Untitled.ipynb

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      "/Users/surajnair/anaconda/envs/py27/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.\n",
      "  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')\n",
      "/Users/surajnair/anaconda/envs/py27/lib/python2.7/site-packages/skimage/viewer/utils/core.py:10: UserWarning: Recommended matplotlib backend is `Agg` for full skimage.viewer functionality.\n",
      "  warn(\"Recommended matplotlib backend is `Agg` for full \"\n"
     ]
    }
   ],
   "source": [
    "import openslide\n",
    "import numpy as np\n",
    "import skimage\n",
    "from skimage.viewer import ImageViewer\n",
    "import PIL\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "slide = openslide.open_slide(\"../CAMELYON/data/patient_013/patient_013_node_2.tif\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
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   "source": [
    "slide\n",
    "level = 6\n",
    "dims = slide.level_dimensions[level]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
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     "execution_count": 40,
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     "output_type": "execute_result"
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   ],
   "source": [
    "slide.level_downsamples[level]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
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   "source": [
    "pixelarray = np.array(slide.read_region((0,0), level, dims))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
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     "data": {
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       "(3290, 1483, 4)"
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     "execution_count": 42,
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   ],
   "source": [
    "pixelarray.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
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    {
     "data": {
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       "[]"
      ]
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     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "viewer = ImageViewer(pixelarray)\n",
    "viewer.show()"
   ]
  },
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   "cell_type": "code",
   "execution_count": null,
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    "collapsed": true
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   "cell_type": "code",
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