run_nnUNet_statistics_on_validation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import multiprocessing\n",
    "import os\n",
    "from copy import deepcopy\n",
    "from multiprocessing import Pool\n",
    "from typing import Tuple, List, Union, Optional\n",
    "\n",
    "import numpy as np\n",
    "from batchgenerators.utilities.file_and_folder_operations import subfiles, join, save_json, load_json, isfile\n",
    "from nnunetv2.configuration import default_num_processes\n",
    "from nnunetv2.imageio.base_reader_writer import BaseReaderWriter\n",
    "from nnunetv2.imageio.reader_writer_registry import determine_reader_writer_from_dataset_json, determine_reader_writer_from_file_ending\n",
    "from nnunetv2.imageio.simpleitk_reader_writer import SimpleITKIO\n",
    "# the Evaluator class of the previous nnU-Net was great and all but man was it overengineered. Keep it simple\n",
    "from nnunetv2.utilities.json_export import recursive_fix_for_json_export\n",
    "from nnunetv2.utilities.plans_handling.plans_handler import PlansManager\n",
    "from nnunetv2.evaluation.evaluate_predictions import compute_metrics_on_folder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'metric_per_case': [{'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0004.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0004.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5243258270781207,\n",
       "     'IoU': 0.3553127354935946,\n",
       "     'FP': 1632,\n",
       "     'TP': 943,\n",
       "     'FN': 79,\n",
       "     'TN': 42988962,\n",
       "     'n_pred': 2575,\n",
       "     'n_ref': 1022}}},\n",
       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0007.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0007.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.571897570584373,\n",
       "     'IoU': 0.40045977011494255,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0014.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0014.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.626486915146709,\n",
       "     'IoU': 0.4561200923787529,\n",
       "     'FP': 350,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0017.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0017.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5641025641025641,\n",
       "     'IoU': 0.39285714285714285,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0024.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0024.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.22195704057279236,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0029.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0029.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.6992561105207227,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0037.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0037.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.48157248157248156,\n",
       "     'IoU': 0.31715210355987056,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0039.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0039.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.6287967289719626,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0049.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0049.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.8026424442609413,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0050.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0050.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5859872611464968,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0051.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0051.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5779897101267412,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0052.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0052.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.8759163725224002,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0059.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0059.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.7378169790518192,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0062.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0062.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.7068024199498303,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0067.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0067.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.713819812474521,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0072.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0072.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5517525773195876,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0073.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0073.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.7194874532835024,\n",
       "     'IoU': 0.5618745830553702,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0075.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0075.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5191168551427033,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0076.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0076.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5543665861235761,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0084.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0084.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.6871846619576185,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0088.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0088.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.6969790382244143,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0092.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0092.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.8810833685992383,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0093.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0093.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.666073546856465,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0095.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0095.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.5930962343096234,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0102.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0102.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.014148980441115273,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0919.nrrd',\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0920.nrrd',\n",
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       "   'metrics': {1: {'Dice': 0.6960127591706539,\n",
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       "  {'reference_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr/0922.nrrd',\n",
       "   'prediction_file': '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation/0922.nrrd',\n",
       "   'metrics': {1: {'Dice': 0.7644552647595861,\n",
       "     'IoU': 0.6187192118226601,\n",
       "     'FP': 288,\n",
       "     'TP': 628,\n",
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       "     'n_pred': 916,\n",
       "     'n_ref': 727}}}],\n",
       " 'mean': {1: {'Dice': 0.5399219717151396,\n",
       "   'IoU': 0.40691089197653835,\n",
       "   'FP': 1052.7368421052631,\n",
       "   'TP': 1038.0485829959514,\n",
       "   'FN': 444.07287449392715,\n",
       "   'TN': 41019220.21862348,\n",
       "   'n_pred': 2090.7854251012145,\n",
       "   'n_ref': 1482.1214574898786}},\n",
       " 'foreground_mean': {'Dice': 0.5399219717151396,\n",
       "  'IoU': 0.40691089197653835,\n",
       "  'FP': 1052.7368421052631,\n",
       "  'TP': 1038.0485829959514,\n",
       "  'FN': 444.07287449392715,\n",
       "  'TN': 41019220.21862348,\n",
       "  'n_pred': 2090.7854251012145,\n",
       "  'n_ref': 1482.1214574898786}}"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "folder_ref = '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_raw/Dataset117_smal_tumors_MRI_lighter_next_stage/labelsTr'\n",
    "folder_pred = '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/validation'\n",
    "output_file = '/media/immersive/KINGSTON/nnUnetData-and-Models/dataset/nnUNet_trained_models/Dataset117_smal_tumors_MRI_lighter_next_stage/nnUNetTrainer_probabilisticOversampling_LastLayerMask__nnUNetPlans__3d_fullres_small_patch/fold_all/summary.json'\n",
    "image_reader_writer = SimpleITKIO()\n",
    "file_ending = '.nrrd'\n",
    "labels = [1]\n",
    "ignore_label = None\n",
    "num_processes = 12\n",
    "compute_metrics_on_folder(folder_ref, folder_pred, output_file, image_reader_writer, file_ending, labels, ignore_label, num_processes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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