device=device)
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batch_size=1,
num_workers=2,
save_root=save_root,
exp_name=args.exp_name,
example_input=example_input,
enable_save_trace=enable_save_trace,
schedulers={'lr': lr_sched},
valid_metrics=valid_metrics,
preview_batch=preview_batch,
preview_interval=5,
inference_kwargs=inference_kwargs,
hparams=hparams,
# enable_videos=True, # Uncomment to enable videos in tensorboard
out_channels=out_channels,
ipython_shell=args.ipython,
# extra_save_steps=range(0, max_steps, 10_000),
# mixed_precision=True, # Enable to use Apex for mixed precision training
)
if args.deterministic:
assert trainer.num_workers <= 1, 'num_workers > 1 introduces indeterministic behavior'
criterion = CombinedLoss([crossentropy, dice], weight=[0.5, 0.5], device=device)
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=1,
num_workers=1,
save_root=save_root,
exp_name=args.exp_name,
example_input=example_input,
enable_save_trace=enable_save_trace,
schedulers={'lr': lr_sched},
valid_metrics=valid_metrics,
preview_batch=preview_batch,
preview_interval=5,
# enable_videos=True, # Uncomment to enable videos in tensorboard
offset=train_dataset.offset,
apply_softmax_for_prediction=True,
num_classes=train_dataset.num_classes,
# TODO: Tune these:
preview_tile_shape=(32, 64, 64),
preview_overlap_shape=(32, 64, 64),
# mixed_precision=True, # Enable to use Apex for mixed precision training
)
# Archiving training script, src folder, env info
Backup(script_path=__file__,save_path=trainer.save_path).archive_backup()
]:
valid_metrics[f'val_{evaluator.name}_mean'] = evaluator() # Mean metrics
for c in range(out_channels):
valid_metrics[f'val_{evaluator.name}_c{c}'] = evaluator(c)
criterion = nn.CrossEntropyLoss().to(device)
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batch_size=batch_size,
num_workers=1,
save_root=save_root,
exp_name=args.exp_name,
save_jit='script',
schedulers={"lr": lr_sched},
valid_metrics=valid_metrics,
out_channels=out_channels,
)
# Archiving training script, src folder, env info
bk = Backup(script_path=__file__, save_path=trainer.save_path).archive_backup()
# Start training
trainer.run(max_steps)
valid_metrics = {}
criterion = HybridDiceLoss()
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=4,
num_workers=8,
save_root=save_root,
exp_name=args.exp_name,
example_input=example_input,
enable_save_trace=enable_save_trace,
schedulers=schedulers,
valid_metrics=valid_metrics,
enable_videos=False, # Uncomment to get rid of videos in tensorboard
offset=train_dataset.offset,
apply_softmax_for_prediction=True,
num_classes=train_dataset.num_classes,
ipython_shell=False,
)
# Archiving training script, src folder, env info
Backup(script_path=__file__, save_path=trainer.save_path).archive_backup()
# Start training
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=1,
num_workers=1,
save_root=save_root,
exp_name=args.exp_name,
example_input=example_input,
enable_save_trace=enable_save_trace,
schedulers=
schedulers, #{"lr": optim.lr_scheduler.StepLR(optimizer, 1000, 0.995)},
valid_metrics=valid_metrics,
#preview_batch=preview_batch,
#preview_interval=5,
enable_videos=False, # Uncomment to get rid of videos in tensorboard
offset=train_dataset.offset,
apply_softmax_for_prediction=True,
num_classes=train_dataset.num_classes,
ipython_shell=False,
# TODO: Tune these:
#preview_tile_shape=(48, 96, 96),
#preview_overlap_shape=(48, 96, 96),
#sample_plotting_handler = handlers._tb_log_sample_images_Synapse,
#mixed_precision=True, # Enable to use Apex for mixed precision training
)
weight_decay=0.5e-4,
lr=lr,
amsgrad=True)
lr_sched = optim.lr_scheduler.StepLR(optimizer, lr_stepsize, lr_dec)
# criterion = LovaszLoss().to(device)
criterion = DiceLoss().to(device)
# Create and run trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=batch_size,
num_workers=2,
save_root=save_root,
exp_name=args.exp_name,
schedulers={"lr": lr_sched},
ipython_shell=False,
mixed_precision=False, # Enable to use Apex for mixed precision training
)
# Archiving training script, src folder, env info
bk = Backup(script_path=__file__,
save_path=trainer.save_path).archive_backup()
trainer.run(max_steps)
}
# Class weights for imbalanced dataset
class_weights = torch.tensor([0.2653, 0.7347])
# criterion = nn.CrossEntropyLoss(weight=class_weights)
criterion = DiceLoss()
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=batch_size,
num_workers=2,
save_root=save_root,
exp_name=args.exp_name,
schedulers={"lr": lr_sched},
valid_metrics=valid_metrics,
)
# Archiving training script, src folder, env info
Backup(script_path=__file__,save_path=trainer.save_path).archive_backup()
# Start training
trainer.train(max_steps=max_steps, max_runtime=max_runtime)
# How to re-calculate mean, std and class_weights for other datasets:
crossentropy = nn.CrossEntropyLoss() # weight=torch.tensor((0.2, 0.8)))
dice = DiceLoss() # weight=torch.tensor((0.2, 0.8)), apply_softmax=True)
criterion = CombinedLoss([crossentropy, dice],
weight=[0.5, 0.5],
device=device)
# Create trainer
trainer = Trainer(
model=model,
criterion=criterion,
optimizer=optimizer,
device=device,
train_dataset=train_dataset,
valid_dataset=valid_dataset,
batchsize=1,
num_workers=1,
save_root=save_root,
exp_name=args.exp_name,
schedulers={'lr': lr_sched},
valid_metrics=valid_metrics,
enable_videos=True,
offset=train_dataset.offset,
apply_softmax_for_prediction=True,
num_classes=train_dataset.num_classes,
)
# Archiving training script, src folder, env info
Backup(script_path=__file__, save_path=trainer.save_path).archive_backup()
# Start training
trainer.run(max_steps=max_steps, max_runtime=max_runtime)
