hack cell image segmentation

nate_image.ipynb

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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%matplotlib"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Using matplotlib backend: Qt4Agg\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from functools import partial\n",
      "from skimage.io import imread\n",
      "from skimage.filter import canny, rank, threshold_otsu\n",
      "from skimage import exposure as expos\n",
      "from skimage.feature import blob_dog\n",
      "from skimage.morphology import disk\n",
      "from skimage.segmentation import felzenszwalb, slic, quickshift\n",
      "from skimage.segmentation import mark_boundaries\n",
      "\n",
      "from matplotlib.widgets import RectangleSelector\n",
      "import matplotlib.pyplot as plt\n",
      "\n",
      "def segment(img, stepsize=8, **kwargs):\n",
      "    sub = img[::stepsize, ::stepsize]\n",
      "    return felzenszwalb(sub, **kwargs), sub"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "img = imread('DATA_SET_2_0841.tif')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 48
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def onselect(ax, click, release):\n",
      "    column_slice = slice(click.xdata, release.xdata)\n",
      "    row_slice = slice(click.ydata, release.ydata)\n",
      "    indexer = row_slice, column_slice\n",
      "    \n",
      "    print('equalizing image subset ...')\n",
      "    sub = img[indexer]\n",
      "    im_eq = rank.autolevel(sub, disk(20))\n",
      "#     im_eq = expos.equalize_hist(sub)\n",
      "    \n",
      "    print('segmenting image subset ...')\n",
      "    res, sub = segment(im_eq, stepsize=2, scale=300, sigma=3.5)\n",
      "    \n",
      "    print('marking boundaries ...')\n",
      "    bounds = mark_boundaries(sub, res)\n",
      "    \n",
      "    print('drawing boundaries ...')\n",
      "    plt.imshow(bounds, cmap=plt.cm.jet)\n",
      "    \n",
      "    \n",
      "def toggle_selector(event):\n",
      "    if event.key in ['Q', 'q'] and toggle_selector.RS.active:\n",
      "        toggle_selector.RS.set_active(False)\n",
      "    if event.key in ['A', 'a'] and not toggle_selector.RS.active:\n",
      "        toggle_selector.RS.set_active(True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 53
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fig, ax = plt.subplots(1, 1)\n",
      "ax.imshow(img, cmap=plt.cm.gray)\n",
      "ax.axis('off')\n",
      "fig.tight_layout()\n",
      "toggle_selector.RS = RectangleSelector(ax, partial(onselect, ax),\n",
      "                                       drawtype='box')\n",
      "# plt.connect('key_press_event', toggle_selector)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "equalizing image subset ...\n",
        "segmenting image subset ..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "marking boundaries ..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "drawing boundaries ..."
       ]
      }
     ],
     "prompt_number": 54
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sub = expos.equalize_hist(img[indexer])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 105
    },
    {
     "cell_type": "code",
     "collapsed": true,
     "input": [
      "res, sub = segment(sub, stepsize=2, scale=1000, sigma=1.5)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 106
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "bounds = mark_boundaries(sub, res)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 107
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "plt.imshow(bounds, cmap=plt.cm.jet)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 108,
       "text": [
        "<matplotlib.image.AxesImage at 0x7fe95ca39d90>"
       ]
      }
     ],
     "prompt_number": 108
    }
   ],
   "metadata": {}
  }
 ]
}