def main():
"""
Image Classification Prediction
"""
cli_args = get_test_args(__author__, __version__)
# Variables
image_path = cli_args.input
checkpoint_path = cli_args.checkpoint
top_k = cli_args.top_k
categories_names = cli_args.categories_names
# LOAD THE PRE-TRAINED MODEL
model = load_ckp(checkpoint_path, optimizer=None)
# PREDICT THE TOP_K PROBABILITY AND ITS CORRESPONDING CLASS FROM WHICH IT IS BELONG
probs, classes = predict(image_path, model, top_k)
# Check the categories file
if not os.path.isfile(categories_names):
print(f'Categories file {categories_names} was not found.')
exit(1)
# Label mapping
with open(categories_names, 'r') as f:
cat_to_name = json.load(f)
class_names = [cat_to_name[idx] for idx in classes]
# Display prediction
data = pd.DataFrame({' Classes': classes, ' Flower': class_names, 'Probability': probs })
data = data.sort_values('Probability', ascending = False)
print('The item identified in the image file is:')
print(data)
def predict_use(args):
model_name = args.model_name
patient_path = args.patient_path
config_file = 'config.yaml'
cfg = load_config(config_file)
input_modalites = int(cfg['PARAMETERS']['input_modalites'])
output_channels = int(cfg['PARAMETERS']['output_channels'])
base_channels = int(cfg['PARAMETERS']['base_channels'])
patience = int(cfg['PARAMETERS']['patience'])
ROOT = cfg['PATH']['root']
best_dir = cfg['PATH']['best_model_path']
best_model_dir = os.path.join(ROOT, best_dir)
device = 'cuda:0' if torch.cuda.is_available() else 'cpu'
# load best trained model
net = init_U_Net(input_modalites, output_channels, base_channels)
net.to(device)
optimizer = optim.Adam(net.parameters())
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
verbose=True,
patience=patience)
ckp_path = os.path.join(best_model_dir, model_name + '_best_model.pth.tar')
net, _, _, _, _, _ = load_ckp(ckp_path, net, optimizer, scheduler)
# predict
predict(net, model_name, patient_path, ROOT, save_mask=True)
def main():
os.environ["CUDA_VISIBLE_DEVICES"] = opt.gpus
test_image_dataset = image_preprocessing(opt.dataset, 'val')
data_loader = DataLoader(test_image_dataset,
batch_size=opt.batch_size,
shuffle=False,
num_workers=opt.num_workers)
G = Generator(ResidualBlock, layer_count=9)
F = Generator(ResidualBlock, layer_count=9)
if torch.cuda.is_available():
G = nn.DataParallel(G)
F = nn.DataParallel(F)
G = G.cuda()
F = F.cuda()
G, F, _, _, _, _, _, _, _ = load_ckp(opt.model_path, G, F)
G.eval()
F.eval()
if not os.path.exists(opt.save_path):
os.mkdir(opt.save_path)
for step, data in enumerate(tqdm(data_loader)):
real_A = to_variable(data['A'])
real_B = to_variable(data['B'])
fake_B = G(real_A)
fake_A = F(real_B)
batch_image = torch.cat((torch.cat(
(real_A, real_B), 3), torch.cat((fake_A, fake_B), 3)), 2)
for i in range(batch_image.shape[0]):
torchvision.utils.save_image(
denorm(batch_image[i]),
opt.save_path + '{result_name}_{step}.jpg'.format(
result_name=opt.result_name,
step=step * opt.batch_size + i))
def main(_config,_run):
logger = _run
SAVE_NAME = _config['SAVE_NAME']
LOAD_SAVED_MODEL = _config['LOAD_SAVED_MODEL']
MODEL_PATH_FINAL = _config['MODEL_PATH_FINAL']
total_steps = 1000000
params = common.HYPERPARAMS['gamePlay2']
params['epsilon_frames'] *= 2
parser = argparse.ArgumentParser()
parser.add_argument("--cuda", default=False, action="store_true", help="Enable cuda")
args = parser.parse_args()
env = gym.make(params['env_name'],glob_conf=_config,logger=logger)
#env = ptan.common.wrappers.wrap_dqn(env)
writer = SummaryWriter(comment="-" + params['run_name'] + "-rainbow-beta200")
net = RainbowDQN(env.observation_space.shape, env.action_space.n).to(device)
#net.load_state_dict(torch.load( ))
name_load = current_path +"/models" +MODEL_PATH_FINAL
if _config['LOAD_SAVED_MODEL']:
mdl, opt, lss = load_ckp(MODEL_PATH_FINAL, net, optimizer)
net = mdl
optimizer = opt
tgt_net = ptan.agent.TargetNet(net)
agent = ptan.agent.DQNAgent(lambda x: net.qvals(x), ptan.actions.ArgmaxActionSelector(), device=device)
# change the step_counts to change multi step prediction
exp_source = ptan.experience.ExperienceSourceFirstLast(env, agent, gamma=params['gamma'], steps_count=REWARD_STEPS)
buffer = ptan.experience.PrioritizedReplayBuffer(exp_source, params['replay_size'], PRIO_REPLAY_ALPHA)
optimizer = optim.Adam(net.parameters(), lr=params['learning_rate'])
today = datetime.datetime.now()
todays_date_full = str(today.year) + "_" + str(today.month) + "_" + str(today.day) + "_"
todays_date_full += str(today.hour) + "_" + str(today.minute) + "_" + str(today.second)
folder_name = todays_date_full +"_"+experiment_name
results_dir = current_path + "/results/" + folder_name
results_dir_weights = results_dir + "/weights"
os.makedirs(results_dir)
os.makedirs(results_dir_weights)
frame_idx = 0
beta = BETA_START
best_mean_reward = 0.0
eval_states = None
with common.RewardTracker(writer, params['stop_reward']) as reward_tracker:
while frame_idx < total_steps:
frame_idx += 1
buffer.populate(1)
beta = min(1.0, BETA_START + frame_idx * (1.0 - BETA_START) / BETA_FRAMES)
new_rewards = exp_source.pop_total_rewards()
if new_rewards:
# start saving the model after actual training begins
if frame_idx > 100:
if best_mean_reward is None or best_mean_reward < reward_tracker.mean_reward:
torch.save(net.state_dict(),
SAVE_NAME + "-best.dat")
if best_mean_reward is not None:
print("Best mean reward updated %.3f -> %.3f, model saved" % \
(best_mean_reward, reward_tracker.mean_reward))
if not reward_tracker.mean_reward == 0:
best_mean_reward = reward_tracker.mean_reward
if reward_tracker.reward(new_rewards[0], frame_idx):
break
if len(buffer) < params['replay_initial']:
continue
if eval_states is None:
eval_states, _, _ = buffer.sample(STATES_TO_EVALUATE, beta)
eval_states = [np.array(transition.state, copy=False) for transition in eval_states]
eval_states = np.array(eval_states, copy=False)
optimizer.zero_grad()
batch, batch_indices, batch_weights = buffer.sample(params['batch_size'], beta)
loss_v, sample_prios_v = calc_loss(batch, batch_weights, net, tgt_net.target_model,
params['gamma'] ** REWARD_STEPS, device=device)
# if frame_idx % 10000 == 0:
if frame_idx % 5000 == 0:
checkpoint = ({
'model': net.state_dict(),
'optimizer': optimizer.state_dict(),
'loss': loss_v,
'num_step': frame_idx
})
torch.save(checkpoint, results_dir_weights + "/rainbow" + str(frame_idx) + "step.dat")
# Save network parameters as histogram
for name, param in net.named_parameters():
writer.add_histogram(name, param.clone().cpu().data.numpy(), frame_idx)
loss_v.backward()
optimizer.step()
buffer.update_priorities(batch_indices, sample_prios_v.data.cpu().numpy())
if frame_idx % params['target_net_sync'] == 0:
tgt_net.sync()
if logger:
loss_v.item()
logger.log_scalar("loss", loss_v.item())
logger.log_scalar("mean_reward", reward_tracker.mean_reward)
def main(ckp_path=None):
"""ckp_path (str): checkpoint_path
Train the model from scratch if ckp_path is None else
Re-Train the model from previous checkpoint
"""
cli_args = get_train_args(__author__, __version__)
# Variables
data_dir = cli_args.data_dir
save_dir = cli_args.save_dir
file_name = cli_args.file_name
use_gpu = cli_args.use_gpu
# LOAD DATA
data_loaders = load_data(data_dir, config.IMG_SIZE, config.BATCH_SIZE)
# BUILD MODEL
if ckp_path == None:
model = initialize_model(model_name=config.MODEL_NAME,
num_classes=config.NO_OF_CLASSES,
feature_extract=True,
use_pretrained=True)
else:
model = load_ckp(ckp_path)
# Device is available or not
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
# If the user wants the gpu mode, check if cuda is available
if (use_gpu == True) and (torch.cuda.is_available() == False):
print("GPU mode is not available, using CPU...")
use_gpu = False
# MOVE MODEL TO AVAILBALE DEVICE
model.to(device)
# DEFINE OPTIMIZER
optimizer = optimizer_fn(model_name=config.MODEL_NAME,
model=model,
lr_rate=config.LR_RATE)
# DEFINE SCHEDULER
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
mode="min",
patience=5,
factor=0.3,
verbose=True)
# DEFINE LOSS FUNCTION
criterion = loss_fn()
# LOAD BEST MODEL'S WEIGHTS
best_model_wts = copy.deepcopy(model.state_dict())
# BEST VALIDATION SCORE
if ckp_path == None:
best_score = -1 # IF MODEL IS TRAIN FROM SCRATCH
else:
best_score = model.best_score # IF MODEL IS RE-TRAIN
# NO OF ITERATION
no_epochs = config.EPOCHS
# KEEP TRACK OF LOSS AND ACCURACY IN EACH EPOCH
stats = {
'train_losses': [],
'valid_losses': [],
'train_accuracies': [],
'valid_accuracies': []
}
print("Models's Training Start......")
for epoch in range(1, no_epochs + 1):
train_loss, train_score = train_fn(data_loaders,
model,
optimizer,
criterion,
device,
phase='train')
val_loss, val_score = eval_fn(data_loaders,
model,
criterion,
device=config.DEVICE,
phase='valid')
scheduler.step(val_loss)
# SAVE MODEL'S WEIGHTS IF MODEL' VALIDATION ACCURACY IS INCREASED
if val_score > best_score:
print(
'Validation score increased ({:.6f} --> {:.6f}). Saving model ...'
.format(best_score, val_score))
best_score = val_score
best_model_wts = copy.deepcopy(
model.state_dict()) #Saving the best model' weights
# MAKE A RECORD OF AVERAGE LOSSES AND ACCURACY IN EACH EPOCH FOR PLOTING
stats['train_losses'].append(train_loss)
stats['valid_losses'].append(val_loss)
stats['train_accuracies'].append(train_score)
stats['valid_accuracies'].append(val_score)
# PRINT TRAINING AND VALIDATION LOOS/ACCURACIES AFTER EACH EPOCH
epoch_len = len(str(no_epochs))
print_msg = (f'[{epoch:>{epoch_len}}/{no_epochs:>{epoch_len}}] ' +
'\t' + f'train_loss: {train_loss:.5f} ' + '\t' +
f'train_score: {train_score:.5f} ' + '\t' +
f'valid_loss: {val_loss:.5f} ' + '\t' +
f'valid_score: {val_score:.5f}')
print(print_msg)
# load best model weights
model.load_state_dict(best_model_wts)
# create checkpoint variable and add important data
model.class_to_idx = data_loaders['train'].dataset.class_to_idx
model.best_score = best_score
model.model_name = config.MODEL_NAME
checkpoint = {
'epoch': no_epochs,
'lr_rate': config.LR_RATE,
'model_name': config.MODEL_NAME,
'batch_size': config.BATCH_SIZE,
'valid_score': best_score,
'optimizer': optimizer.state_dict(),
'state_dict': model.state_dict(),
'class_to_idx': model.class_to_idx
}
# SAVE CHECKPOINT
save_ckp(checkpoint, save_dir, file_name)
print("Models's Training is Successfull......")
return model
from modules.models import get_model
from utils import load_ckp
import torch.onnx
import onnx
import torch
OPSET_VERSION = 8
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
model = get_model(cfg.model_name, embeddings_size=cfg.embeddings_size)
model = model.to(device)
model.effnet.set_swish(False)
print(f'Load checkpoint : {cfg.WEIGHTS_LOAD_PATH}')
model, _, _, _, _, _ = load_ckp('../' + cfg.WEIGHTS_LOAD_PATH,
model,
remove_module=True)
model.eval()
with torch.no_grad():
# Input to the model
x = torch.randn(10, 3, 48, 48).to(device).float()
print('Start onnx conversion')
print(f'Save model to : {cfg.WEIGHTS_SAVE_PATH}')
torch.onnx.export(model,
x,
os.path.join('..', cfg.WEIGHTS_SAVE_PATH, 'model.onnx'),
opset_version=OPSET_VERSION,
verbose=False,
export_params=True,
input_names=['input'],
def train(args):
torch.cuda.manual_seed(1)
torch.manual_seed(1)
# user defined parameters
model_name = args.model_name
model_type = args.model_type
lstm_backbone = args.lstmbase
unet_backbone = args.unetbase
layer_num = args.layer_num
nb_shortcut = args.nb_shortcut
loss_fn = args.loss_fn
world_size = args.world_size
rank = args.rank
base_channel = args.base_channels
crop_size = args.crop_size
ignore_idx = args.ignore_idx
return_sequence = args.return_sequence
variant = args.LSTM_variant
epochs = args.epoch
is_pretrain = args.is_pretrain
# system setup parameters
config_file = 'config.yaml'
config = load_config(config_file)
labels = config['PARAMETERS']['labels']
root_path = config['PATH']['model_root']
model_dir = config['PATH']['save_ckp']
best_dir = config['PATH']['save_best_model']
input_modalites = int(config['PARAMETERS']['input_modalites'])
output_channels = int(config['PARAMETERS']['output_channels'])
batch_size = int(config['PARAMETERS']['batch_size'])
is_best = bool(config['PARAMETERS']['is_best'])
is_resume = bool(config['PARAMETERS']['resume'])
patience = int(config['PARAMETERS']['patience'])
time_step = int(config['PARAMETERS']['time_step'])
num_workers = int(config['PARAMETERS']['num_workers'])
early_stop_patience = int(config['PARAMETERS']['early_stop_patience'])
lr = int(config['PARAMETERS']['lr'])
optimizer = config['PARAMETERS']['optimizer']
connect = config['PARAMETERS']['connect']
conv_type = config['PARAMETERS']['lstm_convtype']
# build up dirs
model_path = os.path.join(root_path, model_dir)
best_path = os.path.join(root_path, best_dir)
intermidiate_data_save = os.path.join(root_path, 'train_newdata',
model_name)
train_info_file = os.path.join(intermidiate_data_save,
'{}_train_info.json'.format(model_name))
log_path = os.path.join(root_path, 'logfiles')
if not os.path.exists(model_path):
os.mkdir(model_path)
if not os.path.exists(best_path):
os.mkdir(best_path)
if not os.path.exists(intermidiate_data_save):
os.makedirs(intermidiate_data_save)
if not os.path.exists(log_path):
os.mkdir(log_path)
log_name = model_name + '_' + config['PATH']['log_file']
logger = logfile(os.path.join(log_path, log_name))
logger.info('labels {} are ignored'.format(ignore_idx))
logger.info('Dataset is loading ...')
writer = SummaryWriter('ProcessVisu/%s' % model_name)
# load training set and validation set
data_class = data_split()
train, val, test = data_construction(data_class)
train_dict = time_parser(train, time_patch=time_step)
val_dict = time_parser(val, time_patch=time_step)
# LSTM initilization
if model_type == 'LSTM':
net = LSTMSegNet(lstm_backbone=lstm_backbone,
input_dim=input_modalites,
output_dim=output_channels,
hidden_dim=base_channel,
kernel_size=3,
num_layers=layer_num,
conv_type=conv_type,
return_sequence=return_sequence)
elif model_type == 'UNet_LSTM':
if variant == 'back':
net = BackLSTM(input_dim=input_modalites,
hidden_dim=base_channel,
output_dim=output_channels,
kernel_size=3,
num_layers=layer_num,
conv_type=conv_type,
lstm_backbone=lstm_backbone,
unet_module=unet_backbone,
base_channel=base_channel,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
logger.info(
'the pretrained status of backbone is {}'.format(is_pretrain))
elif variant == 'center':
net = CenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'bicenter':
net = BiCenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
connect=connect,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'directcenter':
net = DirectCenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'bidirectcenter':
net = BiDirectCenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
connect=connect,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'rescenter':
net = ResCenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'birescenter':
net = BiResCenterLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
connect=connect,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
elif variant == 'shortcut':
net = ShortcutLSTM(input_modalites=input_modalites,
output_channels=output_channels,
base_channel=base_channel,
num_layers=layer_num,
num_connects=nb_shortcut,
conv_type=conv_type,
return_sequence=return_sequence,
is_pretrain=is_pretrain)
else:
raise NotImplementedError()
# loss and optimizer setup
if loss_fn == 'Dice':
criterion = DiceLoss(labels=labels, ignore_idx=ignore_idx)
elif loss_fn == 'GDice':
criterion = GneralizedDiceLoss(labels=labels)
elif loss_fn == 'WCE':
criterion = WeightedCrossEntropyLoss(labels=labels)
else:
raise NotImplementedError()
if optimizer == 'adam':
optimizer = optim.Adam(net.parameters(), lr=0.001)
# optimizer = optim.Adam(net.parameters())
elif optimizer == 'sgd':
optimizer = optim.SGD(net.parameters(), momentum=0.9, lr=lr)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
verbose=True,
patience=patience)
# device setup
device = 'cuda:0' if torch.cuda.is_available() else 'cpu'
# net, optimizer = amp.initialize(net, optimizer, opt_level="O1")
if torch.cuda.device_count() > 1:
torch.distributed.init_process_group(
backend='nccl',
init_method='tcp://127.0.0.1:38366',
rank=rank,
world_size=world_size)
if distributed_is_initialized():
print('distributed is initialized')
net.to(device)
net = nn.parallel.DistributedDataParallel(net,
find_unused_parameters=True)
else:
print('data parallel')
net = nn.DataParallel(net)
net.to(device)
min_loss = float('Inf')
early_stop_count = 0
global_step = 0
start_epoch = 0
start_loss = 0
train_info = {
'train_loss': [],
'val_loss': [],
'label_0_acc': [],
'label_1_acc': [],
'label_2_acc': [],
'label_3_acc': [],
'label_4_acc': []
}
if is_resume:
try:
# open previous check points
ckp_path = os.path.join(model_path,
'{}_model_ckp.pth.tar'.format(model_name))
net, optimizer, scheduler, start_epoch, min_loss, start_loss = load_ckp(
ckp_path, net, optimizer, scheduler)
# open previous training records
with open(train_info_file) as f:
train_info = json.load(f)
logger.info(
'Training loss from last time is {}'.format(start_loss) +
'\n' +
'Mininum training loss from last time is {}'.format(min_loss))
logger.info(
'Training accuracies from last time are: label 0: {}, label 1: {}, label 2: {}, label 3: {}, label 4: {}'
.format(train_info['label_0_acc'][-1],
train_info['label_1_acc'][-1],
train_info['label_2_acc'][-1],
train_info['label_3_acc'][-1],
train_info['label_4_acc'][-1]))
except:
logger.warning(
'No checkpoint available, strat training from scratch')
for epoch in range(start_epoch, epochs):
train_set = data_loader(train_dict,
batch_size=batch_size,
key='train',
num_works=num_workers,
time_step=time_step,
patch=crop_size,
model_type='RNN')
n_train = len(train_set)
val_set = data_loader(val_dict,
batch_size=batch_size,
key='val',
num_works=num_workers,
time_step=time_step,
patch=crop_size,
model_type='CNN')
n_val = len(val_set)
logger.info('Dataset loading finished!')
nb_batches = np.ceil(n_train / batch_size)
n_total = n_train + n_val
logger.info(
'{} images will be used in total, {} for trainning and {} for validation'
.format(n_total, n_train, n_val))
train_loader = train_set.load()
# setup to train mode
net.train()
running_loss = 0
dice_score_label_0 = 0
dice_score_label_1 = 0
dice_score_label_2 = 0
dice_score_label_3 = 0
dice_score_label_4 = 0
logger.info('Training epoch {} will begin'.format(epoch + 1))
with tqdm(total=n_train,
desc=f'Epoch {epoch+1}/{epochs}',
unit='patch') as pbar:
for i, data in enumerate(train_loader, 0):
# i : patient
images, segs = data['image'].to(device), data['seg'].to(device)
outputs = net(images)
loss = criterion(outputs, segs)
loss.backward()
optimizer.step()
# if i == 0:
# in_images = images.detach().cpu().numpy()[0]
# in_segs = segs.detach().cpu().numpy()[0]
# in_pred = outputs.detach().cpu().numpy()[0]
# heatmap_plot(image=in_images, mask=in_segs, pred=in_pred, name=model_name, epoch=epoch+1, is_train=True)
running_loss += loss.detach().item()
outputs = outputs.view(-1, outputs.shape[-4],
outputs.shape[-3], outputs.shape[-2],
outputs.shape[-1])
segs = segs.view(-1, segs.shape[-3], segs.shape[-2],
segs.shape[-1])
_, preds = torch.max(outputs.data, 1)
dice_score = dice(preds.data.cpu(),
segs.data.cpu(),
ignore_idx=None)
dice_score_label_0 += dice_score['bg']
dice_score_label_1 += dice_score['csf']
dice_score_label_2 += dice_score['gm']
dice_score_label_3 += dice_score['wm']
dice_score_label_4 += dice_score['tm']
# show progress bar
pbar.set_postfix(
**{
'training loss': loss.detach().item(),
'Training accuracy': dice_score['avg']
})
pbar.update(images.shape[0])
global_step += 1
if global_step % nb_batches == 0:
net.eval()
val_loss, val_acc, val_info = validation(net,
val_set,
criterion,
device,
batch_size,
ignore_idx=None,
name=model_name,
epoch=epoch + 1)
net.train()
train_info['train_loss'].append(running_loss / nb_batches)
train_info['val_loss'].append(val_loss)
train_info['label_0_acc'].append(dice_score_label_0 / nb_batches)
train_info['label_1_acc'].append(dice_score_label_1 / nb_batches)
train_info['label_2_acc'].append(dice_score_label_2 / nb_batches)
train_info['label_3_acc'].append(dice_score_label_3 / nb_batches)
train_info['label_4_acc'].append(dice_score_label_4 / nb_batches)
# save bast trained model
scheduler.step(running_loss / nb_batches)
logger.info('Epoch: {}, LR: {}'.format(
epoch + 1, optimizer.param_groups[0]['lr']))
if min_loss > running_loss / nb_batches:
min_loss = running_loss / nb_batches
is_best = True
early_stop_count = 0
else:
is_best = False
early_stop_count += 1
state = {
'epoch': epoch + 1,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'scheduler_state_dict': scheduler.state_dict(),
'loss': running_loss / nb_batches,
'min_loss': min_loss
}
verbose = save_ckp(state,
is_best,
early_stop_count=early_stop_count,
early_stop_patience=early_stop_patience,
save_model_dir=model_path,
best_dir=best_path,
name=model_name)
# summarize the training results of this epoch
logger.info('The average training loss for this epoch is {}'.format(
running_loss / nb_batches))
logger.info('The best training loss till now is {}'.format(min_loss))
logger.info(
'Validation dice loss: {}; Validation (avg) accuracy of the last timestep: {}'
.format(val_loss, val_acc))
# save the training info every epoch
logger.info('Writing the training info into file ...')
val_info_file = os.path.join(intermidiate_data_save,
'{}_val_info.json'.format(model_name))
with open(train_info_file, 'w') as fp:
json.dump(train_info, fp)
with open(val_info_file, 'w') as fp:
json.dump(val_info, fp)
for name, layer in net.named_parameters():
if layer.requires_grad:
writer.add_histogram(name + '_grad',
layer.grad.cpu().data.numpy(), epoch)
writer.add_histogram(name + '_data',
layer.cpu().data.numpy(), epoch)
if verbose:
logger.info(
'The validation loss has not improved for {} epochs, training will stop here.'
.format(early_stop_patience))
break
loss_plot(train_info_file, name=model_name)
logger.info('finish training!')
return
def main():
os.environ["CUDA_VISIBLE_DEVICES"] = opt.gpus
start_epoch = 0
train_image_dataset = image_preprocessing(opt.dataset, 'train')
data_loader = DataLoader(train_image_dataset, batch_size=opt.batch_size,
shuffle=True, num_workers=opt.num_workers)
criterion = least_squares
euclidean_l1 = nn.L1Loss()
G = Generator(ResidualBlock, layer_count=9)
F = Generator(ResidualBlock, layer_count=9)
Dx = Discriminator()
Dy = Discriminator()
G_optimizer = optim.Adam(G.parameters(), lr=opt.lr, betas=(opt.beta1, opt.beta2))
F_optimizer = optim.Adam(F.parameters(), lr=opt.lr, betas=(opt.beta1, opt.beta2))
Dx_optimizer = optim.Adam(Dx.parameters(), lr=opt.lr, betas=(opt.beta1, opt.beta2))
Dy_optimizer = optim.Adam(Dy.parameters(), lr=opt.lr, betas=(opt.beta1, opt.beta2))
if torch.cuda.is_available():
G = nn.DataParallel(G)
F = nn.DataParallel(F)
Dx = nn.DataParallel(Dx)
Dy = nn.DataParallel(Dy)
G = G.cuda()
F = F.cuda()
Dx = Dx.cuda()
Dy = Dy.cuda()
if opt.checkpoint is not None:
G, F, Dx, Dy, G_optimizer, F_optimizer, Dx_optimizer, Dy_optimizer, start_epoch = load_ckp(opt.checkpoint, G, F, Dx, Dy, G_optimizer, F_optimizer, Dx_optimizer, Dy_optimizer)
print('[Start] : Cycle GAN Training')
logger = Logger(opt.epochs, len(data_loader), image_step=10)
for epoch in range(opt.epochs):
epoch = epoch + start_epoch + 1
print("Epoch[{epoch}] : Start".format(epoch=epoch))
for step, data in enumerate(data_loader):
real_A = to_variable(data['A'])
real_B = to_variable(data['B'])
fake_B = G(real_A)
fake_A = F(real_B)
# Train Dx
Dx_optimizer.zero_grad()
Dx_real = Dx(real_A)
Dx_fake = Dx(fake_A)
Dx_loss = patch_loss(criterion, Dx_real, True) + patch_loss(criterion, Dx_fake, 0)
Dx_loss.backward(retain_graph=True)
Dx_optimizer.step()
# Train Dy
Dy_optimizer.zero_grad()
Dy_real = Dy(real_B)
Dy_fake = Dy(fake_B)
Dy_loss = patch_loss(criterion, Dy_real, True) + patch_loss(criterion, Dy_fake, 0)
Dy_loss.backward(retain_graph=True)
Dy_optimizer.step()
# Train G
G_optimizer.zero_grad()
Dy_fake = Dy(fake_B)
G_loss = patch_loss(criterion, Dy_fake, True)
# Train F
F_optimizer.zero_grad()
Dx_fake = Dx(fake_A)
F_loss = patch_loss(criterion, Dx_fake, True)
# identity loss
loss_identity = euclidean_l1(real_A, fake_A) + euclidean_l1(real_B, fake_B)
# cycle consistency
loss_cycle = euclidean_l1(F(fake_B), real_A) + euclidean_l1(G(fake_A), real_B)
# Optimize G & F
loss = G_loss + F_loss + opt.lamda * loss_cycle + opt.lamda * loss_identity * (0.5)
loss.backward()
G_optimizer.step()
F_optimizer.step()
if (step + 1 ) % opt.save_step == 0:
print("Epoch[{epoch}]| Step [{now}/{total}]| Dx Loss: {Dx_loss}, Dy_Loss: {Dy_loss}, G_Loss: {G_loss}, F_Loss: {F_loss}".format(
epoch=epoch, now=step + 1, total=len(data_loader), Dx_loss=Dx_loss.item(), Dy_loss=Dy_loss,
G_loss=G_loss.item(), F_loss=F_loss.item()))
batch_image = torch.cat((torch.cat((real_A, real_B), 3), torch.cat((fake_A, fake_B), 3)), 2)
torchvision.utils.save_image(denorm(batch_image[0]), opt.training_result + 'result_{result_name}_ep{epoch}_{step}.jpg'.format(result_name=opt.result_name,epoch=epoch, step=(step + 1) * opt.batch_size))
# http://localhost:8097
logger.log(
losses={
'loss_G': G_loss,
'loss_F': F_loss,
'loss_identity': loss_identity,
'loss_cycle': loss_cycle,
'total_G_loss': loss,
'loss_Dx': Dx_loss,
'loss_Dy': Dy_loss,
'total_D_loss': (Dx_loss + Dy_loss),
},
images={
'real_A': real_A,
'real_B': real_B,
'fake_A': fake_A,
'fake_ B': fake_B,
},
)
torch.save({
'epoch': epoch,
'G_model': G.state_dict(),
'G_optimizer': G_optimizer.state_dict(),
'F_model': F.state_dict(),
'F_optimizer': F_optimizer.state_dict(),
'Dx_model': Dx.state_dict(),
'Dx_optimizer': Dx_optimizer.state_dict(),
'Dy_model': Dy.state_dict(),
'Dy_optimizer': Dy_optimizer.state_dict(),
}, opt.save_model + 'model_{result_name}_CycleGAN_ep{epoch}.ckp'.format(result_name=opt.result_name, epoch=epoch))
def train(args):
torch.cuda.manual_seed(1)
torch.manual_seed(1)
# user defined
model_name = args.model_name
model_loss_fn = args.loss_fn
config_file = 'config.yaml'
config = load_config(config_file)
data_root = config['PATH']['data_root']
labels = config['PARAMETERS']['labels']
root_path = config['PATH']['root']
model_dir = config['PATH']['model_path']
best_dir = config['PATH']['best_model_path']
data_class = config['PATH']['data_class']
input_modalites = int(config['PARAMETERS']['input_modalites'])
output_channels = int(config['PARAMETERS']['output_channels'])
base_channel = int(config['PARAMETERS']['base_channels'])
crop_size = int(config['PARAMETERS']['crop_size'])
batch_size = int(config['PARAMETERS']['batch_size'])
epochs = int(config['PARAMETERS']['epoch'])
is_best = bool(config['PARAMETERS']['is_best'])
is_resume = bool(config['PARAMETERS']['resume'])
patience = int(config['PARAMETERS']['patience'])
ignore_idx = int(config['PARAMETERS']['ignore_index'])
early_stop_patience = int(config['PARAMETERS']['early_stop_patience'])
# build up dirs
model_path = os.path.join(root_path, model_dir)
best_path = os.path.join(root_path, best_dir)
intermidiate_data_save = os.path.join(root_path, 'train_data', model_name)
train_info_file = os.path.join(intermidiate_data_save,
'{}_train_info.json'.format(model_name))
log_path = os.path.join(root_path, 'logfiles')
if not os.path.exists(model_path):
os.mkdir(model_path)
if not os.path.exists(best_path):
os.mkdir(best_path)
if not os.path.exists(intermidiate_data_save):
os.makedirs(intermidiate_data_save)
if not os.path.exists(log_path):
os.mkdir(log_path)
log_name = model_name + '_' + config['PATH']['log_file']
logger = logfile(os.path.join(log_path, log_name))
logger.info('Dataset is loading ...')
# split dataset
dir_ = os.path.join(data_root, data_class)
data_content = train_split(dir_)
# load training set and validation set
train_set = data_loader(data_content=data_content,
key='train',
form='LGG',
crop_size=crop_size,
batch_size=batch_size,
num_works=8)
n_train = len(train_set)
train_loader = train_set.load()
val_set = data_loader(data_content=data_content,
key='val',
form='LGG',
crop_size=crop_size,
batch_size=batch_size,
num_works=8)
logger.info('Dataset loading finished!')
n_val = len(val_set)
nb_batches = np.ceil(n_train / batch_size)
n_total = n_train + n_val
logger.info(
'{} images will be used in total, {} for trainning and {} for validation'
.format(n_total, n_train, n_val))
net = init_U_Net(input_modalites, output_channels, base_channel)
device = 'cuda:0' if torch.cuda.is_available() else 'cpu'
if torch.cuda.device_count() > 1:
logger.info('{} GPUs available.'.format(torch.cuda.device_count()))
net = nn.DataParallel(net)
net.to(device)
if model_loss_fn == 'Dice':
criterion = DiceLoss(labels=labels, ignore_index=ignore_idx)
elif model_loss_fn == 'CrossEntropy':
criterion = CrossEntropyLoss(labels=labels, ignore_index=ignore_idx)
elif model_loss_fn == 'FocalLoss':
criterion = FocalLoss(labels=labels, ignore_index=ignore_idx)
elif model_loss_fn == 'Dice_CE':
criterion = Dice_CE(labels=labels, ignore_index=ignore_idx)
elif model_loss_fn == 'Dice_FL':
criterion = Dice_FL(labels=labels, ignore_index=ignore_idx)
else:
raise NotImplementedError()
optimizer = optim.Adam(net.parameters(), lr=1e-4, weight_decay=1e-5)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
verbose=True,
patience=patience)
net, optimizer = amp.initialize(net, optimizer, opt_level='O1')
min_loss = float('Inf')
early_stop_count = 0
global_step = 0
start_epoch = 0
start_loss = 0
train_info = {
'train_loss': [],
'val_loss': [],
'BG_acc': [],
'NET_acc': [],
'ED_acc': [],
'ET_acc': []
}
if is_resume:
try:
ckp_path = os.path.join(model_dir,
'{}_model_ckp.pth.tar'.format(model_name))
net, optimizer, scheduler, start_epoch, min_loss, start_loss = load_ckp(
ckp_path, net, optimizer, scheduler)
# open previous training records
with open(train_info_file) as f:
train_info = json.load(f)
logger.info(
'Training loss from last time is {}'.format(start_loss) +
'\n' +
'Mininum training loss from last time is {}'.format(min_loss))
except:
logger.warning(
'No checkpoint available, strat training from scratch')
# start training
for epoch in range(start_epoch, epochs):
# setup to train mode
net.train()
running_loss = 0
dice_coeff_bg = 0
dice_coeff_net = 0
dice_coeff_ed = 0
dice_coeff_et = 0
logger.info('Training epoch {} will begin'.format(epoch + 1))
with tqdm(total=n_train,
desc=f'Epoch {epoch+1}/{epochs}',
unit='patch') as pbar:
for i, data in enumerate(train_loader, 0):
images, segs = data['image'].to(device), data['seg'].to(device)
# zero the parameter gradients
optimizer.zero_grad()
outputs = net(images)
loss = criterion(outputs, segs)
# loss.backward()
with amp.scale_loss(loss, optimizer) as scaled_loss:
scaled_loss.backward()
optimizer.step()
# save the output at the begining of each epoch to visulize it
if i == 0:
in_images = images.detach().cpu().numpy()[:, 0, ...]
in_segs = segs.detach().cpu().numpy()
in_pred = outputs.detach().cpu().numpy()
heatmap_plot(image=in_images,
mask=in_segs,
pred=in_pred,
name=model_name,
epoch=epoch + 1)
running_loss += loss.detach().item()
dice_score = dice_coe(outputs.detach().cpu(),
segs.detach().cpu())
dice_coeff_bg += dice_score['BG']
dice_coeff_ed += dice_score['ED']
dice_coeff_et += dice_score['ET']
dice_coeff_net += dice_score['NET']
# show progress bar
pbar.set_postfix(
**{
'Training loss': loss.detach().item(),
'Training (avg) accuracy': dice_score['avg']
})
pbar.update(images.shape[0])
global_step += 1
if global_step % nb_batches == 0:
# validate
net.eval()
val_loss, val_acc = validation(net, val_set, criterion,
device, batch_size)
train_info['train_loss'].append(running_loss / nb_batches)
train_info['val_loss'].append(val_loss)
train_info['BG_acc'].append(dice_coeff_bg / nb_batches)
train_info['NET_acc'].append(dice_coeff_net / nb_batches)
train_info['ED_acc'].append(dice_coeff_ed / nb_batches)
train_info['ET_acc'].append(dice_coeff_et / nb_batches)
# save bast trained model
scheduler.step(running_loss / nb_batches)
if min_loss > val_loss:
min_loss = val_loss
is_best = True
early_stop_count = 0
else:
is_best = False
early_stop_count += 1
state = {
'epoch': epoch + 1,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'scheduler_state_dict': scheduler.state_dict(),
'loss': running_loss / nb_batches,
'min_loss': min_loss
}
verbose = save_ckp(state,
is_best,
early_stop_count=early_stop_count,
early_stop_patience=early_stop_patience,
save_model_dir=model_path,
best_dir=best_path,
name=model_name)
logger.info('The average training loss for this epoch is {}'.format(
running_loss / (np.ceil(n_train / batch_size))))
logger.info(
'Validation dice loss: {}; Validation (avg) accuracy: {}'.format(
val_loss, val_acc))
logger.info('The best validation loss till now is {}'.format(min_loss))
# save the training info every epoch
logger.info('Writing the training info into file ...')
with open(train_info_file, 'w') as fp:
json.dump(train_info, fp)
loss_plot(train_info_file, name=model_name)
if verbose:
logger.info(
'The validation loss has not improved for {} epochs, training will stop here.'
.format(early_stop_patience))
break
logger.info('finish training!')
def train(args):
torch.cuda.manual_seed(1)
torch.manual_seed(1)
# user defined
model_name = args.model_name
model_type = args.model_type
loss_func = args.loss
world_size = args.world_size
rank = args.rank
base_channel = args.base_channels
crop_size = args.crop_size
ignore_idx = args.ignore_idx
epochs = args.epoch
# system setup
config_file = 'config.yaml'
config = load_config(config_file)
labels = config['PARAMETERS']['labels']
root_path = config['PATH']['model_root']
model_dir = config['PATH']['save_ckp']
best_dir = config['PATH']['save_best_model']
output_channels = int(config['PARAMETERS']['output_channels'])
batch_size = int(config['PARAMETERS']['batch_size'])
is_best = bool(config['PARAMETERS']['is_best'])
is_resume = bool(config['PARAMETERS']['resume'])
patience = int(config['PARAMETERS']['patience'])
time_step = int(config['PARAMETERS']['time_step'])
num_workers = int(config['PARAMETERS']['num_workers'])
early_stop_patience = int(config['PARAMETERS']['early_stop_patience'])
pad_method = config['PARAMETERS']['pad_method']
lr = int(config['PARAMETERS']['lr'])
optimizer = config['PARAMETERS']['optimizer']
softmax = True
modalities = ['flair', 't1', 't1gd', 't2']
input_modalites = len(modalities)
# build up dirs
model_path = os.path.join(root_path, model_dir)
best_path = os.path.join(root_path, best_dir)
intermidiate_data_save = os.path.join(root_path, 'train_newdata',
model_name)
train_info_file = os.path.join(intermidiate_data_save,
'{}_train_info.json'.format(model_name))
log_path = os.path.join(root_path, 'logfiles')
if not os.path.exists(model_path):
os.mkdir(model_path)
if not os.path.exists(best_path):
os.mkdir(best_path)
if not os.path.exists(intermidiate_data_save):
os.makedirs(intermidiate_data_save)
if not os.path.exists(log_path):
os.mkdir(log_path)
log_name = model_name + '_' + config['PATH']['log_file']
logger = logfile(os.path.join(log_path, log_name))
logger.info('Dataset is loading ...')
writer = SummaryWriter('ProcessVisu/%s' % model_name)
logger.info('patch size: {}'.format(crop_size))
# load training set and validation set
data_class = data_split()
train, val, test = data_construction(data_class)
train_dict = time_parser(train, time_patch=time_step)
val_dict = time_parser(val, time_patch=time_step)
# groups = 4
if model_type == 'UNet':
net = init_U_Net(input_modalites, output_channels, base_channel,
pad_method, softmax)
elif model_type == 'ResUNet':
net = ResUNet(input_modalites, output_channels, base_channel,
pad_method, softmax)
elif model_type == 'DResUNet':
net = DResUNet(input_modalites, output_channels, base_channel,
pad_method, softmax)
elif model_type == 'direct_concat':
net = U_Net_direct_concat(input_modalites, output_channels,
base_channel, pad_method, softmax)
elif model_type == 'Inception':
net = Inception_UNet(input_modalites, output_channels, base_channel,
softmax)
elif model_type == 'Simple_Inception':
net = Simplified_Inception_UNet(input_modalites, output_channels,
base_channel, softmax)
# device setup
device = 'cuda:0' if torch.cuda.is_available() else 'cpu'
net.to(device)
# print model structure
summary(net, input_size=(input_modalites, crop_size, crop_size, crop_size))
dummy_input = torch.rand(1, input_modalites, crop_size, crop_size,
crop_size).to(device)
writer.add_graph(net, (dummy_input, ))
# loss and optimizer setup
if loss_func == 'Dice' and softmax:
criterion = DiceLoss(labels=labels, ignore_idx=ignore_idx)
elif loss_func == 'GDice' and softmax:
criterion = GneralizedDiceLoss(labels=labels)
elif loss_func == 'CrossEntropy':
criterion = WeightedCrossEntropyLoss(labels=labels)
if not softmax:
criterion = nn.CrossEntropyLoss().cuda()
else:
raise NotImplementedError()
if optimizer == 'adam':
optimizer = optim.Adam(net.parameters())
elif optimizer == 'sgd':
optimizer = optim.SGD(net.parameters(),
momentum=0.9,
lr=lr,
weight_decay=1e-5)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
verbose=True,
patience=patience)
# net, optimizer = amp.initialize(net, optimizer, opt_level='O1')
if torch.cuda.device_count() > 1:
logger.info('{} GPUs avaliable'.format(torch.cuda.device_count()))
torch.distributed.init_process_group(
backend='nccl',
init_method='tcp://127.0.0.1:38366',
rank=rank,
world_size=world_size)
if distributed_is_initialized():
logger.info('distributed is initialized')
net.to(device)
net = nn.parallel.DistributedDataParallel(net)
else:
logger.info('data parallel')
net = nn.DataParallel(net)
net.to(device)
min_loss = float('Inf')
early_stop_count = 0
global_step = 0
start_epoch = 0
start_loss = 0
train_info = {
'train_loss': [],
'val_loss': [],
'label_0_acc': [],
'label_1_acc': [],
'label_2_acc': [],
'label_3_acc': [],
'label_4_acc': []
}
if is_resume:
try:
# open previous check points
ckp_path = os.path.join(model_path,
'{}_model_ckp.pth.tar'.format(model_name))
net, optimizer, scheduler, start_epoch, min_loss, start_loss = load_ckp(
ckp_path, net, optimizer, scheduler)
# open previous training records
with open(train_info_file) as f:
train_info = json.load(f)
logger.info(
'Training loss from last time is {}'.format(start_loss) +
'\n' +
'Mininum training loss from last time is {}'.format(min_loss))
logger.info(
'Training accuracies from last time are: label 0: {}, label 1: {}, label 2: {}, label 3: {}, label 4: {}'
.format(train_info['label_0_acc'][-1],
train_info['label_1_acc'][-1],
train_info['label_2_acc'][-1],
train_info['label_3_acc'][-1],
train_info['label_4_acc'][-1]))
# min_loss = float('Inf')
except:
logger.warning(
'No checkpoint available, strat training from scratch')
# start training
for epoch in range(start_epoch, epochs):
# every epoch generate a new set of images
train_set = data_loader(train_dict,
batch_size=batch_size,
key='train',
num_works=num_workers,
time_step=time_step,
patch=crop_size,
modalities=modalities,
model_type='CNN')
n_train = len(train_set)
train_loader = train_set.load()
val_set = data_loader(val_dict,
batch_size=batch_size,
key='val',
num_works=num_workers,
time_step=time_step,
patch=crop_size,
modalities=modalities,
model_type='CNN')
n_val = len(val_set)
nb_batches = np.ceil(n_train / batch_size)
n_total = n_train + n_val
logger.info(
'{} images will be used in total, {} for trainning and {} for validation'
.format(n_total, n_train, n_val))
logger.info('Dataset loading finished!')
# setup to train mode
net.train()
running_loss = 0
dice_score_label_0 = 0
dice_score_label_1 = 0
dice_score_label_2 = 0
dice_score_label_3 = 0
dice_score_label_4 = 0
logger.info('Training epoch {} will begin'.format(epoch + 1))
with tqdm(total=n_train,
desc=f'Epoch {epoch+1}/{epochs}',
unit='patch') as pbar:
for i, data in enumerate(train_loader, 0):
images, segs = data['image'].to(device), data['seg'].to(device)
if model_type == 'SkipDenseSeg' and not softmax:
segs = segs.long()
# combine the batch and time step
batch, time, channel, z, y, x = images.shape
images = images.view(-1, channel, z, y, x)
segs = segs.view(-1, z, y, x)
# zero the parameter gradients
optimizer.zero_grad()
outputs = net(images)
loss = criterion(outputs, segs)
loss.backward()
# with amp.scale_loss(loss, optimizer) as scaled_loss:
# scaled_loss.backward()
optimizer.step()
running_loss += loss.detach().item()
_, preds = torch.max(outputs.data, 1)
dice_score = dice(preds.data.cpu(),
segs.data.cpu(),
ignore_idx=ignore_idx)
dice_score_label_0 += dice_score['bg']
dice_score_label_1 += dice_score['csf']
dice_score_label_2 += dice_score['gm']
dice_score_label_3 += dice_score['wm']
dice_score_label_4 += dice_score['tm']
# show progress bar
pbar.set_postfix(
**{
'Training loss': loss.detach().item(),
'Training accuracy': dice_score['avg']
})
pbar.update(images.shape[0])
del images, segs
global_step += 1
if global_step % nb_batches == 0:
net.eval()
val_loss, val_acc, val_info = validation(
net,
val_set,
criterion,
device,
batch_size,
model_type=model_type,
softmax=softmax,
ignore_idx=ignore_idx)
train_info['train_loss'].append(running_loss / nb_batches)
train_info['val_loss'].append(val_loss)
train_info['label_0_acc'].append(dice_score_label_0 / nb_batches)
train_info['label_1_acc'].append(dice_score_label_1 / nb_batches)
train_info['label_2_acc'].append(dice_score_label_2 / nb_batches)
train_info['label_3_acc'].append(dice_score_label_3 / nb_batches)
train_info['label_4_acc'].append(dice_score_label_4 / nb_batches)
# save bast trained model
if model_type == 'SkipDenseSeg':
scheduler.step()
else:
scheduler.step(val_loss)
# debug
for param_group in optimizer.param_groups:
logger.info('%0.6f | %6d ' % (param_group['lr'], epoch))
if min_loss > running_loss / nb_batches + 1e-2:
min_loss = running_loss / nb_batches
is_best = True
early_stop_count = 0
else:
is_best = False
early_stop_count += 1
# save the check point
state = {
'epoch': epoch + 1,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'scheduler_state_dict': scheduler.state_dict(),
'loss': running_loss / nb_batches,
'min_loss': min_loss
}
verbose = save_ckp(state,
is_best,
early_stop_count=early_stop_count,
early_stop_patience=early_stop_patience,
save_model_dir=model_path,
best_dir=best_path,
name=model_name)
# summarize the training results of this epoch
logger.info('Average training loss of this epoch is {}'.format(
running_loss / nb_batches))
logger.info('Best training loss till now is {}'.format(min_loss))
logger.info('Validation dice loss: {}; Validation accuracy: {}'.format(
val_loss, val_acc))
# save the training info every epoch
logger.info('Writing the training info into file ...')
val_info_file = os.path.join(intermidiate_data_save,
'{}_val_info.json'.format(model_name))
with open(train_info_file, 'w') as fp:
json.dump(train_info, fp)
with open(val_info_file, 'w') as fp:
json.dump(val_info, fp)
loss_plot(train_info_file, name=model_name)
for name, layer in net.named_parameters():
writer.add_histogram(name + '_grad',
layer.grad.cpu().data.numpy(), epoch)
writer.add_histogram(name + '_data',
layer.cpu().data.numpy(), epoch)
if verbose:
logger.info(
'The validation loss has not improved for {} epochs, training will stop here.'
.format(early_stop_patience))
break
writer.close()
logger.info('finish training!')
pretrained_dynamic = a1[0]
# flow_dataset = FlowDataset(transform = transforms.Compose([ToTensor(),Rescale((cnvrt_size,cnvrt_size))]))
flow_dataset = FlowDataset(transform = transforms.Compose([ToTensor()]))
dataloader = DataLoader(flow_dataset, batch_size=batch_size,shuffle=True, num_workers=workers)
net_dynamic = createDeepLabv3().to(device)
net_dynamic.apply(weights_init)
net_impainter = Inpainter(ngpu=1).to(device)
# net_impainter.apply(weights_init)
optimizerD = optim.Adam(net_dynamic.parameters(), lr=lr, betas=(beta1, beta2))
optimizerI = optim.Adam(net_impainter.parameters(), lr=lr, betas=(beta1, beta2))
if(pretrained_dynamic!=None):
net_dynamic, optimizerD, start_epoch = load_ckp(checkpoint_dynamic_path+pretrained_dynamic, net_dynamic, optimizerD)
print("Loaded pretrained: " + pretrained_dynamic)
if(pretrained_inpainter!=None):
net_impainter, optimizerI, start_epoch = load_ckp(checkpoint_inpainter_path+pretrained_inpainter, net_impainter, optimizerI)
print("Loaded pretrained: " + pretrained_inpainter)
loss_l1 = nn.L1Loss()
loss_l2 = nn.MSELoss()
I_losses = []
D_losses = []
iters = 0
print("Starting Training Loop... from" + str(start_epoch))
net_dynamic.train()