def log(logname, dice, results="/results"):
dllogger = Logger(backends=[
JSONStreamBackend(Verbosity.VERBOSE, os.path.join(results, logname)),
StdOutBackend(Verbosity.VERBOSE, step_format=lambda step: ""),
])
metrics = {}
metrics.update({"Mean dice": round(dice.mean().item(), 2)})
metrics.update({f"L{j+1}": round(m.item(), 2) for j, m in enumerate(dice)})
dllogger.log(step=(), data=metrics)
dllogger.flush()
def log(logname, dice, epoch=None, dice_tta=None):
dllogger = Logger(backends=[
JSONStreamBackend(Verbosity.VERBOSE, os.path.join(
args.results, logname)),
StdOutBackend(Verbosity.VERBOSE, step_format=lambda step: ""),
])
metrics = {}
if epoch is not None:
metrics.update({"Epoch": epoch})
metrics.update({"Mean dice": round(dice.mean().item(), 2)})
if dice_tta is not None:
metrics.update({"Mean TTA dice": round(dice_tta.mean().item(), 2)})
metrics.update({f"L{j+1}": round(m.item(), 2) for j, m in enumerate(dice)})
if dice_tta is not None:
metrics.update({
f"TTA_L{j+1}": round(m.item(), 2)
for j, m in enumerate(dice_tta)
})
dllogger.log(step=(), data=metrics)
dllogger.flush()
def setup_logger(config):
log_path = config.get("log_path", os.getcwd())
if is_main_process():
backends = [
TensorBoardBackend(verbosity=dllogger.Verbosity.VERBOSE,
log_dir=log_path),
JSONStreamBackend(verbosity=dllogger.Verbosity.VERBOSE,
filename=os.path.join(log_path, "log.json")),
AggregatorBackend(verbosity=dllogger.Verbosity.VERBOSE,
agg_dict={"loss": AverageMeter}),
StdOutBackend(
verbosity=dllogger.Verbosity.DEFAULT,
step_format=empty_step_format,
metric_format=no_string_metric_format,
prefix_format=empty_prefix_format,
),
]
logger = Logger(backends=backends)
else:
logger = Logger(backends=[])
container_setup_info = get_framework_env_vars()
logger.log(step="PARAMETER",
data=container_setup_info,
verbosity=dllogger.Verbosity.DEFAULT)
logger.metadata("loss", {
"unit": "nat",
"GOAL": "MINIMIZE",
"STAGE": "TRAIN"
})
logger.metadata("val_loss", {
"unit": "nat",
"GOAL": "MINIMIZE",
"STAGE": "VAL"
})
return logger
class Model(pl.LightningModule):
def __init__(self, args):
super(Model, self).__init__()
self.save_hyperparameters()
self.args = args
self.f1_score = F1(args)
self.model = UNetLoc(args) if args.type == "pre" else get_dmg_unet(
args)
self.loss = Loss(args)
self.best_f1 = torch.tensor(0)
self.best_epoch = 0
self.tta_flips = [[2], [3], [2, 3]]
self.lr = args.lr
self.n_class = 2 if self.args.type == "pre" else 5
self.softmax = nn.Softmax(dim=1)
self.test_idx = 0
self.dllogger = Logger(backends=[
JSONStreamBackend(
Verbosity.VERBOSE,
os.path.join(args.results, f"{args.logname}.json")),
StdOutBackend(Verbosity.VERBOSE,
step_format=lambda step: f"Epoch: {step} "),
])
def forward(self, img):
pred = self.model(img)
if self.args.tta:
for flip_idx in self.tta_flips:
pred += self.flip(self.model(self.flip(img, flip_idx)),
flip_idx)
pred /= len(self.tta_flips) + 1
return pred
def training_step(self, batch, _):
img, lbl = batch["image"], batch["mask"]
pred = self.model(img)
loss = self.compute_loss(pred, lbl)
return loss
def validation_step(self, batch, _):
img, lbl = batch["image"], batch["mask"]
pred = self.forward(img)
loss = self.loss(pred, lbl)
self.f1_score.update(pred, lbl)
return {"val_loss": loss}
def test_step(self, batch, batch_idx):
img, lbl = batch["image"], batch["mask"]
pred = self.forward(img)
self.f1_score.update(pred, lbl)
self.save(pred, lbl)
def compute_loss(self, preds, label):
if self.args.deep_supervision:
loss = self.loss(preds[0], label)
for i, pred in enumerate(preds[1:]):
downsampled_label = torch.nn.functional.interpolate(
label.unsqueeze(1), pred.shape[2:])
loss += 0.5**(i + 1) * self.loss(pred,
downsampled_label.squeeze(1))
c_norm = 1 / (2 - 2**(-len(preds)))
return c_norm * loss
return self.loss(preds, label)
@staticmethod
def metric_mean(name, outputs):
return torch.stack([out[name] for out in outputs]).mean(dim=0)
@staticmethod
def update_damage_scores(metrics, dmgs_f1):
if dmgs_f1 is not None:
for i in range(4):
metrics.update({f"D{i+1}": round(dmgs_f1[i].item(), 3)})
def on_validation_epoch_start(self):
self.f1_score.reset()
def on_test_epoch_start(self):
self.f1_score.reset()
def validation_epoch_end(self, outputs):
loss = self.metric_mean("val_loss", outputs)
f1_score, dmgs_f1 = self.f1_score.compute()
self.f1_score.reset()
if f1_score >= self.best_f1:
self.best_f1 = f1_score
self.best_epoch = self.current_epoch
if int(os.getenv("LOCAL_RANK", "0")) == 0:
metrics = {
"f1": round(f1_score.item(), 3),
"val_loss": round(loss.item(), 3),
"top_f1": round(self.best_f1.item(), 3),
}
self.update_damage_scores(metrics, dmgs_f1)
self.dllogger.log(step=self.current_epoch, data=metrics)
self.dllogger.flush()
self.log("f1_score", f1_score.cpu())
self.log("val_loss", loss.cpu())
def test_epoch_end(self, _):
f1_score, dmgs_f1 = self.f1_score.compute()
self.f1_score.reset()
if int(os.getenv("LOCAL_RANK", "0")) == 0:
metrics = {"f1": round(f1_score.item(), 3)}
self.update_damage_scores(metrics, dmgs_f1)
self.dllogger.log(step=(), data=metrics)
self.dllogger.flush()
def save(self, preds, targets):
if self.args.type == "pre":
probs = torch.sigmoid(preds[:, 1])
else:
if self.args.loss_str == "coral":
probs = torch.sum(torch.sigmoid(preds) > 0.5, dim=1) + 1
elif self.args.loss_str == "mse":
probs = torch.round(F.relu(preds[:, 0], inplace=True)) + 1
else:
probs = self.softmax(preds)
probs = probs.cpu().detach().numpy()
targets = targets.cpu().detach().numpy().astype(np.uint8)
for prob, target in zip(probs, targets):
task = "localization" if self.args.type == "pre" else "damage"
fname = os.path.join(self.args.results, "probs",
f"test_{task}_{self.test_idx:05d}")
self.test_idx += 1
np.save(fname, prob)
Image.fromarray(target).save(
fname.replace("probs", "targets") + "_target.png")
@staticmethod
def flip(data, axis):
return torch.flip(data, dims=axis)
def configure_optimizers(self):
optimizer = {
"sgd":
FusedSGD(self.parameters(),
lr=self.lr,
momentum=self.args.momentum),
"adam":
FusedAdam(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"adamw":
torch.optim.AdamW(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"radam":
RAdam(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"adabelief":
AdaBelief(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"adabound":
AdaBound(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"adamp":
AdamP(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
"novograd":
FusedNovoGrad(self.parameters(),
lr=self.lr,
weight_decay=self.args.weight_decay),
}[self.args.optimizer.lower()]
if not self.args.use_scheduler:
return optimizer
scheduler = {
"scheduler":
NoamLR(
optimizer=optimizer,
warmup_epochs=self.args.warmup,
total_epochs=self.args.epochs,
steps_per_epoch=len(self.train_dataloader()) // self.args.gpus,
init_lr=self.args.init_lr,
max_lr=self.args.lr,
final_lr=self.args.final_lr,
),
"interval":
"step",
"frequency":
1,
}
return {"optimizer": optimizer, "lr_scheduler": scheduler}
@staticmethod
def add_model_specific_args(parent_parser):
parser = ArgumentParser(parents=[parent_parser], add_help=False)
arg = parser.add_argument
arg(
"--optimizer",
type=str,
default="adamw",
choices=[
"sgd", "adam", "adamw", "radam", "adabelief", "adabound",
"adamp", "novograd"
],
)
arg(
"--dmg_model",
type=str,
default="siamese",
choices=[
"siamese", "siameseEnc", "fused", "fusedEnc", "parallel",
"parallelEnc", "diff", "cat"
],
help="U-Net variant for damage assessment task",
)
arg(
"--encoder",
type=str,
default="resnest200",
choices=[
"resnest50", "resnest101", "resnest200", "resnest269",
"resnet50", "resnet101", "resnet152"
],
help="U-Net encoder",
)
arg(
"--loss_str",
type=str,
default="focal+dice",
help=
"Combination of: dice, focal, ce, ohem, mse, coral, e.g focal+dice creates the loss function as sum of focal and dice",
)
arg("--use_scheduler",
action="store_true",
help="Enable Noam learning rate scheduler")
arg("--warmup",
type=int,
default=1,
help="Warmup epochs for Noam learning rate scheduler")
arg("--init_lr",
type=float,
default=1e-4,
help="Initial learning rate for Noam scheduler")
arg("--final_lr",
type=float,
default=1e-4,
help="Final learning rate for Noam scheduler")
arg("--lr",
type=float,
default=3e-4,
help="Learning rate, or a target learning rate for Noam scheduler")
arg("--weight_decay",
type=float,
default=0,
help="Weight decay (L2 penalty)")
arg("--momentum",
type=float,
default=0.9,
help="Momentum for SGD optimizer")
arg(
"--dilation",
type=int,
choices=[1, 2, 4],
default=1,
help=
"Dilation rate for a encoder, e.g dilation=2 uses dilation instead of stride in the last encoder block",
)
arg("--tta", action="store_true", help="Enable test time augmentation")
arg("--ppm", action="store_true", help="Use pyramid pooling module")
arg("--aspp",
action="store_true",
help="Use atrous spatial pyramid pooling")
arg("--no_skip",
action="store_true",
help="Disable skip connections in UNet")
arg("--deep_supervision",
action="store_true",
help="Enable deep supervision")
arg("--attention",
action="store_true",
help="Enable attention module at the decoder")
arg("--autoaugment",
action="store_true",
help="Use imageNet autoaugment pipeline")
arg("--interpolate",
action="store_true",
help="Interpolate feature map from encoder without a decoder")
arg("--dec_interp",
action="store_true",
help=
"Use interpolation instead of transposed convolution in a decoder")
return parser
class NNUnet(pl.LightningModule):
def __init__(self, args):
super(NNUnet, self).__init__()
self.args = args
self.save_hyperparameters()
self.build_nnunet()
self.loss = Loss()
self.dice = Dice(self.n_class)
self.best_sum = 0
self.eval_dice = 0
self.best_sum_epoch = 0
self.best_dice = self.n_class * [0]
self.best_epoch = self.n_class * [0]
self.best_sum_dice = self.n_class * [0]
self.learning_rate = args.learning_rate
if self.args.exec_mode in ["train", "evaluate"]:
self.dllogger = Logger(backends=[
JSONStreamBackend(Verbosity.VERBOSE,
os.path.join(args.results, "logs.json")),
StdOutBackend(Verbosity.VERBOSE,
step_format=lambda step: f"Epoch: {step} "),
])
self.tta_flips = ([[2], [3], [2, 3]] if self.args.dim == 2 else
[[2], [3], [4], [2, 3], [2, 4], [3, 4], [2, 3, 4]])
def forward(self, img):
if self.args.benchmark:
return self.model(img)
return self.tta_inference(img) if self.args.tta else self.do_inference(
img)
def training_step(self, batch, batch_idx):
img, lbl = batch["image"], batch["label"]
pred = self.model(img)
loss = self.compute_loss(pred, lbl)
return loss
def validation_step(self, batch, batch_idx):
img, lbl = batch["image"], batch["label"]
pred = self.forward(img)
loss = self.loss(pred, lbl)
dice = self.dice(pred, lbl[:, 0])
return {"val_loss": loss, "val_dice": dice}
def test_step(self, batch, batch_idx):
if self.args.exec_mode == "evaluate":
return self.validation_step(batch, batch_idx)
img = batch["image"]
pred = self.forward(img)
if self.args.save_preds:
self.save_mask(pred, batch["fname"])
def build_unet(self, in_channels, n_class, kernels, strides):
return UNet(
in_channels=in_channels,
n_class=n_class,
kernels=kernels,
strides=strides,
normalization_layer=self.args.norm,
negative_slope=self.args.negative_slope,
deep_supervision=self.args.deep_supervision,
dimension=self.args.dim,
)
def get_unet_params(self):
config = get_config_file(self.args)
in_channels = config["in_channels"]
patch_size = config["patch_size"]
spacings = config["spacings"]
n_class = config["n_class"]
strides, kernels, sizes = [], [], patch_size[:]
while True:
spacing_ratio = [spacing / min(spacings) for spacing in spacings]
stride = [
2 if ratio <= 2 and size >= 8 else 1
for (ratio, size) in zip(spacing_ratio, sizes)
]
kernel = [3 if ratio <= 2 else 1 for ratio in spacing_ratio]
if all(s == 1 for s in stride):
break
sizes = [i / j for i, j in zip(sizes, stride)]
spacings = [i * j for i, j in zip(spacings, stride)]
kernels.append(kernel)
strides.append(stride)
if len(strides) == 5:
break
strides.insert(0, len(spacings) * [1])
kernels.append(len(spacings) * [3])
return in_channels, n_class, kernels, strides, patch_size
def build_nnunet(self):
in_channels, n_class, kernels, strides, self.patch_size = self.get_unet_params(
)
self.model = self.build_unet(in_channels, n_class, kernels, strides)
self.n_class = n_class - 1
if is_main_process():
print(f"Filters: {self.model.filters}")
print(f"Kernels: {kernels}")
print(f"Strides: {strides}")
def compute_loss(self, preds, label):
if self.args.deep_supervision:
loss = self.loss(preds[0], label)
for i, pred in enumerate(preds[1:]):
downsampled_label = nn.functional.interpolate(
label, pred.shape[2:])
loss += 0.5**(i + 1) * self.loss(pred, downsampled_label)
c_norm = 1 / (2 - 2**(-len(preds)))
return c_norm * loss
return self.loss(preds, label)
def do_inference(self, image):
if self.args.dim == 2:
if self.args.exec_mode == "predict" and not self.args.benchmark:
return self.inference2d_test(image)
return self.inference2d(image)
return self.sliding_window_inference(image)
def tta_inference(self, img):
pred = self.do_inference(img)
for flip_idx in self.tta_flips:
pred += flip(self.do_inference(flip(img, flip_idx)), flip_idx)
pred /= len(self.tta_flips) + 1
return pred
def inference2d(self, image):
batch_modulo = image.shape[2] % self.args.val_batch_size
if self.args.benchmark:
image = image[:, :, batch_modulo:]
elif batch_modulo != 0:
batch_pad = self.args.val_batch_size - batch_modulo
image = nn.ConstantPad3d((0, 0, 0, 0, batch_pad, 0), 0)(image)
image = torch.transpose(image.squeeze(0), 0, 1)
preds_shape = (image.shape[0], self.n_class + 1, *image.shape[2:])
preds = torch.zeros(preds_shape,
dtype=image.dtype,
device=image.device)
for start in range(0, image.shape[0] - self.args.val_batch_size + 1,
self.args.val_batch_size):
end = start + self.args.val_batch_size
pred = self.model(image[start:end])
preds[start:end] = pred.data
if batch_modulo != 0 and not self.args.benchmark:
preds = preds[batch_pad:]
return torch.transpose(preds, 0, 1).unsqueeze(0)
def inference2d_test(self, image):
preds_shape = (image.shape[0], self.n_class + 1, *image.shape[2:])
preds = torch.zeros(preds_shape,
dtype=image.dtype,
device=image.device)
for depth in range(image.shape[2]):
preds[:, :, depth] = self.sliding_window_inference(image[:, :,
depth])
return preds
def sliding_window_inference(self, image):
return sliding_window_inference(
inputs=image,
roi_size=self.patch_size,
sw_batch_size=self.args.val_batch_size,
predictor=self.model,
overlap=self.args.overlap,
mode=self.args.val_mode,
)
@staticmethod
def metric_mean(name, outputs):
return torch.stack([out[name] for out in outputs]).mean(dim=0)
def validation_epoch_end(self, outputs):
loss = self.metric_mean("val_loss", outputs)
dice = 100 * self.metric_mean("val_dice", outputs)
dice_sum = torch.sum(dice)
if dice_sum >= self.best_sum:
self.best_sum = dice_sum
self.best_sum_dice = dice[:]
self.best_sum_epoch = self.current_epoch
for i, dice_i in enumerate(dice):
if dice_i > self.best_dice[i]:
self.best_dice[i], self.best_epoch[
i] = dice_i, self.current_epoch
if is_main_process():
metrics = {}
metrics.update({"mean dice": round(torch.mean(dice).item(), 2)})
metrics.update(
{"TOP_mean": round(torch.mean(self.best_sum_dice).item(), 2)})
metrics.update(
{f"L{i+1}": round(m.item(), 2)
for i, m in enumerate(dice)})
metrics.update({
f"TOP_L{i+1}": round(m.item(), 2)
for i, m in enumerate(self.best_sum_dice)
})
metrics.update({"val_loss": round(loss.item(), 4)})
self.dllogger.log(step=self.current_epoch, data=metrics)
self.dllogger.flush()
self.log("val_loss", loss)
self.log("dice_sum", dice_sum)
def test_epoch_end(self, outputs):
if self.args.exec_mode == "evaluate":
self.eval_dice = 100 * self.metric_mean("val_dice", outputs)
def configure_optimizers(self):
optimizer = {
"sgd":
torch.optim.SGD(self.parameters(),
lr=self.learning_rate,
momentum=self.args.momentum),
"adam":
torch.optim.Adam(self.parameters(),
lr=self.learning_rate,
weight_decay=self.args.weight_decay),
"adamw":
torch.optim.AdamW(self.parameters(),
lr=self.learning_rate,
weight_decay=self.args.weight_decay),
"radam":
optim.RAdam(self.parameters(),
lr=self.learning_rate,
weight_decay=self.args.weight_decay),
"fused_adam":
apex.optimizers.FusedAdam(self.parameters(),
lr=self.learning_rate,
weight_decay=self.args.weight_decay),
}[self.args.optimizer.lower()]
scheduler = {
"none":
None,
"multistep":
torch.optim.lr_scheduler.MultiStepLR(optimizer,
self.args.steps,
gamma=self.args.factor),
"cosine":
torch.optim.lr_scheduler.CosineAnnealingLR(optimizer,
self.args.max_epochs),
"plateau":
torch.optim.lr_scheduler.ReduceLROnPlateau(
optimizer,
factor=self.args.factor,
patience=self.args.lr_patience),
}[self.args.scheduler.lower()]
opt_dict = {"optimizer": optimizer, "monitor": "val_loss"}
if scheduler is not None:
opt_dict.update({"lr_scheduler": scheduler})
return opt_dict
def save_mask(self, pred, fname):
fname = str(fname[0].cpu().detach().numpy(),
"utf-8").replace("_x", "_pred")
pred = nn.functional.softmax(torch.tensor(pred), dim=1)
pred = pred.squeeze().cpu().detach().numpy()
np.save(os.path.join(self.save_dir, fname), pred, allow_pickle=False)
if len(step) > 1:
s += "Iteration: {} ".format(step[1])
if len(step) > 2:
s += "Validation Iteration: {} ".format(step[2])
return s
l = Logger(
[
StdOutBackend(Verbosity.DEFAULT, step_format=format_step),
JSONStreamBackend(Verbosity.VERBOSE, "tmp.json"),
]
)
# You can log metrics in separate calls
l.log(step="PARAMETER", data={"HP1": 17}, verbosity=Verbosity.DEFAULT)
l.log(step="PARAMETER", data={"HP2": 23}, verbosity=Verbosity.DEFAULT)
# or together
l.log(step="PARAMETER", data={"HP3": 1, "HP4": 2}, verbosity=Verbosity.DEFAULT)
l.metadata("loss", {"unit": "nat", "GOAL": "MINIMIZE", "STAGE": "TRAIN"})
l.metadata("val.loss", {"unit": "nat", "GOAL": "MINIMIZE", "STAGE": "VAL"})
l.metadata(
"speed",
{"unit": "speeds/s", "format": ":.3f", "GOAL": "MAXIMIZE", "STAGE": "TRAIN"},
)
for epoch in range(0, 2):
for it in range(0, 10):
l.log(