def get_optimizer(self, stage: str, model: nn.Module) -> _Optimizer:
optimizer_params = \
self.stages_config[stage].get("optimizer_params", {})
layerwise_params = \
optimizer_params.pop("layerwise_params", OrderedDict())
no_bias_weight_decay = \
optimizer_params.pop("no_bias_weight_decay", True)
# linear scaling rule from https://arxiv.org/pdf/1706.02677.pdf
lr_scaling_params = optimizer_params.pop("lr_linear_scaling", None)
if lr_scaling_params:
data_params = dict(self.stages_config[stage]["data_params"])
batch_size = data_params.get("batch_size")
per_gpu_scaling = data_params.get("per_gpu_scaling", False)
distributed_rank = self.distributed_params.get("rank", -1)
distributed = distributed_rank > -1
if per_gpu_scaling and not distributed:
num_gpus = max(1, torch.cuda.device_count())
batch_size *= num_gpus
base_lr = lr_scaling_params.get("lr")
base_batch_size = lr_scaling_params.get("base_batch_size", 256)
lr_scaling = batch_size / base_batch_size
optimizer_params["lr"] = base_lr * lr_scaling # scale default lr
else:
lr_scaling = 1.0
model_params = process_model_params(model, layerwise_params,
no_bias_weight_decay, lr_scaling)
optimizer = self._get_optimizer(model_params=model_params,
**optimizer_params)
return optimizer
def create_optimizer(args, model, filter_bias_and_bn=True):
opt_lower = args.opt.lower()
weight_decay = args.weight_decay
layerwise_params = {
"encoder*": dict(lr=args.lr * args.ev, weight_decay=args.weight_decay)
}
parameters = process_model_params(model, layerwise_params=layerwise_params)
opt_args = dict(lr=args.lr, weight_decay=weight_decay)
if hasattr(args, 'opt_eps') and args.opt_eps is not None:
opt_args['eps'] = args.opt_eps
if hasattr(args, 'opt_betas') and args.opt_betas is not None:
opt_args['betas'] = args.opt_betas
opt_split = opt_lower.split('_')
opt_lower = opt_split[-1]
if opt_lower == 'sgd' or opt_lower == 'nesterov':
opt_args.pop('eps', None)
optimizer = SGD(parameters,
momentum=args.momentum,
nesterov=True,
**opt_args)
elif opt_lower == 'momentum':
opt_args.pop('eps', None)
optimizer = SGD(parameters,
momentum=args.momentum,
nesterov=False,
**opt_args)
elif opt_lower == 'adam':
optimizer = Adam(parameters, **opt_args)
elif opt_lower == 'adamw':
optimizer = AdamW(parameters, **opt_args)
elif opt_lower == 'radam':
optimizer = RAdam(parameters, **opt_args)
elif opt_lower == 'radam':
optimizer = RAdam(parameters, **opt_args)
else:
assert False and "Invalid optimizer"
raise ValueError
if len(opt_split) > 1:
if opt_split[0] == 'lookahead':
_logger.info('Using lookahead')
optimizer = Lookahead(optimizer)
return optimizer
def smart_way():
args = parse_arguments()
SEED = args.seed
ROOT = Path(args.dataset)
img_paths, targets = retrieve_dataset(ROOT)
train_transforms = compose(
[resize_transforms(),
hard_transforms(),
post_transforms()])
valid_transforms = compose([pre_transforms(), post_transforms()])
loaders = get_loaders(
img_paths=img_paths,
targets=targets,
random_state=SEED,
batch_size=8,
train_transforms_fn=train_transforms,
valid_transforms_fn=valid_transforms,
)
logdir = './table_recognition/nn/regression/logs6/'
model = torch.load(
f'./table_recognition/nn/segmentation/logs/resnet18_PSPNet/save/best_model.pth'
)
model: RegressionFromSegmentation = RegressionFromSegmentation(model)
model.to(utils.get_device())
learning_rate = 0.001
encoder_learning_rate = 0.0005
layerwise_params = {
"encoder*": dict(lr=encoder_learning_rate, weight_decay=0.00003)
}
model_params = utils.process_model_params(
model, layerwise_params=layerwise_params)
base_optimizer = RAdam(model_params, lr=learning_rate, weight_decay=0.0003)
optimizer = Lookahead(base_optimizer)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
factor=0.25,
patience=2)
device = utils.get_device()
runner = CustomRunner2(device=device)
runner.train(model=model,
optimizer=optimizer,
scheduler=scheduler,
loaders=loaders,
logdir=logdir,
num_epochs=1000,
verbose=True,
load_best_on_end=True,
main_metric='loss')
best_model_save_dir = os.path.join(logdir, 'save')
os.makedirs(best_model_save_dir, exist_ok=True)
torch.save(model, os.path.join(
best_model_save_dir,
'best_model.pth')) # save best model (by valid loss)
batch = next(iter(loaders["valid"]))
try:
runner.trace(
model=model, batch=batch, logdir=logdir,
fp16=False) # optimized version (not all models can be traced)
except Exception:
pass
criterion = {
"dice": DiceLoss(),
"iou": IoULoss(),
"bce": nn.BCEWithLogitsLoss()
}
learning_rate = 0.001
encoder_learning_rate = 0.0005
# Since we use a pre-trained encoder, we will reduce the learning rate on it.
layerwise_params = {
"encoder*": dict(lr=encoder_learning_rate, weight_decay=0.00003)
}
# This function removes weight_decay for biases and applies our layerwise_params
model_params = utils.process_model_params(model,
layerwise_params=layerwise_params)
# Catalyst has new SOTA optimizers out of box
base_optimizer = RAdam(model_params, lr=learning_rate, weight_decay=0.0003)
optimizer = Lookahead(base_optimizer)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer,
factor=0.25,
patience=2)
num_epochs = 3
logdir = "./logs/segmentation"
device = utils.get_device()
print(f"device: {device}")
def main(cfg: DictConfig):
cwd = Path(get_original_cwd())
# overwrite config if continue training from checkpoint
resume_cfg = None
if "resume" in cfg:
cfg_path = cwd / cfg.resume / ".hydra/config.yaml"
print(f"Continue from: {cfg.resume}")
# Overwrite everything except device
# TODO config merger (perhaps continue training with the same optimizer but other lrs?)
resume_cfg = OmegaConf.load(cfg_path)
cfg.model = resume_cfg.model
if cfg.train.num_epochs == 0:
cfg.data.scale_factor = resume_cfg.data.scale_factor
OmegaConf.save(cfg, ".hydra/config.yaml")
print(OmegaConf.to_yaml(cfg))
device = set_device_id(cfg.device)
set_seed(cfg.seed, device=device)
# Augmentations
if cfg.data.aug == "auto":
transforms = albu.load(cwd / "autoalbument/autoconfig.json")
else:
transforms = D.get_training_augmentations()
if OmegaConf.is_missing(cfg.model, "convert_bottleneck"):
cfg.model.convert_bottleneck = (0, 0, 0)
# Model
print(f"Setup model {cfg.model.arch} {cfg.model.encoder_name} "
f"convert_bn={cfg.model.convert_bn} "
f"convert_bottleneck={cfg.model.convert_bottleneck} ")
model = get_segmentation_model(
arch=cfg.model.arch,
encoder_name=cfg.model.encoder_name,
encoder_weights=cfg.model.encoder_weights,
classes=1,
convert_bn=cfg.model.convert_bn,
convert_bottleneck=cfg.model.convert_bottleneck,
# decoder_attention_type="scse", # TODO to config
)
model = model.to(device)
model.train()
print(model)
# Optimization
# Reduce LR for pretrained encoder
layerwise_params = {
"encoder*":
dict(lr=cfg.optim.lr_encoder, weight_decay=cfg.optim.wd_encoder)
}
model_params = cutils.process_model_params(
model, layerwise_params=layerwise_params)
# Select optimizer
optimizer = get_optimizer(
name=cfg.optim.name,
model_params=model_params,
lr=cfg.optim.lr,
wd=cfg.optim.wd,
lookahead=cfg.optim.lookahead,
)
criterion = {
"dice": DiceLoss(),
# "dice": SoftDiceLoss(mode="binary", smooth=1e-7),
"iou": IoULoss(),
"bce": nn.BCEWithLogitsLoss(),
"lovasz": LovaszLossBinary(),
"focal_tversky": FocalTverskyLoss(eps=1e-7, alpha=0.7, gamma=0.75),
}
# Load states if resuming training
if "resume" in cfg:
checkpoint_path = (cwd / cfg.resume / cfg.train.logdir /
"checkpoints/best_full.pth")
if checkpoint_path.exists():
print(f"\nLoading checkpoint {str(checkpoint_path)}")
checkpoint = cutils.load_checkpoint(checkpoint_path)
cutils.unpack_checkpoint(
checkpoint=checkpoint,
model=model,
optimizer=optimizer
if resume_cfg.optim.name == cfg.optim.name else None,
criterion=criterion,
)
else:
raise ValueError("Nothing to resume, checkpoint missing")
# We could only want to validate resume, in this case skip training routine
best_th = 0.5
stats = None
if cfg.data.stats:
print(f"Use statistics from file: {cfg.data.stats}")
stats = cwd / cfg.data.stats
if cfg.train.num_epochs is not None:
callbacks = [
# Each criterion is calculated separately.
CriterionCallback(input_key="mask",
prefix="loss_dice",
criterion_key="dice"),
CriterionCallback(input_key="mask",
prefix="loss_iou",
criterion_key="iou"),
CriterionCallback(input_key="mask",
prefix="loss_bce",
criterion_key="bce"),
CriterionCallback(input_key="mask",
prefix="loss_lovasz",
criterion_key="lovasz"),
CriterionCallback(
input_key="mask",
prefix="loss_focal_tversky",
criterion_key="focal_tversky",
),
# And only then we aggregate everything into one loss.
MetricAggregationCallback(
prefix="loss",
mode="weighted_sum", # can be "sum", "weighted_sum" or "mean"
# because we want weighted sum, we need to add scale for each loss
metrics={
"loss_dice": cfg.loss.dice,
"loss_iou": cfg.loss.iou,
"loss_bce": cfg.loss.bce,
"loss_lovasz": cfg.loss.lovasz,
"loss_focal_tversky": cfg.loss.focal_tversky,
},
),
# metrics
DiceCallback(input_key="mask"),
IouCallback(input_key="mask"),
# gradient accumulation
OptimizerCallback(accumulation_steps=cfg.optim.accumulate),
# early stopping
SchedulerCallback(reduced_metric="loss_dice",
mode=cfg.scheduler.mode),
EarlyStoppingCallback(**cfg.scheduler.early_stopping,
minimize=False),
# TODO WandbLogger works poorly with multistage right now
WandbLogger(project=cfg.project, config=dict(cfg)),
# CheckpointCallback(save_n_best=cfg.checkpoint.save_n_best),
]
# Training
runner = SupervisedRunner(device=device,
input_key="image",
input_target_key="mask")
# TODO Scheduler does not work now, every stage restarts from base lr
scheduler_warm_restart = optim.lr_scheduler.MultiStepLR(
optimizer,
milestones=[1, 2],
gamma=10,
)
for i, (size, num_epochs) in enumerate(
zip(cfg.data.sizes, cfg.train.num_epochs)):
scale = size / 1024
print(
f"Training stage {i}, scale {scale}, size {size}, epochs {num_epochs}"
)
# Datasets
(
train_ds,
valid_ds,
train_images,
val_images,
) = D.get_train_valid_datasets_from_path(
# path=(cwd / cfg.data.path),
path=(cwd / f"data/hubmap-{size}x{size}/"),
train_ids=cfg.data.train_ids,
valid_ids=cfg.data.valid_ids,
seed=cfg.seed,
valid_split=cfg.data.valid_split,
mean=cfg.data.mean,
std=cfg.data.std,
transforms=transforms,
stats=stats,
)
train_bs = int(cfg.loader.train_bs / (scale**2))
valid_bs = int(cfg.loader.valid_bs / (scale**2))
print(
f"train: {len(train_ds)}; bs {train_bs}",
f"valid: {len(valid_ds)}, bs {valid_bs}",
)
# Data loaders
data_loaders = D.get_data_loaders(
train_ds=train_ds,
valid_ds=valid_ds,
train_bs=train_bs,
valid_bs=valid_bs,
num_workers=cfg.loader.num_workers,
)
# Select scheduler
scheduler = get_scheduler(
name=cfg.scheduler.type,
optimizer=optimizer,
num_epochs=num_epochs * (len(data_loaders["train"]) if
cfg.scheduler.mode == "batch" else 1),
eta_min=scheduler_warm_restart.get_last_lr()[0] /
cfg.scheduler.eta_min_factor,
plateau=cfg.scheduler.plateau,
)
runner.train(
model=model,
criterion=criterion,
optimizer=optimizer,
scheduler=scheduler,
callbacks=callbacks,
logdir=cfg.train.logdir,
loaders=data_loaders,
num_epochs=num_epochs,
verbose=True,
main_metric=cfg.train.main_metric,
load_best_on_end=True,
minimize_metric=False,
check=cfg.check,
fp16=dict(amp=cfg.amp),
)
# Set new initial LR for optimizer after restart
scheduler_warm_restart.step()
print(
f"New LR for warm restart {scheduler_warm_restart.get_last_lr()[0]}"
)
# Find optimal threshold for dice score
model.eval()
best_th, dices = find_dice_threshold(model, data_loaders["valid"])
print("Best dice threshold", best_th, np.max(dices[1]))
np.save(f"dices_{size}.npy", dices)
else:
print("Validation only")
# Datasets
size = cfg.data.sizes[-1]
train_ds, valid_ds = D.get_train_valid_datasets_from_path(
# path=(cwd / cfg.data.path),
path=(cwd / f"data/hubmap-{size}x{size}/"),
train_ids=cfg.data.train_ids,
valid_ids=cfg.data.valid_ids,
seed=cfg.seed,
valid_split=cfg.data.valid_split,
mean=cfg.data.mean,
std=cfg.data.std,
transforms=transforms,
stats=stats,
)
train_bs = int(cfg.loader.train_bs / (cfg.data.scale_factor**2))
valid_bs = int(cfg.loader.valid_bs / (cfg.data.scale_factor**2))
print(
f"train: {len(train_ds)}; bs {train_bs}",
f"valid: {len(valid_ds)}, bs {valid_bs}",
)
# Data loaders
data_loaders = D.get_data_loaders(
train_ds=train_ds,
valid_ds=valid_ds,
train_bs=train_bs,
valid_bs=valid_bs,
num_workers=cfg.loader.num_workers,
)
# Find optimal threshold for dice score
model.eval()
best_th, dices = find_dice_threshold(model, data_loaders["valid"])
print("Best dice threshold", best_th, np.max(dices[1]))
np.save(f"dices_val.npy", dices)
#
# # Load best checkpoint
# checkpoint_path = Path(cfg.train.logdir) / "checkpoints/best.pth"
# if checkpoint_path.exists():
# print(f"\nLoading checkpoint {str(checkpoint_path)}")
# state_dict = torch.load(checkpoint_path, map_location=torch.device("cpu"))[
# "model_state_dict"
# ]
# model.load_state_dict(state_dict)
# del state_dict
# model = model.to(device)
# Load config for updating with threshold and metric
# (otherwise loading do not work)
cfg = OmegaConf.load(".hydra/config.yaml")
cfg.threshold = float(best_th)
# Evaluate on full-size image if valid_ids is non-empty
df_train = pd.read_csv(cwd / "data/train.csv")
df_train = {
r["id"]: r["encoding"]
for r in df_train.to_dict(orient="record")
}
dices = []
unique_ids = sorted(
set(
str(p).split("/")[-1].split("_")[0]
for p in (cwd / cfg.data.path / "train").iterdir()))
size = cfg.data.sizes[-1]
scale = size / 1024
for image_id in cfg.data.valid_ids:
image_name = unique_ids[image_id]
print(f"\nValidate for {image_name}")
rle_pred, shape = inference_one(
image_path=(cwd / f"data/train/{image_name}.tiff"),
target_path=Path("."),
cfg=cfg,
model=model,
scale_factor=scale,
tile_size=cfg.data.tile_size,
tile_step=cfg.data.tile_step,
threshold=best_th,
save_raw=False,
tta_mode=None,
weight="pyramid",
device=device,
filter_crops="tissue",
stats=stats,
)
print("Predict", shape)
pred = rle_decode(rle_pred["predicted"], shape)
mask = rle_decode(df_train[image_name], shape)
assert pred.shape == mask.shape, f"pred {pred.shape}, mask {mask.shape}"
assert pred.shape == shape, f"pred {pred.shape}, expected {shape}"
dices.append(
dice(
torch.from_numpy(pred).type(torch.uint8),
torch.from_numpy(mask).type(torch.uint8),
threshold=None,
activation="none",
))
print("Full image dice:", np.mean(dices))
OmegaConf.save(cfg, ".hydra/config.yaml")
return
def train_segmentation_model(
model: torch.nn.Module,
logdir: str,
num_epochs: int,
loaders: Dict[str, DataLoader]
):
criterion = {
"dice": DiceLoss(),
"iou": IoULoss(),
"bce": nn.BCEWithLogitsLoss()
}
learning_rate = 0.001
encoder_learning_rate = 0.0005
layerwise_params = {"encoder*": dict(lr=encoder_learning_rate, weight_decay=0.00003)}
model_params = utils.process_model_params(model, layerwise_params=layerwise_params)
base_optimizer = RAdam(model_params, lr=learning_rate, weight_decay=0.0003)
optimizer = Lookahead(base_optimizer)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer, factor=0.25, patience=2)
device = utils.get_device()
runner = SupervisedRunner(device=device, input_key='image', input_target_key='mask')
callbacks = [
CriterionCallback(
input_key="mask",
prefix="loss_dice",
criterion_key="dice"
),
CriterionCallback(
input_key="mask",
prefix="loss_iou",
criterion_key="iou"
),
CriterionCallback(
input_key="mask",
prefix="loss_bce",
criterion_key="bce"
),
MetricAggregationCallback(
prefix="loss",
mode="weighted_sum",
metrics={"loss_dice": 1.0, "loss_iou": 1.0, "loss_bce": 0.8},
),
# metrics
DiceCallback(input_key='mask'),
IouCallback(input_key='mask'),
]
runner.train(
model=model,
criterion=criterion,
optimizer=optimizer,
scheduler=scheduler,
loaders=loaders,
callbacks=callbacks,
logdir=logdir,
num_epochs=num_epochs,
main_metric="iou",
minimize_metric=False,
verbose=True,
load_best_on_end=True,
)
best_model_save_dir = os.path.join(logdir, 'save')
os.makedirs(best_model_save_dir, True)
torch.save(model, os.path.join(best_model_save_dir, 'best_model.pth')) # save best model (by valid loss)
batch = next(iter(loaders["valid"]))
try:
runner.trace(model=model, batch=batch, logdir=logdir, fp16=False) # optimized version (not all models can be traced)
except Exception:
pass
:shape_copy[3]] = state_dict[key][
:shape_copy[0],
:shape_copy[1],
:shape_copy[2],
:shape_copy[3]]
else:
model_state[key] = state_dict[key]
model.load_state_dict(model_state, strict=False)
model_wrapper = ModelWrapper(model)
##############################
learning_rate = 0.001
# This function removes weight_decay for biases and applies our layerwise_params
model_params = utils.process_model_params(model_wrapper)
# Catalyst has new SOTA optimizers out of box
base_optimizer = RAdam(model_params, lr=learning_rate, weight_decay=0.0003)
optimizer = Lookahead(base_optimizer, k=5, alpha=0.5)
scheduler = optim.lr_scheduler.ReduceLROnPlateau(optimizer, factor=0.25, patience=2)
#########################
num_epochs = 50
logdir = "logs_pretrain/segmentation"
resume_path = f"{logdir}/checkpoints/last_full.pth"
if not os.path.isfile(resume_path):
resume_path = None
