{
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   "cell_type": "code",
   "execution_count": null,
   "id": "40fce609-1142-4746-a912-70481ff809be",
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   "outputs": [],
   "source": [
    "#generate NPZ for entry from Imaging1, start in row n1 (from 0) and end before n2 (up to nrows), a total of n2-n1 files will be created in directory outdir\n",
    "#files will have random name with random id stored in the same dataset for subsequent data retrieval\n",
    "import generateNPZ\n",
    "import importlib\n",
    "importlib.reload(generateNPZ)\n",
    "project='iPNUMMretro/Study'\n",
    "outdir='Z:'\n",
    "db=generateNPZ.initDB('onko-nix')\n",
    "odb=generateNPZ.initOrthanc('onko-nix')\n",
    "\n",
    "files=generateNPZ.getFile(db,odb,project,outdir,n1=1,n2=2)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "05cb025f-1c44-4ddf-b859-8b8e9d2584a6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import parseNPZ\n",
    "import os\n",
    "import importlib\n",
    "importlib.reload(parseNPZ)\n",
    "\n",
    "infile=os.path.join('Z:','6ebf549213805ee0.npz')\n",
    "infile=os.path.join('Z:','7c8a7ead6849be2c.npz')\n",
    "parseNPZ.generateNiftyFromNPZ(infile)\n",
    "#this will generate Z:/6ebf549213805ee0_CT.nii.gz and Z:/6ebf549213805ee0_PET.nii.gz\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6d523d18-ede0-41aa-a93c-96123fa6abbc",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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