NIH_Test_Average.ipynb

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    {
     "ename": "ModuleNotFoundError",
     "evalue": "Couldn't locate OpenSlide DLL.  Did you call os.add_dll_directory()?  https://openslide.org/api/python/#installing",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python311\\site-packages\\openslide\\lowlevel.py:65\u001b[0m, in \u001b[0;36m_load_library\u001b[1;34m()\u001b[0m\n\u001b[0;32m     64\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m---> 65\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m try_load([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide-1.dll\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide-0.dll\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[0;32m     66\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m:\n",
      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python311\\site-packages\\openslide\\lowlevel.py:58\u001b[0m, in \u001b[0;36m_load_library.<locals>.try_load\u001b[1;34m(names)\u001b[0m\n\u001b[0;32m     57\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m---> 58\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m cdll\u001b[38;5;241m.\u001b[39mLoadLibrary(name)\n\u001b[0;32m     59\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m:\n",
      "File \u001b[1;32mC:\\ProgramData\\anaconda3\\Lib\\ctypes\\__init__.py:454\u001b[0m, in \u001b[0;36mLibraryLoader.LoadLibrary\u001b[1;34m(self, name)\u001b[0m\n\u001b[0;32m    453\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mLoadLibrary\u001b[39m(\u001b[38;5;28mself\u001b[39m, name):\n\u001b[1;32m--> 454\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_dlltype(name)\n",
      "File \u001b[1;32mC:\\ProgramData\\anaconda3\\Lib\\ctypes\\__init__.py:376\u001b[0m, in \u001b[0;36mCDLL.__init__\u001b[1;34m(self, name, mode, handle, use_errno, use_last_error, winmode)\u001b[0m\n\u001b[0;32m    375\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m handle \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m--> 376\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_handle \u001b[38;5;241m=\u001b[39m _dlopen(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_name, mode)\n\u001b[0;32m    377\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
      "\u001b[1;31mFileNotFoundError\u001b[0m: Could not find module 'libopenslide-0.dll' (or one of its dependencies). Try using the full path with constructor syntax.",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[1;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
      "Cell \u001b[1;32mIn[3], line 2\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mos\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mopenslide\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m open_slide\n\u001b[0;32m      3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPIL\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Image\n\u001b[0;32m      4\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnumpy\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mnp\u001b[39;00m\n",
      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python311\\site-packages\\openslide\\__init__.py:31\u001b[0m\n\u001b[0;32m     27\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mio\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m BytesIO\n\u001b[0;32m     29\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mPIL\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Image, ImageCms\n\u001b[1;32m---> 31\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mopenslide\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m lowlevel\n\u001b[0;32m     33\u001b[0m \u001b[38;5;66;03m# For the benefit of library users\u001b[39;00m\n\u001b[0;32m     34\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mopenslide\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_version\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m __version__  \u001b[38;5;66;03m# noqa: F401  module-imported-but-unused\u001b[39;00m\n",
      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python311\\site-packages\\openslide\\lowlevel.py:92\u001b[0m\n\u001b[0;32m     88\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m     89\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m try_load([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide.so.1\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide.so.0\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[1;32m---> 92\u001b[0m _lib \u001b[38;5;241m=\u001b[39m _load_library()\n\u001b[0;32m     95\u001b[0m \u001b[38;5;28;01mclass\u001b[39;00m \u001b[38;5;21;01mOpenSlideError\u001b[39;00m(\u001b[38;5;167;01mException\u001b[39;00m):\n\u001b[0;32m     96\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"An error produced by the OpenSlide library.\u001b[39;00m\n\u001b[0;32m     97\u001b[0m \n\u001b[0;32m     98\u001b[0m \u001b[38;5;124;03m    Import this from openslide rather than from openslide.lowlevel.\u001b[39;00m\n\u001b[0;32m     99\u001b[0m \u001b[38;5;124;03m    \"\"\"\u001b[39;00m\n",
      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python311\\site-packages\\openslide\\lowlevel.py:67\u001b[0m, in \u001b[0;36m_load_library\u001b[1;34m()\u001b[0m\n\u001b[0;32m     65\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m try_load([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide-1.dll\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlibopenslide-0.dll\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[0;32m     66\u001b[0m     \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m:\n\u001b[1;32m---> 67\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mModuleNotFoundError\u001b[39;00m(\n\u001b[0;32m     68\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCouldn\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt locate OpenSlide DLL.  \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     69\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mDid you call os.add_dll_directory()?  \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     70\u001b[0m             \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhttps://openslide.org/api/python/#installing\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m     71\u001b[0m         )\n\u001b[0;32m     72\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m platform\u001b[38;5;241m.\u001b[39msystem() \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDarwin\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m     73\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n",
      "\u001b[1;31mModuleNotFoundError\u001b[0m: Couldn't locate OpenSlide DLL.  Did you call os.add_dll_directory()?  https://openslide.org/api/python/#installing"
     ]
    }
   ],
   "source": [
    "\n",
    "import os\n",
    "from openslide import open_slide\n",
    "from PIL import Image\n",
    "import numpy as np\n",
    "from matplotlib import pyplot as plt\n",
    "import tifffile as tiff\n",
    "\n",
    "import numpy as np\n",
    "def find_mean_std_pixel_value(img_list):\n",
    "    \n",
    "    avg_pixel_value = []\n",
    "    stddev_pixel_value= []\n",
    "    for file in img_list:\n",
    "        image = tiff.imread(file)\n",
    "        avg = image.mean()\n",
    "        std = image.std()\n",
    "        avg_pixel_value.append(avg)\n",
    "        stddev_pixel_value.append(std)\n",
    "        \n",
    "    avg_pixel_value = np.array(avg_pixel_value)  \n",
    "    stddev_pixel_value=np.array(stddev_pixel_value)\n",
    "        \n",
    "    print(\"Average pixel value for all images is:\", avg_pixel_value.mean())\n",
    "    print(\"Average std dev of pixel value for all images is:\", stddev_pixel_value.mean())\n",
    "    \n",
    "    return(avg_pixel_value, stddev_pixel_value)\n",
    "\n",
    "import glob\n",
    "orig_tile_dir_name = r\"C:\\Users\\cheukjy\\WC25_LLEDGE2_test\"\n",
    "blank_img_list=(glob.glob(orig_tile_dir_name + r\"\\Test_2_H_tiles\\*.tif\"))"
   ]
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   "id": "616b7106-6865-4f65-b778-1daf4b9bd8cf",
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   "source": []
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