NerveSegmentation3D.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 3D Nerve Surface Segmentation "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Add Proper References Here**\n",
    "\n",
    "**NOTICE:** This notebook assumes you are familiar layered surface detection on tubular objects introduced in the *NerveSegmentation2D* notebook. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from matplotlib.image import imsave \n",
    "from skimage.io import imread\n",
    "from scipy.ndimage.interpolation import map_coordinates\n",
    "\n",
    "from qimtools import visualization, inspection, io\n",
    "from slgbuilder import GraphObject,MaxflowBuilder"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The objects (nerves) in the volume have two different sizes which need to be handled differently. With small nerves marked in red an large in blue."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(200, 200, 10)\n"
     ]
    }
   ],
   "source": [
    "in_dir = 'data/'\n",
    "Vol_path = os.path.join(in_dir, 'nerves3D.tiff')\n",
    "\n",
    "# Load the data\n",
    "vol = io.Volume( Vol_path )\n",
    "\n",
    "# Convert the stack of 2D slices to a 3D volume\n",
    "vol = vol.concatenate().astype(np.int32)\n",
    "vol = np.transpose(vol,(1,2,0))\n",
    "\n",
    "print(vol.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "/* Put everything inside the global mpl namespace */\n",
       "window.mpl = {};\n",
       "\n",
       "\n",
       "mpl.get_websocket_type = function() {\n",
       "    if (typeof(WebSocket) !== 'undefined') {\n",
       "        return WebSocket;\n",
       "    } else if (typeof(MozWebSocket) !== 'undefined') {\n",
       "        return MozWebSocket;\n",
       "    } else {\n",
       "        alert('Your browser does not have WebSocket support. ' +\n",
       "              'Please try Chrome, Safari or Firefox ≥ 6. ' +\n",
       "              'Firefox 4 and 5 are also supported but you ' +\n",
       "              'have to enable WebSockets in about:config.');\n",
       "    };\n",
       "}\n",
       "\n",
       "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n",
       "    this.id = figure_id;\n",
       "\n",
       "    this.ws = websocket;\n",
       "\n",
       "    this.supports_binary = (this.ws.binaryType != undefined);\n",
       "\n",
       "    if (!this.supports_binary) {\n",
       "        var warnings = document.getElementById(\"mpl-warnings\");\n",
       "        if (warnings) {\n",
       "            warnings.style.display = 'block';\n",
       "            warnings.textContent = (\n",
       "                \"This browser does not support binary websocket messages. \" +\n",
       "                    \"Performance may be slow.\");\n",
       "        }\n",
       "    }\n",
       "\n",
       "    this.imageObj = new Image();\n",
       "\n",
       "    this.context = undefined;\n",
       "    this.message = undefined;\n",
       "    this.canvas = undefined;\n",
       "    this.rubberband_canvas = undefined;\n",
       "    this.rubberband_context = undefined;\n",
       "    this.format_dropdown = undefined;\n",
       "\n",
       "    this.image_mode = 'full';\n",
       "\n",
       "    this.root = $('<div/>');\n",
       "    this._root_extra_style(this.root)\n",
       "    this.root.attr('style', 'display: inline-block');\n",
       "\n",
       "    $(parent_element).append(this.root);\n",
       "\n",
       "    this._init_header(this);\n",
       "    this._init_canvas(this);\n",
       "    this._init_toolbar(this);\n",
       "\n",
       "    var fig = this;\n",
       "\n",
       "    this.waiting = false;\n",
       "\n",
       "    this.ws.onopen =  function () {\n",
       "            fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n",
       "            fig.send_message(\"send_image_mode\", {});\n",
       "            if (mpl.ratio != 1) {\n",
       "                fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n",
       "            }\n",
       "            fig.send_message(\"refresh\", {});\n",
       "        }\n",
       "\n",
       "    this.imageObj.onload = function() {\n",
       "            if (fig.image_mode == 'full') {\n",
       "                // Full images could contain transparency (where diff images\n",
       "                // almost always do), so we need to clear the canvas so that\n",
       "                // there is no ghosting.\n",
       "                fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n",
       "            }\n",
       "            fig.context.drawImage(fig.imageObj, 0, 0);\n",
       "        };\n",
       "\n",
       "    this.imageObj.onunload = function() {\n",
       "        fig.ws.close();\n",
       "    }\n",
       "\n",
       "    this.ws.onmessage = this._make_on_message_function(this);\n",
       "\n",
       "    this.ondownload = ondownload;\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_header = function() {\n",
       "    var titlebar = $(\n",
       "        '<div class=\"ui-dialog-titlebar ui-widget-header ui-corner-all ' +\n",
       "        'ui-helper-clearfix\"/>');\n",
       "    var titletext = $(\n",
       "        '<div class=\"ui-dialog-title\" style=\"width: 100%; ' +\n",
       "        'text-align: center; padding: 3px;\"/>');\n",
       "    titlebar.append(titletext)\n",
       "    this.root.append(titlebar);\n",
       "    this.header = titletext[0];\n",
       "}\n",
       "\n",
       "\n",
       "\n",
       "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n",
       "\n",
       "}\n",
       "\n",
       "\n",
       "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n",
       "\n",
       "}\n",
       "\n",
       "mpl.figure.prototype._init_canvas = function() {\n",
       "    var fig = this;\n",