodes in/out:  8511 6849\n",
      "    Updated center to [133 363  16]\n",
      "Added appearance for \"n11\" in frame 8 with seed coordinates [ 133.  363.   16.]\n",
      "      Optimum energy:  74230.0\n",
      "      Nodes in/out:  8298 7062\n",
      "    Updated center to [134 361  16]\n",
      "Added appearance for \"n11\" in frame 9 with seed coordinates [ 134.  361.   16.]\n",
      "      Optimum energy:  73342.0\n",
      "      Nodes in/out:  8286 7074\n",
      "    Updated center to [136 359  16]\n",
      "Added appearance for \"n11\" in frame 10 with seed coordinates [ 136.  359.   16.]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Optimum energy:  73711.0\n",
      "      Nodes in/out:  8251 7109\n",
      "    Updated center to [138 356  16]\n",
      "Added appearance for \"n11\" in frame 11 with seed coordinates [ 138.  356.   16.]\n",
      "      Optimum energy:  72743.0\n",
      "      Nodes in/out:  8129 7231\n",
      "    Updated center to [139 353  16]\n"
     ]
    }
   ],
   "source": [
    "nseeds = [( 90,390,12),\n",
    "          (150,410,12),\n",
    "          (200,390,12),\n",
    "          (190,315,12),\n",
    "          (145,265,12),\n",
    "          (110,230,12),\n",
    "          ( 40,255,12),\n",
    "          ( 45,300,18),\n",
    "          ( 67,355,18),\n",
    "          (110,275,24),\n",
    "          (130,315,24),\n",
    "          (125,360,24)]\n",
    "for i in range(len(nseeds)):\n",
    "    data.add_object_at( neighbors[i], min_rs, max_rs, frame=0, seed=nseeds[i], segment_it=True )\n",
    "    data.track(neighbors[i], seed_frame=0, target_frames=range(1,len(data.images)), recenter_iterations=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## adding others"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "others = []\n",
    "for i in range(7):\n",
    "    o = data.init_object(\"o\"+str(i))\n",
    "    objects.append(o)\n",
    "    others.append(o)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added appearance for \"o0\" in frame 0 with seed coordinates [  70.  205.   12.]\n",
      "      Optimum energy:  79859.0\n",
      "      Nodes in/out:  7453 7907\n",
      "Added appearance for \"o0\" in frame 1 with seed coordinates [  70.  205.   12.]\n",
      "      Optimum energy:  79123.0\n",
      "      Nodes in/out:  7182 8178\n",
      "    Updated center to [ 67 204  11]\n",
      "Added appearance for \"o0\" in frame 2 with seed coordinates [  67.  204.   11.]\n",
      "      Optimum energy:  78390.0\n",
      "      Nodes in/out:  7041 8319\n",
      "    Updated center to [ 66 204  11]\n",
      "Added appearance for \"o0\" in frame 3 with seed coordinates [  66.  204.   11.]\n",
      "      Optimum energy:  77943.0\n",
      "      Nodes in/out:  6966 8394\n",
      "    Updated center to [ 66 203  11]\n",
      "Added appearance for \"o0\" in frame 4 with seed coordinates [  66.  203.   11.]\n",
      "      Optimum energy:  76368.0\n",
      "      Nodes in/out:  6878 8482\n",
      "    Updated center to [ 65 203  11]\n",
      "Added appearance for \"o0\" in frame 5 with seed coordinates [  65.  203.   11.]\n",
      "      Optimum energy:  74884.0\n",
      "      Nodes in/out:  6739 8621\n",
      "    Updated center to [ 65 202  11]\n",
      "Added appearance for \"o0\" in frame 6 with seed coordinates [  65.  202.   11.]\n",
      "      Optimum energy:  74215.0\n",
      "      Nodes in/out:  6968 8392\n",
      "    Updated center to [ 64 202  11]\n",
      "Added appearance for \"o0\" in frame 7 with seed coordinates [  64.  202.   11.]\n",
      "      Optimum energy:  74843.0\n",
      "      Nodes in/out:  7122 8238\n",
      "    Updated center to [ 62 202  11]\n",
      "Added appearance for \"o0\" in frame 8 with seed coordinates [  62.  202.   11.]\n",
      "      Optimum energy:  73133.0\n",
      "      Nodes in/out:  6843 8517\n",
      "    Updated center to [ 60 202  11]\n",
      "Added appearance for \"o0\" in frame 9 with seed coordinates [  60.  202.   11.]\n",
      "      Optimum energy:  73853.0\n",
      "      Nodes in/out:  6850 8510\n",
      "    Updated center to [ 58 203  11]\n",
      "Added appearance for \"o0\" in frame 10 with seed coordinates [  58.  203.   11.]\n",
      "      Optimum energy:  73281.0\n",
      "      Nodes in/out:  7048 8312\n",
      "    Updated center to [ 57 204  11]\n",
      "Added appearance for \"o0\" in frame 11 with seed coordinates [  57.  204.   11.]\n",
      "      Optimum energy:  72447.0\n",
      "      Nodes in/out:  7148 8212\n",
      "    Updated center to [ 58 205  11]\n",
      "Added appearance for \"o1\" in frame 0 with seed coordinates [ 145.  170.   12.]\n",
      "      Optimum energy:  79468.0\n",
      "      Nodes in/out:  7463 7897\n",
      "Added appearance for \"o1\" in frame 1 with seed coordinates [ 145.  170.   12.]\n",
      "      Optimum energy:  77890.0\n",
      "      Nodes in/out:  7401 7959\n",
      "    Updated center to [143 170  12]\n",
      "Added appearance for \"o1\" in frame 2 with seed coordinates [ 143.  170.   12.]\n",
      "      Optimum energy:  76299.0\n",
      "      Nodes in/out:  7550 7810\n",
      "    Updated center to [143 170  12]\n",
      "Added appearance for \"o1\" in frame 3 with seed coordinates [ 143.  170.   12.]\n",
      "      Optimum energy:  75716.0\n",
      "      Nodes in/out:  7416 7944\n",
      "    Updated center to [143 171  12]\n",
      "Added appearance for \"o1\" in frame 4 with seed coordinates [ 143.  171.   12.]\n",
      "      Optimum energy:  73819.0\n",
      "      Nodes in/out:  7408 7952\n",
      "    Updated center to [143 170  12]\n",
      "Added appearance for \"o1\" in frame 5 with seed coordinates [ 143.  170.   12.]\n",
      "      Optimum energy:  73959.0\n",
      "      Nodes in/out:  7406 7954\n",
      "    Updated center to [143 169  12]\n",
      "Added appearance for \"o1\" in frame 6 with seed coordinates [ 143.  169.   12.]\n",
      "      Optimum energy:  72926.0\n",
      "      Nodes in/out:  7233 8127\n",
      "    Updated center to [141 169  12]\n",
      "Added appearance for \"o1\" in frame 7 with seed coordinates [ 141.  169.   12.]\n",
      "      Optimum energy:  73685.0\n",
      "      Nodes in/out:  5266 10094\n",
      "    Updated center to [137 174  11]\n",
      "Added appearance for \"o1\" in frame 8 with seed coordinates [ 137.  174.   11.]\n",
      "      Optimum energy:  72566.0\n",
      "      Nodes in/out:  5575 9785\n",
      "    Updated center to [134 177  10]\n",
      "Added appearance for \"o1\" in frame 9 with seed coordinates [ 134.  177.   10.]\n",
      "      Optimum energy:  74338.0\n",
      "      Nodes in/out:  4863 10497\n",
      "    Updated center to [132 180  10]\n",
      "Added appearance for \"o1\" in frame 10 with seed coordinates [ 132.  180.   10.]\n",
      "      Optimum energy:  75345.0\n",
      "      Nodes in/out:  5268 10092\n",
      "    Updated center to [130 183  10]\n",
      "Added appearance for \"o1\" in frame 11 with seed coordinates [ 130.  183.   10.]\n",
      "      Optimum energy:  72213.0\n",
      "      Nodes in/out:  5246 10114\n",
      "    Updated center to [129 185  10]\n",
      "Added appearance for \"o2\" in frame 0 with seed coordinates [  50.  160.   12.]\n",
      "      Optimum energy:  86055.0\n",
      "      Nodes in/out:  4930 10430\n",
      "Added appearance for \"o2\" in frame 1 with seed coordinates [  50.  160.   12.]\n",
      "      Optimum energy:  84946.0\n",
      "      Nodes in/out:  4205 11155\n",
      "    Updated center to [ 51 159  13]\n",
      "Added appearance for \"o2\" in frame 2 with seed coordinates [  51.  159.   13.]\n",
      "      Optimum energy:  75165.0\n",
      "      Nodes in/out:  5974 9386\n",
      "    Updated center to [ 52 160  14]\n",
      "Added appearance for \"o2\" in frame 3 with seed coordinates [  52.  160.   14.]\n",
      "      Optimum energy:  74464.0\n",
      "      Nodes in/out:  6528 8832\n",
      "    Updated center to [ 53 160  15]\n",
      "Added appearance for \"o2\" in frame 4 with seed coordinates [  53.  160.   15.]\n",
      "      Optimum energy:  71279.0\n",
      "      Nodes in/out:  7138 8222\n",
      "    Updated center to [ 54 161  15]\n",
      "Added appearance for \"o2\" in frame 5 with seed coordinates [  54.  161.   15.]\n",
      "      Optimum energy:  74554.0\n",
      "      Nodes in/out:  6271 9089\n",
      "    Updated center to [ 54 163  15]\n",
      "Added appearance for \"o2\" in frame 6 with seed coordinates [  54.  163.   15.]\n",
      "      Optimum energy:  78489.0\n",
      "      Nodes in/out:  3451 11909\n",
      "    Updated center to [ 53 166  15]\n",
      "Added appearance for \"o2\" in frame 7 with seed coordinates [  53.  166.   15.]\n",
      "      Optimum energy:  76633.0\n",
      "      Nodes in/out:  3339 12021\n",
      "    Updated center to [ 51 167  14]\n",
      "Added appearance for \"o2\" in frame 8 with seed coordinates [  51.  167.   14.]\n",
      "      Optimum energy:  73425.0\n",
      "      Nodes in/out:  3249 12111\n",
      "    Updated center to [ 50 166  14]\n",
      "Added appearance for \"o2\" in frame 9 with seed coordinates [  50.  166.   14.]\n",
      "      Optimum energy:  73863.0\n",
      "      Nodes in/out:  3596 11764\n",
      "    Updated center to [ 50 165  14]\n",
      "Added appearance for \"o2\" in frame 10 with seed coordinates [  50.  165.   14.]\n",
      "      Optimum energy:  72200.0\n",
      "      Nodes in/out:  3845 11515\n",
      "    Updated center to [ 49 165  14]\n",
      "Added appearance for \"o2\" in frame 11 with seed coordinates [  49.  165.   14.]\n",
      "      Optimum energy:  71988.0\n",
      "      Nodes in/out:  3580 11780\n",
      "    Updated center to [ 48 163  14]\n",
      "Added appearance for \"o3\" in frame 0 with seed coordinates [ 105.  140.   12.]\n",
      "      Optimum energy:  76778.0\n",
      "      Nodes in/out:  6732 8628\n",
      "Added appearance for \"o3\" in frame 1 with seed coordinates [ 105.  140.   12.]\n",
      "      Optimum energy:  75438.0\n",
      "      Nodes in/out:  6809 8551\n",
      "    Updated center to [104 139  12]\n",
      "Added appearance for \"o3\" in frame 2 with seed coordinates [ 104.  139.   12.]\n",
      "      Optimum energy:  72651.0\n",
      "      Nodes in/out:  6769 8591\n",
      "    Updated center to [103 139  12]\n",
      "Added appearance for \"o3\" in frame 3 with seed coordinates [ 103.  139.   12.]\n",
      "      Optimum energy:  71398.0\n",
      "      Nodes in/out:  6755 8605\n",
      "    Updated center to [103 139  12]\n",
      "Added appearance for \"o3\" in frame 4 with seed coordinates [ 103.  139.   12.]\n",
      "      Optimum energy:  70839.0\n",
      "      Nodes in/out:  6647 8713\n",
      "    Updated center to [103 139  12]\n",
      "Added appearance for \"o3\" in frame 5 with seed coordinates [ 103.  139.   12.]\n",
      "      Optimum energy:  70911.0\n",
      "      Nodes in/out:  6713 8647\n",
      "    Updated center to [102 139  12]\n",
      "Added appearance for \"o3\" in frame 6 with seed coordinates [ 102.  139.   12.]\n",
      "      Optimum energy:  72522.0\n",
      "      Nodes in/out:  5876 9484\n",
      "    Updated center to [ 99 140  12]\n",
      "Added appearance for \"o3\" in frame 7 with seed coordinates [  99.  140.   12.]\n",
      "      Optimum energy:  72124.0\n",
      "      Nodes in/out:  4055 11305\n",
      "    Updated center to [ 96 144  11]\n",
      "Added appearance for \"o3\" in frame 8 with seed coordinates [  96.  144.   11.]\n",
      "      Optimum energy:  72493.0\n",
      "      Nodes in/out:  4220 11140\n",
      "    Updated center to [ 92 148  11]\n",
      "Added appearance for \"o3\" in frame 9 with seed coordinates [  92.  148.   11.]\n",
      "      Optimum energy:  71475.0\n",
      "      Nodes in/out:  5120 10240\n",
      "    Updated center to [ 90 150  11]\n",
      "Added appearance for \"o3\" in frame 10 with seed coordinates [  90.  150.   11.]\n",
      "      Optimum energy:  71518.0\n",
      "      Nodes in/out:  4911 10449\n",
      "    Updated center to [ 89 153  11]\n",
      "Added appearance for \"o3\" in frame 11 with seed coordinates [  89.  153.   11.]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Optimum energy:  71222.0\n",
      "      Nodes in/out:  5111 10249\n",
      "    Updated center to [ 89 154  11]\n",
      "Added appearance for \"o4\" in frame 0 with seed coordinates [ 190.  220.   12.]\n",
      "      Optimum energy:  83505.0\n",
      "      Nodes in/out:  6591 8769\n",
      "Added appearance for \"o4\" in frame 1 with seed coordinates [ 190.  220.   12.]\n",
      "      Optimum energy:  82542.0\n",
      "      Nodes in/out:  6615 8745\n",
      "    Updated center to [186 215  12]\n",
      "Added appearance for \"o4\" in frame 2 with seed coordinates [ 186.  215.   12.]\n",
      "      Optimum energy:  75998.0\n",
      "      Nodes in/out:  7176 8184\n",
      "    Updated center to [184 212  12]\n",
      "Added appearance for \"o4\" in frame 3 with seed coordinates [ 184.  212.   12.]\n",
      "      Optimum energy:  76277.0\n",
      "      Nodes in/out:  7180 8180\n",
      "    Updated center to [183 211  12]\n",
      "Added appearance for \"o4\" in frame 4 with seed coordinates [ 183.  211.   12.]\n",
      "      Optimum energy:  73714.0\n",
      "      Nodes in/out:  7052 8308\n",
      "    Updated center to [183 210  12]\n",
      "Added appearance for \"o4\" in frame 5 with seed coordinates [ 183.  210.   12.]\n",
      "      Optimum energy:  77603.0\n",
      "      Nodes in/out:  6800 8560\n",
      "    Updated center to [182 210  12]\n",
      "Added appearance for \"o4\" in frame 6 with seed coordinates [ 182.  210.   12.]\n",
      "      Optimum energy:  73715.0\n",
      "      Nodes in/out:  5352 10008\n",
      "    Updated center to [180 212  11]\n",
      "Added appearance for \"o4\" in frame 7 with seed coordinates [ 180.  212.   11.]\n",
      "      Optimum energy:  73757.0\n",
      "      Nodes in/out:  5360 10000\n",
      "    Updated center to [179 213  11]\n",
      "Added appearance for \"o4\" in frame 8 with seed coordinates [ 179.  213.   11.]\n",
      "      Optimum energy:  75098.0\n",
      "      Nodes in/out:  5388 9972\n",
      "    Updated center to [178 214  10]\n",
      "Added appearance for \"o4\" in frame 9 with seed coordinates [ 178.  214.   10.]\n",
      "      Optimum energy:  75293.0\n",
      "      Nodes in/out:  4884 10476\n",
      "    Updated center to [177 214  10]\n",
      "Added appearance for \"o4\" in frame 10 with seed coordinates [ 177.  214.   10.]\n",
      "      Optimum energy:  74230.0\n",
      "      Nodes in/out:  5130 10230\n",
      "    Updated center to [176 214  10]\n",
      "Added appearance for \"o4\" in frame 11 with seed coordinates [ 176.  214.   10.]\n",
      "      Optimum energy:  73585.0\n",
      "      Nodes in/out:  4961 10399\n",
      "    Updated center to [176 215  10]\n",
      "Added appearance for \"o5\" in frame 0 with seed coordinates [ 200.  265.   12.]\n",
      "      Optimum energy:  85823.0\n",
      "      Nodes in/out:  7119 8241\n",
      "Added appearance for \"o5\" in frame 1 with seed coordinates [ 200.  265.   12.]\n",
      "      Optimum energy:  81595.0\n",
      "      Nodes in/out:  7233 8127\n",
      "    Updated center to [200 262  12]\n",
      "Added appearance for \"o5\" in frame 2 with seed coordinates [ 200.  262.   12.]\n",
      "      Optimum energy:  78375.0\n",
      "      Nodes in/out:  6818 8542\n",
      "    Updated center to [201 261  12]\n",
      "Added appearance for \"o5\" in frame 3 with seed coordinates [ 201.  261.   12.]\n",
      "      Optimum energy:  79132.0\n",
      "      Nodes in/out:  6269 9091\n",
      "    Updated center to [203 262  13]\n",
      "Added appearance for \"o5\" in frame 4 with seed coordinates [ 203.  262.   13.]\n",
      "      Optimum energy:  77753.0\n",
      "      Nodes in/out:  6995 8365\n",
      "    Updated center to [204 262  13]\n",
      "Added appearance for \"o5\" in frame 5 with seed coordinates [ 204.  262.   13.]\n",
      "      Optimum energy:  75818.0\n",
      "      Nodes in/out:  6519 8841\n",
      "    Updated center to [205 263  13]\n",
      "Added appearance for \"o5\" in frame 6 with seed coordinates [ 205.  263.   13.]\n",
      "      Optimum energy:  77145.0\n",
      "      Nodes in/out:  6269 9091\n",
      "    Updated center to [205 264  12]\n",
      "Added appearance for \"o5\" in frame 7 with seed coordinates [ 205.  264.   12.]\n",
      "      Optimum energy:  75469.0\n",
      "      Nodes in/out:  6202 9158\n",
      "    Updated center to [204 263  12]\n",
      "Added appearance for \"o5\" in frame 8 with seed coordinates [ 204.  263.   12.]\n",
      "      Optimum energy:  73932.0\n",
      "      Nodes in/out:  6021 9339\n",
      "    Updated center to [203 261  12]\n",
      "Added appearance for \"o5\" in frame 9 with seed coordinates [ 203.  261.   12.]\n",
      "      Optimum energy:  73101.0\n",
      "      Nodes in/out:  5907 9453\n",
      "    Updated center to [202 259  12]\n",
      "Added appearance for \"o5\" in frame 10 with seed coordinates [ 202.  259.   12.]\n",
      "      Optimum energy:  72664.0\n",
      "      Nodes in/out:  6250 9110\n",
      "    Updated center to [201 259  12]\n",
      "Added appearance for \"o5\" in frame 11 with seed coordinates [ 201.  259.   12.]\n",
      "      Optimum energy:  73871.0\n",
      "      Nodes in/out:  6114 9246\n",
      "    Updated center to [201 260  12]\n",
      "Added appearance for \"o6\" in frame 0 with seed coordinates [ 220.  335.   20.]\n",
      "      Optimum energy:  83500.0\n",
      "      Nodes in/out:  7189 8171\n",
      "Added appearance for \"o6\" in frame 1 with seed coordinates [ 220.  335.   20.]\n",
      "      Optimum energy:  78491.0\n",
      "      Nodes in/out:  7594 7766\n",
      "    Updated center to [218 333  18]\n",
      "Added appearance for \"o6\" in frame 2 with seed coordinates [ 218.  333.   18.]\n",
      "      Optimum energy:  81945.0\n",
      "      Nodes in/out:  9480 5880\n",
      "    Updated center to [214 332  17]\n",
      "Added appearance for \"o6\" in frame 3 with seed coordinates [ 214.  332.   17.]\n",
      "      Optimum energy:  80342.0\n",
      "      Nodes in/out:  9660 5700\n",
      "    Updated center to [211 330  16]\n",
      "Added appearance for \"o6\" in frame 4 with seed coordinates [ 211.  330.   16.]\n",
      "      Optimum energy:  83728.0\n",
      "      Nodes in/out:  9089 6271\n",
      "    Updated center to [210 328  15]\n",
      "Added appearance for \"o6\" in frame 5 with seed coordinates [ 210.  328.   15.]\n",
      "      Optimum energy:  74070.0\n",
      "      Nodes in/out:  5772 9588\n",
      "    Updated center to [203 325  13]\n",
      "Added appearance for \"o6\" in frame 6 with seed coordinates [ 203.  325.   13.]\n",
      "      Optimum energy:  71882.0\n",
      "      Nodes in/out:  6938 8422\n",
      "    Updated center to [199 323  12]\n",
      "Added appearance for \"o6\" in frame 7 with seed coordinates [ 199.  323.   12.]\n",
      "      Optimum energy:  74564.0\n",
      "      Nodes in/out:  6377 8983\n",
      "    Updated center to [196 321  12]\n",
      "Added appearance for \"o6\" in frame 8 with seed coordinates [ 196.  321.   12.]\n",
      "      Optimum energy:  75542.0\n",
      "      Nodes in/out:  6398 8962\n",
      "    Updated center to [195 320  12]\n",
      "Added appearance for \"o6\" in frame 9 with seed coordinates [ 195.  320.   12.]\n",
      "      Optimum energy:  77198.0\n",
      "      Nodes in/out:  6667 8693\n",
      "    Updated center to [196 321  12]\n",
      "Added appearance for \"o6\" in frame 10 with seed coordinates [ 196.  321.   12.]\n",
      "      Optimum energy:  77276.0\n",
      "      Nodes in/out:  6566 8794\n",
      "    Updated center to [196 321  12]\n",
      "Added appearance for \"o6\" in frame 11 with seed coordinates [ 196.  321.   12.]\n",
      "      Optimum energy:  75354.0\n",
      "      Nodes in/out:  5444 9916\n",
      "    Updated center to [195 321  11]\n"
     ]
    }
   ],
   "source": [
    "oseeds = [( 70,205,12),\n",
    "          (145,170,12),\n",
    "          ( 50,160,12),\n",
    "          (105,140,12),\n",
    "          (190,220,12),\n",
    "          (200,265,12),\n",
    "          (220,335,20)]\n",
    "for i in range(len(oseeds)):\n",
    "    data.add_object_at( others[i], min_rs, max_rs, frame=0, seed=oseeds[i], segment_it=True )\n",
    "    data.track(others[i], seed_frame=0, target_frames=range(1,len(data.images)), recenter_iterations=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Save / Load"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "data.save('/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry.pkl')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "data = Data4d( [], silent=False )\n",
    "data.load('/Users/jug/Dropbox/ProjectGoldstein/2016-09-22_fromMark/092216_PH-mCherry-02_w2SD mCherry.pkl')\n",
    "objects = range(len(data.object_names))\n",
    "ecells = [0,1]\n",
    "neighbors = range(2,2+12)\n",
    "others = range(2+12,2+12+7)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualisation stuff "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "w = data.show_frame(0,stackUnits=[1.,1.,5.],raise_window=True)\n",
    "#data.show_objects(ecells, show_surfaces=True, show_centers=True, colors=data.colors_gold)\n",
    "#try:\n",
    "#    data.show_objects(neighbors, show_surfaces=True, show_centers=True, colors=data.colors_green)\n",
    "#    data.show_objects(others, show_surfaces=True, show_centers=True, colors=data.colors_blue)\n",
    "#except:\n",
    "#    None\n",
    "#data.show_objects(neighbors, show_surfaces=True, show_centers=True, colors=data.colors_green)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  1 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame0.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  2 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame1.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  3 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame2.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  4 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame3.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  5 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame4.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  6 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame5.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  7 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame6.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  8 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame7.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  9 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame8.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  10 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame9.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  11 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame10.jpg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  12 of 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:spimagine.gui.glwidget | saving frame as 3dframes/frame11.jpg\n"
     ]
    }
   ],
   "source": [
    "for f in range(len(data.images)):\n",
    "    print 'Exporting frame ',f+1,'of',len(data.images)\n",
    "    w = data.show_frame(f,stackUnits=[1.,1.,5.],raise_window=False)\n",
    "    data.show_objects(ecells, show_surfaces=True, show_centers=True, colors=data.colors_gold)\n",
    "    try:\n",
    "        data.show_objects(neighbors, show_surfaces=True, show_centers=True, colors=data.colors_green)\n",
    "        data.show_objects(others, show_surfaces=True, show_centers=True, colors=data.colors_blue)\n",
    "    except:\n",
    "        None\n",
    "    data.save_current_visualization( '3dframes/frame'+str(f)+'.jpg' )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.object_volumes[Ea]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}