{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For convinience, I've unified all of the data preprocessing\n",
    "notebooks from [ALPNet](https://github.com/cheng-01037/Self-supervised-Fewshot-Medical-Image-Segmentation.git) into a single notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%reset\n",
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "import numpy as np\n",
    "import os\n",
    "import glob\n",
    "import SimpleITK as sitk\n",
    "import sys\n",
    "\n",
    "sys.path.insert(0, '../')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create dirs for the SABS and CHAOS datasets\n",
    "os.makedirs('./SABS', exist_ok=True)\n",
    "os.makedirs('./CHAOST2', exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def copy_spacing_ori(src, dst):\n",
    "    dst.SetSpacing(src.GetSpacing())\n",
    "    dst.SetOrigin(src.GetOrigin())\n",
    "    dst.SetDirection(src.GetDirection())\n",
    "    return dst\n",
    "\n",
    "# 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",
    "    resample.SetOutputOrigin(mov_img_obj.GetOrigin())\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",
    "## Then crop ROI\n",
    "def get_label_center(label):\n",
    "    nnz = np.sum(label > 1e-5)\n",
    "    return np.int32(np.rint(np.sum(np.nonzero(label), axis = 1) * 1.0 / nnz))\n",
    "\n",
    "def image_crop(ori_vol, crop_size, referece_ctr_idx, padval = 0., only_2d = True):\n",
    "    \"\"\" crop a 3d matrix given the index of the new volume on the original volume\n",
    "        Args:\n",
    "            refernce_ctr_idx: the center of the new volume on the original volume (in indices)\n",
    "            only_2d: only do cropping on first two dimensions\n",
    "    \"\"\"\n",
    "    _expand_cropsize = [x + 1 for x in crop_size] # to deal with boundary case\n",
    "    if only_2d:\n",
    "        assert len(crop_size) == 2, \"Actual len {}\".format(len(crop_size))\n",
    "        assert len(referece_ctr_idx) == 2, \"Actual len {}\".format(len(referece_ctr_idx))\n",
    "        _expand_cropsize.append(ori_vol.shape[-1])\n",
    "        \n",
    "    image_patch = np.ones(tuple(_expand_cropsize)) * padval\n",
    "\n",
    "    half_size = tuple( [int(x * 1.0 / 2) for x in _expand_cropsize] )\n",
    "    _min_idx = [0,0,0]\n",
    "    _max_idx = list(ori_vol.shape)\n",
    "\n",
    "    # bias of actual cropped size to the beginning and the end of this volume\n",
    "    _bias_start = [0,0,0]\n",
    "    _bias_end = [0,0,0]\n",
    "\n",
    "    for dim,hsize in enumerate(half_size):\n",
    "        if dim == 2 and only_2d:\n",
    "            break\n",
    "\n",
    "        _bias_start[dim] = np.min([hsize, referece_ctr_idx[dim]])\n",
    "        _bias_end[dim] = np.min([hsize, ori_vol.shape[dim] - referece_ctr_idx[dim]])\n",
    "\n",
    "        _min_idx[dim] = referece_ctr_idx[dim] - _bias_start[dim]\n",
    "        _max_idx[dim] = referece_ctr_idx[dim] + _bias_end[dim]\n",
    "        \n",
    "    if only_2d:\n",
    "        image_patch[ half_size[0] - _bias_start[0]: half_size[0] +_bias_end[0], \\\n",
    "                half_size[1] - _bias_start[1]: half_size[1] +_bias_end[1], ... ] = \\\n",
    "                ori_vol[ referece_ctr_idx[0] - _bias_start[0]: referece_ctr_idx[0] +_bias_end[0], \\\n",
    "                referece_ctr_idx[1] - _bias_start[1]: referece_ctr_idx[1] +_bias_end[1], ... ]\n",
    "\n",
    "        image_patch = image_patch[ 0: crop_size[0], 0: crop_size[1], : ]\n",
    "    # then goes back to original volume\n",
    "    else:\n",
    "        image_patch[ half_size[0] - _bias_start[0]: half_size[0] +_bias_end[0], \\\n",
    "                half_size[1] - _bias_start[1]: half_size[1] +_bias_end[1], \\\n",
    "                half_size[2] - _bias_start[2]: half_size[2] +_bias_end[2] ] = \\\n",
    "                ori_vol[ referece_ctr_idx[0] - _bias_start[0]: referece_ctr_idx[0] +_bias_end[0], \\\n",
    "                referece_ctr_idx[1] - _bias_start[1]: referece_ctr_idx[1] +_bias_end[1], \\\n",
    "                referece_ctr_idx[2] - _bias_start[2]: referece_ctr_idx[2] +_bias_end[2] ]\n",
    "\n",
    "        image_patch = image_patch[ 0: crop_size[0], 0: crop_size[1], 0: crop_size[2] ]\n",
    "    return image_patch\n",
    "\n",
    "s2n = sitk.GetArrayFromImage\n",
    "\n",
    "\n",
    "def resample_imgs(imgs, segs, pids, scan_dir, BD_BIAS, SPA_FAC, required_res=512):\n",
    "    spa_fac = SPA_FAC\n",
    "    for img_fid, seg_fid, pid in zip(imgs, segs, pids):\n",
    "\n",
    "        # lb_n = nio.read_nii_bysitk(seg_fid)\n",
    "\n",
    "        img_obj = sitk.ReadImage( img_fid )\n",
    "        seg_obj = sitk.ReadImage( seg_fid )\n",
    "        print(img_fid, seg_fid)\n",
    "        ## image\n",
    "        array = sitk.GetArrayFromImage(img_obj)\n",
    "        H = W = array.shape[-1]\n",
    "        if SPA_FAC is None:\n",
    "            spa_fac = (H - 2 * BD_BIAS) / required_res\n",
    "        print(array.shape, f\"label shape {sitk.GetArrayFromImage(seg_obj).shape}\")\n",
    "        # cropping\n",
    "        array = array[:, BD_BIAS: -BD_BIAS, BD_BIAS: -BD_BIAS]\n",
    "        cropped_img_o = sitk.GetImageFromArray(array)\n",
    "        cropped_img_o = copy_spacing_ori(img_obj, cropped_img_o)\n",
    "\n",
    "        # resampling\n",
    "        img_spa_ori = img_obj.GetSpacing()\n",
    "        res_img_o = resample_by_res(cropped_img_o, [img_spa_ori[0] * spa_fac, img_spa_ori[1] * spa_fac, img_spa_ori[-1]], interpolator = sitk.sitkLinear,\n",
    "                                        logging = True)\n",
    "\n",
    "        ## label\n",
    "        lb_arr = sitk.GetArrayFromImage(seg_obj)\n",
    "        # cropping\n",
    "        lb_arr = lb_arr[:,BD_BIAS: -BD_BIAS, BD_BIAS: -BD_BIAS]\n",
    "        cropped_lb_o = sitk.GetImageFromArray(lb_arr)\n",
    "        cropped_lb_o = copy_spacing_ori(seg_obj, cropped_lb_o)\n",
    "\n",
    "        lb_spa_ori = seg_obj.GetSpacing()\n",
    "\n",
    "        # resampling\n",
    "        res_lb_o = resample_lb_by_res(cropped_lb_o,  [lb_spa_ori[0] * spa_fac, lb_spa_ori[1] * spa_fac, lb_spa_ori[-1] ], interpolator = sitk.sitkLinear,\n",
    "                                    ref_img = res_img_o, logging = True)\n",
    "\n",
    "    \n",
    "        out_img_fid = os.path.join( scan_dir, f'image_{pid}.nii.gz' )\n",
    "        out_lb_fid  = os.path.join( scan_dir, f'label_{pid}.nii.gz' ) \n",
    "    \n",
    "        # then save\n",
    "        sitk.WriteImage(res_img_o, out_img_fid, True) \n",
    "        sitk.WriteImage(res_lb_o, out_lb_fid, True) \n",
    "        print(f\"{out_img_fid} has been saved, shape: {res_img_o.GetSize()}\")\n",
    "        print(f\"{out_lb_fid} has been saved\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Intensitiy Normalization for CT Images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# set up directories for images\n",
    "IMG_FOLDER=\"./miccai2015/RawData/Training/img\"\n",
    "SEG_FOLDER=\"./miccai2015/RawData/Training/label\"\n",
    "OUT_FOLDER=\"./SABS/tmp_normalized/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[]\n"
     ]
    }
   ],
   "source": [
    "imgs = sorted(glob.glob(IMG_FOLDER + \"/*.nii.gz\"))\n",
    "segs = sorted(glob.glob(SEG_FOLDER + \"/*.nii.gz\"))\n",
    "pids = [pid.split(\"img\")[-1].split(\".\")[0] for pid in imgs]\n",
    "print(sorted(pids))\n",
    "assert len(imgs) == len(segs)\n",
    "for img, seg in zip(imgs, segs):\n",
    "    print(img, seg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(147, 512, 512) label shape (147, 512, 512)\n",
      "./SABS/tmp_normalized/image_0.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_0.nii.gz has been save\n",
      "(139, 512, 512) label shape (139, 512, 512)\n",
      "./SABS/tmp_normalized/image_1.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_1.nii.gz has been save\n",
      "(198, 512, 512) label shape (198, 512, 512)\n",
      "./SABS/tmp_normalized/image_2.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_2.nii.gz has been save\n",
      "(140, 512, 512) label shape (140, 512, 512)\n",
      "./SABS/tmp_normalized/image_3.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_3.nii.gz has been save\n",
      "(117, 512, 512) label shape (117, 512, 512)\n",
      "./SABS/tmp_normalized/image_4.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_4.nii.gz has been save\n",
      "(131, 512, 512) label shape (131, 512, 512)\n",
      "./SABS/tmp_normalized/image_5.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_5.nii.gz has been save\n",
      "(163, 512, 512) label shape (163, 512, 512)\n",
      "./SABS/tmp_normalized/image_6.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_6.nii.gz has been save\n",
      "(148, 512, 512) label shape (148, 512, 512)\n",
      "./SABS/tmp_normalized/image_7.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_7.nii.gz has been save\n",
      "(149, 512, 512) label shape (149, 512, 512)\n",
      "./SABS/tmp_normalized/image_8.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_8.nii.gz has been save\n",
      "(148, 512, 512) label shape (148, 512, 512)\n",
      "./SABS/tmp_normalized/image_9.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_9.nii.gz has been save\n",
      "(143, 512, 512) label shape (143, 512, 512)\n",
      "./SABS/tmp_normalized/image_10.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_10.nii.gz has been save\n",
      "(89, 512, 512) label shape (89, 512, 512)\n",
      "./SABS/tmp_normalized/image_11.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_11.nii.gz has been save\n",
      "(96, 512, 512) label shape (96, 512, 512)\n",
      "./SABS/tmp_normalized/image_12.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_12.nii.gz has been save\n",
      "(124, 512, 512) label shape (124, 512, 512)\n",
      "./SABS/tmp_normalized/image_13.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_13.nii.gz has been save\n",
      "(85, 512, 512) label shape (85, 512, 512)\n",
      "./SABS/tmp_normalized/image_14.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_14.nii.gz has been save\n",
      "(131, 512, 512) label shape (131, 512, 512)\n",
      "./SABS/tmp_normalized/image_15.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_15.nii.gz has been save\n",
      "(88, 512, 512) label shape (88, 512, 512)\n",
      "./SABS/tmp_normalized/image_16.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_16.nii.gz has been save\n",
      "(89, 512, 512) label shape (89, 512, 512)\n",
      "./SABS/tmp_normalized/image_17.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_17.nii.gz has been save\n",
      "(100, 512, 512) label shape (100, 512, 512)\n",
      "./SABS/tmp_normalized/image_18.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_18.nii.gz has been save\n",
      "(153, 512, 512) label shape (153, 512, 512)\n",
      "./SABS/tmp_normalized/image_19.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_19.nii.gz has been save\n",
      "(93, 512, 512) label shape (93, 512, 512)\n",
      "./SABS/tmp_normalized/image_20.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_20.nii.gz has been save\n",
      "(144, 512, 512) label shape (144, 512, 512)\n",
      "./SABS/tmp_normalized/image_21.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_21.nii.gz has been save\n",
      "(104, 512, 512) label shape (104, 512, 512)\n",
      "./SABS/tmp_normalized/image_22.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_22.nii.gz has been save\n",
      "(98, 512, 512) label shape (98, 512, 512)\n",
      "./SABS/tmp_normalized/image_23.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_23.nii.gz has been save\n",
      "(94, 512, 512) label shape (94, 512, 512)\n",
      "./SABS/tmp_normalized/image_24.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_24.nii.gz has been save\n",
      "(184, 512, 512) label shape (184, 512, 512)\n",
      "./SABS/tmp_normalized/image_25.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_25.nii.gz has been save\n",
      "(99, 512, 512) label shape (99, 512, 512)\n",
      "./SABS/tmp_normalized/image_26.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_26.nii.gz has been save\n",
      "(100, 512, 512) label shape (100, 512, 512)\n",
      "./SABS/tmp_normalized/image_27.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_27.nii.gz has been save\n",
      "(90, 512, 512) label shape (90, 512, 512)\n",
      "./SABS/tmp_normalized/image_28.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_28.nii.gz has been save\n",
      "(195, 512, 512) label shape (195, 512, 512)\n",
      "./SABS/tmp_normalized/image_29.nii.gz has been save\n",
      "./SABS/tmp_normalized/label_29.nii.gz has been save\n"
     ]
    }
   ],
   "source": [
    "import copy\n",
    "scan_dir = OUT_FOLDER\n",
    "LIR = -125\n",
    "HIR = 275\n",
    "os.makedirs(scan_dir, exist_ok = True)\n",
    "\n",
    "reindex = 0\n",
    "for img_fid, seg_fid, pid in zip(imgs, segs, pids):\n",
    "\n",
    "    img_obj = sitk.ReadImage( img_fid )\n",
    "    seg_obj = sitk.ReadImage( seg_fid )\n",
    "\n",
    "    array = sitk.GetArrayFromImage(img_obj)\n",
    "    print(array.shape, f\"label shape {sitk.GetArrayFromImage(seg_obj).shape}\")\n",
    "    array[array > HIR] = HIR\n",
    "    array[array < LIR] = LIR\n",
    "    \n",
    "    array = (array - array.min()) / (array.max() - array.min()) * 255.0\n",
    "    \n",
    "    # then normalize this\n",
    "    \n",
    "    wined_img = sitk.GetImageFromArray(array)\n",
    "    wined_img = copy_spacing_ori(img_obj, wined_img)\n",
    "    \n",
    "    out_img_fid = os.path.join( scan_dir, f'image_{str(reindex)}.nii.gz' )\n",
    "    out_lb_fid  = os.path.join( scan_dir, f'label_{str(reindex)}.nii.gz' ) \n",
    "    \n",
    "    # then save\n",
    "    sitk.WriteImage(wined_img, out_img_fid, True) \n",
    "    sitk.WriteImage(seg_obj, out_lb_fid, True) \n",
    "    print(\"{} has been save\".format(out_img_fid))\n",
    "    print(\"{} has been save\".format(out_lb_fid))\n",
    "    reindex += 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Overview\n",
    "\n",
    "This is the second step of preprocessing\n",
    "\n",
    "Cut out irrelevant empty boundary and resample to 512x512 in axial plane.\n",
    "\n",
    "Input: intensity-normalized images\n",
    "\n",
    "Output: spacially resampled images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['0', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '23', '24', '25', '26', '27', '28', '29', '3', '4', '5', '6', '7', '8', '9']\n",
      "./SABS/tmp_normalized/image_0.nii.gz ./SABS/tmp_normalized/label_0.nii.gz\n",
      "./SABS/tmp_normalized/image_1.nii.gz ./SABS/tmp_normalized/label_1.nii.gz\n",
      "./SABS/tmp_normalized/image_10.nii.gz ./SABS/tmp_normalized/label_10.nii.gz\n",
      "./SABS/tmp_normalized/image_11.nii.gz ./SABS/tmp_normalized/label_11.nii.gz\n",
      "./SABS/tmp_normalized/image_12.nii.gz ./SABS/tmp_normalized/label_12.nii.gz\n",
      "./SABS/tmp_normalized/image_13.nii.gz ./SABS/tmp_normalized/label_13.nii.gz\n",
      "./SABS/tmp_normalized/image_14.nii.gz ./SABS/tmp_normalized/label_14.nii.gz\n",
      "./SABS/tmp_normalized/image_15.nii.gz ./SABS/tmp_normalized/label_15.nii.gz\n",
      "./SABS/tmp_normalized/image_16.nii.gz ./SABS/tmp_normalized/label_16.nii.gz\n",
      "./SABS/tmp_normalized/image_17.nii.gz ./SABS/tmp_normalized/label_17.nii.gz\n",
      "./SABS/tmp_normalized/image_18.nii.gz ./SABS/tmp_normalized/label_18.nii.gz\n",
      "./SABS/tmp_normalized/image_19.nii.gz ./SABS/tmp_normalized/label_19.nii.gz\n",
      "./SABS/tmp_normalized/image_2.nii.gz ./SABS/tmp_normalized/label_2.nii.gz\n",
      "./SABS/tmp_normalized/image_20.nii.gz ./SABS/tmp_normalized/label_20.nii.gz\n",
      "./SABS/tmp_normalized/image_21.nii.gz ./SABS/tmp_normalized/label_21.nii.gz\n",
      "./SABS/tmp_normalized/image_22.nii.gz ./SABS/tmp_normalized/label_22.nii.gz\n",
      "./SABS/tmp_normalized/image_23.nii.gz ./SABS/tmp_normalized/label_23.nii.gz\n",
      "./SABS/tmp_normalized/image_24.nii.gz ./SABS/tmp_normalized/label_24.nii.gz\n",
      "./SABS/tmp_normalized/image_25.nii.gz ./SABS/tmp_normalized/label_25.nii.gz\n",
      "./SABS/tmp_normalized/image_26.nii.gz ./SABS/tmp_normalized/label_26.nii.gz\n",
      "./SABS/tmp_normalized/image_27.nii.gz ./SABS/tmp_normalized/label_27.nii.gz\n",
      "./SABS/tmp_normalized/image_28.nii.gz ./SABS/tmp_normalized/label_28.nii.gz\n",
      "./SABS/tmp_normalized/image_29.nii.gz ./SABS/tmp_normalized/label_29.nii.gz\n",
      "./SABS/tmp_normalized/image_3.nii.gz ./SABS/tmp_normalized/label_3.nii.gz\n",
      "./SABS/tmp_normalized/image_4.nii.gz ./SABS/tmp_normalized/label_4.nii.gz\n",
      "./SABS/tmp_normalized/image_5.nii.gz ./SABS/tmp_normalized/label_5.nii.gz\n",
      "./SABS/tmp_normalized/image_6.nii.gz ./SABS/tmp_normalized/label_6.nii.gz\n",
      "./SABS/tmp_normalized/image_7.nii.gz ./SABS/tmp_normalized/label_7.nii.gz\n",
      "./SABS/tmp_normalized/image_8.nii.gz ./SABS/tmp_normalized/label_8.nii.gz\n",
      "./SABS/tmp_normalized/image_9.nii.gz ./SABS/tmp_normalized/label_9.nii.gz\n"
     ]
    }
   ],
   "source": [
    "IMG_FOLDER = \"./SABS/tmp_normalized\"\n",
    "\n",
    "SEG_FOLDER = IMG_FOLDER\n",
    "imgs = glob.glob(IMG_FOLDER + \"/image_*.nii.gz\")\n",
    "imgs = sorted([ fid for fid in sorted(imgs) ])\n",
    "segs = sorted([ fid for fid in glob.glob(SEG_FOLDER + \"/label_*.nii.gz\")])\n",
    "\n",
    "pids = [pid.split(\"_\")[-1].split(\".\")[0] for pid in imgs]\n",
    "print(pids)\n",
    "for img, seg in zip(imgs, segs):\n",
    "    print(img, seg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "./SABS/tmp_normalized/image_0.nii.gz ./SABS/tmp_normalized/label_0.nii.gz\n",
      "(147, 512, 512) label shape (147, 512, 512)\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "Spacing: (0.66796875, 0.66796875, 3.0) -> [0.66796875, 0.66796875, 3.0]\n",
      "Size (448, 448, 147) -> [448. 448. 147.]\n",
      "./SABS/sabs_CT_normalized/image_0.nii.gz has been saved, shape: (449, 449, 148)\n",
      "./SABS/sabs_CT_normalized/label_0.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_1.nii.gz ./SABS/tmp_normalized/label_1.nii.gz\n",
      "(139, 512, 512) label shape (139, 512, 512)\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "Spacing: (0.720703125, 0.720703125, 3.0) -> [0.720703125, 0.720703125, 3.0]\n",
      "Size (448, 448, 139) -> [448. 448. 139.]\n",
      "./SABS/sabs_CT_normalized/image_1.nii.gz has been saved, shape: (449, 449, 140)\n",
      "./SABS/sabs_CT_normalized/label_1.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_10.nii.gz ./SABS/tmp_normalized/label_10.nii.gz\n",
      "(143, 512, 512) label shape (143, 512, 512)\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "Spacing: (0.68359375, 0.68359375, 3.0) -> [0.68359375, 0.68359375, 3.0]\n",
      "Size (448, 448, 143) -> [448. 448. 143.]\n",
      "./SABS/sabs_CT_normalized/image_10.nii.gz has been saved, shape: (449, 449, 144)\n",
      "./SABS/sabs_CT_normalized/label_10.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_11.nii.gz ./SABS/tmp_normalized/label_11.nii.gz\n",
      "(89, 512, 512) label shape (89, 512, 512)\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.7675780057907104, 0.7675780057907104, 5.0) -> [0.7675780057907104, 0.7675780057907104, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "./SABS/sabs_CT_normalized/image_11.nii.gz has been saved, shape: (449, 449, 90)\n",
      "./SABS/sabs_CT_normalized/label_11.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_12.nii.gz ./SABS/tmp_normalized/label_12.nii.gz\n",
      "(96, 512, 512) label shape (96, 512, 512)\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Label values: [ 0  1  2  3  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "Spacing: (0.70703125, 0.70703125, 5.0) -> [0.70703125, 0.70703125, 5.0]\n",
      "Size (448, 448, 96) -> [448. 448.  96.]\n",
      "./SABS/sabs_CT_normalized/image_12.nii.gz has been saved, shape: (449, 449, 97)\n",
      "./SABS/sabs_CT_normalized/label_12.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_13.nii.gz ./SABS/tmp_normalized/label_13.nii.gz\n",
      "(124, 512, 512) label shape (124, 512, 512)\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "Spacing: (0.685546875, 0.685546875, 3.0) -> [0.685546875, 0.685546875, 3.0]\n",
      "Size (448, 448, 124) -> [448. 448. 124.]\n",
      "./SABS/sabs_CT_normalized/image_13.nii.gz has been saved, shape: (449, 449, 125)\n",
      "./SABS/sabs_CT_normalized/label_13.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_14.nii.gz ./SABS/tmp_normalized/label_14.nii.gz\n",
      "(85, 512, 512) label shape (85, 512, 512)\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "Spacing: (0.83203125, 0.83203125, 5.0) -> [0.83203125, 0.83203125, 5.0]\n",
      "Size (448, 448, 85) -> [448. 448.  85.]\n",
      "./SABS/sabs_CT_normalized/image_14.nii.gz has been saved, shape: (449, 449, 86)\n",
      "./SABS/sabs_CT_normalized/label_14.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_15.nii.gz ./SABS/tmp_normalized/label_15.nii.gz\n",
      "(131, 512, 512) label shape (131, 512, 512)\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.7792969942092896, 0.7792969942092896, 5.0) -> [0.7792969942092896, 0.7792969942092896, 5.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "./SABS/sabs_CT_normalized/image_15.nii.gz has been saved, shape: (449, 449, 132)\n",
      "./SABS/sabs_CT_normalized/label_15.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_16.nii.gz ./SABS/tmp_normalized/label_16.nii.gz\n",
      "(88, 512, 512) label shape (88, 512, 512)\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "Spacing: (0.7753909826278687, 0.7753909826278687, 5.0) -> [0.7753909826278687, 0.7753909826278687, 5.0]\n",
      "Size (448, 448, 88) -> [448. 448.  88.]\n",
      "./SABS/sabs_CT_normalized/image_16.nii.gz has been saved, shape: (449, 449, 89)\n",
      "./SABS/sabs_CT_normalized/label_16.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_17.nii.gz ./SABS/tmp_normalized/label_17.nii.gz\n",
      "(89, 512, 512) label shape (89, 512, 512)\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "Spacing: (0.796875, 0.796875, 5.0) -> [0.796875, 0.796875, 5.0]\n",
      "Size (448, 448, 89) -> [448. 448.  89.]\n",
      "./SABS/sabs_CT_normalized/image_17.nii.gz has been saved, shape: (449, 449, 90)\n",
      "./SABS/sabs_CT_normalized/label_17.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_18.nii.gz ./SABS/tmp_normalized/label_18.nii.gz\n",
      "(100, 512, 512) label shape (100, 512, 512)\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.875, 0.875, 3.0) -> [0.875, 0.875, 3.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "./SABS/sabs_CT_normalized/image_18.nii.gz has been saved, shape: (449, 449, 101)\n",
      "./SABS/sabs_CT_normalized/label_18.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_19.nii.gz ./SABS/tmp_normalized/label_19.nii.gz\n",
      "(153, 512, 512) label shape (153, 512, 512)\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 153) -> [448. 448. 153.]\n",
      "./SABS/sabs_CT_normalized/image_19.nii.gz has been saved, shape: (449, 449, 154)\n",
      "./SABS/sabs_CT_normalized/label_19.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_2.nii.gz ./SABS/tmp_normalized/label_2.nii.gz\n",
      "(198, 512, 512) label shape (198, 512, 512)\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "Spacing: (0.8984375, 0.8984375, 3.0) -> [0.8984375, 0.8984375, 3.0]\n",
      "Size (448, 448, 198) -> [448. 448. 198.]\n",
      "./SABS/sabs_CT_normalized/image_2.nii.gz has been saved, shape: (449, 449, 199)\n",
      "./SABS/sabs_CT_normalized/label_2.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_20.nii.gz ./SABS/tmp_normalized/label_20.nii.gz\n",
      "(93, 512, 512) label shape (93, 512, 512)\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "Spacing: (0.837890625, 0.837890625, 3.0) -> [0.837890625, 0.837890625, 3.0]\n",
      "Size (448, 448, 93) -> [448. 448.  93.]\n",
      "./SABS/sabs_CT_normalized/image_20.nii.gz has been saved, shape: (449, 449, 94)\n",
      "./SABS/sabs_CT_normalized/label_20.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_21.nii.gz ./SABS/tmp_normalized/label_21.nii.gz\n",
      "(144, 512, 512) label shape (144, 512, 512)\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "Spacing: (0.740234375, 0.740234375, 3.0) -> [0.740234375, 0.740234375, 3.0]\n",
      "Size (448, 448, 144) -> [448. 448. 144.]\n",
      "./SABS/sabs_CT_normalized/image_21.nii.gz has been saved, shape: (449, 449, 145)\n",
      "./SABS/sabs_CT_normalized/label_21.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_22.nii.gz ./SABS/tmp_normalized/label_22.nii.gz\n",
      "(104, 512, 512) label shape (104, 512, 512)\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "Spacing: (0.8144530057907104, 0.8144530057907104, 5.0) -> [0.8144530057907104, 0.8144530057907104, 5.0]\n",
      "Size (448, 448, 104) -> [448. 448. 104.]\n",
      "./SABS/sabs_CT_normalized/image_22.nii.gz has been saved, shape: (449, 449, 105)\n",
      "./SABS/sabs_CT_normalized/label_22.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_23.nii.gz ./SABS/tmp_normalized/label_23.nii.gz\n",
      "(98, 512, 512) label shape (98, 512, 512)\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "Spacing: (0.671875, 0.671875, 5.0) -> [0.671875, 0.671875, 5.0]\n",
      "Size (448, 448, 98) -> [448. 448.  98.]\n",
      "./SABS/sabs_CT_normalized/image_23.nii.gz has been saved, shape: (449, 449, 99)\n",
      "./SABS/sabs_CT_normalized/label_23.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_24.nii.gz ./SABS/tmp_normalized/label_24.nii.gz\n",
      "(94, 512, 512) label shape (94, 512, 512)\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Label values: [ 0  1  2  3  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "Spacing: (0.9199219942092896, 0.9199219942092896, 5.0) -> [0.9199219942092896, 0.9199219942092896, 5.0]\n",
      "Size (448, 448, 94) -> [448. 448.  94.]\n",
      "./SABS/sabs_CT_normalized/image_24.nii.gz has been saved, shape: (449, 449, 95)\n",
      "./SABS/sabs_CT_normalized/label_24.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_25.nii.gz ./SABS/tmp_normalized/label_25.nii.gz\n",
      "(184, 512, 512) label shape (184, 512, 512)\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "Spacing: (0.74609375, 0.74609375, 3.0) -> [0.74609375, 0.74609375, 3.0]\n",
      "Size (448, 448, 184) -> [448. 448. 184.]\n",
      "./SABS/sabs_CT_normalized/image_25.nii.gz has been saved, shape: (449, 449, 185)\n",
      "./SABS/sabs_CT_normalized/label_25.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_26.nii.gz ./SABS/tmp_normalized/label_26.nii.gz\n",
      "(99, 512, 512) label shape (99, 512, 512)\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "Spacing: (0.703125, 0.703125, 5.0) -> [0.703125, 0.703125, 5.0]\n",
      "Size (448, 448, 99) -> [448. 448.  99.]\n",
      "./SABS/sabs_CT_normalized/image_26.nii.gz has been saved, shape: (449, 449, 100)\n",
      "./SABS/sabs_CT_normalized/label_26.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_27.nii.gz ./SABS/tmp_normalized/label_27.nii.gz\n",
      "(100, 512, 512) label shape (100, 512, 512)\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 5.0) -> [0.9765620231628418, 0.9765620231628418, 5.0]\n",
      "Size (448, 448, 100) -> [448. 448. 100.]\n",
      "./SABS/sabs_CT_normalized/image_27.nii.gz has been saved, shape: (449, 449, 101)\n",
      "./SABS/sabs_CT_normalized/label_27.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_28.nii.gz ./SABS/tmp_normalized/label_28.nii.gz\n",
      "(90, 512, 512) label shape (90, 512, 512)\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "Spacing: (0.9760000109672546, 0.9760000109672546, 5.0) -> [0.9760000109672546, 0.9760000109672546, 5.0]\n",
      "Size (448, 448, 90) -> [448. 448.  90.]\n",
      "./SABS/sabs_CT_normalized/image_28.nii.gz has been saved, shape: (449, 449, 91)\n",
      "./SABS/sabs_CT_normalized/label_28.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_29.nii.gz ./SABS/tmp_normalized/label_29.nii.gz\n",
      "(195, 512, 512) label shape (195, 512, 512)\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "Spacing: (0.7421875, 0.7421875, 3.0) -> [0.7421875, 0.7421875, 3.0]\n",
      "Size (448, 448, 195) -> [448. 448. 195.]\n",
      "./SABS/sabs_CT_normalized/image_29.nii.gz has been saved, shape: (449, 449, 196)\n",
      "./SABS/sabs_CT_normalized/label_29.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_3.nii.gz ./SABS/tmp_normalized/label_3.nii.gz\n",
      "(140, 512, 512) label shape (140, 512, 512)\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "Spacing: (0.59375, 0.59375, 3.0) -> [0.59375, 0.59375, 3.0]\n",
      "Size (448, 448, 140) -> [448. 448. 140.]\n",
      "./SABS/sabs_CT_normalized/image_3.nii.gz has been saved, shape: (449, 449, 141)\n",
      "./SABS/sabs_CT_normalized/label_3.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_4.nii.gz ./SABS/tmp_normalized/label_4.nii.gz\n",
      "(117, 512, 512) label shape (117, 512, 512)\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "Spacing: (0.90625, 0.90625, 3.0) -> [0.90625, 0.90625, 3.0]\n",
      "Size (448, 448, 117) -> [448. 448. 117.]\n",
      "./SABS/sabs_CT_normalized/image_4.nii.gz has been saved, shape: (449, 449, 118)\n",
      "./SABS/sabs_CT_normalized/label_4.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_5.nii.gz ./SABS/tmp_normalized/label_5.nii.gz\n",
      "(131, 512, 512) label shape (131, 512, 512)\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "Spacing: (0.701171875, 0.701171875, 3.0) -> [0.701171875, 0.701171875, 3.0]\n",
      "Size (448, 448, 131) -> [448. 448. 131.]\n",
      "./SABS/sabs_CT_normalized/image_5.nii.gz has been saved, shape: (449, 449, 132)\n",
      "./SABS/sabs_CT_normalized/label_5.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_6.nii.gz ./SABS/tmp_normalized/label_6.nii.gz\n",
      "(163, 512, 512) label shape (163, 512, 512)\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "Spacing: (0.748046875, 0.748046875, 3.0) -> [0.748046875, 0.748046875, 3.0]\n",
      "Size (448, 448, 163) -> [448. 448. 163.]\n",
      "./SABS/sabs_CT_normalized/image_6.nii.gz has been saved, shape: (449, 449, 164)\n",
      "./SABS/sabs_CT_normalized/label_6.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_7.nii.gz ./SABS/tmp_normalized/label_7.nii.gz\n",
      "(148, 512, 512) label shape (148, 512, 512)\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.728515625, 0.728515625, 3.0) -> [0.728515625, 0.728515625, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "./SABS/sabs_CT_normalized/image_7.nii.gz has been saved, shape: (449, 449, 149)\n",
      "./SABS/sabs_CT_normalized/label_7.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_8.nii.gz ./SABS/tmp_normalized/label_8.nii.gz\n",
      "(149, 512, 512) label shape (149, 512, 512)\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "Spacing: (0.9765620231628418, 0.9765620231628418, 2.5) -> [0.9765620231628418, 0.9765620231628418, 2.5]\n",
      "Size (448, 448, 149) -> [448. 448. 149.]\n",
      "./SABS/sabs_CT_normalized/image_8.nii.gz has been saved, shape: (449, 449, 150)\n",
      "./SABS/sabs_CT_normalized/label_8.nii.gz has been saved\n",
      "./SABS/tmp_normalized/image_9.nii.gz ./SABS/tmp_normalized/label_9.nii.gz\n",
      "(148, 512, 512) label shape (148, 512, 512)\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Label values: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "Spacing: (0.78125, 0.78125, 3.0) -> [0.78125, 0.78125, 3.0]\n",
      "Size (448, 448, 148) -> [448. 448. 148.]\n",
      "./SABS/sabs_CT_normalized/image_9.nii.gz has been saved, shape: (449, 449, 149)\n",
      "./SABS/sabs_CT_normalized/label_9.nii.gz has been saved\n"
     ]
    }
   ],
   "source": [
    "import copy\n",
    "OUT_FOLDER = \"./SABS/sabs_CT_normalized\"\n",
    "BD_BIAS = 32 # cut irrelavent empty boundary to make roi stands out\n",
    "\n",
    "# SPA_FAC = (512 - 2 * BD_BIAS) / 512 # spacing factor\n",
    "for res in (256, 672):\n",
    "    if res == 672:\n",
    "        OUT_FOLDER += \"_672\"\n",
    "    scan_dir = OUT_FOLDER\n",
    "    os.makedirs(OUT_FOLDER, exist_ok = True)\n",
    "\n",
    "    resample_imgs(imgs, segs, pids, scan_dir, BD_BIAS, SPA_FAC=None, required_res=res)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Synapse Classmap Generation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pid 0 finished!\n",
      "pid 1 finished!\n",
      "pid 2 finished!\n",
      "pid 3 finished!\n",
      "pid 4 finished!\n",
      "pid 5 finished!\n",
      "pid 6 finished!\n",
      "pid 7 finished!\n",
      "pid 8 finished!\n",
      "pid 9 finished!\n",
      "pid 10 finished!\n",
      "pid 11 finished!\n",
      "pid 12 finished!\n",
      "pid 13 finished!\n",
      "pid 14 finished!\n",
      "pid 15 finished!\n",
      "pid 16 finished!\n",
      "pid 17 finished!\n",
      "pid 18 finished!\n",
      "pid 19 finished!\n",
      "pid 20 finished!\n",
      "pid 21 finished!\n",
      "pid 22 finished!\n",
      "pid 23 finished!\n",
      "pid 24 finished!\n",
      "pid 25 finished!\n",
      "pid 26 finished!\n",
      "pid 27 finished!\n",
      "pid 28 finished!\n",
      "pid 29 finished!\n",
      "pid 30 finished!\n",
      "pid 31 finished!\n",
      "pid 32 finished!\n",
      "pid 33 finished!\n",
      "pid 34 finished!\n",
      "pid 35 finished!\n",
      "pid 36 finished!\n",
      "pid 37 finished!\n"
     ]
    }
   ],
   "source": [
    "import json\n",
    "# import niftiio as nio\n",
    "import SimpleITK as sitk\n",
    "\n",
    "# normalization: cut top 2% of histogram, then doing volume-wise normalization\n",
    "IMG_BNAMES = (\"./SABS/sabs_CT_normalized/image_*.nii.gz\", \"./SABS/sabs_CT_normalized_672/image_*.nii.gz\")\n",
    "SEG_NAMES = (\"./SABS/sabs_CT_normalized/label_*.nii.gz\", \"./SABS/sabs_CT_normalized_672/label_*.nii.gz\")\n",
    "for IMG_BNAME, SEG_BNAME in zip(IMG_BNAMES, SEG_NAMES):\n",
    "    imgs = glob.glob(IMG_BNAME)\n",
    "    segs = glob.glob(SEG_BNAME)\n",
    "    imgs = [ fid for fid in sorted(imgs, key = lambda x: int(x.split(\"_\")[-1].split(\".nii.gz\")[0])  ) ]\n",
    "    segs = [ fid for fid in sorted(segs, key = lambda x: int(x.split(\"_\")[-1].split(\".nii.gz\")[0])  ) ]\n",
    "    for img, seg in zip(imgs, segs):\n",
    "        print(img, seg)\n",
    "\n",
    "    classmap = {}\n",
    "    LABEL_NAME = [\"BGD\", \"SPLEEN\", \"KID_R\", \"KID_l\", \"GALLBLADDER\", \"ESOPHAGUS\", \"LIVER\", \"STOMACH\", \"AORTA\", \"IVC\", \"PS_VEIN\", \"PANCREAS\", \"AG_R\", \"AG_L\"]     \n",
    "\n",
    "    MIN_TP=1 # minimum number of true positive pixels in a slice\n",
    "\n",
    "    fid = os.path.dirname(IMG_BNAME) + f'/classmap_{MIN_TP}.json'\n",
    "    for _lb in LABEL_NAME:\n",
    "        classmap[_lb] = {}\n",
    "        for pid in range(len(segs)):\n",
    "            classmap[_lb][str(pid)] = []\n",
    "\n",
    "    for pid, seg in enumerate(segs):\n",
    "        # lb_vol = nio.read_nii_bysitk(seg)\n",
    "        lb_vol = sitk.GetArrayFromImage(sitk.ReadImage(seg))\n",
    "        n_slice = lb_vol.shape[0]\n",
    "        for slc in range(n_slice):\n",
    "            for cls in range(len(LABEL_NAME)):\n",
    "                if cls in lb_vol[slc, ...]:\n",
    "                    if np.sum( lb_vol[slc, ...] == cls) >= MIN_TP:\n",
    "                        classmap[LABEL_NAME[cls]][str(pid)].append(slc)\n",
    "        print(f'pid {str(pid)} finished!')\n",
    "    \n",
    "    with open(fid, 'w') as fopen:\n",
    "        json.dump(classmap, fopen)\n",
    "        fopen.close()  \n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# MRI Image Normalization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "## PLEASE RUN dcm_img_to_nii.sh to convert dicom to nii.gz\n",
    "! ./dcm_img_to_nii.sh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [316.         316.          35.99999911]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_1.nii.gz has been saved\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 36) -> [348.         348.          35.99999911]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_10.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_13.nii.gz has been saved\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_15.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_19.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_2.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 26) -> [348.         348.          30.38961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_20.nii.gz has been saved\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 31) -> [340.         340.          32.20779221]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_21.nii.gz has been saved\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 33) -> [356.         356.          37.28571347]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_22.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 30) -> [348.         348.          35.06493506]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_3.nii.gz has been saved\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [332.        332.         33.8961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_31.nii.gz has been saved\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 39) -> [372.         372.          45.58441558]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_32.nii.gz has been saved\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 29) -> [356.        356.         33.8961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_33.nii.gz has been saved\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [356.         356.          34.28571503]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_34.nii.gz has been saved\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 38) -> [332.         332.          44.41558442]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_36.nii.gz has been saved\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 32) -> [300.        300.         37.4025974]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_37.nii.gz has been saved\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (320, 320, 34) -> [348.         348.          39.74025974]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_38.nii.gz has been saved\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 26) -> [324.         324.          30.38961039]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_39.nii.gz has been saved\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [1.25, 1.25, 7.7]\n",
      "Size (256, 256, 30) -> [340.         340.          35.06493506]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_5.nii.gz has been saved\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [1.25, 1.25, 7.7]\n",
      "Size (288, 288, 32) -> [324.         324.          33.24675325]\n",
      "./CHAOST2/chaos_MR_T2_normalized/image_8.nii.gz has been saved\n"
     ]
    }
   ],
   "source": [
    "import copy\n",
    "\n",
    "IMG_FOLDER = \"./CHAOST2/niis/T2SPIR\" #, path of nii-like images from step 1\n",
    "OUT_FOLDER=\"./CHAOST2/chaos_MR_T2_normalized/\" # output directory\n",
    "\n",
    "imgs = glob.glob(IMG_FOLDER + f'/image_*.nii.gz')\n",
    "imgs = [ fid for fid in sorted(imgs) ]\n",
    "segs = [ fid for fid in sorted(glob.glob(IMG_FOLDER + f'/label_*.nii.gz')) ]\n",
    "\n",
    "pids = [pid.split(\"_\")[-1].split(\".\")[0] for pid in imgs]\n",
    "for img, seg in zip(imgs, segs):\n",
    "    print(img, seg)\n",
    "\n",
    "os.makedirs(OUT_FOLDER, exist_ok = True)\n",
    "    \n",
    "HIST_CUT_TOP = 0.5 # cut top 0.5% of intensity historgam to alleviate off-resonance effect\n",
    "\n",
    "NEW_SPA = [1.25, 1.25, 7.70] # unified voxel spacing\n",
    "\n",
    "for img_fid, seg_fid, pid in zip(imgs, segs, pids):\n",
    "\n",
    "    resample_flg = True\n",
    "\n",
    "    img_obj = sitk.ReadImage( img_fid )\n",
    "    seg_obj = sitk.ReadImage( seg_fid )\n",
    "\n",
    "    array = sitk.GetArrayFromImage(img_obj)\n",
    "\n",
    "    # cut histogram\n",
    "    hir = float(np.percentile(array, 100.0 - HIST_CUT_TOP))\n",
    "    array[array > hir] = hir\n",
    "\n",
    "    his_img_o = sitk.GetImageFromArray(array)\n",
    "    his_img_o = copy_spacing_ori(img_obj, his_img_o)\n",
    "\n",
    "    # resampling\n",
    "    img_spa_ori = img_obj.GetSpacing()\n",
    "    res_img_o = resample_by_res(his_img_o, [NEW_SPA[0], NEW_SPA[1], NEW_SPA[2]],\n",
    "                            interpolator = sitk.sitkLinear, logging = True)\n",
    "    ## label\n",
    "    lb_arr = sitk.GetArrayFromImage(seg_obj)\n",
    "\n",
    "    # resampling\n",
    "    res_lb_o = resample_lb_by_res(seg_obj,  [NEW_SPA[0], NEW_SPA[1], NEW_SPA[2] ], interpolator = sitk.sitkLinear,\n",
    "                                  ref_img = None, logging = True)\n",
    "\n",
    "    # crop out rois\n",
    "    res_img_a = s2n(res_img_o)\n",
    "\n",
    "    crop_img_a = image_crop(res_img_a.transpose(1,2,0), [256, 256],\n",
    "                            referece_ctr_idx = [res_img_a.shape[1] // 2, res_img_a.shape[2] //2],\n",
    "                            padval = res_img_a.min(), only_2d = True).transpose(2,0,1)\n",
    "\n",
    "    out_img_obj = copy_spacing_ori(res_img_o, sitk.GetImageFromArray(crop_img_a))\n",
    "\n",
    "    res_lb_a = s2n(res_lb_o)\n",
    "\n",
    "    crop_lb_a = image_crop(res_lb_a.transpose(1,2,0), [256, 256],\n",
    "                            referece_ctr_idx = [res_lb_a.shape[1] // 2, res_lb_a.shape[2] //2],\n",
    "                            padval = 0, only_2d = True).transpose(2,0,1)\n",
    "\n",
    "    out_lb_obj = copy_spacing_ori(res_img_o, sitk.GetImageFromArray(crop_lb_a))\n",
    "\n",
    "\n",
    "    out_img_fid = os.path.join( OUT_FOLDER, f'image_{pid}.nii.gz' )\n",
    "    out_lb_fid  = os.path.join( OUT_FOLDER, f'label_{pid}.nii.gz' ) \n",
    "\n",
    "    # then save pre-processed images\n",
    "    sitk.WriteImage(out_img_obj, out_img_fid, True) \n",
    "    sitk.WriteImage(out_lb_obj, out_lb_fid, True) \n",
    "    print(\"{} has been saved\".format(out_img_fid))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## MRI Resampling and ROI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "./CHAOST2/niis/T2SPIR/image_1.nii.gz ./CHAOST2/niis/T2SPIR/label_1.nii.gz\n",
      "(36, 256, 256) label shape (36, 256, 256)\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.54296875, 1.54296875, 7.699999809265137) -> [0.5832054501488095, 0.5832054501488095, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "./SABS/sabs_CT_normalized/image_1.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_1.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_10.nii.gz ./CHAOST2/niis/T2SPIR/label_10.nii.gz\n",
      "(36, 256, 256) label shape (36, 256, 256)\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "Spacing: (1.69921875, 1.69921875, 7.699999809265137) -> [0.6422642299107143, 0.6422642299107143, 7.699999809265137]\n",
      "Size (254, 254, 36) -> [672. 672.  36.]\n",
      "./SABS/sabs_CT_normalized/image_10.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_10.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_13.nii.gz ./CHAOST2/niis/T2SPIR/label_13.nii.gz\n",
      "(30, 320, 320) label shape (30, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "./SABS/sabs_CT_normalized/image_13.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_13.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_15.nii.gz ./CHAOST2/niis/T2SPIR/label_15.nii.gz\n",
      "(26, 256, 256) label shape (26, 256, 256)\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "./SABS/sabs_CT_normalized/image_15.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_15.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_19.nii.gz ./CHAOST2/niis/T2SPIR/label_19.nii.gz\n",
      "(30, 320, 320) label shape (30, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "./SABS/sabs_CT_normalized/image_19.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_19.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_2.nii.gz ./CHAOST2/niis/T2SPIR/label_2.nii.gz\n",
      "(26, 320, 320) label shape (26, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "./SABS/sabs_CT_normalized/image_2.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_2.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_20.nii.gz ./CHAOST2/niis/T2SPIR/label_20.nii.gz\n",
      "(26, 320, 320) label shape (26, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 26) -> [672. 672.  26.]\n",
      "./SABS/sabs_CT_normalized/image_20.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_20.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_21.nii.gz ./CHAOST2/niis/T2SPIR/label_21.nii.gz\n",
      "(31, 256, 256) label shape (31, 256, 256)\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "Spacing: (1.66015625, 1.66015625, 8.0) -> [0.627499534970238, 0.627499534970238, 8.0]\n",
      "Size (254, 254, 31) -> [672. 672.  31.]\n",
      "./SABS/sabs_CT_normalized/image_21.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_21.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_22.nii.gz ./CHAOST2/niis/T2SPIR/label_22.nii.gz\n",
      "(33, 256, 256) label shape (33, 256, 256)\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.699999809265137) -> [0.6570289248511905, 0.6570289248511905, 8.699999809265137]\n",
      "Size (254, 254, 33) -> [672. 672.  33.]\n",
      "./SABS/sabs_CT_normalized/image_22.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_22.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_3.nii.gz ./CHAOST2/niis/T2SPIR/label_3.nii.gz\n",
      "(30, 320, 320) label shape (30, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 30) -> [672. 672.  30.]\n",
      "./SABS/sabs_CT_normalized/image_3.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_3.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_31.nii.gz ./CHAOST2/niis/T2SPIR/label_31.nii.gz\n",
      "(29, 256, 256) label shape (29, 256, 256)\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "./SABS/sabs_CT_normalized/image_31.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_31.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_32.nii.gz ./CHAOST2/niis/T2SPIR/label_32.nii.gz\n",
      "(39, 256, 256) label shape (39, 256, 256)\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "Spacing: (1.81640625, 1.81640625, 9.0) -> [0.6865583147321428, 0.6865583147321428, 9.0]\n",
      "Size (254, 254, 39) -> [672. 672.  39.]\n",
      "./SABS/sabs_CT_normalized/image_32.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_32.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_33.nii.gz ./CHAOST2/niis/T2SPIR/label_33.nii.gz\n",
      "(29, 256, 256) label shape (29, 256, 256)\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "Spacing: (1.73828125, 1.73828125, 9.0) -> [0.6570289248511905, 0.6570289248511905, 9.0]\n",
      "Size (254, 254, 29) -> [672. 672.  29.]\n",
      "./SABS/sabs_CT_normalized/image_33.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_33.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_34.nii.gz ./CHAOST2/niis/T2SPIR/label_34.nii.gz\n",
      "(30, 256, 256) label shape (30, 256, 256)\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.73828125, 1.73828125, 8.800000190734863) -> [0.6570289248511905, 0.6570289248511905, 8.800000190734863]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "./SABS/sabs_CT_normalized/image_34.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_34.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_36.nii.gz ./CHAOST2/niis/T2SPIR/label_36.nii.gz\n",
      "(38, 256, 256) label shape (38, 256, 256)\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "Spacing: (1.62109375, 1.62109375, 9.0) -> [0.6127348400297619, 0.6127348400297619, 9.0]\n",
      "Size (254, 254, 38) -> [672. 672.  38.]\n",
      "./SABS/sabs_CT_normalized/image_36.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_36.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_37.nii.gz ./CHAOST2/niis/T2SPIR/label_37.nii.gz\n",
      "(32, 256, 256) label shape (32, 256, 256)\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.46484375, 1.46484375, 9.0) -> [0.5536760602678571, 0.5536760602678571, 9.0]\n",
      "Size (254, 254, 32) -> [672. 672.  32.]\n",
      "./SABS/sabs_CT_normalized/image_37.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_37.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_38.nii.gz ./CHAOST2/niis/T2SPIR/label_38.nii.gz\n",
      "(34, 320, 320) label shape (34, 320, 320)\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "Spacing: (1.359375, 1.359375, 9.0) -> [0.6432756696428571, 0.6432756696428571, 9.0]\n",
      "Size (318, 318, 34) -> [672. 672.  34.]\n",
      "./SABS/sabs_CT_normalized/image_38.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_38.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_39.nii.gz ./CHAOST2/niis/T2SPIR/label_39.nii.gz\n",
      "(26, 256, 256) label shape (26, 256, 256)\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "Spacing: (1.58203125, 1.58203125, 9.0) -> [0.5979701450892857, 0.5979701450892857, 9.0]\n",
      "Size (254, 254, 26) -> [672. 672.  26.]\n",
      "./SABS/sabs_CT_normalized/image_39.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_39.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_5.nii.gz ./CHAOST2/niis/T2SPIR/label_5.nii.gz\n",
      "(30, 256, 256) label shape (30, 256, 256)\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "Spacing: (1.66015625, 1.66015625, 9.0) -> [0.627499534970238, 0.627499534970238, 9.0]\n",
      "Size (254, 254, 30) -> [672. 672.  30.]\n",
      "./SABS/sabs_CT_normalized/image_5.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_5.nii.gz has been saved\n",
      "./CHAOST2/niis/T2SPIR/image_8.nii.gz ./CHAOST2/niis/T2SPIR/label_8.nii.gz\n",
      "(32, 288, 288) label shape (32, 288, 288)\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "Label values: [0 1 2 3 4]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "Spacing: (1.40625, 1.40625, 8.0) -> [0.5984933035714286, 0.5984933035714286, 8.0]\n",
      "Size (286, 286, 32) -> [672. 672.  32.]\n",
      "./SABS/sabs_CT_normalized/image_8.nii.gz has been saved\n",
      "./SABS/sabs_CT_normalized/label_8.nii.gz has been saved\n"
     ]
    }
   ],
   "source": [
    "# SPA_FAC = (256 - 2 * BD_BIAS) / 512 # spacing factor\n",
    "BD_BIAS = 1\n",
    "scan_dir = OUT_FOLDER\n",
    "for res in (256, 672):\n",
    "    if res == 672:\n",
    "        scan_dir += \"_672\"\n",
    "    resample_imgs(imgs, segs, pids, scan_dir,\n",
    "                BD_BIAS, SPA_FAC=None, required_res=res)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## MRI Classmap Generation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pid 1 finished!\n",
      "pid 2 finished!\n",
      "pid 3 finished!\n",
      "pid 5 finished!\n",
      "pid 8 finished!\n",
      "pid 10 finished!\n",
      "pid 13 finished!\n",
      "pid 15 finished!\n",
      "pid 19 finished!\n",
      "pid 20 finished!\n",
      "pid 21 finished!\n",
      "pid 22 finished!\n",
      "pid 31 finished!\n",
      "pid 32 finished!\n",
      "pid 33 finished!\n",
      "pid 34 finished!\n",
      "pid 36 finished!\n",
      "pid 37 finished!\n",
      "pid 38 finished!\n",
      "pid 39 finished!\n"
     ]
    }
   ],
   "source": [
    "IMG_BNAMES = (\"./CHAOST2/chaos_MR_T2_normalized/image_*.nii.gz\", \"./CHAOST2/chaos_MR_T2_normalized_672/image_*.nii.gz\")\n",
    "SEG_NAMES = (\"./CHAOST2/chaos_MR_T2_normalized/label_*.nii.gz\", \"./CHAOST2/chaos_MR_T2_normalized_672/label_*.nii.gz\")\n",
    "\n",
    "for IMG_BNAME, SEG_BNAME in zip(IMG_BNAMES, SEG_NAMES):\n",
    "    imgs = glob.glob(IMG_BNAME)\n",
    "    segs = glob.glob(SEG_BNAME)\n",
    "    imgs = [ fid for fid in sorted(imgs, key = lambda x: int(x.split(\"_\")[-1].split(\".nii.gz\")[0])  ) ]\n",
    "    segs = [ fid for fid in sorted(segs, key = lambda x: int(x.split(\"_\")[-1].split(\".nii.gz\")[0])  ) ]\n",
    "\n",
    "\n",
    "    classmap = {}\n",
    "    LABEL_NAME = [\"BG\", \"LIVER\", \"RK\", \"LK\", \"SPLEEN\"]     \n",
    "\n",
    "    MIN_TP = 1 # minimum number of positive label pixels to be recorded. Use >100 when training with manual annotations for more stable training\n",
    "\n",
    "    fid = os.path.join(OUT_FOLDER,f'.classmap_{MIN_TP}.json') # name of the output file. \n",
    "    for _lb in LABEL_NAME:\n",
    "        classmap[_lb] = {}\n",
    "        for _sid in segs:\n",
    "            pid = _sid.split(\"_\")[-1].split(\".nii.gz\")[0]\n",
    "            classmap[_lb][pid] = []\n",
    "\n",
    "    for seg in segs:\n",
    "        pid = seg.split(\"_\")[-1].split(\".nii.gz\")[0]\n",
    "        lb_vol = sitk.GetArrayFromImage(sitk.ReadImage(seg))\n",
    "        n_slice = lb_vol.shape[0]\n",
    "        for slc in range(n_slice):\n",
    "            for cls in range(len(LABEL_NAME)):\n",
    "                if cls in lb_vol[slc, ...]:\n",
    "                    if np.sum( lb_vol[slc, ...]) >= MIN_TP:\n",
    "                        classmap[LABEL_NAME[cls]][str(pid)].append(slc)\n",
    "        print(f'pid {str(pid)} finished!')\n",
    "    \n",
    "    with open(fid, 'w') as fopen:\n",
    "        json.dump(classmap, fopen)\n",
    "        fopen.close()  \n",
    "\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Psuedo label generation for Encoder Finetuning"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import copy\n",
    "import skimage\n",
    "\n",
    "from skimage.segmentation import slic\n",
    "from skimage.segmentation import mark_boundaries\n",
    "from skimage.util import img_as_float\n",
    "from skimage.measure import label \n",
    "import scipy.ndimage.morphology as snm\n",
    "from skimage import io\n",
    "import argparse\n",
    "\n",
    "\n",
    "to01 = lambda x: (x - x.min()) / (x.max() - x.min())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Summary\n",
    "\n",
    "a. Generate a mask of the patient to avoid pseudolabels of empty regions in the background\n",
    "\n",
    "b. Generate superpixels as pseudolabels\n",
    "\n",
    "Configurations of pseudlabels\n",
    "\n",
    "default setting of minimum superpixel sizes\n",
    "`segs = seg_func(img[ii, ...], min_size = 400, sigma = 1)`\n",
    "\n",
    "you can also try other configs\n",
    "`segs = seg_func(img[ii, ...], min_size = 100, sigma = 0.8)`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [],
   "source": [
    "MODE = 'MIDDLE' # minimum size of pesudolabels. 'MIDDLE' is the default setting\n",
    "\n",
    "# wrapper for process 3d image in 2d\n",
    "def superpix_vol(img, method = 'fezlen', **kwargs):\n",
    "    \"\"\"\n",
    "    loop through the entire volume\n",
    "    assuming image with axis z, x, y\n",
    "    \"\"\"\n",
    "    if method =='fezlen':\n",
    "        seg_func = skimage.segmentation.felzenszwalb\n",
    "    else:\n",
    "        raise NotImplementedError\n",
    "        \n",
    "    out_vol = np.zeros(img.shape)\n",
    "    for ii in range(img.shape[0]):\n",
    "        if MODE == 'MIDDLE':\n",
    "            segs = seg_func(img[ii, ...], min_size = 400, sigma = 1)\n",
    "        else:\n",
    "            raise NotImplementedError\n",
    "        out_vol[ii, ...] = segs\n",
    "        \n",
    "    return out_vol\n",
    "\n",
    "# thresholding the intensity values to get a binary mask of the patient\n",
    "def fg_mask2d(img_2d, thresh): # change this by your need\n",
    "    mask_map = np.float32(img_2d > thresh)\n",
    "    \n",
    "    def getLargestCC(segmentation): # largest connected components\n",
    "        labels = label(segmentation)\n",
    "        assert( labels.max() != 0 ) # assume at least 1 CC\n",
    "        largestCC = labels == np.argmax(np.bincount(labels.flat)[1:])+1\n",
    "        return largestCC\n",
    "    if mask_map.max() < 0.999:\n",
    "        return mask_map\n",
    "    else:\n",
    "        post_mask = getLargestCC(mask_map)\n",
    "        fill_mask = snm.binary_fill_holes(post_mask)\n",
    "    return fill_mask\n",
    "\n",
    "# remove superpixels within the empty regions\n",
    "def superpix_masking(raw_seg2d, mask2d):\n",
    "    raw_seg2d = np.int32(raw_seg2d)\n",
    "    lbvs = np.unique(raw_seg2d)\n",
    "    max_lb = lbvs.max()\n",
    "    raw_seg2d[raw_seg2d == 0] = max_lb + 1\n",
    "    lbvs = list(lbvs)\n",
    "    lbvs.append( max_lb )\n",
    "    raw_seg2d = raw_seg2d * mask2d\n",
    "    lb_new = 1\n",
    "    out_seg2d = np.zeros(raw_seg2d.shape)\n",
    "    for lbv in lbvs:\n",
    "        if lbv == 0:\n",
    "            continue\n",
    "        else:\n",
    "            out_seg2d[raw_seg2d == lbv] = lb_new\n",
    "            lb_new += 1\n",
    "    \n",
    "    return out_seg2d\n",
    "            \n",
    "def superpix_wrapper(img, verbose = False, fg_thresh = 1e-4):\n",
    "    raw_seg = superpix_vol(img)\n",
    "    fg_mask_vol = np.zeros(raw_seg.shape)\n",
    "    processed_seg_vol = np.zeros(raw_seg.shape)\n",
    "    for ii in range(raw_seg.shape[0]):\n",
    "        if verbose:\n",
    "            print(\"doing {} slice\".format(ii))\n",
    "        _fgm = fg_mask2d(img[ii, ...], fg_thresh )\n",
    "        _out_seg = superpix_masking(raw_seg[ii, ...], _fgm)\n",
    "        fg_mask_vol[ii] = _fgm\n",
    "        processed_seg_vol[ii] = _out_seg\n",
    "    return fg_mask_vol, processed_seg_vol\n",
    "        \n",
    "# copy spacing and orientation info between sitk objects\n",
    "def copy_info(src, dst):\n",
    "    dst.SetSpacing(src.GetSpacing())\n",
    "    dst.SetOrigin(src.GetOrigin())\n",
    "    dst.SetDirection(src.GetDirection())\n",
    "    # dst.CopyInfomation(src)\n",
    "    return dst\n",
    "\n",
    "\n",
    "def strip_(img, lb):\n",
    "    img = np.int32(img)\n",
    "    if isinstance(lb, float):\n",
    "        lb = int(lb)\n",
    "        return np.float32(img == lb) * float(lb)\n",
    "    elif isinstance(lb, list):\n",
    "        out = np.zeros(img.shape)\n",
    "        for _lb in lb:\n",
    "            out += np.float32(img == int(_lb)) * float(_lb)\n",
    "            \n",
    "        return out\n",
    "    else:\n",
    "        raise Exception"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "DATASET_CONFIG = {'SABS':{\n",
    "                    'img_bname': f'./SABS/sabs_CT_normalized/image_*.nii.gz',\n",
    "                    'out_dir': './SABS/sabs_CT_normalized',\n",
    "                    'fg_thresh': 1e-4\n",
    "                    },\n",
    "                  'CHAOST2':{\n",
    "                      'img_bname': f'./CHAOST2/chaos_MR_T2_normalized/image_*.nii.gz',\n",
    "                      'out_dir': './CHAOST2/chaos_MR_T2_normalized',\n",
    "                      'fg_thresh': 1e-4 + 50\n",
    "                    },\n",
    "                  'SABS_672':{\n",
    "                    'img_bname': f'./SABS/sabs_CT_normalized_672/image_*.nii.gz',\n",
    "                    'out_dir': './SABS/sabs_CT_normalized_672',\n",
    "                    'fg_thresh': 1e-4\n",
    "                    },\n",
    "                  'CHAOST2_672':{\n",
    "                      'img_bname': f'./CHAOST2/chaos_MR_T2_normalized_672/image_*.nii.gz',\n",
    "                      'out_dir': './CHAOST2/chaos_MR_T2_normalized_672',\n",
    "                      'fg_thresh': 1e-4 + 50\n",
    "                    }\n",
    "}\n",
    "\n",
    "for DOMAIN in DATASET_CONFIG.keys():\n",
    "  img_bname = DATASET_CONFIG[DOMAIN]['img_bname']\n",
    "  imgs = glob.glob(img_bname)\n",
    "  out_dir = DATASET_CONFIG[DOMAIN]['out_dir']\n",
    "\n",
    "  imgs = sorted(imgs, key = lambda x: int(x.split('_')[-1].split('.nii.gz')[0]) )\n",
    "  print(imgs)\n",
    "\n",
    "  # Generate pseudolabels for every image and save them\n",
    "  for img_fid in imgs:\n",
    "  # img_fid = imgs[0]\n",
    "\n",
    "      idx = os.path.basename(img_fid).split(\"_\")[-1].split(\".nii.gz\")[0]\n",
    "      im_obj = sitk.ReadImage(img_fid)\n",
    "\n",
    "      out_fg, out_seg = superpix_wrapper(sitk.GetArrayFromImage(im_obj), fg_thresh = DATASET_CONFIG[DOMAIN]['fg_thresh'] )\n",
    "      out_fg_o = sitk.GetImageFromArray(out_fg ) \n",
    "      out_seg_o = sitk.GetImageFromArray(out_seg )\n",
    "\n",
    "      out_fg_o = copy_info(im_obj, out_fg_o)\n",
    "      out_seg_o = copy_info(im_obj, out_seg_o)\n",
    "      seg_fid = os.path.join(out_dir, f'superpix-{MODE}_{idx}.nii.gz')\n",
    "      msk_fid = os.path.join(out_dir, f'fgmask_{idx}.nii.gz')\n",
    "      sitk.WriteImage(out_fg_o, msk_fid)\n",
    "      sitk.WriteImage(out_seg_o, seg_fid)\n",
    "      print(f'image with id {idx} has finished')\n"
   ]
  }
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