n-ary_mask_generation.ipynb

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    "# Script to generate n-ary masks for each cell-type\n",
    "# Created by Ruchika Verma\n",
    "\n",
    "This code will create separate folder for each patient and subfolders for annotated images under each patient's folder.\n",
    "\n",
    "Each sub-folder corresponding to patient (image name) will contain 4 sub-subfolders (Epithelial, Lymphocyte, Neutrophil and Macrophage) to save their corresponding n-ary-masks with unique values for each instance and with value 0 for background\n",
    "\n",
    "# Input\n",
    "data_path: Specify the path of downloaded images\n",
    "\n",
    "destination_path = Specify the path to save corresponding n-ary masks\n",
    "\n",
    "# Output\n",
    "MoNuSAC_masks directory in the destination_path\n",
    "\n",
    "n-ary masks will be saved in each sub-sub-folder\n",
    "\n",
    "Folder -> Patient name\n",
    "\n",
    "Sub-folder -> Sub-images under each patient\n",
    "\n",
    "Sub-Sub-folder -> Annotated cell-type on each sub-image\n"
   ]
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   "cell_type": "code",
   "execution_count": 13,
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   "source": [
    "#Process whole slide images\n",
    "import os\n",
    "import openslide\n",
    "from xml.dom import minidom\n",
    "import numpy as np\n",
    "import openslide\n",
    "from openslide import open_slide  \n",
    "from glob import glob\n",
    "import cv2\n",
    "import matplotlib.pyplot as plt\n",
    "import scipy.io as sio\n",
    "from PIL import Image\n",
    "import scipy\n",
    "import scipy.ndimage\n",
    "from shapely.geometry import Polygon\n",
    "from skimage import draw\n",
    "import xml.etree.ElementTree as ET"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
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    {
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       "51"
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   "source": [
    "# Read svs files from the desired path\n",
    "count = 0\n",
    "data_path = 'D:\\MoNuSAC_annotations' #Path to read data from\n",
    "destination_path = 'D:\\MoNuSAC' # Path to save n-ary masks corresponding to xml files\n",
    "os.chdir(destination_path)\n",
    "\n",
    "try:\n",
    "    os.mkdir(destination_path+'\\MoNuSAC_masks')\n",
    "except OSError:\n",
    "    print (\"Creation of the mask directory %s failed\" % destination_path)\n",
    "    \n",
    "os.chdir(destination_path+'\\MoNuSAC_masks')#Create folder named as MoNuSAC_masks\n",
    "patients = [x[0] for x in os.walk(data_path)]#Total patients in the data_path\n",
    "len(patients)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Epithelial\n",
      "Creation of the directory Epithelial failed\n",
      "2\n",
      "Lymphocyte\n",
      "Successfully created the directory Lymphocyte \n",
      "3\n",
      "Neutrophil\n",
      "Successfully created the directory Neutrophil \n",
      "4\n",
      "Macrophage\n",
      "Successfully created the directory Macrophage \n",
      "\\TCGA-55-1594-01Z-00-DX1_002\n",
      "5\n",
      "Epithelial\n",
      "Successfully created the directory Epithelial \n",
      "6\n",
      "Lymphocyte\n",
      "Successfully created the directory Lymphocyte \n"
     ]
    }
   ],
   "source": [
    "for patient_loc in patients:\n",
    "    patient_name = patient_loc[len(data_path)+1:]#Patient name\n",
    "    print(patient_name)\n",
    "    \n",
    "    ## To make patient's name directory in the destination folder\n",
    "    try:\n",
    "        os.mkdir(patient_name)\n",
    "    except OSError:\n",
    "        print (\"\\n Creation of the patient's directory %s failed\" % patient_name)\n",
    "        \n",
    "    ## Read sub-images of each patient in the data path        \n",
    "    sub_images = glob(patient_loc+'/*.svs')\n",
    "    for sub_image_loc in sub_images:\n",
    "        gt = 0\n",
    "        sub_image_name = sub_image_loc[len(data_path)+len(patient_name)+1:-4]        \n",
    "        print(sub_image_name)\n",
    "        \n",
    "        ## To make sub_image directory under the patient's folder\n",
    "        sub_image = './'+patient_name+'/'+sub_image_name #Destination path\n",
    "        try:\n",
    "            os.mkdir(sub_image)\n",
    "        except OSError:\n",
    "            print (\"\\n Creation of the patient's directory %s failed\" % sub_image)\n",
    "            \n",
    "        image_name = sub_image_loc\n",
    "        img = openslide.OpenSlide(image_name)\n",
    "                                  \n",
    "        # If svs image needs to save in tif\n",
    "        cv2.imwrite(sub_image_loc[:-4]+'.tif', np.array(img.read_region((0,0),0,img.level_dimensions[0])))      \n",
    "   \n",
    "        # Read xml file\n",
    "        xml_file_name  = image_name[:-4]\n",
    "        xml_file_name = xml_file_name+'.xml'\n",
    "        tree = ET.parse(xml_file_name)\n",
    "        root = tree.getroot()\n",
    "        \n",
    "        #Generate n-ary mask for each cell-type                         \n",
    "        for k in range(len(root)):\n",
    "            label = [x.attrib['Name'] for x in root[k][0]]\n",
    "            label = label[0]\n",
    "            \n",
    "            for child in root[k]:\n",
    "                for x in child:\n",
    "                    r = x.tag\n",
    "                    if r == 'Attribute':\n",
    "                        count = count+1\n",
    "                        print(count)\n",
    "                        label = x.attrib['Name']\n",
    "                        n_ary_mask = np.transpose(np.zeros((img.read_region((0,0),0,img.level_dimensions[0]).size))) \n",
    "                        print(label)\n",
    "                        \n",
    "                        # Create directory for each label\n",
    "                        sub_path = sub_image+'/'+label\n",
    "                        \n",
    "                        try:\n",
    "                            os.mkdir(sub_path)\n",
    "                        except OSError:\n",
    "                            print (\"Creation of the directory %s failed\" % label)\n",
    "                        else:\n",
    "                            print (\"Successfully created the directory %s \" % label) \n",
    "                                          \n",
    "                        \n",
    "                    if r == 'Region':\n",
    "                        regions = []\n",
    "                        vertices = x[1]\n",
    "                        coords = np.zeros((len(vertices), 2))\n",
    "                        for i, vertex in enumerate(vertices):\n",
    "                            coords[i][0] = vertex.attrib['X']\n",
    "                            coords[i][1] = vertex.attrib['Y']        \n",
    "                        regions.append(coords)\n",
    "                        poly = Polygon(regions[0])  \n",
    "                        \n",
    "                        vertex_row_coords = regions[0][:,0]\n",
    "                        vertex_col_coords = regions[0][:,1]\n",
    "                        fill_row_coords, fill_col_coords = draw.polygon(vertex_col_coords, vertex_row_coords, n_ary_mask.shape)\n",
    "                        gt = gt+1 #Keep track of giving unique valu to each instance in an image\n",
    "                        n_ary_mask[fill_row_coords, fill_col_coords] = gt\n",
    "                        mask_path = sub_path+'/'+str(count)+'_mask.tif'\n",
    "                        cv2.imwrite(mask_path, n_ary_mask)                       \n",
    "    "
   ]
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