# some code from nnU-Net: https://github.com/MIC-DKFZ/nnUNet from time import time, sleep from datetime import datetime import os import sys import pandas as pd import numpy as np import matplotlib.pyplot as plt class Logger(): def __init__(self, output_folder): self.output_folder = output_folder os.makedirs(self.output_folder, exist_ok=True) timestamp = datetime.now() self.log_file = os.path.join( self.output_folder, "training_log_%d_%d_%d_%02.0d_%02.0d_%02.0d.txt" % (timestamp.year, timestamp.month, timestamp.day, timestamp.hour, timestamp.minute, timestamp.second) ) with open(self.log_file, 'w') as f: f.write("Starting... \n") def print_to_log_file(self, *args, also_print_to_console=True, add_timestamp=True): timestamp = time() dt_object = datetime.fromtimestamp(timestamp) if add_timestamp: args = ("%s:" % dt_object, *args) successful = False max_attempts = 5 ctr = 0 while not successful and ctr < max_attempts: try: with open(self.log_file, 'a+') as f: for a in args: f.write(str(a)) f.write(" ") f.write("\n") successful = True except IOError: print("%s: failed to log: " % datetime.fromtimestamp(timestamp), sys.exc_info()) sleep(0.5) ctr += 1 if also_print_to_console: print(*args) def poly_lr(epoch, max_epochs, initial_lr, exponent=0.9): return initial_lr * (1 - epoch / max_epochs)**exponent def split_prostatedataset(data_root, patientid_path, center=1, seed=0, random_validation=False): all_centers = ['A-ISBI', 'B-ISBI_1.5', 'C-I2CVB', 'D-UCL', 'E-BIDMC', 'F-HK'] train_centers = [all_centers[center-1]] patientid = pd.read_csv(patientid_path) all_patientid = [] train_patientid = [] val_patientid = [] for c in train_centers: all_patientid.extend(patientid[patientid.center==c]['patientid'].values.tolist()) if random_validation: np.random.seed(seed) np.random.shuffle(all_patientid) train_patientid = sorted(all_patientid[:int(len(all_patientid)*0.9)]) val_patientid = sorted(all_patientid[int(len(all_patientid)*0.9):]) else: train_patientid = all_patientid[:int(len(all_patientid)*0.9)] val_patientid = all_patientid[int(len(all_patientid)*0.9):] train_patientid = [x for x in os.listdir(data_root) if int(x[9:12]) in train_patientid] val_patientid = [x for x in os.listdir(data_root) if int(x[9:12]) in val_patientid] # exclude centers ood_centers = list(set(all_centers) - set(train_centers)) test_patientid = [] for c in ood_centers: test_patientid.extend(patientid[patientid.center==c]['patientid'].values.tolist()) return train_patientid, val_patientid, test_patientid def plot_loss(train_losses, val_losses, model_save_path): # plot loss plt.plot(train_losses) plt.plot(val_losses) plt.title('Dice CE Loss') plt.xlabel('Epoch') plt.ylabel('Loss') plt.savefig(os.path.join(model_save_path, 'train_loss.png')) plt.close()