Python Course Lecture 6a Image Analysis.ipynb

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   "source": [
    "# Python Course Lecture 6a: Images"
   ]
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   "source": [
    "import skimage\n",
    "from skimage import io\n",
    "from scipy import ndimage\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from IPython.display import HTML, Image\n",
    "\n",
    "%matplotlib inline"
   ]
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    "# Image Analysis Packages\n",
    "\n",
    "There are lots of useful image analysis packages out there, all of which are worthwile.  I'll stick to scikit-image for this lecture, but I also find the following packages very useful:\n",
    "\n",
    "   - Scikit-image\n",
    "   - OpenCV 2 (and 3 is coming out soon!)\n",
    "   - Scipy.ndimage\n",
    "   - Python Imaging Library (PIL) and Pillow\n",
    "   \n",
    "   \n",
    "   \n",
    "Remember: Search for a function before trying to implement it yourself--you'll save a whole lot of time, really!"
   ]
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   "outputs": [
    {
     "ename": "URLError",
     "evalue": "<urlopen error [Errno -2] Name or service not known>",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mgaierror\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36mdo_open\u001b[1;34m(self, http_class, req, **http_conn_args)\u001b[0m\n\u001b[0;32m   1239\u001b[0m             \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1240\u001b[1;33m                 \u001b[0mh\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrequest\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_method\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mselector\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mheaders\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1241\u001b[0m             \u001b[1;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;31m# timeout error\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36mrequest\u001b[1;34m(self, method, url, body, headers)\u001b[0m\n\u001b[0;32m   1082\u001b[0m         \u001b[1;34m\"\"\"Send a complete request to the server.\"\"\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1083\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_send_request\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmethod\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0murl\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mbody\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mheaders\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1084\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36m_send_request\u001b[1;34m(self, method, url, body, headers)\u001b[0m\n\u001b[0;32m   1127\u001b[0m             \u001b[0mbody\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbody\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mencode\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'iso-8859-1'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1128\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mendheaders\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mbody\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1129\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36mendheaders\u001b[1;34m(self, message_body)\u001b[0m\n\u001b[0;32m   1078\u001b[0m             \u001b[1;32mraise\u001b[0m \u001b[0mCannotSendHeader\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1079\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_send_output\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmessage_body\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1080\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36m_send_output\u001b[1;34m(self, message_body)\u001b[0m\n\u001b[0;32m    910\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 911\u001b[1;33m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    912\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mmessage_body\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36msend\u001b[1;34m(self, data)\u001b[0m\n\u001b[0;32m    853\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mauto_open\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 854\u001b[1;33m                 \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mconnect\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    855\u001b[0m             \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/http/client.py\u001b[0m in \u001b[0;36mconnect\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    825\u001b[0m         self.sock = self._create_connection(\n\u001b[1;32m--> 826\u001b[1;33m             (self.host,self.port), self.timeout, self.source_address)\n\u001b[0m\u001b[0;32m    827\u001b[0m         \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msock\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msetsockopt\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msocket\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mIPPROTO_TCP\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msocket\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mTCP_NODELAY\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/socket.py\u001b[0m in \u001b[0;36mcreate_connection\u001b[1;34m(address, timeout, source_address)\u001b[0m\n\u001b[0;32m    692\u001b[0m     \u001b[0merr\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 693\u001b[1;33m     \u001b[1;32mfor\u001b[0m \u001b[0mres\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mgetaddrinfo\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mhost\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mport\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mSOCK_STREAM\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    694\u001b[0m         \u001b[0maf\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msocktype\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mproto\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mcanonname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msa\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/socket.py\u001b[0m in \u001b[0;36mgetaddrinfo\u001b[1;34m(host, port, family, type, proto, flags)\u001b[0m\n\u001b[0;32m    731\u001b[0m     \u001b[0maddrlist\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m[\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 732\u001b[1;33m     \u001b[1;32mfor\u001b[0m \u001b[0mres\u001b[0m \u001b[1;32min\u001b[0m \u001b[0m_socket\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetaddrinfo\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mhost\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mport\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfamily\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtype\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mproto\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mflags\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    733\u001b[0m         \u001b[0maf\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msocktype\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mproto\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mcanonname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msa\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mgaierror\u001b[0m: [Errno -2] Name or service not known",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[1;31mURLError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-2-05d47af354a9>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mcell\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mio\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mimread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"http://www.public.asu.edu/~wtyler/lab/Optical%20Imaging_files/ca3-ca3-dualpatch-slice-filtered.png\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[0mcell\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcell\u001b[0m \u001b[1;33m/\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0marray\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0muint8\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[0mcell\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcell\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0muint8\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[0mplt\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mimshow\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mcell\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mtype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mcell\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/site-packages/skimage/io/_io.py\u001b[0m in \u001b[0;36mimread\u001b[1;34m(fname, as_grey, plugin, flatten, **plugin_args)\u001b[0m\n\u001b[0;32m     58\u001b[0m             \u001b[0mplugin\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m'tifffile'\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     59\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 60\u001b[1;33m     \u001b[1;32mwith\u001b[0m \u001b[0mfile_or_url_context\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mfname\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     61\u001b[0m         \u001b[0mimg\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcall_plugin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'imread'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mplugin\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mplugin\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0mplugin_args\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     62\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/contextlib.py\u001b[0m in \u001b[0;36m__enter__\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m     57\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m__enter__\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[0;32m     58\u001b[0m         \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 59\u001b[1;33m             \u001b[1;32mreturn\u001b[0m \u001b[0mnext\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgen\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     60\u001b[0m         \u001b[1;32mexcept\u001b[0m \u001b[0mStopIteration\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     61\u001b[0m             \u001b[1;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"generator didn't yield\"\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/site-packages/skimage/io/util.py\u001b[0m in \u001b[0;36mfile_or_url_context\u001b[1;34m(resource_name)\u001b[0m\n\u001b[0;32m     27\u001b[0m         \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     28\u001b[0m             \u001b[1;32mwith\u001b[0m \u001b[0mtempfile\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mNamedTemporaryFile\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdelete\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mFalse\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msuffix\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mext\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 29\u001b[1;33m                 \u001b[0mu\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0murlopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mresource_name\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     30\u001b[0m                 \u001b[0mf\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mu\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     31\u001b[0m             \u001b[1;31m# f must be closed before yielding\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36murlopen\u001b[1;34m(url, data, timeout, cafile, capath, cadefault, context)\u001b[0m\n\u001b[0;32m    160\u001b[0m     \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    161\u001b[0m         \u001b[0mopener\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0m_opener\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 162\u001b[1;33m     \u001b[1;32mreturn\u001b[0m \u001b[0mopener\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0murl\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    163\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    164\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0minstall_opener\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mopener\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36mopen\u001b[1;34m(self, fullurl, data, timeout)\u001b[0m\n\u001b[0;32m    463\u001b[0m             \u001b[0mreq\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mmeth\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mreq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    464\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 465\u001b[1;33m         \u001b[0mresponse\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_open\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mreq\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    466\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    467\u001b[0m         \u001b[1;31m# post-process response\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36m_open\u001b[1;34m(self, req, data)\u001b[0m\n\u001b[0;32m    481\u001b[0m         \u001b[0mprotocol\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtype\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    482\u001b[0m         result = self._call_chain(self.handle_open, protocol, protocol +\n\u001b[1;32m--> 483\u001b[1;33m                                   '_open', req)\n\u001b[0m\u001b[0;32m    484\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mresult\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    485\u001b[0m             \u001b[1;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36m_call_chain\u001b[1;34m(self, chain, kind, meth_name, *args)\u001b[0m\n\u001b[0;32m    441\u001b[0m         \u001b[1;32mfor\u001b[0m \u001b[0mhandler\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mhandlers\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    442\u001b[0m             \u001b[0mfunc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mhandler\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmeth_name\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 443\u001b[1;33m             \u001b[0mresult\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m*\u001b[0m\u001b[0margs\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    444\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    445\u001b[0m                 \u001b[1;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36mhttp_open\u001b[1;34m(self, req)\u001b[0m\n\u001b[0;32m   1266\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1267\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0mhttp_open\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1268\u001b[1;33m         \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdo_open\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mhttp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mclient\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mHTTPConnection\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1269\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1270\u001b[0m     \u001b[0mhttp_request\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mAbstractHTTPHandler\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdo_request_\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/nickdg/anaconda3/lib/python3.5/urllib/request.py\u001b[0m in \u001b[0;36mdo_open\u001b[1;34m(self, http_class, req, **http_conn_args)\u001b[0m\n\u001b[0;32m   1240\u001b[0m                 \u001b[0mh\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrequest\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_method\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mselector\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mheaders\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1241\u001b[0m             \u001b[1;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;31m# timeout error\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1242\u001b[1;33m                 \u001b[1;32mraise\u001b[0m \u001b[0mURLError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0merr\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1243\u001b[0m             \u001b[0mr\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mh\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgetresponse\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1244\u001b[0m         \u001b[1;32mexcept\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mURLError\u001b[0m: <urlopen error [Errno -2] Name or service not known>"
     ]
    }
   ],
   "source": [
    "cell = io.imread(\"http://www.public.asu.edu/~wtyler/lab/Optical%20Imaging_files/ca3-ca3-dualpatch-slice-filtered.png\") \n",
    "cell = cell / np.array([2, 2, 2, 1], dtype=np.uint8)\n",
    "cell = cell.astype(np.uint8)\n",
    "plt.imshow(cell)\n",
    "print(type(cell))\n",
    "print(cell.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell.dtype"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## The Relative Weights in the Brightness of Each Color produces a wide Color Range"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Image(url=\"https://www.kirupa.com/images/rgb_image.png\", width=300)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Images are 2D (grayscale) or 3D (color) Arrays"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.imshow(cell[:, :, 0], cmap='gray')\n",
    "\n",
    "fig, axes = plt.subplots(nrows=1, ncols=cell.shape[2])\n",
    "for img, ax in zip(cell.swapaxes(0,2), axes):\n",
    "    ax.imshow(img.T, cmap='gray')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Image DType: 8-bit Unsiged Int\n",
    "Color brightness levels are often encoded using the integers 0-255.  To guarantee this, and to save space, the DType of image data is an **unsigned, 8-bit integer**.\n",
    "  - **unsigned** means the numbers are all positive (they can't contain a negative sign)\n",
    "  - **8-bit** is the number of bits that encode the value in binary.  An 8-bit number can code the values 2^8, which is 255."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'0b101000'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bin(40)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Aside: Binary Encoding has Maximum Range\n",
    "Make sure that the encoding you choose can represent the full range of your data, or you'll get unexpected results."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[  0  25  50  75 100]\n",
      "[  0 100 200  44 144]\n"
     ]
    }
   ],
   "source": [
    "increasing = np.linspace(0, 100, 5, dtype=np.uint8)\n",
    "print(increasing)\n",
    "print(increasing * 4)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Aside: Binary Encoding has Maximum Precision\n",
    "Performing multiple mathematical steps on data can result in **floating point errors**.  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "69.82 69.82000000000001\n"
     ]
    }
   ],
   "source": [
    "a = 69.82\n",
    "b = 69.2 + .62\n",
    "print(a, b)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Be Aware of Floating Point Errors When:\n",
    "  - Rounding\n",
    "  - Subracting two almost-equal values (ex: .1235 - .1234)\n",
    "  - Exceeding Max and Min Values of the Encoding Scheme\n",
    "  - Dividing by very small numbers (ex: 112000000. - 100000. / .0009)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Demo: Simple Image Processing Algorithms using NumPy"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "### Brightening"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell_bright = cell * 2\n",
    "plt.imshow(cell_bright)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "### Cropping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell_cropped = cell_bright[90:-40, 5:-5, :]\n",
    "plt.imshow(cell_cropped)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "### Downsampling, without Interpolation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell_small = cell_bright[::7, ::7, :]\n",
    "plt.imshow(cell_small)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## RGB-Specific Selection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "green = cell_bright[:, :, 1]\n",
    "plt.imshow(green, cmap='gray')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## In Short: Analysis Boils Down to Array Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell_mean = np.mean(cell_bright, axis=0)\n",
    "fig, ax = plt.subplots()\n",
    "plt.plot(cell_mean[:, 0], 'r', label='Red')\n",
    "plt.plot(cell_mean[:, 1], 'g', label='Green')\n",
    "plt.title(\"Average Fluorescence over Horizontal Axis of Image\"); plt.ylabel('Image Brightness'); plt.legend()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Image Analysis Demos using Image-Specific Packages"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Image Rotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cell45 = ndimage.rotate(cell_bright, 45)\n",
    "plt.imshow(cell45)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Gaussian Blurring"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "red_blurred = ndimage.gaussian_filter(cell_bright[:, :, 0], 2, order=0)\n",
    "plt.imshow(red_blurred, cmap='gray')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Edge Detection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from skimage import feature\n",
    "red_edges = feature.canny(red_blurred, 2)\n",
    "plt.imshow(red_edges, cmap='gray')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Skeletonization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from skimage.morphology import convex_hull_image, skeletonize\n",
    "\n",
    "red_neuron = skeletonize(red_blurred > 50)\n",
    "plt.imshow(red_neuron, cmap='gray')\n"
   ]
  }
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