datapreprocessing_KiTS.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "datadownloadpath = './datadownload/KiTS/'\n",
    "datasavepath = './datapreprocessed/KiTS/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import glob\n",
    "import SimpleITK as sitk\n",
    "import numpy as np\n",
    "from scipy.ndimage import label, binary_fill_holes\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.exists(datasavepath) == False:\n",
    "    os.mkdir(datasavepath)\n",
    "if os.path.exists(datasavepath + 'Image') == False:\n",
    "    os.mkdir(datasavepath + 'Image')\n",
    "    os.mkdir(datasavepath + 'Label')\n",
    "    os.mkdir(datasavepath + 'processed')\n",
    "    os.mkdir(datasavepath + 'mask')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# helper functions copy pasted\n",
    "def resample_by_res(mov_img_obj, new_spacing, interpolator = sitk.sitkLinear, logging = True):\n",
    "    resample = sitk.ResampleImageFilter()\n",
    "    resample.SetInterpolator(interpolator)\n",
    "    resample.SetOutputDirection(mov_img_obj.GetDirection())\n",
    "    # fix the direction.\n",
    "#     resample.SetOutputDirection(tuple(np.abs(mov_img_obj.GetDirection())))\n",
    "    resample.SetOutputOrigin(mov_img_obj.GetOrigin())\n",
    "    resample.SetUseNearestNeighborExtrapolator(True)\n",
    "    mov_spacing = mov_img_obj.GetSpacing()\n",
    "\n",
    "    resample.SetOutputSpacing(new_spacing)\n",
    "    RES_COE = np.array(mov_spacing) * 1.0 / np.array(new_spacing)\n",
    "    new_size = np.array(mov_img_obj.GetSize()) *  RES_COE \n",
    "\n",
    "    resample.SetSize( [int(sz+1) for sz in new_size] )\n",
    "    if logging:\n",
    "        print(\"Spacing: {} -> {}\".format(mov_spacing, new_spacing))\n",
    "        print(\"Size {} -> {}\".format( mov_img_obj.GetSize(), new_size ))\n",
    "\n",
    "    return resample.Execute(mov_img_obj)\n",
    "\n",
    "def resample_lb_by_res(mov_lb_obj, new_spacing, interpolator = sitk.sitkLinear, ref_img = None, logging = True):\n",
    "    src_mat = sitk.GetArrayFromImage(mov_lb_obj)\n",
    "    lbvs = np.unique(src_mat)\n",
    "    if logging:\n",
    "        print(\"Label values: {}\".format(lbvs))\n",
    "    for idx, lbv in enumerate(lbvs):\n",
    "        _src_curr_mat = np.float32(src_mat == lbv) \n",
    "        _src_curr_obj = sitk.GetImageFromArray(_src_curr_mat)\n",
    "        _src_curr_obj.CopyInformation(mov_lb_obj)\n",
    "        _tar_curr_obj = resample_by_res( _src_curr_obj, new_spacing, interpolator, logging )\n",
    "        _tar_curr_mat = np.rint(sitk.GetArrayFromImage(_tar_curr_obj)) * lbv\n",
    "        if idx == 0:\n",
    "            out_vol = _tar_curr_mat\n",
    "        else:\n",
    "            out_vol[_tar_curr_mat == lbv] = lbv\n",
    "    out_obj = sitk.GetImageFromArray(out_vol)\n",
    "    out_obj.SetSpacing( _tar_curr_obj.GetSpacing() )\n",
    "    if ref_img != None:\n",
    "        out_obj.CopyInformation(ref_img)\n",
    "    return out_obj\n",
    "\n",
    "def remove_all_but_the_largest_connected_component(image: np.ndarray, for_which_classes: list, volume_per_voxel: float,\n",
    "                                                   minimum_valid_object_size: dict = None):\n",
    "    \"\"\"\n",
    "    removes all but the largest connected component, individually for each class\n",
    "    :param image:\n",
    "    :param for_which_classes: can be None. Should be list of int. Can also be something like [(1, 2), 2, 4].\n",
    "    Here (1, 2) will be treated as a joint region, not individual classes (example LiTS here we can use (1, 2)\n",
    "    to use all foreground classes together)\n",
    "    :param minimum_valid_object_size: Only objects larger than minimum_valid_object_size will be removed. Keys in\n",
    "    minimum_valid_object_size must match entries in for_which_classes\n",
    "    :return:\n",
    "    \"\"\"\n",
    "    if for_which_classes is None:\n",
    "        for_which_classes = np.unique(image)\n",
    "        for_which_classes = for_which_classes[for_which_classes > 0]\n",
    "\n",
    "    assert 0 not in for_which_classes, \"cannot remove background\"\n",
    "    largest_removed = {}\n",
    "    kept_size = {}\n",
    "    for c in for_which_classes:\n",
    "        if isinstance(c, (list, tuple)):\n",
    "            c = tuple(c)  # otherwise it cant be used as key in the dict\n",
    "            mask = np.zeros_like(image, dtype=bool)\n",
    "            for cl in c:\n",
    "                mask[image == cl] = True\n",
    "        else:\n",
    "            mask = image == c\n",
    "        # get labelmap and number of objects\n",
    "        lmap, num_objects = label(mask.astype(int))\n",
    "\n",
    "        # collect object sizes\n",
    "        object_sizes = {}\n",
    "        for object_id in range(1, num_objects + 1):\n",
    "            object_sizes[object_id] = (lmap == object_id).sum() * volume_per_voxel\n",
    "\n",
    "        largest_removed[c] = None\n",
    "        kept_size[c] = None\n",
    "\n",
    "        if num_objects > 0:\n",
    "            # we always keep the largest object. We could also consider removing the largest object if it is smaller\n",
    "            # than minimum_valid_object_size in the future but we don't do that now.\n",
    "            maximum_size = max(object_sizes.values())\n",
    "            kept_size[c] = maximum_size\n",
    "\n",
    "            for object_id in range(1, num_objects + 1):\n",
    "                # we only remove objects that are not the largest\n",
    "                if object_sizes[object_id] != maximum_size:\n",
    "                    # we only remove objects that are smaller than minimum_valid_object_size\n",
    "                    remove = True\n",
    "                    if minimum_valid_object_size is not None:\n",
    "                        remove = object_sizes[object_id] < minimum_valid_object_size[c]\n",
    "                    if remove:\n",
    "                        image[(lmap == object_id) & mask] = 0\n",
    "                        if largest_removed[c] is None:\n",
    "                            largest_removed[c] = object_sizes[object_id]\n",
    "                        else:\n",
    "                            largest_removed[c] = max(largest_removed[c], object_sizes[object_id])\n",
    "    return image, largest_removed, kept_size"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "IMG_FOLDER = datadownloadpath\n",
    "SEG_FOLDER = datadownloadpath\n",
    "imgs = glob.glob(IMG_FOLDER + \"case_*/imaging.nii.gz\")\n",
    "imgs = [ fid for fid in sorted(imgs) ]\n",
    "segs = [ fid for fid in sorted(glob.glob(SEG_FOLDER + \"case_*/segmentation.nii.gz\")) ]\n",
    "\n",
    "pids = [pid.split(\"_\")[-1].split(\"/\")[0] for pid in imgs]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['./datadownload/KiTS/case_00000/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00001/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00002/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00003/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00004/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00005/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00006/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00007/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00008/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00009/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00010/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00011/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00012/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00013/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00014/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00015/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00016/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00017/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00018/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00019/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00020/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00021/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00022/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00023/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00024/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00025/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00026/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00027/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00028/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00029/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00030/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00031/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00032/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00033/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00034/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00035/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00036/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00037/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00038/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00039/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00040/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00041/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00042/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00043/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00044/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00045/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00046/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00047/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00048/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00049/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00050/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00051/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00052/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00053/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00054/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00055/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00056/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00057/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00058/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00059/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00060/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00061/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00062/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00063/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00064/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00065/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00066/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00067/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00068/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00069/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00070/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00071/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00072/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00073/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00074/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00075/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00076/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00077/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00078/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00079/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00080/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00081/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00082/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00083/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00084/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00085/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00086/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00087/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00088/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00089/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00090/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00091/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00092/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00093/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00094/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00095/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00096/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00097/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00098/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00099/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00100/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00101/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00102/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00103/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00104/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00105/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00106/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00107/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00108/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00109/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00110/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00111/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00112/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00113/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00114/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00115/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00116/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00117/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00118/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00119/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00120/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00121/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00122/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00123/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00124/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00125/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00126/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00127/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00128/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00129/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00130/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00131/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00132/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00133/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00134/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00135/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00136/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00137/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00138/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00139/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00140/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00141/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00142/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00143/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00144/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00145/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00146/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00147/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00148/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00149/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00150/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00151/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00152/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00153/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00154/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00155/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00156/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00157/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00158/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00159/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00160/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00161/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00162/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00163/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00164/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00165/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00166/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00167/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00168/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00169/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00170/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00171/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00172/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00173/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00174/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00175/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00176/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00177/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00178/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00179/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00180/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00181/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00182/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00183/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00184/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00185/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00186/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00187/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00188/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00189/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00190/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00191/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00192/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00193/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00194/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00195/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00196/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00197/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00198/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00199/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00200/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00201/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00202/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00203/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00204/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00205/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00206/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00207/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00208/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00209/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00210/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00211/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00212/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00213/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00214/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00215/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00216/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00217/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00218/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00219/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00220/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00221/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00222/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00223/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00224/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00225/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00226/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00227/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00228/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00229/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00230/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00231/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00232/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00233/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00234/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00235/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00236/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00237/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00238/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00239/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00240/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00241/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00242/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00243/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00244/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00245/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00246/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00247/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00248/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00249/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00250/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00251/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00252/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00253/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00254/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00255/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00256/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00257/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00258/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00259/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00260/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00261/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00262/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00263/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00264/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00265/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00266/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00267/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00268/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00269/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00270/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00271/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00272/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00273/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00274/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00275/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00276/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00277/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00278/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00279/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00280/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00281/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00282/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00283/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00284/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00285/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00286/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00287/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00288/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00289/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00290/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00291/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00292/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00293/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00294/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00295/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00296/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00297/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00298/imaging.nii.gz',\n",
       " './datadownload/KiTS/case_00299/imaging.nii.gz']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "imgs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['./datadownload/KiTS/case_00000/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00001/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00002/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00003/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00004/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00005/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00006/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00007/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00008/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00009/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00010/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00011/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00012/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00013/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00014/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00015/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00016/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00017/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00018/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00019/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00020/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00021/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00022/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00023/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00024/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00025/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00026/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00027/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00028/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00029/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00030/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00031/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00032/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00033/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00034/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00035/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00036/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00037/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00038/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00039/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00040/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00041/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00042/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00043/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00044/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00045/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00046/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00047/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00048/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00049/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00050/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00051/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00052/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00053/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00054/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00055/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00056/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00057/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00058/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00059/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00060/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00061/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00062/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00063/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00064/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00065/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00066/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00067/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00068/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00069/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00070/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00071/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00072/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00073/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00074/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00075/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00076/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00077/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00078/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00079/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00080/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00081/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00082/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00083/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00084/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00085/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00086/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00087/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00088/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00089/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00090/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00091/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00092/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00093/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00094/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00095/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00096/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00097/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00098/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00099/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00100/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00101/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00102/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00103/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00104/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00105/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00106/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00107/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00108/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00109/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00110/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00111/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00112/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00113/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00114/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00115/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00116/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00117/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00118/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00119/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00120/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00121/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00122/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00123/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00124/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00125/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00126/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00127/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00128/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00129/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00130/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00131/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00132/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00133/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00134/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00135/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00136/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00137/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00138/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00139/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00140/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00141/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00142/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00143/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00144/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00145/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00146/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00147/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00148/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00149/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00150/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00151/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00152/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00153/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00154/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00155/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00156/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00157/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00158/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00159/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00160/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00161/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00162/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00163/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00164/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00165/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00166/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00167/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00168/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00169/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00170/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00171/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00172/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00173/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00174/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00175/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00176/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00177/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00178/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00179/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00180/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00181/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00182/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00183/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00184/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00185/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00186/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00187/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00188/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00189/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00190/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00191/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00192/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00193/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00194/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00195/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00196/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00197/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00198/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00199/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00200/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00201/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00202/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00203/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00204/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00205/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00206/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00207/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00208/segmentation.nii.gz',\n",
       " './datadownload/KiTS/case_00209/segmentation.nii.gz']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "segs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
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     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
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   ],
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    "pids"
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  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 1, Data resample"
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  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "targetspacing = [1.6, 1.6, 3.2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "pid = pids[0]\n",
    "imgfile = imgs[0]\n",
    "img_obj = sitk.ReadImage( imgfile )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "Size (512, 512, 611) -> [294.375   294.375    95.46875]\n",
      "Spacing: (0.919921875, 0.919921875, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 611) -> [294.375   294.375    95.46875]\n",
      "Spacing: (0.919921875, 0.919921875, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 602) -> [255.625  255.625   94.0625]\n",
      "Spacing: (0.939453125, 0.939453125, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.939453125, 0.939453125, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 261) -> [300.625  300.625   81.5625]\n",
      "Spacing: (0.939453125, 0.939453125, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 261) -> [300.625  300.625   81.5625]\n",
      "Spacing: (0.939453125, 0.939453125, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 270) -> [273.75  273.75   84.375]\n",
      "Spacing: (0.85546875, 0.85546875, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9765625, 0.9765625, 4.0) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 64) -> [312.5 312.5  80. ]\n",
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      "Size (512, 512, 157) -> [237.5    237.5    147.1875]\n",
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      "Size (512, 512, 61) -> [300.625  300.625   57.1875]\n",
      "Spacing: (0.939453125, 0.939453125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 61) -> [300.625  300.625   57.1875]\n",
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      "Size (512, 512, 227) -> [261.25   261.25   212.8125]\n",
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      "Spacing: (0.7578125, 0.7578125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 50) -> [242.5   242.5    46.875]\n",
      "Spacing: (0.7578125, 0.7578125, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Size (512, 512, 80) -> [225. 225. 125.]\n",
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      "Size (512, 512, 80) -> [225. 225. 125.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.849609375, 0.849609375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 439) -> [271.875  271.875  137.1875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.849609375, 0.849609375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 439) -> [271.875  271.875  137.1875]\n",
      "Spacing: (0.849609375, 0.849609375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 439) -> [271.875  271.875  137.1875]\n",
      "Spacing: (0.849609375, 0.849609375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 439) -> [271.875  271.875  137.1875]\n",
      "Spacing: (0.705078125, 0.705078125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [225.625  225.625   70.3125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.705078125, 0.705078125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [225.625  225.625   70.3125]\n",
      "Spacing: (0.705078125, 0.705078125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [225.625  225.625   70.3125]\n",
      "Spacing: (0.705078125, 0.705078125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [225.625  225.625   70.3125]\n",
      "Spacing: (0.650390625, 0.650390625, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.650390625, 0.650390625, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 178) -> [208.125  208.125  139.0625]\n",
      "Spacing: (0.650390625, 0.650390625, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 178) -> [208.125  208.125  139.0625]\n",
      "Spacing: (0.650390625, 0.650390625, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 178) -> [208.125  208.125  139.0625]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [212.5    212.5    151.5625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [212.5    212.5    151.5625]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [212.5    212.5    151.5625]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [212.5    212.5    151.5625]\n"
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     "name": "stdout",
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      "Spacing: (0.8613280057907104, 0.8613280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [275.62496185 275.62496185  94.53125   ]\n",
      "Spacing: (0.8613280057907104, 0.8613280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [275.62496185 275.62496185  94.53125   ]\n",
      "Spacing: (0.8613280057907104, 0.8613280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [275.62496185 275.62496185  94.53125   ]\n",
      "Spacing: (0.9375, 0.9375, 3.75) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.9375, 0.9375, 3.75) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 129) -> [300.       300.       151.171875]\n",
      "Spacing: (0.9375, 0.9375, 3.75) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 129) -> [300.       300.       151.171875]\n",
      "Spacing: (0.9375, 0.9375, 3.75) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 129) -> [300.       300.       151.171875]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [268.75 268.75 150.  ]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [268.75 268.75 150.  ]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [268.75 268.75 150.  ]\n",
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      "Spacing: (0.822265625, 0.822265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 38) -> [263.125 263.125  59.375]\n",
      "Spacing: (0.822265625, 0.822265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 38) -> [263.125 263.125  59.375]\n",
      "Spacing: (0.833984375, 0.833984375, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.833984375, 0.833984375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 541) -> [266.875   266.875    84.53125]\n",
      "Spacing: (0.833984375, 0.833984375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 541) -> [266.875   266.875    84.53125]\n",
      "Spacing: (0.7820000052452087, 0.7820000052452087, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.7820000052452087, 0.7820000052452087, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [250.24000168 250.24000168 100.3125    ]\n",
      "Spacing: (0.7820000052452087, 0.7820000052452087, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [250.24000168 250.24000168 100.3125    ]\n",
      "Spacing: (0.7820000052452087, 0.7820000052452087, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [250.24000168 250.24000168 100.3125    ]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [212.5    212.5    132.8125]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [212.5    212.5    132.8125]\n",
      "Spacing: (0.6640625, 0.6640625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [212.5    212.5    132.8125]\n",
      "Spacing: (0.7363280057907104, 0.7363280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.7363280057907104, 0.7363280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [235.62496185 235.62496185  80.46875   ]\n",
      "Spacing: (0.7363280057907104, 0.7363280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [235.62496185 235.62496185  80.46875   ]\n",
      "Spacing: (0.7363280057907104, 0.7363280057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [235.62496185 235.62496185  80.46875   ]\n",
      "Spacing: (0.875, 0.875, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.875, 0.875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 302) -> [280.     280.     235.9375]\n",
      "Spacing: (0.875, 0.875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 302) -> [280.     280.     235.9375]\n",
      "Spacing: (0.89453125, 0.89453125, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.89453125, 0.89453125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 723) -> [286.25    286.25    112.96875]\n",
      "Spacing: (0.89453125, 0.89453125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 723) -> [286.25    286.25    112.96875]\n",
      "Spacing: (0.89453125, 0.89453125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 723) -> [286.25    286.25    112.96875]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [268.75  268.75  153.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [268.75  268.75  153.125]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [268.75  268.75  153.125]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [268.75  268.75  153.125]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 131) -> [241.25   241.25   204.6875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 131) -> [241.25   241.25   204.6875]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 131) -> [241.25   241.25   204.6875]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 131) -> [241.25   241.25   204.6875]\n",
      "Spacing: (0.73046875, 0.73046875, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.73046875, 0.73046875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 38) -> [233.75  233.75   59.375]\n",
      "Spacing: (0.73046875, 0.73046875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 38) -> [233.75  233.75   59.375]\n",
      "Spacing: (0.73046875, 0.73046875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 38) -> [233.75  233.75   59.375]\n",
      "Spacing: (0.5180000066757202, 0.5180000066757202, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 117) -> [165.76000214 165.76000214 109.6875    ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.5180000066757202, 0.5180000066757202, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 117) -> [165.76000214 165.76000214 109.6875    ]\n",
      "Spacing: (0.5180000066757202, 0.5180000066757202, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 117) -> [165.76000214 165.76000214 109.6875    ]\n",
      "Spacing: (0.5180000066757202, 0.5180000066757202, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 117) -> [165.76000214 165.76000214 109.6875    ]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 189) -> [249.37503815 249.37503815 147.65625   ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 189) -> [249.37503815 249.37503815 147.65625   ]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 189) -> [249.37503815 249.37503815 147.65625   ]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 189) -> [249.37503815 249.37503815 147.65625   ]\n",
      "Spacing: (0.80859375, 0.80859375, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.80859375, 0.80859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 423) -> [258.75   258.75   132.1875]\n",
      "Spacing: (0.80859375, 0.80859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 423) -> [258.75   258.75   132.1875]\n",
      "Spacing: (0.80859375, 0.80859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 423) -> [258.75   258.75   132.1875]\n",
      "Spacing: (0.8359375, 0.8359375, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.8359375, 0.8359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 110) -> [267.5   267.5   171.875]\n",
      "Spacing: (0.8359375, 0.8359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 110) -> [267.5   267.5   171.875]\n"
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      "Spacing: (0.8359375, 0.8359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 110) -> [267.5   267.5   171.875]\n",
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      "Size (512, 512, 98) -> [308.75  308.75  153.125]\n",
      "Spacing: (0.96484375, 0.96484375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [308.75  308.75  153.125]\n",
      "Spacing: (0.96484375, 0.96484375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [308.75  308.75  153.125]\n",
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      "Spacing: (0.798828125, 0.798828125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 163) -> [255.625  255.625  152.8125]\n",
      "Spacing: (0.798828125, 0.798828125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 163) -> [255.625  255.625  152.8125]\n",
      "Spacing: (0.798828125, 0.798828125, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 163) -> [255.625  255.625  152.8125]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [300.     300.     151.5625]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [300.     300.     151.5625]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 97) -> [300.     300.     151.5625]\n",
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      "Size (512, 512, 32) -> [249.375 249.375  50.   ]\n",
      "Spacing: (0.779296875, 0.779296875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 32) -> [249.375 249.375  50.   ]\n",
      "Spacing: (0.779296875, 0.779296875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 32) -> [249.375 249.375  50.   ]\n",
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      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 90) -> [225.    225.    140.625]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 90) -> [225.    225.    140.625]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 2.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7409999966621399, 0.7409999966621399, 2.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7409999966621399, 0.7409999966621399, 2.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 207) -> [237.11999893 237.11999893 129.375     ]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 2.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 207) -> [237.11999893 237.11999893 129.375     ]\n",
      "Spacing: (0.677734375, 0.677734375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 52) -> [216.875 216.875  48.75 ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.677734375, 0.677734375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 52) -> [216.875 216.875  48.75 ]\n",
      "Spacing: (0.677734375, 0.677734375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 52) -> [216.875 216.875  48.75 ]\n",
      "Spacing: (0.677734375, 0.677734375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 52) -> [216.875 216.875  48.75 ]\n",
      "Spacing: (0.859375, 0.859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 301) -> [275.     275.      94.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.859375, 0.859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 301) -> [275.     275.      94.0625]\n",
      "Spacing: (0.859375, 0.859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 301) -> [275.     275.      94.0625]\n",
      "Spacing: (0.859375, 0.859375, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 301) -> [275.     275.      94.0625]\n",
      "Spacing: (0.7379999756813049, 0.7379999756813049, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 172) -> [236.15999222 236.15999222 161.25      ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7379999756813049, 0.7379999756813049, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 172) -> [236.15999222 236.15999222 161.25      ]\n",
      "Spacing: (0.7379999756813049, 0.7379999756813049, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 172) -> [236.15999222 236.15999222 161.25      ]\n",
      "Spacing: (0.7379999756813049, 0.7379999756813049, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 172) -> [236.15999222 236.15999222 161.25      ]\n",
      "Spacing: (0.966796875, 0.966796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [309.375  309.375  157.8125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.966796875, 0.966796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [309.375  309.375  157.8125]\n",
      "Spacing: (0.966796875, 0.966796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [309.375  309.375  157.8125]\n",
      "Spacing: (0.966796875, 0.966796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [309.375  309.375  157.8125]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 62) -> [237.11999893 237.11999893  58.125     ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 62) -> [237.11999893 237.11999893  58.125     ]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 62) -> [237.11999893 237.11999893  58.125     ]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 62) -> [237.11999893 237.11999893  58.125     ]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [312.5    312.5    149.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [312.5    312.5    149.0625]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [312.5    312.5    149.0625]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [312.5    312.5    149.0625]\n",
      "Spacing: (0.85546875, 0.85546875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 142) -> [273.75  273.75  221.875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.85546875, 0.85546875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 142) -> [273.75  273.75  221.875]\n",
      "Spacing: (0.85546875, 0.85546875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 142) -> [273.75  273.75  221.875]\n",
      "Spacing: (0.85546875, 0.85546875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 142) -> [273.75  273.75  221.875]\n",
      "Spacing: (1.0410000085830688, 1.0410000085830688, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [333.12000275 333.12000275 132.8125    ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (1.0410000085830688, 1.0410000085830688, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [333.12000275 333.12000275 132.8125    ]\n",
      "Spacing: (1.0410000085830688, 1.0410000085830688, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [333.12000275 333.12000275 132.8125    ]\n",
      "Spacing: (1.0410000085830688, 1.0410000085830688, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 85) -> [333.12000275 333.12000275 132.8125    ]\n",
      "Spacing: (0.861328125, 0.861328125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 670) -> [275.625  275.625  104.6875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.861328125, 0.861328125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 670) -> [275.625  275.625  104.6875]\n",
      "Spacing: (0.861328125, 0.861328125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 670) -> [275.625  275.625  104.6875]\n",
      "Spacing: (0.861328125, 0.861328125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 670) -> [275.625  275.625  104.6875]\n",
      "Spacing: (0.6894530057907104, 0.6894530057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [220.62496185 220.62496185  75.        ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.6894530057907104, 0.6894530057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [220.62496185 220.62496185  75.        ]\n",
      "Spacing: (0.6894530057907104, 0.6894530057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [220.62496185 220.62496185  75.        ]\n",
      "Spacing: (0.6894530057907104, 0.6894530057907104, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [220.62496185 220.62496185  75.        ]\n",
      "Spacing: (0.9609375, 0.9609375, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 68) -> [307.5   307.5    53.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9609375, 0.9609375, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 68) -> [307.5   307.5    53.125]\n",
      "Spacing: (0.9609375, 0.9609375, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 68) -> [307.5   307.5    53.125]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Spacing: (0.9609375, 0.9609375, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 68) -> [307.5   307.5    53.125]\n",
      "Spacing: (0.95703125, 0.95703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 673) -> [306.25    306.25    105.15625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.95703125, 0.95703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 673) -> [306.25    306.25    105.15625]\n",
      "Spacing: (0.95703125, 0.95703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 673) -> [306.25    306.25    105.15625]\n",
      "Spacing: (0.95703125, 0.95703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 673) -> [306.25    306.25    105.15625]\n",
      "Spacing: (0.7734375, 0.7734375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 553) -> [247.5     247.5      86.40625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7734375, 0.7734375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 553) -> [247.5     247.5      86.40625]\n",
      "Spacing: (0.7734375, 0.7734375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 553) -> [247.5     247.5      86.40625]\n",
      "Spacing: (0.7734375, 0.7734375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 553) -> [247.5     247.5      86.40625]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 104) -> [312.5 312.5 162.5]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 104) -> [312.5 312.5 162.5]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 104) -> [312.5 312.5 162.5]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 104) -> [312.5 312.5 162.5]\n",
      "Spacing: (0.87890625, 0.87890625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [281.25   281.25   157.8125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.87890625, 0.87890625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [281.25   281.25   157.8125]\n",
      "Spacing: (0.87890625, 0.87890625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [281.25   281.25   157.8125]\n",
      "Spacing: (0.87890625, 0.87890625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [281.25   281.25   157.8125]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 90) -> [250.    250.    140.625]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 90) -> [250.    250.    140.625]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 90) -> [250.    250.    140.625]\n",
      "Spacing: (0.822265625, 0.822265625, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.822265625, 0.822265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 80) -> [263.125 263.125  75.   ]\n",
      "Spacing: (0.822265625, 0.822265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 80) -> [263.125 263.125  75.   ]\n",
      "Spacing: (0.822265625, 0.822265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 80) -> [263.125 263.125  75.   ]\n",
      "Spacing: (0.951171875, 0.951171875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [304.375  304.375  160.9375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.951171875, 0.951171875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [304.375  304.375  160.9375]\n",
      "Spacing: (0.951171875, 0.951171875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [304.375  304.375  160.9375]\n",
      "Spacing: (0.951171875, 0.951171875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [304.375  304.375  160.9375]\n",
      "Spacing: (0.7890625, 0.7890625, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.7890625, 0.7890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 738) -> [252.5    252.5    115.3125]\n",
      "Spacing: (0.7890625, 0.7890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 738) -> [252.5    252.5    115.3125]\n",
      "Spacing: (0.7890625, 0.7890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 738) -> [252.5    252.5    115.3125]\n",
      "Spacing: (0.833984375, 0.833984375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 145) -> [266.875  266.875  135.9375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.833984375, 0.833984375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 145) -> [266.875  266.875  135.9375]\n",
      "Spacing: (0.833984375, 0.833984375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 145) -> [266.875  266.875  135.9375]\n",
      "Spacing: (0.833984375, 0.833984375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 145) -> [266.875  266.875  135.9375]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 29) -> [312.49984741 312.49984741  45.3125    ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 29) -> [312.49984741 312.49984741  45.3125    ]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 29) -> [312.49984741 312.49984741  45.3125    ]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 29) -> [312.49984741 312.49984741  45.3125    ]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5   134.375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5   134.375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5   134.375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5   134.375]\n",
      "Spacing: (0.859375, 0.859375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 527) -> [275.      275.       82.34375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.859375, 0.859375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 527) -> [275.      275.       82.34375]\n",
      "Spacing: (0.859375, 0.859375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 527) -> [275.      275.       82.34375]\n",
      "Spacing: (0.859375, 0.859375, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 527) -> [275.      275.       82.34375]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [225.     225.      82.8125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [225.     225.      82.8125]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [225.     225.      82.8125]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [225.     225.      82.8125]\n",
      "Spacing: (0.8203120231628418, 0.8203120231628418, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [262.49984741 262.49984741  80.46875   ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.8203120231628418, 0.8203120231628418, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [262.49984741 262.49984741  80.46875   ]\n",
      "Spacing: (0.8203120231628418, 0.8203120231628418, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [262.49984741 262.49984741  80.46875   ]\n",
      "Spacing: (0.8203120231628418, 0.8203120231628418, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [262.49984741 262.49984741  80.46875   ]\n",
      "Spacing: (0.8632810115814209, 0.8632810115814209, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 445) -> [276.24992371 276.24992371 173.828125  ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.8632810115814209, 0.8632810115814209, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 445) -> [276.24992371 276.24992371 173.828125  ]\n",
      "Spacing: (0.8632810115814209, 0.8632810115814209, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 445) -> [276.24992371 276.24992371 173.828125  ]\n",
      "Spacing: (0.8632810115814209, 0.8632810115814209, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 445) -> [276.24992371 276.24992371 173.828125  ]\n",
      "Spacing: (0.76171875, 0.76171875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 285) -> [243.75   243.75    89.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.76171875, 0.76171875, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.76171875, 0.76171875, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.703125, 0.703125, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.64453125, 0.64453125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.703125, 0.703125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.6859999895095825, 0.6859999895095825, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 79) -> [219.51999664 219.51999664 123.4375    ]\n",
      "Spacing: (0.72265625, 0.72265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 50) -> [231.25  231.25   78.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.72265625, 0.72265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 50) -> [231.25  231.25   78.125]\n",
      "Spacing: (0.72265625, 0.72265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 50) -> [231.25  231.25   78.125]\n",
      "Spacing: (0.72265625, 0.72265625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 50) -> [231.25  231.25   78.125]\n",
      "Spacing: (0.8691409826278687, 0.8691409826278687, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 389) -> [278.12511444 278.12511444 151.953125  ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.8691409826278687, 0.8691409826278687, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 389) -> [278.12511444 278.12511444 151.953125  ]\n",
      "Spacing: (0.8691409826278687, 0.8691409826278687, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 389) -> [278.12511444 278.12511444 151.953125  ]\n",
      "Spacing: (0.8691409826278687, 0.8691409826278687, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 389) -> [278.12511444 278.12511444 151.953125  ]\n",
      "Spacing: (0.703125, 0.703125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 262) -> [225.     225.     204.6875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.703125, 0.703125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 262) -> [225.     225.     204.6875]\n",
      "Spacing: (0.703125, 0.703125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 262) -> [225.     225.     204.6875]\n",
      "Spacing: (0.703125, 0.703125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 262) -> [225.     225.     204.6875]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 171) -> [312.5    312.5    160.3125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 171) -> [312.5    312.5    160.3125]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 171) -> [312.5    312.5    160.3125]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 171) -> [312.5    312.5    160.3125]\n",
      "Spacing: (0.94140625, 0.94140625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [301.25   301.25   167.1875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.94140625, 0.94140625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [301.25   301.25   167.1875]\n",
      "Spacing: (0.94140625, 0.94140625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [301.25   301.25   167.1875]\n",
      "Spacing: (0.94140625, 0.94140625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 107) -> [301.25   301.25   167.1875]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 105) -> [312.5    312.5     98.4375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 105) -> [312.5    312.5     98.4375]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 105) -> [312.5    312.5     98.4375]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 105) -> [312.5    312.5     98.4375]\n",
      "Spacing: (0.8789060115814209, 0.8789060115814209, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.8789060115814209, 0.8789060115814209, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 206) -> [281.24992371 281.24992371 160.9375    ]\n",
      "Spacing: (0.8789060115814209, 0.8789060115814209, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 206) -> [281.24992371 281.24992371 160.9375    ]\n",
      "Spacing: (0.8789060115814209, 0.8789060115814209, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 206) -> [281.24992371 281.24992371 160.9375    ]\n",
      "Spacing: (0.736328125, 0.736328125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 48) -> [235.625 235.625  75.   ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.736328125, 0.736328125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 48) -> [235.625 235.625  75.   ]\n",
      "Spacing: (0.736328125, 0.736328125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 48) -> [235.625 235.625  75.   ]\n",
      "Spacing: (0.736328125, 0.736328125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 48) -> [235.625 235.625  75.   ]\n",
      "Spacing: (0.546875, 0.546875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [175.     175.      49.6875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.546875, 0.546875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [175.     175.      49.6875]\n",
      "Spacing: (0.546875, 0.546875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [175.     175.      49.6875]\n",
      "Spacing: (0.546875, 0.546875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 53) -> [175.     175.      49.6875]\n",
      "Spacing: (0.6679999828338623, 0.6679999828338623, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [213.75999451 213.75999451 149.0625    ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.6679999828338623, 0.6679999828338623, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [213.75999451 213.75999451 149.0625    ]\n",
      "Spacing: (0.6679999828338623, 0.6679999828338623, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [213.75999451 213.75999451 149.0625    ]\n",
      "Spacing: (0.6679999828338623, 0.6679999828338623, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 159) -> [213.75999451 213.75999451 149.0625    ]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 532) -> [228.125 228.125  83.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 532) -> [228.125 228.125  83.125]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 532) -> [228.125 228.125  83.125]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 532) -> [228.125 228.125  83.125]\n",
      "Spacing: (0.8496090173721313, 0.8496090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 186) -> [271.87488556 271.87488556 145.3125    ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.8496090173721313, 0.8496090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 186) -> [271.87488556 271.87488556 145.3125    ]\n",
      "Spacing: (0.8496090173721313, 0.8496090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 186) -> [271.87488556 271.87488556 145.3125    ]\n",
      "Spacing: (0.8496090173721313, 0.8496090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 186) -> [271.87488556 271.87488556 145.3125    ]\n",
      "Spacing: (0.947265625, 0.947265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 61) -> [303.125  303.125   57.1875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.947265625, 0.947265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 61) -> [303.125  303.125   57.1875]\n",
      "Spacing: (0.947265625, 0.947265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 61) -> [303.125  303.125   57.1875]\n",
      "Spacing: (0.947265625, 0.947265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 61) -> [303.125  303.125   57.1875]\n",
      "Spacing: (0.837890625, 0.837890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 634) -> [268.125  268.125   99.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.837890625, 0.837890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 634) -> [268.125  268.125   99.0625]\n",
      "Spacing: (0.837890625, 0.837890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 634) -> [268.125  268.125   99.0625]\n",
      "Spacing: (0.837890625, 0.837890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 634) -> [268.125  268.125   99.0625]\n",
      "Spacing: (0.68359375, 0.68359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [218.75   218.75   157.8125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.68359375, 0.68359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [218.75   218.75   157.8125]\n",
      "Spacing: (0.68359375, 0.68359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [218.75   218.75   157.8125]\n",
      "Spacing: (0.68359375, 0.68359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 101) -> [218.75   218.75   157.8125]\n",
      "Spacing: (0.7421875, 0.7421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 109) -> [237.5     237.5      85.15625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7421875, 0.7421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 109) -> [237.5     237.5      85.15625]\n",
      "Spacing: (0.7421875, 0.7421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 109) -> [237.5     237.5      85.15625]\n",
      "Spacing: (0.7421875, 0.7421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 109) -> [237.5     237.5      85.15625]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "Size (512, 512, 76) -> [218.75 218.75  71.25]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 76) -> [218.75 218.75  71.25]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 76) -> [218.75 218.75  71.25]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 76) -> [218.75 218.75  71.25]\n",
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      "Spacing: (0.80078125, 0.80078125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [256.25   256.25   160.9375]\n",
      "Spacing: (0.80078125, 0.80078125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [256.25   256.25   160.9375]\n",
      "Spacing: (0.82421875, 0.82421875, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.82421875, 0.82421875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 279) -> [263.75   263.75    87.1875]\n",
      "Spacing: (0.82421875, 0.82421875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 279) -> [263.75   263.75    87.1875]\n",
      "Spacing: (0.82421875, 0.82421875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 279) -> [263.75   263.75    87.1875]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 581) -> [228.125   228.125    90.78125]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 581) -> [228.125   228.125    90.78125]\n",
      "Spacing: (0.712890625, 0.712890625, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 581) -> [228.125   228.125    90.78125]\n",
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      "Spacing: (0.80859375, 0.80859375, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.91796875, 0.91796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 92) -> [293.75 293.75 143.75]\n",
      "Spacing: (0.91796875, 0.91796875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 92) -> [293.75 293.75 143.75]\n",
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      "Spacing: (0.791015625, 0.791015625, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 197) -> [253.125   253.125   153.90625]\n",
      "Spacing: (0.791015625, 0.791015625, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 197) -> [253.125   253.125   153.90625]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5    80.625]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5    80.625]\n",
      "Spacing: (0.9765625, 0.9765625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 86) -> [312.5   312.5    80.625]\n",
      "Spacing: (0.703125, 0.703125, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.703125, 0.703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 591) -> [225.      225.       92.34375]\n",
      "Spacing: (0.703125, 0.703125, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 591) -> [225.      225.       92.34375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 70) -> [312.5   312.5   109.375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 70) -> [312.5   312.5   109.375]\n",
      "Spacing: (0.90625, 0.90625, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.90625, 0.90625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 36) -> [290.   290.    56.25]\n",
      "Spacing: (0.90625, 0.90625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 36) -> [290.   290.    56.25]\n",
      "Spacing: (0.90625, 0.90625, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.796875, 0.796875, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 1059) -> [259.375   259.375   165.46875]\n",
      "Spacing: (0.810546875, 0.810546875, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.6640625, 0.6640625, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9375, 0.9375, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9375, 0.9375, 0.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.810546875, 0.810546875, 0.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 538) -> [259.375  259.375   84.0625]\n"
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      "Spacing: (0.8730000257492065, 0.8730000257492065, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.8730000257492065, 0.8730000257492065, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 83) -> [248.12511444 248.12511444 129.6875    ]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [312.5   312.5   159.375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [312.5   312.5   159.375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [312.5   312.5   159.375]\n",
      "Spacing: (0.9765625, 0.9765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [312.5   312.5   159.375]\n",
      "Spacing: (0.673828125, 0.673828125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.673828125, 0.673828125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [215.625 215.625 137.5  ]\n",
      "Spacing: (0.673828125, 0.673828125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [215.625 215.625 137.5  ]\n",
      "Spacing: (0.673828125, 0.673828125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [215.625 215.625 137.5  ]\n",
      "Spacing: (0.865234375, 0.865234375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [276.875 276.875 137.5  ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.865234375, 0.865234375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [276.875 276.875 137.5  ]\n",
      "Spacing: (0.865234375, 0.865234375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [276.875 276.875 137.5  ]\n",
      "Spacing: (0.865234375, 0.865234375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 88) -> [276.875 276.875 137.5  ]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [237.5    237.5    154.6875]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [237.5    237.5    154.6875]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [237.5    237.5    154.6875]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [237.5    237.5    154.6875]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 137) -> [237.11999893 237.11999893 128.4375    ]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 137) -> [237.11999893 237.11999893 128.4375    ]\n",
      "Spacing: (0.7409999966621399, 0.7409999966621399, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 137) -> [237.11999893 237.11999893 128.4375    ]\n",
      "Spacing: (0.693359375, 0.693359375, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.693359375, 0.693359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [221.875  221.875  154.6875]\n",
      "Spacing: (0.693359375, 0.693359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [221.875  221.875  154.6875]\n",
      "Spacing: (0.693359375, 0.693359375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 99) -> [221.875  221.875  154.6875]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [300.     300.     145.3125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [300.     300.     145.3125]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [300.     300.     145.3125]\n",
      "Spacing: (0.9375, 0.9375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [300.     300.     145.3125]\n",
      "Spacing: (0.70703125, 0.70703125, 1.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 195) -> [226.25    226.25     91.40625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.70703125, 0.70703125, 1.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 195) -> [226.25    226.25     91.40625]\n",
      "Spacing: (0.70703125, 0.70703125, 1.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 195) -> [226.25    226.25     91.40625]\n",
      "Spacing: (0.70703125, 0.70703125, 1.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 195) -> [226.25    226.25     91.40625]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [268.75  268.75  228.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [268.75  268.75  228.125]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [268.75  268.75  228.125]\n",
      "Spacing: (0.83984375, 0.83984375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [268.75  268.75  228.125]\n",
      "Spacing: (0.9121090173721313, 0.9121090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 235) -> [291.87488556 291.87488556 183.59375   ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.9121090173721313, 0.9121090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 235) -> [291.87488556 291.87488556 183.59375   ]\n",
      "Spacing: (0.9121090173721313, 0.9121090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 235) -> [291.87488556 291.87488556 183.59375   ]\n",
      "Spacing: (0.9121090173721313, 0.9121090173721313, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 235) -> [291.87488556 291.87488556 183.59375   ]\n",
      "Spacing: (0.734375, 0.734375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 143) -> [235.     235.     223.4375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.734375, 0.734375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 143) -> [235.     235.     223.4375]\n",
      "Spacing: (0.734375, 0.734375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 143) -> [235.     235.     223.4375]\n",
      "Spacing: (0.734375, 0.734375, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 143) -> [235.     235.     223.4375]\n",
      "Spacing: (0.625, 0.625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 82) -> [200.    200.    128.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.625, 0.625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 82) -> [200.    200.    128.125]\n",
      "Spacing: (0.625, 0.625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 82) -> [200.    200.    128.125]\n",
      "Spacing: (0.625, 0.625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 82) -> [200.    200.    128.125]\n",
      "Spacing: (0.6796875, 0.6796875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 365) -> [217.5    217.5    114.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.6796875, 0.6796875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 365) -> [217.5    217.5    114.0625]\n",
      "Spacing: (0.6796875, 0.6796875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 365) -> [217.5    217.5    114.0625]\n",
      "Spacing: (0.6796875, 0.6796875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 365) -> [217.5    217.5    114.0625]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [237.5   237.5   228.125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [237.5   237.5   228.125]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [237.5   237.5   228.125]\n",
      "Spacing: (0.7421875, 0.7421875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 146) -> [237.5   237.5   228.125]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "Size (512, 512, 161) -> [231.25   231.25   150.9375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.72265625, 0.72265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 161) -> [231.25   231.25   150.9375]\n",
      "Spacing: (0.72265625, 0.72265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 161) -> [231.25   231.25   150.9375]\n",
      "Spacing: (0.72265625, 0.72265625, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 161) -> [231.25   231.25   150.9375]\n",
      "Spacing: (0.7421879768371582, 0.7421879768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7421879768371582, 0.7421879768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7421879768371582, 0.7421879768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 349) -> [237.50015259 237.50015259 136.328125  ]\n",
      "Spacing: (0.7421879768371582, 0.7421879768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 349) -> [237.50015259 237.50015259 136.328125  ]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 133) -> [250.     250.     207.8125]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 133) -> [250.     250.     207.8125]\n",
      "Spacing: (0.703125, 0.703125, 1.25) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.703125, 0.703125, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 233) -> [225.       225.        91.015625]\n",
      "Spacing: (0.703125, 0.703125, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 233) -> [225.       225.        91.015625]\n",
      "Spacing: (0.75, 0.75, 5.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.75, 0.75, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 135) -> [240.     240.     210.9375]\n",
      "Spacing: (0.75, 0.75, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 135) -> [240.     240.     210.9375]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.763671875, 0.763671875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [244.375 244.375 153.125]\n",
      "Spacing: (0.763671875, 0.763671875, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 98) -> [244.375 244.375 153.125]\n",
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      "Spacing: (0.818359375, 0.818359375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 178) -> [261.875 261.875 166.875]\n",
      "Spacing: (0.818359375, 0.818359375, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 178) -> [261.875 261.875 166.875]\n",
      "Spacing: (0.873046875, 0.873046875, 3.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
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      "Spacing: (0.873046875, 0.873046875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 162) -> [279.375 279.375 151.875]\n",
      "Spacing: (0.873046875, 0.873046875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 162) -> [279.375 279.375 151.875]\n",
      "Spacing: (0.732421875, 0.732421875, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Size (512, 512, 269) -> [234.375   234.375   210.15625]\n",
      "Spacing: (0.732421875, 0.732421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 269) -> [234.375   234.375   210.15625]\n",
      "Spacing: (0.732421875, 0.732421875, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 269) -> [234.375   234.375   210.15625]\n",
      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
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      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [237.50015259 237.50015259  94.53125   ]\n",
      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [237.50015259 237.50015259  94.53125   ]\n",
      "Spacing: (0.7421879768371582, 0.7421879768371582, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 121) -> [237.50015259 237.50015259  94.53125   ]\n",
      "Spacing: (0.7421875, 0.7421875, 4.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [237.5  237.5  128.75]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.7421875, 0.7421875, 4.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [237.5  237.5  128.75]\n",
      "Spacing: (0.7421875, 0.7421875, 4.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [237.5  237.5  128.75]\n",
      "Spacing: (0.7421875, 0.7421875, 4.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 103) -> [237.5  237.5  128.75]\n",
      "Spacing: (0.78125, 0.78125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [250. 250.  75.]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.78125, 0.78125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [250. 250.  75.]\n",
      "Spacing: (0.78125, 0.78125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [250. 250.  75.]\n",
      "Spacing: (0.78125, 0.78125, 2.5) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 96) -> [250. 250.  75.]\n",
      "Spacing: (0.8984379768371582, 0.8984379768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 383) -> [287.50015259 287.50015259 149.609375  ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.8984379768371582, 0.8984379768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 383) -> [287.50015259 287.50015259 149.609375  ]\n",
      "Spacing: (0.8984379768371582, 0.8984379768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 383) -> [287.50015259 287.50015259 149.609375  ]\n",
      "Spacing: (0.8984379768371582, 0.8984379768371582, 1.25) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 383) -> [287.50015259 287.50015259 149.609375  ]\n",
      "Spacing: (0.63671875, 0.63671875, 1.0) -> [1.6, 1.6, 3.2]\n",
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      "Label values: [0 1 2]\n",
      "Spacing: (0.63671875, 0.63671875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 620) -> [203.75 203.75 193.75]\n",
      "Spacing: (0.63671875, 0.63671875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 620) -> [203.75 203.75 193.75]\n",
      "Spacing: (0.63671875, 0.63671875, 1.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 620) -> [203.75 203.75 193.75]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [280.     280.      70.3125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [280.     280.      70.3125]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [280.     280.      70.3125]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 75) -> [280.     280.      70.3125]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [250.     250.     145.3125]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [250.     250.     145.3125]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [250.     250.     145.3125]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 93) -> [250.     250.     145.3125]\n",
      "Spacing: (0.970703125, 0.970703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 60) -> [310.625 310.625  93.75 ]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.970703125, 0.970703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 60) -> [310.625 310.625  93.75 ]\n",
      "Spacing: (0.970703125, 0.970703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 60) -> [310.625 310.625  93.75 ]\n",
      "Spacing: (0.970703125, 0.970703125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 60) -> [310.625 310.625  93.75 ]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 140) -> [241.25 241.25 218.75]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 140) -> [241.25 241.25 218.75]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 140) -> [241.25 241.25 218.75]\n",
      "Spacing: (0.75390625, 0.75390625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 140) -> [241.25 241.25 218.75]\n",
      "Spacing: (0.884765625, 0.884765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 89) -> [283.125  283.125  139.0625]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.884765625, 0.884765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 89) -> [283.125  283.125  139.0625]\n",
      "Spacing: (0.884765625, 0.884765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 89) -> [283.125  283.125  139.0625]\n",
      "Spacing: (0.884765625, 0.884765625, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 89) -> [283.125  283.125  139.0625]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [250.    250.    159.375]\n",
      "Label values: [0 1 2]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [250.    250.    159.375]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [250.    250.    159.375]\n",
      "Spacing: (0.78125, 0.78125, 5.0) -> [1.6, 1.6, 3.2]\n",
      "Size (512, 512, 102) -> [250.    250.    159.375]\n"
     ]
    }
   ],
   "source": [
    "for (imgfile, lblfile, pid) in zip(imgs, segs, pids):\n",
    "    savename = 'kidney_' + pid + '.nii.gz'\n",
    "    img_obj = sitk.ReadImage( imgfile )\n",
    "    seg_obj = sitk.ReadImage( lblfile )\n",
    "    \n",
    "    pa = sitk.PermuteAxesImageFilter()\n",
    "    pa.SetOrder([2,1,0])\n",
    "    img_obj = pa.Execute(img_obj)\n",
    "    seg_obj = pa.Execute(seg_obj)\n",
    "    \n",
    "    img_spa_ori = img_obj.GetSpacing()\n",
    "    res_img_o = resample_by_res(img_obj, targetspacing, interpolator = sitk.sitkLinear,\n",
    "                                    logging = True)\n",
    "    res_lb_o = resample_lb_by_res(seg_obj, targetspacing, interpolator = sitk.sitkLinear,\n",
    "                                  ref_img = res_img_o, logging = True)\n",
    "    \n",
    "    res_img_o = sitk.Flip(res_img_o, [False, False, True])\n",
    "    res_lb_o = sitk.Flip(res_lb_o, [False, False, True])\n",
    "    \n",
    "    sitk.WriteImage(res_img_o, datasavepath + 'Image/' + savename, True) \n",
    "    sitk.WriteImage(res_lb_o, datasavepath + 'Label/' + savename, True) "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 2, Intensity Normalization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "IMG_FOLDER_SAVE = datasavepath + 'Image/'\n",
    "imgs = glob.glob(IMG_FOLDER_SAVE + \"/kidney_*.nii.gz\")\n",
    "imgs = [ fid for fid in sorted(imgs) ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "pixel_mean = 101\n",
    "pixel_std = 76.9\n",
    "intensity_05percent = -79\n",
    "intensity_995percent = 304"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Id 00000 normalized\n",
      "Id 00001 normalized\n",
      "Id 00002 normalized\n",
      "Id 00003 normalized\n",
      "Id 00004 normalized\n",
      "Id 00005 normalized\n",
      "Id 00006 normalized\n",
      "Id 00007 normalized\n",
      "Id 00008 normalized\n",
      "Id 00009 normalized\n",
      "Id 00010 normalized\n",
      "Id 00011 normalized\n",
      "Id 00012 normalized\n",
      "Id 00013 normalized\n",
      "Id 00014 normalized\n",
      "Id 00015 normalized\n",
      "Id 00016 normalized\n",
      "Id 00017 normalized\n",
      "Id 00018 normalized\n",
      "Id 00019 normalized\n",
      "Id 00020 normalized\n",
      "Id 00021 normalized\n",
      "Id 00022 normalized\n",
      "Id 00023 normalized\n",
      "Id 00024 normalized\n",
      "Id 00025 normalized\n",
      "Id 00026 normalized\n",
      "Id 00027 normalized\n",
      "Id 00028 normalized\n",
      "Id 00029 normalized\n",
      "Id 00030 normalized\n",
      "Id 00031 normalized\n",
      "Id 00032 normalized\n",
      "Id 00033 normalized\n",
      "Id 00034 normalized\n",
      "Id 00035 normalized\n",
      "Id 00036 normalized\n",
      "Id 00037 normalized\n",
      "Id 00038 normalized\n",
      "Id 00039 normalized\n",
      "Id 00040 normalized\n",
      "Id 00041 normalized\n",
      "Id 00042 normalized\n",
      "Id 00043 normalized\n",
      "Id 00044 normalized\n",
      "Id 00045 normalized\n",
      "Id 00046 normalized\n",
      "Id 00047 normalized\n",
      "Id 00048 normalized\n",
      "Id 00049 normalized\n",
      "Id 00050 normalized\n",
      "Id 00051 normalized\n",
      "Id 00052 normalized\n",
      "Id 00053 normalized\n",
      "Id 00054 normalized\n",
      "Id 00055 normalized\n",
      "Id 00056 normalized\n",
      "Id 00057 normalized\n",
      "Id 00058 normalized\n",
      "Id 00059 normalized\n",
      "Id 00060 normalized\n",
      "Id 00061 normalized\n",
      "Id 00062 normalized\n",
      "Id 00063 normalized\n",
      "Id 00064 normalized\n",
      "Id 00065 normalized\n",
      "Id 00066 normalized\n",
      "Id 00067 normalized\n",
      "Id 00068 normalized\n",
      "Id 00069 normalized\n",
      "Id 00070 normalized\n",
      "Id 00071 normalized\n",
      "Id 00072 normalized\n",
      "Id 00073 normalized\n",
      "Id 00074 normalized\n",
      "Id 00075 normalized\n",
      "Id 00076 normalized\n",
      "Id 00077 normalized\n",
      "Id 00078 normalized\n",
      "Id 00079 normalized\n",
      "Id 00080 normalized\n",
      "Id 00081 normalized\n",
      "Id 00082 normalized\n",
      "Id 00083 normalized\n",
      "Id 00084 normalized\n",
      "Id 00085 normalized\n",
      "Id 00086 normalized\n",
      "Id 00087 normalized\n",
      "Id 00088 normalized\n",
      "Id 00089 normalized\n",
      "Id 00090 normalized\n",
      "Id 00091 normalized\n",
      "Id 00092 normalized\n",
      "Id 00093 normalized\n",
      "Id 00094 normalized\n",
      "Id 00095 normalized\n",
      "Id 00096 normalized\n",
      "Id 00097 normalized\n",
      "Id 00098 normalized\n",
      "Id 00099 normalized\n",
      "Id 00100 normalized\n",
      "Id 00101 normalized\n",
      "Id 00102 normalized\n",
      "Id 00103 normalized\n",
      "Id 00104 normalized\n",
      "Id 00105 normalized\n",
      "Id 00106 normalized\n",
      "Id 00107 normalized\n",
      "Id 00108 normalized\n",
      "Id 00109 normalized\n",
      "Id 00110 normalized\n",
      "Id 00111 normalized\n",
      "Id 00112 normalized\n",
      "Id 00113 normalized\n",
      "Id 00114 normalized\n",
      "Id 00115 normalized\n",
      "Id 00116 normalized\n",
      "Id 00117 normalized\n",
      "Id 00118 normalized\n",
      "Id 00119 normalized\n",
      "Id 00120 normalized\n",
      "Id 00121 normalized\n",
      "Id 00122 normalized\n",
      "Id 00123 normalized\n",
      "Id 00124 normalized\n",
      "Id 00125 normalized\n",
      "Id 00126 normalized\n",
      "Id 00127 normalized\n",
      "Id 00128 normalized\n",
      "Id 00129 normalized\n",
      "Id 00130 normalized\n",
      "Id 00131 normalized\n",
      "Id 00132 normalized\n",
      "Id 00133 normalized\n",
      "Id 00134 normalized\n",
      "Id 00135 normalized\n",
      "Id 00136 normalized\n",
      "Id 00137 normalized\n",
      "Id 00138 normalized\n",
      "Id 00139 normalized\n",
      "Id 00140 normalized\n",
      "Id 00141 normalized\n",
      "Id 00142 normalized\n",
      "Id 00143 normalized\n",
      "Id 00144 normalized\n",
      "Id 00145 normalized\n",
      "Id 00146 normalized\n",
      "Id 00147 normalized\n",
      "Id 00148 normalized\n",
      "Id 00149 normalized\n",
      "Id 00150 normalized\n",
      "Id 00151 normalized\n",
      "Id 00152 normalized\n",
      "Id 00153 normalized\n",
      "Id 00154 normalized\n",
      "Id 00155 normalized\n",
      "Id 00156 normalized\n",
      "Id 00157 normalized\n",
      "Id 00158 normalized\n",
      "Id 00159 normalized\n",
      "Id 00160 normalized\n",
      "Id 00161 normalized\n",
      "Id 00162 normalized\n",
      "Id 00163 normalized\n",
      "Id 00164 normalized\n",
      "Id 00165 normalized\n",
      "Id 00166 normalized\n",
      "Id 00167 normalized\n",
      "Id 00168 normalized\n",
      "Id 00169 normalized\n",
      "Id 00170 normalized\n",
      "Id 00171 normalized\n",
      "Id 00172 normalized\n",
      "Id 00173 normalized\n",
      "Id 00174 normalized\n",
      "Id 00175 normalized\n",
      "Id 00176 normalized\n",
      "Id 00177 normalized\n",
      "Id 00178 normalized\n",
      "Id 00179 normalized\n",
      "Id 00180 normalized\n",
      "Id 00181 normalized\n",
      "Id 00182 normalized\n",
      "Id 00183 normalized\n",
      "Id 00184 normalized\n",
      "Id 00185 normalized\n",
      "Id 00186 normalized\n",
      "Id 00187 normalized\n",
      "Id 00188 normalized\n",
      "Id 00189 normalized\n",
      "Id 00190 normalized\n",
      "Id 00191 normalized\n",
      "Id 00192 normalized\n",
      "Id 00193 normalized\n",
      "Id 00194 normalized\n",
      "Id 00195 normalized\n",
      "Id 00196 normalized\n",
      "Id 00197 normalized\n",
      "Id 00198 normalized\n",
      "Id 00199 normalized\n",
      "Id 00200 normalized\n",
      "Id 00201 normalized\n",
      "Id 00202 normalized\n",
      "Id 00203 normalized\n",
      "Id 00204 normalized\n",
      "Id 00205 normalized\n",
      "Id 00206 normalized\n",
      "Id 00207 normalized\n",
      "Id 00208 normalized\n",
      "Id 00209 normalized\n"
     ]
    }
   ],
   "source": [
    "for (imgfile, pid) in zip(imgs, pids):\n",
    "    savename = 'kidney_' + pid + '.nii.gz'\n",
    "    img_obj = sitk.ReadImage( imgfile )\n",
    "    \n",
    "    array = sitk.GetArrayFromImage(img_obj)\n",
    "\n",
    "    array[array < intensity_05percent] = intensity_05percent\n",
    "    array[array > intensity_995percent] = intensity_995percent\n",
    "    array = (array - pixel_mean) / pixel_std\n",
    "\n",
    "    normalized_img = sitk.GetImageFromArray(array)\n",
    "    normalized_img.CopyInformation(img_obj)\n",
    "    \n",
    "    sitk.WriteImage(normalized_img, datasavepath + 'processed/' + savename, True) \n",
    "    print('Id ' + pid + ' normalized')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3, Generate Body Masks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "IMG_FOLDER_SAVE = datasavepath + 'Image/'\n",
    "imgs = glob.glob(IMG_FOLDER_SAVE + \"/kidney_*.nii.gz\")\n",
    "imgs = [ fid for fid in sorted(imgs) ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "threshold = -200"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "for (imgfile, pid) in zip(imgs, pids):\n",
    "    savename = 'kidney_' + pid + '.nii.gz'\n",
    "    img_obj = sitk.ReadImage( imgfile )\n",
    "    array = sitk.GetArrayFromImage(img_obj)\n",
    "    array = array > threshold\n",
    "\n",
    "    array_component = remove_all_but_the_largest_connected_component(array, [1], targetspacing)\n",
    "\n",
    "    array_mask = array_component[0].astype(int)\n",
    "    array_mask = binary_fill_holes(array_mask).astype(float)\n",
    "\n",
    "    mask_img = sitk.GetImageFromArray(array_mask)\n",
    "    mask_img.CopyInformation(img_obj)\n",
    "    \n",
    "    sitk.WriteImage(mask_img, datasavepath + 'mask/' + savename, True) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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