itk.ContourExtractor2DImageFilter example

ContourExtractor2D.ipynb

{
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   "cell_type": "code",
   "execution_count": null,
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   "source": [
    "# Ensure dependencies are installed. If itkwidgets was not installed, reload the browser tab after installation.\n",
    "import sys\n",
    "!{sys.executable} -m pip install itk itkwidgets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "from urllib.request import urlretrieve\n",
    "import os\n",
    "import itk\n",
    "import numpy as np\n",
    "\n",
    "from itkwidgets import view, cm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "file_name = 'cthead1.png'\n",
    "if not os.path.exists(file_name):\n",
    "    url = 'https://data.kitware.com/api/v1/file/57b5d9ef8d777f10f269538f/download'\n",
    "    urlretrieve(url, file_name)"
   ]
  },
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   "cell_type": "code",
   "execution_count": 8,
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    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "e606d650b4024ca5b85dec72d862ed72",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itk.itkImagePython.itkImageUC2; pr…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "cthead1 = itk.imread(file_name)\n",
    "view(cthead1, vmax=150)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "paths = itk.contour_extractor2_d_image_filter(cthead1, contour_value=150)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "3a40809e39fc45a38d9a48d2842c8c2a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Viewer(cmap='gray_Matlab', geometries=[{'vtkClass': 'vtkPolyData', 'points': {'vtkClass': 'vtkPoints', 'name':…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "p0 = paths[0]\n",
    "view(cthead1, geometries=p0, cmap=cm.gray, ui_collapsed=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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