def _train_save_load(self, tmpdir, loss, val_metric, model='UNet3D', max_num_epochs=1, log_after_iters=2,
validate_after_iters=2, max_num_iterations=4, weight_map=False):
binary_loss = loss in ['BCEWithLogitsLoss', 'DiceLoss', 'GeneralizedDiceLoss']
device = torch.device("cuda:0" if torch.cuda.is_available() else 'cpu')
test_config = copy.deepcopy(CONFIG_BASE)
test_config['model']['name'] = model
test_config.update({
# get device to train on
'device': device,
'loss': {'name': loss, 'weight': np.random.rand(2).astype(np.float32), 'pos_weight': 3.},
'eval_metric': {'name': val_metric}
})
test_config['model']['final_sigmoid'] = binary_loss
if weight_map:
test_config['loaders']['weight_internal_path'] = 'weight_map'
loss_criterion = get_loss_criterion(test_config)
eval_criterion = get_evaluation_metric(test_config)
model = get_model(test_config)
model = model.to(device)
if loss in ['BCEWithLogitsLoss']:
label_dtype = 'float32'
else:
label_dtype = 'long'
test_config['loaders']['train']['transformer']['label'][0]['dtype'] = label_dtype
test_config['loaders']['val']['transformer']['label'][0]['dtype'] = label_dtype
train, val = TestUNet3DTrainer._create_random_dataset((3, 128, 128, 128), (3, 64, 64, 64), binary_loss)
test_config['loaders']['train']['file_paths'] = [train]
test_config['loaders']['val']['file_paths'] = [val]
loaders = get_train_loaders(test_config)
optimizer = _create_optimizer(test_config, model)
test_config['lr_scheduler']['name'] = 'MultiStepLR'
lr_scheduler = _create_lr_scheduler(test_config, optimizer)
logger = get_logger('UNet3DTrainer', logging.DEBUG)
formatter = DefaultTensorboardFormatter()
trainer = UNet3DTrainer(model, optimizer, lr_scheduler,
loss_criterion, eval_criterion,
device, loaders, tmpdir,
max_num_epochs=max_num_epochs,
log_after_iters=log_after_iters,
validate_after_iters=validate_after_iters,
max_num_iterations=max_num_iterations,
tensorboard_formatter=formatter)
trainer.fit()
# test loading the trainer from the checkpoint
trainer = UNet3DTrainer.from_checkpoint(os.path.join(tmpdir, 'last_checkpoint.pytorch'),
model, optimizer, lr_scheduler,
loss_criterion, eval_criterion,
loaders, tensorboard_formatter=formatter)
return trainer
def _train_save_load(tmpdir, train_config, loss, val_metric, model, weight_map, shape):
binary_loss = loss in ['BCEWithLogitsLoss', 'DiceLoss', 'BCEDiceLoss', 'GeneralizedDiceLoss']
device = torch.device("cuda:0" if torch.cuda.is_available() else 'cpu')
train_config['model']['name'] = model
train_config.update({
# get device to train on
'device': device,
'loss': {'name': loss, 'weight': np.random.rand(2).astype(np.float32), 'pos_weight': 3.},
'eval_metric': {'name': val_metric}
})
train_config['model']['final_sigmoid'] = binary_loss
if weight_map:
train_config['loaders']['weight_internal_path'] = 'weight_map'
loss_criterion = get_loss_criterion(train_config)
eval_criterion = get_evaluation_metric(train_config)
model = get_model(train_config['model'])
model = model.to(device)
if loss in ['BCEWithLogitsLoss']:
label_dtype = 'float32'
train_config['loaders']['train']['transformer']['label'][0]['dtype'] = label_dtype
train_config['loaders']['val']['transformer']['label'][0]['dtype'] = label_dtype
train = _create_random_dataset(shape, binary_loss)
val = _create_random_dataset(shape, binary_loss)
train_config['loaders']['train']['file_paths'] = [train]
train_config['loaders']['val']['file_paths'] = [val]
loaders = get_train_loaders(train_config)
optimizer = create_optimizer(train_config['optimizer'], model)
lr_scheduler = create_lr_scheduler(train_config.get('lr_scheduler', None), optimizer)
formatter = DefaultTensorboardFormatter()
trainer = UNet3DTrainer(model, optimizer, lr_scheduler,
loss_criterion, eval_criterion,
device, loaders, tmpdir,
max_num_epochs=train_config['trainer']['max_num_epochs'],
log_after_iters=train_config['trainer']['log_after_iters'],
validate_after_iters=train_config['trainer']['log_after_iters'],
max_num_iterations=train_config['trainer']['max_num_iterations'],
tensorboard_formatter=formatter)
trainer.fit()
# test loading the trainer from the checkpoint
trainer = UNet3DTrainer(model, optimizer, lr_scheduler,
loss_criterion, eval_criterion,
device, loaders, tmpdir,
tensorboard_formatter=formatter,
max_num_epochs=train_config['trainer']['max_num_epochs'],
log_after_iters=train_config['trainer']['log_after_iters'],
validate_after_iters=train_config['trainer']['log_after_iters'],
max_num_iterations=train_config['trainer']['max_num_iterations'],
resume=os.path.join(tmpdir, 'last_checkpoint.pytorch'))
return trainer
def main():
# Load and log experiment configuration
config = load_config()
logger.info(config)
manual_seed = config.get('manual_seed', None)
if manual_seed is not None:
logger.info(f'Seed the RNG for all devices with {manual_seed}')
torch.manual_seed(manual_seed)
# see https://pytorch.org/docs/stable/notes/randomness.html
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
# Create the model
model = get_model(config)
# use DataParallel if more than 1 GPU available
device = config['device']
if torch.cuda.device_count() > 1 and not device.type == 'cpu':
model = nn.DataParallel(model)
logger.info(f'Using {torch.cuda.device_count()} GPUs for training')
# put the model on GPUs
logger.info(f"Sending the model to '{config['device']}'")
model = model.to(device)
# Log the number of learnable parameters
logger.info(
f'Number of learnable params {get_number_of_learnable_parameters(model)}'
)
# Create loss criterion
loss_criterion = get_loss_criterion(config)
# Create evaluation metric
eval_criterion = get_evaluation_metric(config)
# Create data loaders
loaders = get_train_loaders(config)
# Create the optimizer
optimizer = _create_optimizer(config, model)
# Create learning rate adjustment strategy
lr_scheduler = _create_lr_scheduler(config, optimizer)
# Create model trainer
trainer = _create_trainer(config,
model=model,
optimizer=optimizer,
lr_scheduler=lr_scheduler,
loss_criterion=loss_criterion,
eval_criterion=eval_criterion,
loaders=loaders)
# Start training
trainer.fit()
def create_trainer(config):
# Create the model
model = get_model(config['model'])
# use DataParallel if more than 1 GPU available
device = config['device']
if torch.cuda.device_count() > 1 and not device.type == 'cpu':
model = nn.DataParallel(model)
logger.info(f'Using {torch.cuda.device_count()} GPUs for training')
# put the model on GPUs
logger.info(f"Sending the model to '{config['device']}'")
model = model.to(device)
# Log the number of learnable parameters
logger.info(
f'Number of learnable params {get_number_of_learnable_parameters(model)}'
)
# Create loss criterion
loss_criterion = get_loss_criterion(config)
# Create evaluation metric
eval_criterion = get_evaluation_metric(config)
# Create data loaders
loaders = get_train_loaders(config)
# Create the optimizer
optimizer = create_optimizer(config['optimizer'], model)
# Create learning rate adjustment strategy
lr_scheduler = create_lr_scheduler(config.get('lr_scheduler', None),
optimizer)
trainer_config = config['trainer']
# Create tensorboard formatter
tensorboard_formatter = get_tensorboard_formatter(
trainer_config.pop('tensorboard_formatter', None))
# Create trainer
resume = trainer_config.pop('resume', None)
pre_trained = trainer_config.pop('pre_trained', None)
return UNet3DTrainer(model=model,
optimizer=optimizer,
lr_scheduler=lr_scheduler,
loss_criterion=loss_criterion,
eval_criterion=eval_criterion,
tensorboard_formatter=tensorboard_formatter,
device=config['device'],
loaders=loaders,
resume=resume,
pre_trained=pre_trained,
**trainer_config)
def build(config):
# Create the model
model = get_model(config['model'])
# use DataParallel if more than 1 GPU available
device = config['device']
if torch.cuda.device_count() > 1 and not device.type == 'cpu':
model = nn.DataParallel(model)
logger.info(f'Using {torch.cuda.device_count()} GPUs for training')
# put the model on GPUs
logger.info(f"Sending the model to '{config['device']}'")
model = model.to(device)
# Log the number of learnable parameters
logger.info(
f'Number of learnable params {get_number_of_learnable_parameters(model)}'
)
# Create loss criterion
loss_criterion = get_loss_criterion(config)
# Create evaluation metric
eval_criterion = get_evaluation_metric(config)
# Create data loaders
loaders = get_train_loaders(config)
# Create the optimizer
optimizer = create_optimizer(config['optimizer'], model)
# Create learning rate adjustment strategy
lr_scheduler = create_lr_scheduler(config.get('lr_scheduler', None),
optimizer)
# Create model trainer
trainer = _create_trainer(config,
model=model,
optimizer=optimizer,
lr_scheduler=lr_scheduler,
loss_criterion=loss_criterion,
eval_criterion=eval_criterion,
loaders=loaders)
return trainer
