main.py

from __future__ import print_function

import argparse
import pdb
import os
import math

# internal imports
from utils.file_utils import save_pkl, load_pkl
from utils.utils import *
from utils.core_utils import train
from datasets.dataset_generic import Generic_WSI_Classification_Dataset, Generic_MIL_Dataset

# pytorch imports
import torch
from torch.utils.data import DataLoader, sampler
import torch.nn as nn
import torch.nn.functional as F

import pandas as pd
import numpy as np
from sklearn.metrics import f1_score


# Generic training settings
parser = argparse.ArgumentParser(description='Configurations for WSI Training')
parser.add_argument('--data_root_dir', type=str, default=None,
                    help='data directory')
parser.add_argument('--data_folder_s', type=str, default=None, help='dir under data directory' )
parser.add_argument('--data_folder_l', type=str, default=None, help='dir under data directory' )
parser.add_argument('--tg_file', type=str, default=None, help='dir under data directory' )
parser.add_argument('--max_epochs', type=int, default=200,
                    help='maximum number of epochs to train (default: 200)')
parser.add_argument('--lr', type=float, default=1e-4,
                    help='learning rate (default: 0.0001)')
parser.add_argument('--label_frac', type=float, default=1.0,
                    help='fraction of training labels (default: 1.0)')
parser.add_argument('--reg', type=float, default=1e-5,
                    help='weight decay (default: 1e-5)')
parser.add_argument('--seed', type=int, default=1,
                    help='random seed for reproducible experiment (default: 1)')
parser.add_argument('--k', type=int, default=10, help='number of folds (default: 10)')
parser.add_argument('--k_start', type=int, default=-1, help='start fold (default: -1, last fold)')
parser.add_argument('--k_end', type=int, default=-1, help='end fold (default: -1, first fold)')
parser.add_argument('--results_dir', default='./results', help='results directory (default: ./results)')
parser.add_argument('--split_dir', type=str, default=None,
                    help='manually specify the set of splits to use, instead of infering from the task and label_frac argument (default: None)')
parser.add_argument('--log_data', action='store_true', default=False, help='log data using tensorboard')
parser.add_argument('--testing', action='store_true', default=False, help='debugging tool')
parser.add_argument('--early_stopping', action='store_true', default=False, help='enable early stopping')
parser.add_argument('--opt', type=str, choices = ['adam', 'sgd'], default='adam')
parser.add_argument('--drop_out', action='store_true', default=False, help='enabel dropout (p=0.25)')
parser.add_argument('--bag_loss', type=str, choices=['svm', 'ce'], default='ce',
                    help='slide-level classification loss function (default: ce)')
parser.add_argument('--model_type', type=str, choices=['clam_sb', 'clam_mb', 'mil', 'patch_gcn', 'dgc'], default='clam_sb',
                    help='type of model (default: clam_sb, clam w/ single attention branch)')
parser.add_argument('--mode', type=str, choices=['clam', 'graph'], default='clam', help='Specifies which modalities to use / collate function in dataloader.')
parser.add_argument('--exp_code', type=str, help='experiment code for saving results')
parser.add_argument('--weighted_sample', action='store_true', default=False, help='enable weighted sampling')
parser.add_argument('--model_size', type=str, choices=['small', 'big'], default='small', help='size of model, does not affect mil')
parser.add_argument('--task', type=str)

### CLAM specific options
parser.add_argument('--no_inst_cluster', action='store_true', default=False,
                    help='disable instance-level clustering')
parser.add_argument('--inst_loss', type=str, choices=['svm', 'ce', None], default=None,
                    help='instance-level clustering loss function (default: None)')
parser.add_argument('--subtyping', action='store_true', default=False,
                    help='subtyping problem')
parser.add_argument('--bag_weight', type=float, default=0.7,
                    help='clam: weight coefficient for bag-level loss (default: 0.7)')
parser.add_argument('--B', type=int, default=1, help='numbr of positive/negative patches to sample for clam')

### patch_gcn specific options
parser.add_argument('--num_gcn_layers',  type=int, default=4, help = '# of GCN layers to use.')
parser.add_argument('--edge_agg',        type=str, default='spatial', help="What edge relationship to use for aggregation.")
parser.add_argument('--resample',        type=float, default=0.00, help='Dropping out random patches.')

### my defined options
parser.add_argument('--cluster_loss', action='store_true', default=False)
args = parser.parse_args()
device=torch.device("cuda" if torch.cuda.is_available() else "cpu")

def seed_torch(seed=7):
    import random
    random.seed(seed)
    os.environ['PYTHONHASHSEED'] = str(seed)
    np.random.seed(seed)
    torch.manual_seed(seed)
    if device.type == 'cuda':
        torch.cuda.manual_seed(seed)
        torch.cuda.manual_seed_all(seed) # if you are using multi-GPU.
    torch.backends.cudnn.benchmark = False
    torch.backends.cudnn.deterministic = True

seed_torch(args.seed)

encoding_size = 1024
settings = {'num_splits': args.k,
            'k_start': args.k_start,
            'k_end': args.k_end,
            'task': args.task,
            'max_epochs': args.max_epochs,
            'results_dir': args.results_dir,
            'lr': args.lr,
            'experiment': args.exp_code,
            'reg': args.reg,
            'label_frac': args.label_frac,
            'bag_loss': args.bag_loss,
            'seed': args.seed,
            'model_type': args.model_type,
            'mode': args.mode,
            'model_size': args.model_size,
            "use_drop_out": args.drop_out,
            'weighted_sample': args.weighted_sample,
            'opt': args.opt}

if args.model_type in ['clam_sb', 'clam_mb']:
    settings.update({'bag_weight': args.bag_weight,
                     'inst_loss': args.inst_loss,
                     'B': args.B})

print('\nLoad Dataset')

if args.task == 'task_1_tumor_vs_normal':
    args.n_classes=2
    dataset = Generic_MIL_Dataset(csv_path = 'dataset_csv/tumor_vs_normal_dummy_clean.csv',
                                  mode = args.mode,
                                  data_dir= os.path.join(args.data_root_dir, 'tumor_vs_normal_resnet_features'),
                                  shuffle = False,
                                  seed = args.seed,
                                  print_info = True,
                                  label_dict = {'normal_tissue':0, 'tumor_tissue':1},
                                  patient_strat=False,
                                  ignore=[])

elif args.task == 'task_2_tumor_subtyping':
    args.n_classes=3
    dataset = Generic_MIL_Dataset(csv_path = '../our_work_yfy/dataset_csv/TCGA_RCC_subtyping.csv',
                                  mode = args.mode,
                                  data_dir_s = os.path.join(args.data_root_dir, args.data_folder_s),
                                  data_dir_l = os.path.join(args.data_root_dir, args.data_folder_l),
                                  TG_file= args.tg_file,
                                  print_info = True,
                                  label_dict = {'CCRCC':0, 'PRCC':1, 'CRCC':2},
                                  patient_strat= False,
                                  ignore=[])

    # if args.model_type in ['clam_sb', 'clam_mb']:
    #     assert args.subtyping

elif args.task == 'task_3_pt_staging_cls3':
    args.n_classes=3
    dataset = Generic_MIL_Dataset(csv_path = '../our_work_yfy/dataset_csv/Yifuyuan_gastric_cancer_pt_staging.csv',
                                  mode = args.mode,
                                  data_dir_s = os.path.join(args.data_root_dir, args.data_folder_s),
                                  data_dir_l = os.path.join(args.data_root_dir, args.data_folder_l),
                                  TG_file= args.tg_file,
                                  shuffle = False,
                                  print_info = True,
                                  label_dict = {'T1ab':0, 'T2':1, 'T34':2},
                                  patient_strat= False,
                                  ignore=[])

elif args.task == 'task_3_pt_staging_TCGA':
    args.n_classes=3
    dataset = Generic_MIL_Dataset(csv_path = '../our_work_yfy/dataset_csv/TCGA_gastric_cancer_pt_staging.csv',
                                  mode = args.mode,
                                  data_dir_s = os.path.join(args.data_root_dir, args.data_folder_s),
                                  data_dir_l = os.path.join(args.data_root_dir, args.data_folder_l),
                                  TG_file= args.tg_file,
                                  shuffle = False,
                                  print_info = True,
                                  label_dict = {'T1ab':0, 'T2':1, 'T34':2},
                                  patient_strat= False,
                                  ignore=[])

elif args.task == 'task_3_pt_staging_cls2':
    args.n_classes=2
    dataset = Generic_MIL_Dataset(csv_path = '../our_work_yfy/dataset_csv/TCGA_BLCA_pt_staging.csv',
                                  mode = args.mode,
                                  data_dir_s = os.path.join(args.data_root_dir, args.data_folder_s),
                                  data_dir_l = os.path.join(args.data_root_dir, args.data_folder_l),
                                  TG_file= args.tg_file,
                                  shuffle = False,
                                  print_info = True,
                                  label_dict = {'T2':0, 'T3':1},
                                  patient_strat= False,
                                  ignore=[])

else:
    raise NotImplementedError

# create results directory if necessary
if not os.path.exists(args.results_dir):
    os.makedirs(args.results_dir)

args.results_dir = os.path.join(args.results_dir, str(args.exp_code) + '_s{}'.format(args.seed))
if not os.path.exists(args.results_dir):
    os.makedirs(args.results_dir)

if args.split_dir is None:
    args.split_dir = os.path.join('splits', args.task+'_{}'.format(int(args.label_frac*100)))
else:
    args.split_dir = os.path.join('splits', args.split_dir)

print('split_dir: ', args.split_dir)
assert os.path.isdir(args.split_dir)

settings.update({'split_dir': args.split_dir})


with open(args.results_dir + '/experiment_{}.txt'.format(args.exp_code), 'w') as f:
    print(settings, file=f)
f.close()

print("################# Settings ###################")
for key, val in settings.items():
    print("{}:  {}".format(key, val))


def main(args):
    if args.k_start == -1:
        start = 0
    else:
        start = args.k_start
    if args.k_end == -1:
        end = args.k
    else:
        end = args.k_end

    all_test_auc = []
    all_val_auc = []
    all_test_f1 = []
    all_test_acc = []
    all_val_acc = []
    all_cls0_acc = []
    all_cls1_acc = []
    all_cls2_acc = []
    folds = np.arange(start, end)
    for i in folds:
        seed_torch(args.seed)
        train_dataset, val_dataset, test_dataset = dataset.return_splits(from_id=False,
                                                                         csv_path='{}/splits_{}.csv'.format(args.split_dir, i))  # 利用生成的dataset划分，训练，测试和验证集。

        datasets = (train_dataset, val_dataset, test_dataset)
        results, test_auc, val_auc, test_acc, val_acc, each_class_acc, test_f1 = train(datasets, i, args)
        all_test_auc.append(test_auc)
        all_test_f1.append(test_f1)
        all_test_acc.append(test_acc)

        #write results to pkl
        filename = os.path.join(args.results_dir, 'split_{}_results.pkl'.format(i))
        save_pkl(filename, results)

    final_df = pd.DataFrame({'folds': folds, 'test_auc': all_test_auc,'test_acc': all_test_acc, 'test_f1': all_test_f1})
    result_df = pd.DataFrame({'metric': ['mean', 'var'],
                              'test_auc': [np.mean(all_test_auc), np.std(all_test_auc)],
                              'test_f1': [np.mean(all_test_f1), np.std(all_test_f1)],
                              'test_acc': [np.mean(all_test_acc), np.std(all_test_acc)]})


    if len(folds) != args.k:
        save_name = 'summary_partial_{}_{}.csv'.format(folds[0], folds[-1])
        result_name = 'result_partial_{}_{}.csv'.format(folds[0], folds[-1])
    else:
        save_name = 'summary.csv'
        result_name = 'result.csv'

    result_df.to_csv(os.path.join(args.results_dir, result_name), index=False)
    final_df.to_csv(os.path.join(args.results_dir, save_name))


if __name__ == "__main__":
    results = main(args)
    print("finished!")
    print("end script")