{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Thresholding"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import numpy as np\n",
    "import skimage\n",
    "import matplotlib.pyplot as plt\n",
    "import pandas as pd\n",
    "import urllib\n",
    "#import ipyvolume as ipv\n",
    "import ipywidgets as ipw\n",
    "if not os.path.isfile('Samples/confocal2.tif'):\n",
    "    if not os.path.isdir('Samples'):\n",
    "        os.mkdir('Samples')\n",
    "    #url = 'https://cildata.crbs.ucsd.edu/media/images/10494/10494.tif'\n",
    "    url = 'https://cildata.crbs.ucsd.edu/media/images/41694/41694.tif'\n",
    "    urllib.request.urlretrieve(url, 'Samples/confocal2.tif');\n",
    "\n",
    "image = skimage.io.imread('Samples/confocal2.tif')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def thresholding(level, image):\n",
    "    fig = plt.figure(figsize=(10,10))\n",
    "    ax1 = plt.subplot(1,2,1)\n",
    "    plt.imshow(image[:,:,2], cmap = 'gray')\n",
    "    ax1 = plt.subplot(1,2,2)\n",
    "    plt.imshow((image[:,:,2]>level).astype(int), cmap = 'gray',vmin = 0, vmax = 1)\n",
    "    plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d8fbb7b05d8b47e680ca7b3e1e7def10",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(IntSlider(value=0, description='level', max=255), Output()), _dom_classes=('widget-inter…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ipw.interactive(thresholding, level = ipw.IntSlider(min =0, max = 255), \n",
    "                image = ipw.fixed(image))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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