Image2Mask.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "def Image2Mask(path,file_name):\n",
    "    input_image = sitk.ReadImage(path+'dicom/'+file_name)\n",
    "    segmentation = mask.apply(input_image)\n",
    "\n",
    "    x = segmentation[0]\n",
    "    img = sitk.GetImageFromArray(x)\n",
    "    sitk.WriteImage(img, path+'/Mask/Mask-'+file_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from lungmask import mask\n",
    "import SimpleITK as sitk\n",
    "import os\n",
    "from matplotlib import pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
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    },
    {
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     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-123-6m4np0.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    {
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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    {
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     "output_type": "stream",
     "text": [
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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    {
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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    {
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     "output_type": "stream",
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-4-6lkac7.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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    {
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     "output_type": "stream",
     "text": [
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-111-6m5fve.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-134-6m6m4z.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    {
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     "output_type": "stream",
     "text": [
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-68-6m26po.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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     "name": "stderr",
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-28-6lljkk.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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     "name": "stderr",
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-66-6m258a.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-48-6lmx93.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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     "name": "stderr",
     "output_type": "stream",
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-31-6lm7as.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-1-6lk844.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
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    },
    {
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     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-43-6lmssx.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-137-6m5f4p.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
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    {
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     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-58-6m0v98.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-63-6m1hi2.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-20-6ll117.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-27-6llo0q.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-81-6m2v6l.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-76-6m1kgu.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-118-6m5bf8.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-73-6m2qqf.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
    {
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     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-49-6lmv10.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-107-6m40ph.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
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    },
    {
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     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-113-6m4reh.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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     "name": "stderr",
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-18-6lkzjt.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-101-6m45wc.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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    },
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-132-6m4ud9.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
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    },
    {
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     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-78-6m1ly8.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-38-6lms28.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
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     "name": "stderr",
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    },
    {
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      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-108-6m6248.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-15-6lkesd.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-35-6lm9iv.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-115-6m4svv.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-119-6m43o9.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-30-6lllsn.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-98-6m3hff.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-71-6m10g3.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-82-6m24hl.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-56-6m1i8r.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-102-6m3iwt.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-19-6lkwl1.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-105-6m3ke7.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.95s/it]\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-33-6lm8s6.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.06s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2489.94it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-39-6lm52p.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.10s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2685.21it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-99-6m44ey.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.21s/it]\n",
      "100%|██████████| 4/4 [00:00<00:00, 1280.80it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-84-6m25yz.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.80s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2801.81it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-75-6m2s7t.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:38<00:00, 38.82s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2593.88it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-94-6m3f7c.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 12.00s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 1465.00it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-95-6m2syi.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.61s/it]\n",
      "100%|██████████| 4/4 [00:00<00:00, 1413.53it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-11-6lkv3n.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.26s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 5679.49it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-116-6m426v.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.21s/it]\n",
      "100%|██████████| 3/3 [00:00<00:00, 1402.31it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-34-6llorf.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.69s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2577.94it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-69-6m0zpe.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.26s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 1549.14it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-122-6m46n1.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.55s/it]\n",
      "100%|██████████| 3/3 [00:00<00:00, 4297.44it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-26-6lli36.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.90s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 4512.43it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-67-6m0yyp.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.60s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2081.02it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-92-6m3egn.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.64s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 3086.32it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-133-6m6lea.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.64s/it]\n",
      "0it [00:00, ?it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-16-6lkxbq.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.28s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 4696.87it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-29-6lm5te.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.58s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 4412.73it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-54-6m1grd.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:11<00:00, 11.61s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2162.57it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-25-6llmjc.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.18s/it]\n",
      "100%|██████████| 3/3 [00:00<00:00, 4552.43it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-131-6m63lm.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.46s/it]\n",
      "0it [00:00, ?it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-59-6m1l7j.dcm\n",
      "INFO:root:No GPU support available, will use CPU. Note, that this is significantly slower!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 1/1 [00:12<00:00, 12.51s/it]\n",
      "100%|██████████| 2/2 [00:00<00:00, 2014.07it/s]\n"
     ]
    }
   ],
   "source": [
    "path='/Users/Alireza/Desktop/Datasets/covid4237/'\n",
    "files = os.listdir(path+'dicom')\n",
    "for name in files:\n",
    "    print(name)\n",
    "    Image2Mask(path,name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.2.826.0.1.3680043.9.3218.1.1.1872364.1022.1591771672055.7043.0-3-10-6lke1o.dcm\n"
     ]
    }
   ],
   "source": [
    "path='/Users/Alireza/Desktop/Datasets/covid4237/'\n",
    "\n",
    "name=files[40]\n",
    "print(name)\n",
    "\n",
    "input_image = sitk.ReadImage(path+'dicom/'+name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "ename": "RuntimeError",
     "evalue": "unexpected EOF, expected 6840338 more bytes. The file might be corrupted.",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-19-55433a437337>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msegmentation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput_image\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/lungmask/mask.py\u001b[0m in \u001b[0;36mapply\u001b[0;34m(image, model, force_cpu, batch_size, volume_postprocessing, noHU)\u001b[0m\n\u001b[1;32m     23\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mimage\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mforce_cpu\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_size\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m20\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvolume_postprocessing\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnoHU\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     24\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 25\u001b[0;31m         \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'unet'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'R231'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     26\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m     \u001b[0minimg_raw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msitk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetArrayFromImage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mimage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/lungmask/mask.py\u001b[0m in \u001b[0;36mget_model\u001b[0;34m(modeltype, modelname)\u001b[0m\n\u001b[1;32m     90\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodeltype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodelname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     91\u001b[0m     \u001b[0mmodel_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn_classes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmodel_urls\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodeltype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodelname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 92\u001b[0;31m     \u001b[0mstate_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhub\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_state_dict_from_url\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprogress\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'cpu'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     93\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mmodeltype\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'unet'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     94\u001b[0m         \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mUNet\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_classes\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mn_classes\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpadding\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdepth\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m5\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mup_mode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'upsample'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_norm\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mresidual\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/hub.py\u001b[0m in \u001b[0;36mload_state_dict_from_url\u001b[0;34m(url, model_dir, map_location, progress, check_hash, file_name)\u001b[0m\n\u001b[1;32m    526\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0m_is_legacy_zip_format\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    527\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0m_legacy_zip_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 528\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmap_location\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/serialization.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(f, map_location, pickle_module, **pickle_load_args)\u001b[0m\n\u001b[1;32m    591\u001b[0m                     \u001b[0;32mreturn\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjit\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    592\u001b[0m                 \u001b[0;32mreturn\u001b[0m \u001b[0m_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_zipfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpickle_module\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mpickle_load_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 593\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0m_legacy_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpickle_module\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mpickle_load_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    594\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    595\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/serialization.py\u001b[0m in \u001b[0;36m_legacy_load\u001b[0;34m(f, map_location, pickle_module, **pickle_load_args)\u001b[0m\n\u001b[1;32m    777\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdeserialized_storage_keys\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    778\u001b[0m         \u001b[0;32massert\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdeserialized_objects\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 779\u001b[0;31m         \u001b[0mdeserialized_objects\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_from_file\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moffset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mf_should_read_directly\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    780\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0moffset\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    781\u001b[0m             \u001b[0moffset\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtell\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mRuntimeError\u001b[0m: unexpected EOF, expected 6840338 more bytes. The file might be corrupted."
     ]
    }
   ],
   "source": [
    "segmentation = mask.apply(input_image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "ename": "RuntimeError",
     "evalue": "unexpected EOF, expected 6840338 more bytes. The file might be corrupted.",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-16-c5607e120993>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mImage2Mask\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m<ipython-input-1-4b7371e8b961>\u001b[0m in \u001b[0;36mImage2Mask\u001b[0;34m(path, file_name)\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mImage2Mask\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mfile_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m     \u001b[0minput_image\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msitk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mReadImage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m'dicom/'\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mfile_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m     \u001b[0msegmentation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput_image\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msegmentation\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/lungmask/mask.py\u001b[0m in \u001b[0;36mapply\u001b[0;34m(image, model, force_cpu, batch_size, volume_postprocessing, noHU)\u001b[0m\n\u001b[1;32m     23\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mimage\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mforce_cpu\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_size\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m20\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvolume_postprocessing\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnoHU\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     24\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 25\u001b[0;31m         \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'unet'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'R231'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     26\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m     \u001b[0minimg_raw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msitk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetArrayFromImage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mimage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/lungmask/mask.py\u001b[0m in \u001b[0;36mget_model\u001b[0;34m(modeltype, modelname)\u001b[0m\n\u001b[1;32m     90\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodeltype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodelname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     91\u001b[0m     \u001b[0mmodel_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn_classes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmodel_urls\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodeltype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodelname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 92\u001b[0;31m     \u001b[0mstate_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhub\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_state_dict_from_url\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprogress\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'cpu'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     93\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mmodeltype\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'unet'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     94\u001b[0m         \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mUNet\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_classes\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mn_classes\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpadding\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdepth\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m5\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mup_mode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'upsample'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_norm\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mresidual\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/hub.py\u001b[0m in \u001b[0;36mload_state_dict_from_url\u001b[0;34m(url, model_dir, map_location, progress, check_hash, file_name)\u001b[0m\n\u001b[1;32m    526\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0m_is_legacy_zip_format\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    527\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0m_legacy_zip_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 528\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcached_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmap_location\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/serialization.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(f, map_location, pickle_module, **pickle_load_args)\u001b[0m\n\u001b[1;32m    591\u001b[0m                     \u001b[0;32mreturn\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjit\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    592\u001b[0m                 \u001b[0;32mreturn\u001b[0m \u001b[0m_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_zipfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpickle_module\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mpickle_load_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 593\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0m_legacy_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopened_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmap_location\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpickle_module\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mpickle_load_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    594\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    595\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/opt/anaconda3/lib/python3.8/site-packages/torch/serialization.py\u001b[0m in \u001b[0;36m_legacy_load\u001b[0;34m(f, map_location, pickle_module, **pickle_load_args)\u001b[0m\n\u001b[1;32m    777\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdeserialized_storage_keys\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    778\u001b[0m         \u001b[0;32massert\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdeserialized_objects\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 779\u001b[0;31m         \u001b[0mdeserialized_objects\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_from_file\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moffset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mf_should_read_directly\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    780\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0moffset\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    781\u001b[0m             \u001b[0moffset\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtell\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mRuntimeError\u001b[0m: unexpected EOF, expected 6840338 more bytes. The file might be corrupted."
     ]
    }
   ],
   "source": [
    "    \n",
    "    \n",
    "\n",
    "    x = segmentation[0]\n",
    "    img = sitk.GetImageFromArray(x)\n",
    "    sitk.WriteImage(img, path+'/Mask/Mask-'+file_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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