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b/eval_mtl_concat.py |
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from __future__ import print_function |
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import numpy as np |
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import argparse |
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import torch |
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import torch.nn as nn |
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import pdb |
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import os |
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import pandas as pd |
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from utils.utils import * |
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from math import floor |
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import matplotlib.pyplot as plt |
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from datasets.dataset_mtl_concat import Generic_MIL_MTL_Dataset, save_splits |
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import h5py |
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from utils.eval_utils_mtl_concat import * |
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# Training settings |
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parser = argparse.ArgumentParser(description='TOAD Evaluation Script') |
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parser.add_argument('--data_root_dir', type=str, help='data directory') |
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parser.add_argument('--results_dir', type=str, default='./results', |
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help='relative path to results folder, i.e. '+ |
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'the directory containing models_exp_code relative to project root (default: ./results)') |
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parser.add_argument('--save_exp_code', type=str, default=None, |
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help='experiment code to save eval results') |
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parser.add_argument('--models_exp_code', type=str, default=None, |
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help='experiment code to load trained models (directory under results_dir containing model checkpoints') |
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parser.add_argument('--splits_dir', type=str, default=None, |
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help='splits directory, if using custom splits other than what matches the task (default: None)') |
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parser.add_argument('--drop_out', action='store_true', default=False, |
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help='whether model uses dropout') |
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parser.add_argument('--k', type=int, default=1, help='number of folds (default: 1)') |
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parser.add_argument('--k_start', type=int, default=-1, help='start fold (default: -1, last fold)') |
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parser.add_argument('--k_end', type=int, default=-1, help='end fold (default: -1, first fold)') |
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parser.add_argument('--fold', type=int, default=-1, help='single fold to evaluate') |
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parser.add_argument('--micro_average', action='store_true', default=False, |
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help='use micro_average instead of macro_avearge for multiclass AUC') |
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parser.add_argument('--split', type=str, choices=['train', 'val', 'test', 'all'], default='test') |
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parser.add_argument('--task', type=str, choices=['dummy_mtl_concat']) |
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args = parser.parse_args() |
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device=torch.device("cuda" if torch.cuda.is_available() else "cpu") |
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encoding_size = 1024 |
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args.save_dir = os.path.join('./eval_results', 'EVAL_' + str(args.save_exp_code)) |
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args.models_dir = os.path.join(args.results_dir, str(args.models_exp_code)) |
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os.makedirs(args.save_dir, exist_ok=True) |
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if args.splits_dir is None: |
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args.splits_dir = args.models_dir |
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assert os.path.isdir(args.models_dir) |
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assert os.path.isdir(args.splits_dir) |
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settings = {'task': args.task, |
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'split': args.split, |
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'save_dir': args.save_dir, |
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'models_dir': args.models_dir, |
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'drop_out': args.drop_out, |
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'micro_avg': args.micro_average} |
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with open(args.save_dir + '/eval_experiment_{}.txt'.format(args.save_exp_code), 'w') as f: |
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print(settings, file=f) |
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f.close() |
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print(settings) |
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if args.task == 'dummy_mtl_concat': |
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args.n_classes=18 |
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dataset = Generic_MIL_MTL_Dataset(csv_path = 'dataset_csv/dummy_dataset.csv', |
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data_dir= os.path.join(args.data_root_dir,'DATASET_DIR'), |
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shuffle = False, |
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print_info = True, |
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label_dicts = [{'Lung':0, 'Breast':1, 'Colorectal':2, 'Ovarian':3, |
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'Pancreatic':4, 'Adrenal':5, |
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'Skin':6, 'Prostate':7, 'Renal':8, 'Bladder':9, |
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'Esophagogastric':10, 'Thyroid':11, |
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'Head Neck':12, 'Glioma':13, |
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'Germ Cell':14, 'Endometrial': 15, 'Cervix': 16, 'Liver': 17}, |
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{'Primary':0, 'Metastatic':1}, |
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{'F':0, 'M':1}], |
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label_cols = ['label', 'site', 'sex'], |
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patient_strat= False) |
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else: |
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raise NotImplementedError |
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if args.k_start == -1: |
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start = 0 |
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else: |
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start = args.k_start |
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if args.k_end == -1: |
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end = args.k |
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else: |
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end = args.k_end |
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if args.fold == -1: |
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folds = range(start, end) |
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else: |
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folds = range(args.fold, args.fold+1) |
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ckpt_paths = [os.path.join(args.models_dir, 's_{}_checkpoint.pt'.format(fold)) for fold in folds] |
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datasets_id = {'train': 0, 'val': 1, 'test': 2, 'all': -1} |
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if __name__ == "__main__": |
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all_cls_auc = [] |
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all_cls_acc = [] |
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all_site_auc = [] |
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all_site_acc = [] |
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all_cls_top3_acc = [] |
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all_cls_top5_acc = [] |
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for ckpt_idx in range(len(ckpt_paths)): |
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if datasets_id[args.split] < 0: |
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split_dataset = dataset |
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csv_path = None |
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else: |
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csv_path = '{}/splits_{}.csv'.format(args.splits_dir, folds[ckpt_idx]) |
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datasets = dataset.return_splits(from_id=False, csv_path=csv_path) |
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split_dataset = datasets[datasets_id[args.split]] |
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model, results_dict = eval(split_dataset, args, ckpt_paths[ckpt_idx]) |
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for cls_idx in range(len(results_dict['cls_aucs'])): |
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print('class {} auc: {}'.format(cls_idx, results_dict['cls_aucs'][cls_idx])) |
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all_cls_auc.append(results_dict['cls_auc']) |
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all_cls_acc.append(1-results_dict['cls_test_error']) |
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all_site_auc.append(results_dict['site_auc']) |
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all_site_acc.append(1-results_dict['site_test_error']) |
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all_cls_top3_acc.append(results_dict['top3_acc']) |
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all_cls_top5_acc.append(results_dict['top5_acc']) |
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df = results_dict['df'] |
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df.to_csv(os.path.join(args.save_dir, 'fold_{}.csv'.format(folds[ckpt_idx])), index=False) |
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df_dict = {'folds': folds, 'cls_test_auc': all_cls_auc, 'cls_test_acc': all_cls_acc, 'cls_top3_acc': all_cls_top3_acc, 'cls_top5_acc': all_cls_top5_acc, |
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'site_test_auc': all_site_auc, 'site_test_acc': all_site_acc} |
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final_df = pd.DataFrame(df_dict) |
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if len(folds) != args.k: |
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save_name = 'summary_partial_{}_{}.csv'.format(folds[0], folds[-1]) |
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else: |
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save_name = 'summary.csv' |
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final_df.to_csv(os.path.join(args.save_dir, save_name)) |