def __init__(self, filePathTrain):
# Hyperparameters
self.batchSize = 1
self.numEpochs = 10
self.learningRate = 0.001
self.validPercent = 0.1
self.trainShuffle = True
self.testShuffle = False
self.momentum = 0.99
self.imageDim = 128
# Variables
self.imageDirectory = filePathTrain
self.labelDirectory = filePathTrain
self.numChannels = 3
self.numClasses = 1
# Device configuration
self.device = torch.device(
'cuda' if torch.cuda.is_available() else 'cpu')
# Load dataset
self.trainLoader = self.getTrainingLoader()
#self.testLoader = self.getTestLoader()
# Setup model
self.model = UNet(n_channels=self.numChannels,
n_classes=self.numClasses,
bilinear=True).to(self.device)
#self.optimizer = torch.optim.RMSprop(self.model.parameters(), lr=self.learningRate, weight_decay=self.weightDecay, momentum=self.momentum)
#self.optimizer = torch.optim.Adam(self.model.parameters(), lr=self.learningRate)
self.optimizer = torch.optim.SGD(self.model.parameters(),
lr=self.learningRate,
momentum=self.momentum)
#self.scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(self.optimizer, 'min' if self.numClasses > 1 else 'max', patience=2)
self.criterion = DiceLoss()
def main(args):
global run
run = Run.get_context()
print("Current directory:", os.getcwd())
print("Data directory:", args.images)
print("Training directory content:", os.listdir(args.images))
makedirs(args)
snapshotargs(args)
device = torch.device(
"cpu" if not torch.cuda.is_available() else args.device)
print("Using device:", device)
loader_train, loader_valid = data_loaders(args)
loaders = {"train": loader_train, "valid": loader_valid}
unet = UNet(in_channels=Dataset.in_channels,
out_channels=Dataset.out_channels)
unet = unet.to(device)
unet = torch.nn.DataParallel(unet)
dsc_loss = DiceLoss()
best_validation_dsc = 0.0
optimizer = optim.Adam(unet.parameters(), lr=args.lr)
logger = Logger(args.logs)
loss_train = []
loss_valid = []
step = 0
for epoch in tqdm(range(args.epochs), total=args.epochs):
for phase in ["train", "valid"]:
start = time.time()
if phase == "train":
unet.train()
else:
unet.eval()
validation_pred = []
validation_true = []
for i, data in enumerate(loaders[phase]):
if phase == "train":
step += 1
x, y_true = data
x, y_true = x.to(device), y_true.to(device)
optimizer.zero_grad()
with torch.set_grad_enabled(phase == "train"):
y_pred = unet(x)
loss = dsc_loss(y_pred, y_true)
if phase == "valid":
loss_valid.append(loss.item())
y_pred_np = y_pred.detach().cpu().numpy()
validation_pred.extend(
[y_pred_np[s] for s in range(y_pred_np.shape[0])])
y_true_np = y_true.detach().cpu().numpy()
validation_true.extend(
[y_true_np[s] for s in range(y_true_np.shape[0])])
if (epoch % args.vis_freq
== 0) or (epoch == args.epochs - 1):
if i * args.batch_size < args.vis_images:
tag = "image/{}".format(i)
num_images = args.vis_images - i * args.batch_size
logger.image_list_summary(
tag,
log_images(x, y_true, y_pred)[:num_images],
step,
)
if phase == "train":
loss_train.append(loss.item())
loss.backward()
optimizer.step()
if phase == "train" and (step + 1) % 10 == 0:
log_loss_summary(logger, loss_train, step)
loss_train = []
if phase == "valid":
log_loss_summary(logger, loss_valid, step, prefix="val_")
mean_dsc = np.mean(
dsc_per_volume(
validation_pred,
validation_true,
loader_valid.dataset.patient_slice_index,
))
logger.scalar_summary("val_dsc", mean_dsc, step)
if mean_dsc > best_validation_dsc:
best_validation_dsc = mean_dsc
#torch.save(unet.state_dict(), os.path.join(args.weights, "unet_epoch_" + str(epoch) + ".pt"))
torch.save(unet.state_dict(),
os.path.join(args.weights, "unet.pt"))
loss_valid = []
run.log("time_" + phase, time.time() - start)
print("Best validation mean DSC: {:4f}".format(best_validation_dsc))
run.log("best_validation_mean_dsv", best_validation_dsc)
def __init__(self, configs):
self.batch_size = configs.get("batch_size", "16")
self.epochs = configs.get("epochs", "100")
self.lr = configs.get("lr", "0.0001")
device_args = configs.get("device", "cuda")
self.device = torch.device(
"cpu" if not torch.cuda.is_available() else device_args)
self.workers = configs.get("workers", "4")
self.vis_images = configs.get("vis_images", "200")
self.vis_freq = configs.get("vis_freq", "10")
self.weights = configs.get("weights", "./weights")
if not os.path.exists(self.weights):
os.mkdir(self.weights)
self.logs = configs.get("logs", "./logs")
if not os.path.exists(self.weights):
os.mkdir(self.weights)
self.images_path = configs.get("images_path", "./data")
self.is_resize = config.get("is_resize", False)
self.image_short_side = config.get("image_short_side", 256)
self.is_padding = config.get("is_padding", False)
is_multi_gpu = config.get("DateParallel", False)
pre_train = config.get("pre_train", False)
model_path = config.get("model_path", './weights/unet_idcard_adam.pth')
# self.image_size = configs.get("image_size", "256")
# self.aug_scale = configs.get("aug_scale", "0.05")
# self.aug_angle = configs.get("aug_angle", "15")
self.step = 0
self.dsc_loss = DiceLoss()
self.model = UNet(in_channels=Dataset.in_channels,
out_channels=Dataset.out_channels)
if pre_train:
self.model.load_state_dict(torch.load(model_path,
map_location=self.device),
strict=False)
if is_multi_gpu:
self.model = nn.DataParallel(self.model)
self.model.to(self.device)
self.best_validation_dsc = 0.0
self.loader_train, self.loader_valid = self.data_loaders()
self.params = [p for p in self.model.parameters() if p.requires_grad]
self.optimizer = optim.Adam(self.params,
lr=self.lr,
weight_decay=0.0005)
# self.optimizer = torch.optim.SGD(self.params, lr=self.lr, momentum=0.9, weight_decay=0.0005)
self.scheduler = lr_scheduler.LR_Scheduler_Head(
'poly', self.lr, self.epochs, len(self.loader_train))
weight = Variable(weight.cuda())
else:
weight = args.weight # weight is None
print("weight: {}".format(weight))
# criterion
if args.criterion == 'nll':
criterion = nn.NLLLoss(weight=weight)
elif args.criterion == 'ce':
criterion = nn.CrossEntropyLoss(weight=weight)
elif args.criterion == 'dice':
criterion = DiceLoss(weight=weight,
ignore_index=None,
weight_type=args.weight_type,
cal_zerogt=args.cal_zerogt)
elif args.criterion == 'gdl_inv_square':
criterion = GeneralizedDiceLoss(weight=weight,
ignore_index=None,
weight_type='inv_square',
alpha=args.alpha)
elif args.criterion == 'gdl_others_one_gt':
criterion = GeneralizedDiceLoss(weight=weight,
ignore_index=None,
weight_type='others_one_gt',
alpha=args.alpha)
elif args.criterion == 'gdl_others_one_pred':
criterion = GeneralizedDiceLoss(weight=weight,
ignore_index=None,
def train(args, model, optimizer, dataloader_train, dataloader_val):
# E' l'oggetto che ci stampa a schermo ciò chee acca
writer = SummaryWriter(
comment=''.format(args.optimizer, args.context_path))
# settiamo la loss
if args.loss == 'dice':
# classe definita da loro nel file loss.py
loss_func = DiceLoss()
elif args.loss == 'crossentropy':
loss_func = torch.nn.CrossEntropyLoss(ignore_index=255)
# inizializziamo i contatori
max_miou = 0
step = 0
# iniziamo il training
for epoch in range(args.num_epochs):
# inizializziamo il learning rate
lr = poly_lr_scheduler(optimizer,
args.learning_rate,
iter=epoch,
max_iter=args.num_epochs)
# iniziamo il train
model.train()
# cosa grafica sequenziale
tq = tqdm(total=len(dataloader_train) * args.batch_size)
tq.set_description('epoch %d, lr %f' % (epoch, lr))
# Crediamo che sia la lista delle loss di ogni batch:
loss_record = []
# per ogni immagine o per ogni batch??? Ipotizziamo sia su ogni singolo mini-batch
for i, (data, label) in enumerate(dataloader_train):
if torch.cuda.is_available() and args.use_gpu:
data = data.cuda()
label = label.cuda().long()
# Prendiamo:
# - risultato finale dopo FFM
# - risultato del 16xdown del contextPath, dopo ARM, modificati (?)
# - risultato del 32xdown del contextPath, dopo ARM, modificati (?)
output, output_sup1, output_sup2 = model(data)
# Calcoliammo la loss
# Principal loss function (l_p in the paper):
loss1 = loss_func(output, label)
# Auxilary loss functions (l_i, for i=2, 3 in the paper):
loss2 = loss_func(output_sup1, label)
loss3 = loss_func(output_sup2, label)
# alfa = 1, compute equation 2:
loss = loss1 + loss2 + loss3
# codice grafica
tq.update(args.batch_size)
tq.set_postfix(loss='%.6f' % loss)
'''
zero_grad clears old gradients from the last step (otherwise you’d just accumulate the gradients from all loss.backward() calls).
loss.backward() computes the derivative of the loss w.r.t. the parameters (or anything requiring gradients) using backpropagation.
opt.step() causes the optimizer to take a step based on the gradients of the parameters.
'''
optimizer.zero_grad()
loss.backward()
optimizer.step()
# incrementiamo il contatore
step += 1
# aggiungiamo i valori per il grafico
writer.add_scalar('loss_step', loss, step)
loss_record.append(loss.item())
tq.close()
loss_train_mean = np.mean(loss_record)
writer.add_scalar('epoch/loss_epoch_train', float(loss_train_mean),
epoch)
print('loss for train : %f' % (loss_train_mean))
# salva il modello fin ora trainato
if epoch % args.checkpoint_step == 0 and epoch != 0:
import os
if not os.path.isdir(args.save_model_path):
os.mkdir(args.save_model_path)
torch.save(model.state_dict(),
os.path.join(args.save_model_path, 'model.pth'))
# compute validation every 10 epochs
if epoch % args.validation_step == 0 and epoch != 0:
# chaiam la funzione val che da in output le metriche
precision, miou = val(args, model, dataloader_val)
# salva miou max e salva il relativo miglior modello
if miou > max_miou:
max_miou = miou
import os
os.makedirs(args.save_model_path, exist_ok=True)
torch.save(
model.state_dict(),
os.path.join(args.save_model_path, 'best_dice_loss.pth'))
writer.add_scalar('epoch/precision_val', precision, epoch)
writer.add_scalar('epoch/miou val', miou, epoch)
# proviamo a terminare il writer per vedere se stampa qualcosa
writer.close()
def main(args):
makedirs(args)
snapshotargs(args)
device = torch.device("cpu" if not torch.cuda.is_available() else args.device)
loader_train, loader_valid = data_loaders(args)
loaders = {"train": loader_train, "valid": loader_valid}
unet = UNet(in_channels=Dataset.in_channels, out_channels=Dataset.out_channels)
unet.to(device)
dsc_loss = DiceLoss()
best_validation_dsc = 0.0
optimizer = optim.Adam(unet.parameters(), lr=args.lr)
print("Learning rate = ", args.lr) #AP knowing lr
print("Batch-size = ", args.batch_size) # AP knowing batch-size
print("Number of visualization images to save in log file = ", args.vis_images) # AP knowing batch-size
logger = Logger(args.logs)
loss_train = []
loss_valid = []
step = 0
for epoch in tqdm(range(args.epochs), total=args.epochs):
for phase in ["train", "valid"]:
if phase == "train":
unet.train()
else:
unet.eval()
validation_pred = []
validation_true = []
for i, data in enumerate(loaders[phase]):
if phase == "train":
step += 1
x, y_true = data
x, y_true = x.to(device), y_true.to(device)
optimizer.zero_grad()
with torch.set_grad_enabled(phase == "train"):
y_pred = unet(x)
loss = dsc_loss(y_pred, y_true)
if phase == "valid":
loss_valid.append(loss.item())
y_pred_np = y_pred.detach().cpu().numpy()
validation_pred.extend(
[y_pred_np[s] for s in range(y_pred_np.shape[0])]
)
y_true_np = y_true.detach().cpu().numpy()
validation_true.extend(
[y_true_np[s] for s in range(y_true_np.shape[0])]
)
if (epoch % args.vis_freq == 0) or (epoch == args.epochs - 1):
if i * args.batch_size < args.vis_images:
tag = "image/{}".format(i)
num_images = args.vis_images - i * args.batch_size
logger.image_list_summary(
tag,
log_images(x, y_true, y_pred)[:num_images],
step,
)
if phase == "train":
loss_train.append(loss.item())
loss.backward()
optimizer.step()
if phase == "train" and (step + 1) % 10 == 0:
log_loss_summary(logger, loss_train, step)
loss_train = []
if phase == "valid":
log_loss_summary(logger, loss_valid, step, prefix="val_")
mean_dsc = np.mean(
dsc_per_volume(
validation_pred,
validation_true,
loader_valid.dataset.patient_slice_index,
)
)
logger.scalar_summary("val_dsc", mean_dsc, step)
if mean_dsc > best_validation_dsc:
best_validation_dsc = mean_dsc
torch.save(unet.state_dict(), os.path.join(args.weights, "unet.pt"))
loss_valid = []
print("Best validation mean DSC: {:4f}".format(best_validation_dsc))
def main(args):
makedirs(args)
snapshotargs(args)
device = torch.device("cpu" if not torch.cuda.is_available() else args.device)
loader_train, loader_valid = data_loaders(args)
loaders = {"train": loader_train, "valid": loader_valid}
unet = UNet(in_channels=Dataset.in_channels, out_channels=Dataset.out_channels)
# unet.apply(weights_init)
unet.to(device)
dsc_loss = DiceLoss()
best_validation_dsc = 0.0
optimizer = optim.Adam(unet.parameters(), lr=args.lr, weight_decay=1e-3)
# optimizer = optim.Adam(unet.parameters(), lr=args.lr)
logger = Logger(args.logs)
loss_train = []
loss_valid = []
log_train = []
log_valid = []
validation_pred = []
validation_true = []
step = 0
for epoch in tqdm(range(args.epochs), total=args.epochs):
for phase in ["train", "valid"]:
if phase == "train":
unet.train()
else:
unet.eval()
for i, data in enumerate(loaders[phase]):
if phase == "train":
step += 1
x, y_true = data
x, y_true = x.to(device), y_true.to(device)
optimizer.zero_grad()
with torch.set_grad_enabled(phase == "train"):
y_pred = unet(x)
loss = dsc_loss(y_pred, y_true)
print(loss)
# if phase == "valid":
if phase == "train":
loss_valid.append(loss.item())
y_pred_np = y_pred.detach().cpu().numpy()
validation_pred.extend(
[y_pred_np[s] for s in range(y_pred_np.shape[0])]
)
y_true_np = y_true.detach().cpu().numpy()
validation_true.extend(
[y_true_np[s] for s in range(y_true_np.shape[0])]
)
if phase == "train":
loss_train.append(loss.item())
loss.backward()
optimizer.step()
if phase == "valid":
dsc, label_dsc = dsc_per_volume(
validation_pred,
validation_true,
# loader_valid.dataset.patient_slice_index,
loader_train.dataset.patient_slice_index,
)
mean_dsc = np.mean(dsc)
print(mean_dsc)
print(np.array(label_dsc).mean(axis=0))
if mean_dsc > best_validation_dsc:
best_validation_dsc = mean_dsc
best_label_dsc = label_dsc
torch.save(unet.state_dict(), os.path.join(args.weights, "unet.pt"))
opt = epoch
log_valid.append(np.mean(loss_valid))
loss_valid = []
validation_pred = []
validation_true = []
log_train.append(np.mean(loss_train))
loss_train=[]
plt.plot(log_valid)
plt.plot(log_train)
plt.savefig("Test")
print("Best validation mean DSC: {:4f}".format(best_validation_dsc))
print(opt)
from torchvision.transforms import transforms as T
import argparse # argparse模块的作用是用于解析命令行参数，例如python parseTest.py input.txt --port=8080
from Newunet import Insensee_3Dunet
from torch import optim
import MRI2IMG_dataset
from torch.utils.data import DataLoader
# from advanced_model import CleanU_Net
from networks.unet_model import UNet
from ResNetUNet import ResNetUNet
from HSC82 import CleanU_Net
from transform import imageaug
from loss import DiceLoss
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
learning_rate = 1e-3
DICE_loss = DiceLoss()
def train_model(model, criterion, optimizer, dataload, num_epochs=200):
# model.load_state_dict(torch.load('./3dunet_model_save/weights_199.pth'))
for epoch in range(num_epochs):
save_loss = []
print('Epoch {}/{}'.format(epoch, num_epochs - 1))
print('learning_rate:',
optimizer.state_dict()['param_groups'][0]['lr'])
print('-' * 10)
dataset_size = len(dataload.dataset)
epoch_loss = 0
step = 0
for img, label, _, _ in dataload:
img_train_tensor = img
def main(args):
presentParameters(vars(args))
results_path = args.results
if not os.path.exists(results_path):
os.makedirs(results_path)
save_args(args, modelpath=results_path)
device = torch.device(args.device)
if args.model == 'u-net':
from unet.model import UNet
model = UNet(in_channels=3, n_classes=1).to(device)
elif args.model == 'fcd-net':
from tiramisu.model import FCDenseNet
# select model archictecture so it can be trained in 16gb ram GPU
model = FCDenseNet(in_channels=3,
n_classes=1,
n_filter_first_conv=48,
n_pool=4,
growth_rate=8,
n_layers_per_block=3,
dropout_p=0.2).to(device)
else:
print(
'Parsed model argument "{}" invalid. Possible choices are "u-net" or "fcd-net"'
.format(args.model))
# Init weights for model
model = model.apply(weights_init)
transforms = my_transforms(scale=args.aug_scale,
angle=args.aug_angle,
flip_prob=args.aug_flip)
print('Trainable parameters for model {}: {}'.format(
args.model, get_number_params(model)))
# create pytorch dataset
dataset = DataSetfromNumpy(
image_npy_path='data/train_img_{}x{}.npy'.format(
args.image_size, args.image_size),
mask_npy_path='data/train_mask_{}x{}.npy'.format(
args.image_size, args.image_size),
transform=transforms)
# create training and validation set
n_val = int(len(dataset) * args.val_percent)
n_train = len(dataset) - n_val
train, val = random_split(dataset, [n_train, n_val])
## hacky solution: only add CustomToTensor transform in validation
from utils.transform import CustomToTensor
val.dataset.transform = CustomToTensor()
print('Training the model with n_train: {} and n_val: {} images/masks'.
format(n_train, n_val))
train_loader = DataLoader(train,
batch_size=args.batch_size,
shuffle=True,
num_workers=args.workers)
val_loader = DataLoader(val,
batch_size=args.batch_size,
shuffle=False,
num_workers=args.workers)
dc_loss = DiceLoss()
writer = SummaryWriter(log_dir=os.path.join(args.logs, args.model))
optimizer = Adam(params=model.parameters(), lr=args.lr)
# Learning rate scheduler
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,
mode='min',
factor=0.9,
patience=5)
loss_train = []
loss_valid = []
# training loop:
global_step = 0
for epoch in range(args.epochs):
eval_count = 0
epoch_start_time = datetime.datetime.now().replace(microsecond=0)
# set model into train mode
model = model.train()
train_epoch_loss = 0
valid_epoch_loss = 0
# tqdm progress bar
with tqdm(total=n_train,
desc=f'Epoch {epoch + 1}/{args.epochs}',
unit='img') as pbar:
for batch in train_loader:
# retrieve images and masks and send to pytorch device
imgs = batch['image'].to(device=device, dtype=torch.float32)
true_masks = batch['mask'].to(
device=device,
dtype=torch.float32
if model.n_classes == 1 else torch.long)
# compute prediction masks
predicted_masks = model(imgs)
if model.n_classes == 1:
predicted_masks = torch.sigmoid(predicted_masks)
elif model.n_classes > 1:
predicted_masks = F.softmax(predicted_masks, dim=1)
# compute dice loss
loss = dc_loss(y_true=true_masks, y_pred=predicted_masks)
train_epoch_loss += loss.item()
# update model network weights
optimizer.zero_grad()
loss.backward()
optimizer.step()
# logging
writer.add_scalar('Loss/train', loss.item(), global_step)
# update progress bar
pbar.update(imgs.shape[0])
# Do evaluation every 25 training steps
if global_step % 25 == 0:
eval_count += 1
val_loss = np.mean(
eval_net(model, val_loader, device, dc_loss))
valid_epoch_loss += val_loss
writer.add_scalar('Loss/validation', val_loss, global_step)
if model.n_classes > 1:
pbar.set_postfix(
**{
'Training CE loss (batch)': loss.item(),
'Validation CE (val set)': val_loss
})
else:
pbar.set_postfix(
**{
'Training dice loss (batch)': loss.item(),
'Validation dice loss (val set)': val_loss
})
global_step += 1
# save images as well as true + predicted masks into writer
if global_step % args.vis_images == 0:
writer.add_images('images', imgs, global_step)
if model.n_classes == 1:
writer.add_images('masks/true', true_masks,
global_step)
writer.add_images('masks/pred', predicted_masks > 0.5,
global_step)
# Get estimation of training and validation loss for entire epoch
valid_epoch_loss /= eval_count
train_epoch_loss /= len(train_loader)
# Apply learning rate scheduler per epoch
scheduler.step(valid_epoch_loss)
# Only save the model in case the validation metric is best. For the first epoch, directly save
if epoch > 0:
best_model_bool = [valid_epoch_loss < l for l in loss_valid]
best_model_bool = np.all(best_model_bool)
else:
best_model_bool = True
# append
loss_train.append(train_epoch_loss)
loss_valid.append(valid_epoch_loss)
if best_model_bool:
print(
'\nSaving model and optimizers at epoch {} with best validation loss of {}'
.format(epoch, valid_epoch_loss))
torch.save(obj={
'model_state_dict': model.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'lr_scheduler': scheduler.state_dict(),
},
f=results_path +
'/model_epoch-{}_val_loss-{}.pth'.format(
epoch, np.round(valid_epoch_loss, 4)))
epoch_time_difference = datetime.datetime.now().replace(
microsecond=0) - epoch_start_time
print('Epoch: {:3d} time execution: {}'.format(
epoch, epoch_time_difference))
print(
'Finished training the segmentation model.\nAll results can be found at: {}'
.format(results_path))
# save scalars dictionary as json file
scalars = {'loss_train': loss_train, 'loss_valid': loss_valid}
with open('{}/all_scalars.json'.format(results_path), 'w') as fp:
json.dump(scalars, fp)
print('Logging file for tensorboard is stored at {}'.format(args.logs))
writer.close()
def forward(
self,
input_ids=None,
attention_mask=None,
token_type_ids=None,
position_ids=None,
head_mask=None,
inputs_embeds=None,
labels=None,
):
r"""
labels (:obj:`torch.LongTensor` of shape :obj:`(batch_size, sequence_length)`, `optional`, defaults to :obj:`None`):
Labels for computing the token classification loss.
Indices should be in ``[0, ..., config.num_labels - 1]``.
Returns:
:obj:`tuple(torch.FloatTensor)` comprising various elements depending on the configuration (:class:`~transformers.BertConfig`) and inputs:
loss (:obj:`torch.FloatTensor` of shape :obj:`(1,)`, `optional`, returned when ``labels`` is provided) :
Classification loss.
scores (:obj:`torch.FloatTensor` of shape :obj:`(batch_size, sequence_length, config.num_labels)`)
Classification scores (before SoftMax).
hidden_states (:obj:`tuple(torch.FloatTensor)`, `optional`, returned when ``config.output_hidden_states=True``):
Tuple of :obj:`torch.FloatTensor` (one for the output of the embeddings + one for the output of each layer)
of shape :obj:`(batch_size, sequence_length, hidden_size)`.
Hidden-states of the model at the output of each layer plus the initial embedding outputs.
attentions (:obj:`tuple(torch.FloatTensor)`, `optional`, returned when ``config.output_attentions=True``):
Tuple of :obj:`torch.FloatTensor` (one for each layer) of shape
:obj:`(batch_size, num_heads, sequence_length, sequence_length)`.
Attentions weights after the attention softmax, used to compute the weighted average in the self-attention
heads.
Examples::
from transformers import BertTokenizer, BertForTokenClassification
import torch
tokenizer = BertTokenizer.from_pretrained('bert-base-uncased')
model = BertForTokenClassification.from_pretrained('bert-base-uncased')
input_ids = torch.tensor(tokenizer.encode("Hello, my dog is cute", add_special_tokens=True)).unsqueeze(0) # Batch size 1
labels = torch.tensor([1] * input_ids.size(1)).unsqueeze(0) # Batch size 1
outputs = model(input_ids, labels=labels)
loss, scores = outputs[:2]
"""
outputs = self.bert(
input_ids,
attention_mask=attention_mask,
token_type_ids=token_type_ids,
position_ids=position_ids,
head_mask=head_mask,
inputs_embeds=inputs_embeds,
)
sequence_output = outputs[0]
sequence_output = self.dropout(sequence_output)
logits = self.classifier(sequence_output)
outputs = (logits, ) + outputs[
2:] # add hidden states and attention if they are here
if labels is not None:
# loss_fct = CrossEntropyLoss()
# loss_fct = FocalLoss()
loss_fct = DiceLoss()
# loss_fct = DSCLoss()
# loss_fct= LabelSmoothingCrossEntropy()
# Only keep active parts of the loss
if attention_mask is not None:
active_loss = attention_mask.view(-1) == 1
active_logits = logits.view(-1, self.num_labels)
active_labels = torch.where(
active_loss, labels.view(-1),
torch.tensor(loss_fct.ignore_index).type_as(labels))
# print(active_loss, active_loss.shape, \
# active_logits,active_logits.shape,\
# active_labels,active_labels.shape,\
# labels, labels.shape)
#2048 2048*435 2048 8*256
loss = loss_fct(active_logits, active_labels)
else:
loss = loss_fct(logits.view(-1, self.num_labels),
labels.view(-1))
outputs = (loss, ) + outputs
return outputs # (loss), scores, (hidden_states), (attentions)
def train(args, model_G, model_D, optimizer_G, optimizer_D, CamVid_dataloader_train, CamVid_dataloader_val, IDDA_dataloader, curr_epoch, max_miou):
# we need the camvid data loader an modify the dataloadrer val we don't need the data loader train because we use Idda dataloader
writer = SummaryWriter(comment=''.format(args.optimizer_G,args.optimizer_D, args.context_path))#not important for now
scaler = amp.GradScaler()
if args.loss_G == 'dice':
loss_func_G = DiceLoss()
elif args.loss_G == 'crossentropy':
loss_func_G = torch.nn.CrossEntropyLoss()
loss_func_adv = torch.nn.BCEWithLogitsLoss()
loss_func_D = torch.nn.BCEWithLogitsLoss()
step = 0
for epoch in range(curr_epoch + 1, args.num_epochs + 1): # added +1 shift to finish with an eval
lr_G = poly_lr_scheduler(optimizer_G, args.learning_rate_G, iter=epoch, max_iter=args.num_epochs)
lr_D = poly_lr_scheduler(optimizer_D, args.learning_rate_D, iter=epoch, max_iter=args.num_epochs)
model_G.train()
model_D.train()
tq = tqdm(total=len(CamVid_dataloader_train) * args.batch_size)
tq.set_description('epoch %d, lr_G %f , lr_D %f' % (epoch, lr_G ,lr_D ))
# set the ground truth for the discriminator
source_label = 0
target_label = 1
# iniate lists to track the losses
loss_G_record = []
loss_adv_record = [] # we added a new list to track the advarsirial loss of generator
loss_D_record = [] # we added a new list to track the discriminator loss
source_train_loader = enumerate(IDDA_dataloader)
s_size = len(IDDA_dataloader)
target_loader = enumerate(CamVid_dataloader_train)
t_size = len(CamVid_dataloader_train)
for i in range(t_size):
optimizer_G.zero_grad()
optimizer_D.zero_grad()
#train G:
for param in model_D.parameters():
param.requires_grad = False
#train with source:
_, batch = next(source_train_loader)
data, label = batch
#label = label.type(torch.LongTensor)
data = data.cuda()
label = label.long().cuda()
with amp.autocast():
output_s, output_sup1, output_sup2 = model_G(data)
loss1 = loss_func_G(output_s, label)
loss2 = loss_func_G(output_sup1, label)
loss3 = loss_func_G(output_sup2, label)
loss_G = loss1 + loss2 + loss3
scaler.scale(loss_G).backward()
#train with target:
#try:
_, batch = next(target_loader)
#except:
# target_loader = enumerate(CamVid_dataloader_train)
# _, batch = next(target_loader)
data, _ = batch
data = data.cuda()
with amp.autocast():
output_t, output_sup1, output_sup2 = model_G(data)
D_out = model_D(F.softmax(output_t))
loss_adv = loss_func_adv(D_out , Variable(torch.FloatTensor(D_out.data.size()).fill_(source_label)).cuda() ) # I MIDIFIED THOSE TRY TO FOOL THE DISC
loss_adv = loss_adv * args.lambda_adv#0.001 or 0.01 CHECK
scaler.scale(loss_adv).backward()
# train D:
for param in model_D.parameters():
param.requires_grad = True
#train with source:
output_s = output_s.detach()
with amp.autocast():
D_out = model_D(F.softmax(output_s)) # we feed the discriminator with the output of the model
loss_D = loss_func_D(D_out, Variable(torch.FloatTensor(D_out.data.size()).fill_(source_label)).cuda()) # add the adversarial loss
loss_D = loss_D / 2
scaler.scale(loss_D).backward()
#train with target:
output_t = output_t.detach()
with amp.autocast():
D_out = model_D(F.softmax(output_t)) # we feed the discriminator with the output of the model
loss_D = loss_func_D(D_out, Variable(torch.FloatTensor(D_out.data.size()).fill_(target_label)).cuda()) # add the adversarial loss
loss_D = loss_D / 2
scaler.scale(loss_D).backward()
tq.update(args.batch_size)
losses = {"loss_seg" : '%.6f' %(loss_G.item()) , "loss_adv" : '%.6f' %(loss_adv.item()) , "loss_D" : '%.6f'%(loss_D.item()) } # add dictionary to print losses
tq.set_postfix(losses)
loss_G_record.append(loss_G.item())
loss_adv_record.append(loss_adv.item())
loss_D_record.append(loss_D.item())
step += 1
writer.add_scalar('loss_G_step', loss_G, step) # track the segmentation loss
writer.add_scalar('loss_adv_step', loss_adv, step) # track the adversarial loss
writer.add_scalar('loss_D_step', loss_D, step) # track the discreminator loss
scaler.step(optimizer_G) # update the optimizer for genarator
scaler.step(optimizer_D) # update the optimizer for discriminator
scaler.update()
tq.close()
loss_G_train_mean = np.mean(loss_G_record)
loss_adv_train_mean = np.mean(loss_adv_record)
loss_D_train_mean = np.mean(loss_D_record)
writer.add_scalar('epoch/loss_G_train_mean', float(loss_G_train_mean), epoch)
writer.add_scalar('epoch/loss_adv_train_mean', float(loss_adv_train_mean), epoch)
writer.add_scalar('epoch/loss_D_train_mean', float(loss_D_train_mean), epoch)
#the checkpoint needs rewriting
if epoch % args.checkpoint_step == 0 and epoch != 0:
if not os.path.isdir(args.save_model_path):
os.mkdir(args.save_model_path)
state = {
"epoch": epoch,
"model_G_state": model_G.module.state_dict(),
"optimizer_G": optimizer_G.state_dict() ,
"model_D_state": model_D.module.state_dict(),
"optimizer_D": optimizer_D.state_dict(),
"max_miou": max_miou
}
torch.save(state, os.path.join(args.save_model_path, 'latest_dice_loss.pth'))
print("*** epoch " + str(epoch) + " saved as recent checkpoint!!!")
if epoch % args.validation_step == 0 and epoch != 0:
precision, miou = val(args, model_G, CamVid_dataloader_val)
if miou > max_miou:
max_miou = miou
os.makedirs(args.save_model_path, exist_ok=True)
state = {
"epoch": epoch,
"model_state": model_G.module.state_dict(),
"optimizer": optimizer_G.state_dict(),
"max_miou": max_miou
}
torch.save(state, os.path.join(args.save_model_path, 'best_dice_loss.pth'))
print("*** epoch " + str(epoch) + " saved as best checkpoint!!!")
writer.add_scalar('epoch/precision_val', precision, epoch)
writer.add_scalar('epoch/miou val', miou, epoch)
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 train(args, model, optimizer, dataloader_train, dataloader_val):
writer = SummaryWriter(
comment=''.format(args.optimizer, args.context_path))
if args.loss == 'dice':
loss_func = DiceLoss()
elif args.loss == 'crossentropy':
loss_func = torch.nn.CrossEntropyLoss(ignore_index=255)
max_miou = 0
step = 0
for epoch in range(args.num_epochs):
lr = poly_lr_scheduler(optimizer,
args.learning_rate,
iter=epoch,
max_iter=args.num_epochs)
model.train()
tq = tqdm(total=len(dataloader_train) * args.batch_size)
tq.set_description('epoch %d, lr %f' % (epoch, lr))
loss_record = []
for i, (data, label) in enumerate(dataloader_train):
if torch.cuda.is_available() and args.use_gpu:
data = data.cuda()
label = label.cuda().long()
with torch.cuda.amp.autocast():
output, output_sup1, output_sup2 = model(data)
loss1 = loss_func(output, label)
loss2 = loss_func(output_sup1, label)
loss3 = loss_func(output_sup2, label)
loss = loss1 + loss2 + loss3
tq.update(args.batch_size)
tq.set_postfix(loss='%.6f' % loss)
optimizer.zero_grad()
loss.backward()
optimizer.step()
step += 1
writer.add_scalar('loss_step', loss, step)
loss_record.append(loss.item())
tq.close()
loss_train_mean = np.mean(loss_record)
writer.add_scalar('epoch/loss_epoch_train', float(loss_train_mean),
epoch)
print('loss for train : %f' % (loss_train_mean))
if epoch % args.checkpoint_step == 0 and epoch != 0:
import os
if not os.path.isdir(args.save_model_path):
import os
os.mkdir(args.save_model_path)
torch.save(model.module.state_dict(),
os.path.join(args.save_model_path, 'model.pth'))
if epoch % args.validation_step == 0 and epoch != 0:
precision, miou = val(args, model, dataloader_val)
if miou > max_miou:
max_miou = miou
import os
os.makedirs(args.save_model_path, exist_ok=True)
torch.save(
model.module.state_dict(),
os.path.join(args.save_model_path, 'best_dice_loss.pth'))
writer.add_scalar('epoch/precision_val', precision, epoch)
writer.add_scalar('epoch/miou val', miou, epoch)
def main():
axis = 'ax1'
# CUDA for PyTorch
device = train_device()
# Training dataset
train_params = {'batch_size': 10, 'shuffle': True, 'num_workers': 4}
data_path = './dataset/dataset_' + axis + '/train/'
train_dataset = Dataset(data_path,
transform=transforms.Compose([Preprocessing()]))
lenght = int(len(train_dataset))
train_loader = torch.utils.data.DataLoader(train_dataset, **train_params)
# Validation dataset
data_path = './dataset/dataset_' + axis + '/valid/'
valid_dataset = Dataset(data_path,
transform=transforms.Compose([Preprocessing()]))
valid_params = {'batch_size': 10, 'shuffle': True, 'num_workers': 4}
val_loader = torch.utils.data.DataLoader(valid_dataset, **valid_params)
# Training params
learning_rate = 1e-4
max_epochs = 100
# Used pretrained model and modify channels from 3 to 1
model = torch.hub.load('mateuszbuda/brain-segmentation-pytorch',
'unet',
in_channels=3,
out_channels=1,
init_features=32,
pretrained=True)
model.encoder1.enc1conv1 = nn.Conv2d(1,
32,
kernel_size=(3, 3),
stride=(1, 1),
padding=(1, 1),
bias=False)
model.to(device)
# Optimizer and loss function
optimizer = torch.optim.Adam(model.parameters(), lr=learning_rate)
dsc_loss = DiceLoss()
# Metrics
train_loss = AverageMeter('Training loss', ':.6f')
val_loss = AverageMeter('Validation loss', ':.6f')
best_loss = float('inf')
nb_of_batches = lenght // train_params['batch_size']
for epoch in range(max_epochs):
val_loss.avg = 0
train_loss.avg = 0
if not epoch:
logg_file = loggs.Loggs(['epoch', 'train_loss', 'val_loss'])
model.train()
for i, (image, label) in enumerate(train_loader):
torch.cuda.empty_cache()
image, label = image.to(device), label.to(device)
optimizer.zero_grad()
y_pred = model(image)
loss = dsc_loss(y_pred, label)
del y_pred
train_loss.update(loss.item(), image.size(0))
loss.backward()
optimizer.step()
loggs.training_bar(i,
nb_of_batches,
prefix='Epoch: %d/%d' % (epoch, max_epochs),
suffix='Loss: %.6f' % loss.item())
print(train_loss.avg)
with torch.no_grad():
for i, (x_val, y_val) in enumerate(val_loader):
x_val, y_val = x_val.to(device), y_val.to(device)
model.eval()
yhat = model(x_val)
loss = dsc_loss(yhat, y_val)
val_loss.update(loss.item(), x_val.size(0))
print(val_loss)
logg_file.save([epoch, train_loss.avg, val_loss.avg])
# Save the best model with minimum validation loss
if best_loss > val_loss.avg:
print('Updated model with validation loss %.6f ---> %.6f' %
(best_loss, val_loss.avg))
best_loss = val_loss.avg
torch.save(model, './model_' + axis + '/best_model.pt')
def train():
# 训练的epoch数
epoch = 500
# 数据文件夹
img_dir = "./data/training/images"
# 掩模文件夹
mask_dir = "./data/training/1st_manual"
# 网络输入图片大小
img_size = (512, 512)
# 创建训练loader和验证loader
tr_loader = DataLoader(DRIVE_Loader(img_dir, mask_dir, img_size, 'train'),
batch_size=4,
shuffle=True,
num_workers=2,
pin_memory=True,
drop_last=True)
val_loader = DataLoader(DRIVE_Loader(img_dir, mask_dir, img_size, 'val'),
batch_size=4,
shuffle=True,
num_workers=2,
pin_memory=True,
drop_last=True)
# 定义损失函数
criterion = DiceBCELoss()
# 把网络加载到显卡
network = UNet().cuda()
# 定义优化器
optimizer = Adam(network.parameters(), weight_decay=0.0001)
best_score = 1.0
for i in range(epoch):
# 设置为训练模式，会更新BN和Dropout参数
network.train()
train_step = 0
train_loss = 0
val_loss = 0
val_step = 0
# 训练
for batch in tr_loader:
# 读取每个batch的数据和掩模
imgs, mask = batch
# 把数据加载到显卡
imgs = imgs.cuda()
mask = mask.cuda()
# 把数据喂入网络，获得一个预测结果
mask_pred = network(imgs)
# 根据预测结果与掩模求出Loss
loss = criterion(mask_pred, mask)
# 统计训练loss
train_loss += loss.item()
train_step += 1
# 梯度清零
optimizer.zero_grad()
# 通过loss求出梯度
loss.backward()
# 使用Adam进行梯度回传
optimizer.step()
# 设置为验证模式，不更新BN和Dropout参数
network.eval()
# 验证
with torch.no_grad():
for batch in val_loader:
imgs, mask = batch
imgs = imgs.cuda()
mask = mask.cuda()
# 求出评价指标，这里用的是dice
val_loss += DiceLoss()(network(imgs), mask).item()
val_step += 1
# 分别求出整个epoch的训练loss以及验证指标
train_loss /= train_step
val_loss /= val_step
# 如果验证指标比最优值更好，那么保存当前模型参数
if val_loss < best_score:
best_score = val_loss
torch.save(network.state_dict(), "./checkpoint.pth")
# 输出
print(str(i), "train_loss:", train_loss, "val_dice", val_loss)
def compute_loss(self, start_logits, end_logits, start_labels, end_labels,
label_mask):
"""compute loss on squad task."""
if len(start_labels.size()) > 1:
start_labels = start_labels.squeeze(-1)
if len(end_labels.size()) > 1:
end_labels = end_labels.squeeze(-1)
# sometimes the start/end positions are outside our model inputs, we ignore these terms
batch_size, ignored_index = start_logits.shape # ignored_index: seq_len
start_labels.clamp_(0, ignored_index)
end_labels.clamp_(0, ignored_index)
if self.loss_type != "ce":
# start_labels/end_labels: position index of answer starts/ends among the document.
# F.one_hot will map the postion index to a sequence of 0, 1 labels.
start_labels = F.one_hot(start_labels, num_classes=ignored_index)
end_labels = F.one_hot(end_labels, num_classes=ignored_index)
if self.loss_type == "ce":
loss_fct = CrossEntropyLoss(ignore_index=ignored_index)
start_loss = loss_fct(start_logits, start_labels)
end_loss = loss_fct(end_logits, end_labels)
elif self.loss_type == "bce":
start_loss = F.binary_cross_entropy_with_logits(
start_logits.view(-1),
start_labels.view(-1).float(),
reduction="none")
end_loss = F.binary_cross_entropy_with_logits(
end_logits.view(-1),
end_labels.view(-1).float(),
reduction="none")
start_loss = (start_loss *
label_mask.view(-1)).sum() / label_mask.sum()
end_loss = (end_loss *
label_mask.view(-1)).sum() / label_mask.sum()
elif self.loss_type == "focal":
loss_fct = FocalLoss(gamma=self.args.focal_gamma, reduction="none")
start_loss = loss_fct(
FocalLoss.convert_binary_pred_to_two_dimension(
start_logits.view(-1)), start_labels.view(-1))
end_loss = loss_fct(
FocalLoss.convert_binary_pred_to_two_dimension(
end_logits.view(-1)), end_labels.view(-1))
start_loss = (start_loss *
label_mask.view(-1)).sum() / label_mask.sum()
end_loss = (end_loss *
label_mask.view(-1)).sum() / label_mask.sum()
elif self.loss_type in ["dice", "adaptive_dice"]:
loss_fct = DiceLoss(with_logits=True,
smooth=self.args.dice_smooth,
ohem_ratio=self.args.dice_ohem,
alpha=self.args.dice_alpha,
square_denominator=self.args.dice_square)
# add to test
# start_logits, end_logits = start_logits.view(batch_size, -1), end_logits.view(batch_size, -1)
# start_labels, end_labels = start_labels.view(batch_size, -1), end_labels.view(batch_size, -1)
start_logits, end_logits = start_logits.view(-1,
1), end_logits.view(
-1, 1)
start_labels, end_labels = start_labels.view(-1,
1), end_labels.view(
-1, 1)
# label_mask = label_mask.view(batch_size, -1)
label_mask = label_mask.view(-1, 1)
start_loss = loss_fct(start_logits, start_labels, mask=label_mask)
end_loss = loss_fct(end_logits, end_labels, mask=label_mask)
else:
raise ValueError("This type of loss func donot exists.")
total_loss = (start_loss + end_loss) / 2
return total_loss, start_loss, end_loss
def train(model, setting, optimizer, scheduler, epochs, batchSize, logger,
resultsPath, testResults, testResultsTTA, tbWriter,
allClassEvaluators):
model.to(device)
if torch.cuda.device_count() > 1 and useAllAvailableGPU:
logger.info('# {} GPUs utilized! #'.format(torch.cuda.device_count()))
model = nn.DataParallel(model)
# mandatory to produce random numpy numbers during training, otherwise batches will contain equal random numbers (originally: numpy issue)
def worker_init_fn(worker_id):
np.random.seed(np.random.get_state()[1][0] + worker_id)
# allocate and separately load train / val / test data sets
dataset_Train = CustomDataSetRAM('train', logger)
dataloader_Train = DataLoader(dataset=dataset_Train,
batch_size=batchSize,
shuffle=True,
num_workers=4,
worker_init_fn=worker_init_fn)
if 'val' in setting:
dataset_Val = CustomDataSetRAM('val', logger)
dataloader_Val = DataLoader(dataset=dataset_Val,
batch_size=batchSize,
shuffle=False,
num_workers=1,
worker_init_fn=worker_init_fn)
if 'test' in setting:
dataset_Test = CustomDataSetRAM('test', logger)
dataloader_Test = DataLoader(dataset=dataset_Test,
batch_size=batchSize,
shuffle=False,
num_workers=1,
worker_init_fn=worker_init_fn)
logger.info('####### DATA LOADED - TRAINING STARTS... #######')
# Utilize dice loss and weighted cross entropy loss
Dice_Loss = DiceLoss(ignore_index=8).to(device)
CE_Loss = nn.CrossEntropyLoss(weight=torch.FloatTensor(
[1., 1., 1., 1., 1., 1., 1., 10.]),
ignore_index=8).to(device)
# WCE_Loss = nn.CrossEntropyLoss(weight=getWeightsForCEloss(dataset, train_idx, areLabelsOnehotEncoded=False, device=device, logger=logger)).to(device)
for epoch in range(epochs):
model.train(True)
epochCELoss = 0
epochDiceLoss = 0
epochLoss = 0
np.random.seed()
start = time.time()
for batch in dataloader_Train:
# get data and put onto device
imgBatch, segBatch = batch
imgBatch = imgBatch.to(device)
segBatch = segBatch.to(device)
optimizer.zero_grad()
# forward image batch, compute loss and backprop
prediction = model(imgBatch)
CEloss = CE_Loss(prediction, segBatch)
diceLoss = Dice_Loss(prediction, segBatch)
loss = CEloss + diceLoss
epochCELoss += CEloss.item()
epochDiceLoss += diceLoss.item()
epochLoss += loss.item()
loss.backward()
# nn.utils.clip_grad_norm(model.parameters(), 10)
optimizer.step()
epochTrainLoss = epochLoss / dataloader_Train.__len__()
end = time.time()
# print current loss
logger.info('[Epoch ' + str(epoch + 1) + '] Train-Loss: ' +
str(round(epochTrainLoss, 5)) + ', DiceLoss: ' +
str(round(epochDiceLoss / dataloader_Train.__len__(), 5)) +
', CELoss: ' +
str(round(epochCELoss / dataloader_Train.__len__(), 5)) +
' [took ' + str(round(end - start, 3)) + 's]')
# use tensorboard for visualization of training progress
tbWriter.add_scalars(
'Plot/train', {
'loss': epochTrainLoss,
'CEloss': epochCELoss / dataloader_Train.__len__(),
'DiceLoss': epochDiceLoss / dataloader_Train.__len__()
}, epoch)
# each 50th epoch add prediction image to tensorboard
if epoch % 50 == 0:
with torch.no_grad():
tbWriter.add_image(
'Train/_img',
torch.round(
(imgBatch[0, :, :, :] + 1.6) / 3.2 * 255.0).byte(),
epoch)
tbWriter.add_image(
'Train/GT',
convert_labelmap_to_rgb(segBatch[0, :, :].cpu()), epoch)
tbWriter.add_image(
'Train/pred',
convert_labelmap_to_rgb(
prediction[0, :, :, :].argmax(0).cpu()), epoch)
if epoch % 100 == 0:
logger.info('[Epoch ' + str(epoch + 1) + '] ' +
parse_nvidia_smi(GPUno))
logger.info('[Epoch ' + str(epoch + 1) + '] ' + parse_RAM_info())
# if validation is active, compute dice scores on validation data
if 'val' in setting:
model.train(False)
diceScores_Val = []
start = time.time()
for batch in dataloader_Val:
imgBatch, segBatch = batch
imgBatch = imgBatch.to(device)
# segBatch = segBatch.to(device)
with torch.no_grad():
prediction = model(imgBatch).to('cpu')
diceScores_Val.append(getDiceScores(prediction, segBatch))
diceScores_Val = np.concatenate(
diceScores_Val, 0
) # <- all dice scores of val data (batchSize x amountClasses-1)
diceScores_Val = diceScores_Val[:, :
-1] # ignore last coloum=border dice scores
mean_DiceScores_Val, epoch_val_mean_score = getMeanDiceScores(
diceScores_Val, logger)
end = time.time()
logger.info('[Epoch ' + str(epoch + 1) +
'] Val-Score (mean label dice scores): ' +
str(np.round(mean_DiceScores_Val, 4)) + ', Mean: ' +
str(round(epoch_val_mean_score, 4)) + ' [took ' +
str(round(end - start, 3)) + 's]')
tbWriter.add_scalar('Plot/val', epoch_val_mean_score, epoch)
if epoch % 50 == 0:
with torch.no_grad():
tbWriter.add_image(
'Val/_img',
torch.round(
(imgBatch[0, :, :, :] + 1.6) / 3.2 * 255.0).byte(),
epoch)
tbWriter.add_image(
'Val/GT',
convert_labelmap_to_rgb(segBatch[0, :, :].cpu()),
epoch)
tbWriter.add_image(
'Val/pred',
convert_labelmap_to_rgb(
prediction[0, :, :, :].argmax(0).cpu()), epoch)
if epoch % 100 == 0:
logger.info('[Epoch ' + str(epoch + 1) +
' - After Validation] ' + parse_nvidia_smi(GPUno))
logger.info('[Epoch ' + str(epoch + 1) +
' - After Validation] ' + parse_RAM_info())
# scheduler.step()
if 'val' in setting:
endLoop = scheduler.stepTrainVal(epoch_val_mean_score, logger)
else:
endLoop = scheduler.stepTrain(epochTrainLoss, logger)
if epoch == (
epochs - 1
): #when no early stop is performed, load bestValModel into current model for later save
logger.info(
'### No early stop performed! Best val model loaded... ####')
if 'val' in setting:
scheduler.loadBestValIntoModel()
# if test is active, compute global dice scores on test data for fast and coarse performance check
if 'test' in setting:
model.train(False)
diceScores_Test = []
start = time.time()
for batch in dataloader_Test:
imgBatch, segBatch = batch
imgBatch = imgBatch.to(device)
# segBatch = segBatch.to(device)
with torch.no_grad():
prediction = model(imgBatch).to('cpu')
diceScores_Test.append(getDiceScores(prediction, segBatch))
diceScores_Test = np.concatenate(
diceScores_Test, 0
) # <- all dice scores of test data (amountTestData x amountClasses-1)
diceScores_Test = diceScores_Test[:, :
-1] #ignore last coloum=border dice scores
mean_DiceScores_Test, test_mean_score = getMeanDiceScores(
diceScores_Test, logger)
end = time.time()
logger.info('[Epoch ' + str(epoch + 1) +
'] Test-Score (mean label dice scores): ' +
str(np.round(mean_DiceScores_Test, 4)) + ', Mean: ' +
str(round(test_mean_score, 4)) + ' [took ' +
str(round(end - start, 3)) + 's]')
tbWriter.add_scalar('Plot/test', test_mean_score, epoch)
if epoch % 50 == 0:
with torch.no_grad():
tbWriter.add_image(
'Test/_img',
torch.round(
(imgBatch[0, :, :, :] + 1.6) / 3.2 * 255.0).byte(),
epoch)
tbWriter.add_image(
'Test/GT',
convert_labelmap_to_rgb(segBatch[0, :, :].cpu()),
epoch)
tbWriter.add_image(
'Test/pred',
convert_labelmap_to_rgb(
prediction[0, :, :, :].argmax(0).cpu()), epoch)
if epoch % 100 == 0:
logger.info('[Epoch ' + str(epoch + 1) + ' - After Testing] ' +
parse_nvidia_smi(GPUno))
logger.info('[Epoch ' + str(epoch + 1) + ' - After Testing] ' +
parse_RAM_info())
with torch.no_grad():
### if training is over ###
if endLoop or (epoch == epochs - 1):
diceScores_Test = []
diceScores_Test_TTA = []
test_idx = np.arange(sum(testDatasetsSizes))
for sampleNo in test_idx:
diseaseID = -1
if sampleNo < sum(testDatasetsSizes[:1]):
diseaseID = 0 # Healthy test sample
elif sampleNo < sum(testDatasetsSizes[:2]):
diseaseID = 2 # UUO test sample
elif sampleNo < sum(testDatasetsSizes[:3]):
diseaseID = 4 # Adenine test sample
elif sampleNo < sum(testDatasetsSizes[:4]):
diseaseID = 6 # Alport test sample
elif sampleNo < sum(testDatasetsSizes[:5]):
diseaseID = 8 # IRI test sample
elif sampleNo < sum(testDatasetsSizes[:6]):
diseaseID = 10 # NTN test sample
# get test sample, forward it through network in evaluation mode, and compute performance
imgBatch, segBatch = dataset_Test.__getitem__(sampleNo)
imgBatch = imgBatch.unsqueeze(0).to(device)
segBatch = segBatch.unsqueeze(0)
prediction = model(imgBatch)
predictionCPU = prediction.to("cpu")
# apply post-processing
postprocessedPrediction, outputPrediction, preprocessedGT = postprocessPredictionAndGT(
prediction,
segBatch.squeeze(0).numpy(),
device=device,
predictionsmoothing=True,
holefilling=True)
classInstancePredictionList, classInstanceGTList, finalPredictionRGB, preprocessedGTrgb = extractInstanceChannels(
postprocessedPrediction,
preprocessedGT,
tubuliDilation=True)
# evaluate performance (TP, NP, FP counting and dice score computation)
for i in range(6): #number classes to evaluate = 6
allClassEvaluators[diseaseID][i].add_example(
classInstancePredictionList[i],
classInstanceGTList[i])
# compute global dice scores as coarse performance check
diceScores_Test.append(
getDiceScores(predictionCPU, segBatch))
if saveFinalTestResults:
figFolder = resultsPath + '/' + diseaseModels[
diseaseID // 2]
if not os.path.exists(figFolder):
os.makedirs(figFolder)
imgBatchCPU = torch.round(
(imgBatch[0, :, :, :].to("cpu") + 1.6) / 3.2 *
255.0).byte().numpy().transpose(1, 2, 0)
figPath = figFolder + '/test_idx_' + str(
sampleNo) + '_result.png'
saveFigureResults(imgBatchCPU,
outputPrediction,
postprocessedPrediction,
finalPredictionRGB,
segBatch.squeeze(0).numpy(),
preprocessedGT,
preprocessedGTrgb,
fullResultPath=figPath,
alpha=0.4)
# perform exactly the same when applying TTA
if applyTestTimeAugmentation:
prediction = torch.softmax(prediction, 1)
imgBatch = imgBatch.flip(2)
prediction += torch.softmax(model(imgBatch),
1).flip(2)
imgBatch = imgBatch.flip(3)
prediction += torch.softmax(model(imgBatch),
1).flip(3).flip(2)
imgBatch = imgBatch.flip(2)
prediction += torch.softmax(model(imgBatch),
1).flip(3)
prediction /= 4.
predictionCPU = prediction.to("cpu")
postprocessedPrediction, outputPrediction, preprocessedGT = postprocessPredictionAndGT(
prediction,
segBatch.squeeze(0).numpy(),
device=device,
predictionsmoothing=False,
holefilling=True)
classInstancePredictionList, classInstanceGTList, finalPredictionRGB, preprocessedGTrgb = extractInstanceChannels(
postprocessedPrediction,
preprocessedGT,
tubuliDilation=False)
for i in range(6):
allClassEvaluators[
diseaseID + 1][i].add_example(
classInstancePredictionList[i],
classInstanceGTList[i])
diceScores_Test_TTA.append(
getDiceScores(predictionCPU, segBatch))
if saveFinalTestResults:
figPath = figFolder + '/test_idx_' + str(
sampleNo) + '_result_TTA.png'
saveFigureResults(imgBatchCPU,
outputPrediction,
postprocessedPrediction,
finalPredictionRGB,
segBatch.squeeze(0).numpy(),
preprocessedGT,
preprocessedGTrgb,
fullResultPath=figPath,
alpha=0.4)
# print global dice scores as coarse performance check
diceScores_Test = np.concatenate(
diceScores_Test, 0
) # <- all dice scores of test data (amountTestData x amountClasses-1)
diceScores_Test = diceScores_Test[:, :
-1] # ignore last coloum=border dice scores
mean_DiceScores_Test, test_mean_score = getMeanDiceScores(
diceScores_Test, logger)
logger.info('[FINAL RESULT] [Epoch ' + str(epoch + 1) +
'] Test-Score (mean label dice scores): ' +
str(np.round(mean_DiceScores_Test, 4)) +
', Mean: ' + str(round(test_mean_score, 4)))
testResults.append(diceScores_Test)
# print global dice scores of TTA as coarse performance check
if applyTestTimeAugmentation:
diceScores_Test_TTA = np.concatenate(
diceScores_Test_TTA, 0
) # <- all dice scores of test data (amountTestData x amountClasses-1)
diceScores_Test_TTA = diceScores_Test_TTA[:, :
-1] # ignore last coloum=border dice scores
mean_DiceScores_Test_TTA, test_mean_score_TTA = getMeanDiceScores(
diceScores_Test_TTA, logger)
logger.info(
'[FINAL TTA RESULT] [Epoch ' + str(epoch + 1) +
'] Test-Score (mean label dice scores): ' +
str(np.round(mean_DiceScores_Test_TTA, 4)) +
', Mean: ' + str(round(test_mean_score_TTA, 4)))
testResultsTTA.append(diceScores_Test_TTA)
if endLoop:
logger.info('### Early network training stop at epoch ' +
str(epoch + 1) + '! ###')
break
logger.info('[Epoch ' + str(epoch + 1) + '] ### Training done! ###')
return model
def train_net(args):
cropsize = [cfgs.crop_height, cfgs.crop_width]
# dataset_train = CityScapes(cfgs.data_dir, cropsize=cropsize, mode='train')
dataset_train = ContextVoc(cfgs.train_file,
cropsize=cropsize,
mode='train')
dataloader_train = DataLoader(dataset_train,
batch_size=args.batch_size,
shuffle=True,
num_workers=args.num_workers,
drop_last=True)
# dataset_val = CityScapes(cfgs.data_dir, mode='val')
dataset_val = ContextVoc(cfgs.val_file, cropsize=cropsize, mode='train')
dataloader_val = DataLoader(dataset_val,
batch_size=1,
shuffle=True,
num_workers=args.num_workers,
drop_last=True)
# build net
os.environ['CUDA_VISIBLE_DEVICES'] = args.cuda
if torch.cuda.is_available() and args.use_gpu:
device = torch.device('cuda')
else:
device = torch.device('cpu')
# model = BiSeNet(args.num_classes, args.context_path)
net = DeeplabV3plus(cfgs).to(device)
# net = SCAR(load_weights=True).to(device)
if args.pretrained_model_path is not None:
print('load model from %s ...' % args.pretrained_model_path)
state_dict = torch.load(args.pretrained_model_path,
map_location=device)
state_dict = renamedict(state_dict)
net.load_state_dict(state_dict, strict=False)
# net.load_state_dict(torch.load(args.pretrained_model_path))
print('Done!')
if args.mulgpu:
net = torch.nn.DataParallel(net)
net.train()
# build optimizer
if args.optimizer == 'rmsprop':
optimizer = torch.optim.RMSprop(net.parameters(), args.learning_rate)
elif args.optimizer == 'sgd':
optimizer = torch.optim.SGD(net.parameters(),
args.learning_rate,
momentum=0.9,
weight_decay=1e-4)
elif args.optimizer == 'adam':
optimizer = torch.optim.Adam(net.parameters(), args.learning_rate)
else:
print('not supported optimizer \n')
optimizer = None
#build loss
if args.losstype == 'dice':
criterion = DiceLoss()
elif args.losstype == 'crossentropy':
criterion = torch.nn.CrossEntropyLoss()
elif args.losstype == 'ohem':
score_thres = 0.7
n_min = args.batch_size * cfgs.crop_height * cfgs.crop_width // 16
criterion = OhemCELoss(thresh=score_thres, n_min=n_min)
elif args.losstype == 'focal':
# criterion = SoftmaxFocalLoss()
criterion = FocalLoss()
elif args.losstype == 'multi':
criterion = Multiloss(4)
return net, optimizer, criterion, dataloader_train, dataloader_val
def train_val(config):
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
train_loader = get_dataloader(img_dir=config.train_img_dir,
mask_dir=config.train_mask_dir,
mode="train",
batch_size=config.batch_size,
num_workers=config.num_workers)
val_loader = get_dataloader(img_dir=config.val_img_dir,
mask_dir=config.val_mask_dir,
mode="val",
batch_size=config.batch_size,
num_workers=config.num_workers)
writer = SummaryWriter(
comment="LR_%f_BS_%d_MODEL_%s_DATA_%s" %
(config.lr, config.batch_size, config.model_type, config.data_type))
if config.model_type not in [
'UNet', 'R2UNet', 'AUNet', 'R2AUNet', 'SEUNet', 'SEUNet++',
'UNet++', 'DAUNet', 'DANet', 'AUNetR', 'RendDANet', "BASNet"
]:
print('ERROR!! model_type should be selected in supported models')
print('Choose model %s' % config.model_type)
return
if config.model_type == "UNet":
model = UNet()
elif config.model_type == "AUNet":
model = AUNet()
elif config.model_type == "R2UNet":
model = R2UNet()
elif config.model_type == "SEUNet":
model = SEUNet(useCSE=False, useSSE=False, useCSSE=True)
elif config.model_type == "UNet++":
model = UNetPP()
elif config.model_type == "DANet":
model = DANet(backbone='resnet101', nclass=1)
elif config.model_type == "AUNetR":
model = AUNet_R16(n_classes=1, learned_bilinear=True)
elif config.model_type == "RendDANet":
model = RendDANet(backbone='resnet101', nclass=1)
elif config.model_type == "BASNet":
model = BASNet(n_channels=3, n_classes=1)
else:
model = UNet()
if torch.cuda.device_count() > 1:
print("Let's use", torch.cuda.device_count(), "GPUs!")
model = nn.DataParallel(model)
model = model.to(device, dtype=torch.float)
if config.optimizer == "sgd":
optimizer = SGD(model.parameters(),
lr=config.lr,
weight_decay=1e-6,
momentum=0.9)
else:
optimizer = torch.optim.Adam(model.parameters(), lr=config.lr)
if config.loss == "dice":
criterion = DiceLoss()
elif config.loss == "bce":
criterion = nn.BCELoss()
elif config.loss == "bas":
criterion = BasLoss()
else:
criterion = MixLoss()
scheduler = lr_scheduler.StepLR(optimizer, step_size=40, gamma=0.1)
global_step = 0
best_dice = 0.0
for epoch in range(config.num_epochs):
epoch_loss = 0.0
with tqdm(total=config.num_train,
desc="Epoch %d / %d" % (epoch + 1, config.num_epochs),
unit='img') as train_pbar:
model.train()
for image, mask in train_loader:
image = image.to(device, dtype=torch.float)
mask = mask.to(device, dtype=torch.float)
d0, d1, d2, d3, d4, d5, d6, d7 = model(image)
loss = criterion(d0, d1, d2, d3, d4, d5, d6, d7, mask)
epoch_loss += loss.item()
writer.add_scalar('Loss/train', loss.item(), global_step)
train_pbar.set_postfix(**{'loss (batch)': loss.item()})
optimizer.zero_grad()
loss.backward()
optimizer.step()
train_pbar.update(image.shape[0])
global_step += 1
# if global_step % 100 == 0:
# writer.add_images('masks/true', mask, global_step)
# writer.add_images('masks/pred', d0 > 0.5, global_step)
scheduler.step()
epoch_dice = 0.0
epoch_acc = 0.0
epoch_sen = 0.0
epoch_spe = 0.0
epoch_pre = 0.0
current_num = 0
with tqdm(total=config.num_val,
desc="Epoch %d / %d validation round" %
(epoch + 1, config.num_epochs),
unit='img') as val_pbar:
model.eval()
locker = 0
for image, mask in val_loader:
current_num += image.shape[0]
image = image.to(device, dtype=torch.float)
mask = mask.to(device, dtype=torch.float)
d0, d1, d2, d3, d4, d5, d6, d7 = model(image)
batch_dice = dice_coeff(mask, d0).item()
epoch_dice += batch_dice * image.shape[0]
epoch_acc += get_accuracy(pred=d0, true=mask) * image.shape[0]
epoch_sen += get_sensitivity(pred=d0,
true=mask) * image.shape[0]
epoch_spe += get_specificity(pred=d0,
true=mask) * image.shape[0]
epoch_pre += get_precision(pred=d0, true=mask) * image.shape[0]
if locker == 200:
writer.add_images('masks/true', mask, epoch + 1)
writer.add_images('masks/pred', d0 > 0.5, epoch + 1)
val_pbar.set_postfix(**{'dice (batch)': batch_dice})
val_pbar.update(image.shape[0])
locker += 1
epoch_dice /= float(current_num)
epoch_acc /= float(current_num)
epoch_sen /= float(current_num)
epoch_spe /= float(current_num)
epoch_pre /= float(current_num)
epoch_f1 = get_F1(SE=epoch_sen, PR=epoch_pre)
if epoch_dice > best_dice:
best_dice = epoch_dice
writer.add_scalar('Best Dice/test', best_dice, epoch + 1)
torch.save(
model, config.result_path + "/%s_%s_%d.pth" %
(config.model_type, str(epoch_dice), epoch + 1))
logging.info('Validation Dice Coeff: {}'.format(epoch_dice))
print("epoch dice: " + str(epoch_dice))
writer.add_scalar('Dice/test', epoch_dice, epoch + 1)
writer.add_scalar('Acc/test', epoch_acc, epoch + 1)
writer.add_scalar('Sen/test', epoch_sen, epoch + 1)
writer.add_scalar('Spe/test', epoch_spe, epoch + 1)
writer.add_scalar('Pre/test', epoch_pre, epoch + 1)
writer.add_scalar('F1/test', epoch_f1, epoch + 1)
writer.close()
print("Training finished")
def train(args, model, optimizer, dataloader_train, dataloader_val):
plotting.output_file('learning_curve_%s_%s.html' %
(args.optimizer, args.context_path))
fig_loss = plotting.figure(title='Loss Curve',
x_axis_label='epochs',
y_axis_label='loss',
plot_width=600,
plot_height=600)
fig_precision = plotting.figure(title='Precision Curve',
x_axis_label='epochs',
y_axis_label='precision',
plot_width=600,
plot_height=600)
fig_miou = plotting.figure(title='mIOU Curve',
x_axis_label='epochs',
y_axis_label='mIOU',
plot_width=600,
plot_height=600)
if args.loss == 'dice':
loss_func = DiceLoss()
elif args.loss == 'crossentropy':
loss_func = torch.nn.CrossEntropyLoss()
max_miou = 0
loss_list = []
epoch_x = []
precision_list = []
miou_list = []
for epoch in range(args.num_epochs):
lr = poly_lr_scheduler(optimizer,
args.learning_rate,
iter=epoch,
max_iter=args.num_epochs)
model.train()
tq = tqdm.tqdm(total=len(dataloader_train) * args.batch_size)
tq.set_description('epoch %d, lr %f' % (epoch, lr))
loss_record = []
for i, (data, label) in enumerate(dataloader_train):
if torch.cuda.is_available() and args.use_gpu:
data = data.cuda()
label = label.cuda()
output, output_sup1, output_sup2 = model(data)
loss1 = loss_func(output, label)
loss2 = loss_func(output_sup1, label)
loss3 = loss_func(output_sup2, label)
loss = loss1 + loss2 + loss3
tq.update(args.batch_size)
tq.set_postfix(loss='%.6f' % loss)
optimizer.zero_grad()
loss.backward()
optimizer.step()
loss_record.append(loss.item())
tq.close()
loss_train_mean = np.mean(loss_record)
loss_list.append(loss_train_mean)
print('loss for train : %f' % (loss_train_mean))
if epoch % args.checkpoint_step == 0 and epoch != 0:
if not os.path.isdir(args.save_model_path):
os.mkdir(args.save_model_path)
torch.save(
model.module.state_dict(),
os.path.join(args.save_model_path, 'latest_dice_loss.pth'))
if epoch % args.validation_step == 0 or epoch == (args.num_epochs - 1):
precision, miou = val(args, model, dataloader_val)
if miou > max_miou:
max_miou = miou
torch.save(
model.module.state_dict(),
os.path.join(args.save_model_path, 'best_dice_loss.pth'))
precision_list.append(precision)
miou_list.append(miou)
epoch_x.append(epoch)
fig_loss.line(range(len(loss_list)),
loss_list,
legend_label='train loss, min: %.4f' % min(loss_list),
line_width=2,
line_color='red')
fig_precision.line(epoch_x,
precision_list,
legend_label='precision, max: %.4f' %
max(precision_list),
line_width=2,
line_color='blue')
fig_miou.line(epoch_x,
miou_list,
legend_label='miou, max: %.4f' % max(miou_list),
line_width=2,
line_color='green')
plotting.save(row(fig_loss, fig_precision, fig_miou))
def main():
# load data
print('\nloading the dataset ...')
assert opt.dataset == "ISIC2016" or opt.dataset == "ISIC2017"
if opt.dataset == "ISIC2016":
num_aug = 5
normalize = Normalize((0.7012, 0.5517, 0.4875),
(0.0942, 0.1331, 0.1521))
elif opt.dataset == "ISIC2017":
num_aug = 2
normalize = Normalize((0.6820, 0.5312, 0.4736),
(0.0840, 0.1140, 0.1282))
if opt.over_sample:
print('data is offline oversampled ...')
train_file = 'train_oversample.csv'
else:
print('no offline oversampling ...')
train_file = 'train.csv'
im_size = 224
transform_train = torch_transforms.Compose([
RatioCenterCrop(0.8),
Resize((256, 256)),
RandomCrop((224, 224)),
RandomRotate(),
RandomHorizontalFlip(),
RandomVerticalFlip(),
ToTensor(), normalize
])
transform_val = torch_transforms.Compose([
RatioCenterCrop(0.8),
Resize((256, 256)),
CenterCrop((224, 224)),
ToTensor(), normalize
])
trainset = ISIC(csv_file=train_file, transform=transform_train)
trainloader = torch.utils.data.DataLoader(
trainset,
batch_size=opt.batch_size,
shuffle=True,
num_workers=8,
worker_init_fn=_worker_init_fn_(),
drop_last=True)
valset = ISIC(csv_file='val.csv', transform=transform_val)
valloader = torch.utils.data.DataLoader(valset,
batch_size=64,
shuffle=False,
num_workers=8)
print('done\n')
# load models
print('\nloading the model ...')
if not opt.no_attention:
print('turn on attention ...')
if opt.normalize_attn:
print('use softmax for attention map ...')
else:
print('use sigmoid for attention map ...')
else:
print('turn off attention ...')
net = AttnVGG(num_classes=2,
attention=not opt.no_attention,
normalize_attn=opt.normalize_attn)
dice = DiceLoss()
if opt.focal_loss:
print('use focal loss ...')
criterion = FocalLoss(gama=2., size_average=True, weight=None)
else:
print('use cross entropy loss ...')
criterion = nn.CrossEntropyLoss()
print('done\n')
# move to GPU
print('\nmoving models to GPU ...')
model = nn.DataParallel(net, device_ids=device_ids).to(device)
criterion.to(device)
dice.to(device)
print('done\n')
# optimizer
optimizer = optim.SGD(model.parameters(),
lr=opt.lr,
momentum=0.9,
weight_decay=1e-4,
nesterov=True)
lr_lambda = lambda epoch: np.power(0.1, epoch // 10)
scheduler = lr_scheduler.LambdaLR(optimizer, lr_lambda=lr_lambda)
# training
print('\nstart training ...\n')
step = 0
EMA_accuracy = 0
AUC_val = 0
writer = SummaryWriter(opt.outf)
if opt.log_images:
data_iter = iter(valloader)
fixed_batch = next(data_iter)
fixed_batch = fixed_batch['image'][0:16, :, :, :].to(device)
for epoch in range(opt.epochs):
torch.cuda.empty_cache()
# adjust learning rate
scheduler.step()
current_lr = optimizer.param_groups[0]['lr']
writer.add_scalar('train/learning_rate', current_lr, epoch)
print("\nepoch %d learning rate %f\n" % (epoch + 1, current_lr))
# run for one epoch
for aug in range(num_aug):
for i, data in enumerate(trainloader, 0):
# warm up
model.train()
model.zero_grad()
optimizer.zero_grad()
inputs, seg, labels = data['image'], data['image_seg'], data[
'label']
seg = seg[:, -1:, :, :]
seg_1 = F.adaptive_avg_pool2d(seg,
im_size // opt.base_up_factor)
seg_2 = F.adaptive_avg_pool2d(
seg, im_size // opt.base_up_factor // 2)
inputs, seg_1, seg_2, labels = inputs.to(device), seg_1.to(
device), seg_2.to(device), labels.to(device)
# forward
pred, a1, a2 = model(inputs)
# backward
loss_c = criterion(pred, labels)
loss_seg1 = dice(a1, seg_1)
loss_seg2 = dice(a2, seg_2)
loss = loss_c + 0.001 * loss_seg1 + 0.01 * loss_seg2
loss.backward()
optimizer.step()
# display results
if i % 10 == 0:
model.eval()
pred, __, __ = model(inputs)
predict = torch.argmax(pred, 1)
total = labels.size(0)
correct = torch.eq(predict, labels).sum().double().item()
accuracy = correct / total
EMA_accuracy = 0.9 * EMA_accuracy + 0.1 * accuracy
writer.add_scalar('train/loss_c', loss_c.item(), step)
writer.add_scalar('train/loss_seg1', loss_seg1.item(),
step)
writer.add_scalar('train/loss_seg2', loss_seg2.item(),
step)
writer.add_scalar('train/accuracy', accuracy, step)
writer.add_scalar('train/EMA_accuracy', EMA_accuracy, step)
print(
"[epoch %d][aug %d/%d][iter %d/%d] loss_c %.4f loss_seg1 %.4f loss_seg2 %.4f accuracy %.2f%% EMA %.2f%%"
%
(epoch + 1, aug + 1, num_aug, i + 1, len(trainloader),
loss.item(), loss_seg1.item(), loss_seg2.item(),
(100 * accuracy), (100 * EMA_accuracy)))
step += 1
# the end of each epoch - validation results
model.eval()
total = 0
correct = 0
with torch.no_grad():
with open('val_results.csv', 'wt', newline='') as csv_file:
csv_writer = csv.writer(csv_file, delimiter=',')
for i, data in enumerate(valloader, 0):
images_val, labels_val = data['image'], data['label']
images_val, labels_val = images_val.to(
device), labels_val.to(device)
pred_val, __, __ = model(images_val)
predict = torch.argmax(pred_val, 1)
total += labels_val.size(0)
correct += torch.eq(predict,
labels_val).sum().double().item()
# record predictions
responses = F.softmax(pred_val,
dim=1).squeeze().cpu().numpy()
responses = [
responses[i] for i in range(responses.shape[0])
]
csv_writer.writerows(responses)
AP, AUC, precision_mean, precision_mel, recall_mean, recall_mel = compute_metrics(
'val_results.csv', 'val.csv')
# save checkpoints
print('\nsaving checkpoints ...\n')
checkpoint = {
'state_dict': model.module.state_dict(),
'opt_state_dict': optimizer.state_dict(),
}
torch.save(checkpoint,
os.path.join(opt.outf, 'checkpoint_latest.pth'))
if AUC > AUC_val: # save optimal validation model
torch.save(checkpoint, os.path.join(opt.outf,
'checkpoint.pth'))
AUC_val = AUC
# log scalars
writer.add_scalar('val/accuracy', correct / total, epoch)
writer.add_scalar('val/mean_precision', precision_mean, epoch)
writer.add_scalar('val/mean_recall', recall_mean, epoch)
writer.add_scalar('val/precision_mel', precision_mel, epoch)
writer.add_scalar('val/recall_mel', recall_mel, epoch)
writer.add_scalar('val/AP', AP, epoch)
writer.add_scalar('val/AUC', AUC, epoch)
print("\n[epoch %d] val result: accuracy %.2f%%" %
(epoch + 1, 100 * correct / total))
print(
"\nmean precision %.2f%% mean recall %.2f%% \nprecision for mel %.2f%% recall for mel %.2f%%"
% (100 * precision_mean, 100 * recall_mean,
100 * precision_mel, 100 * recall_mel))
print("\nAP %.4f AUC %.4f\n optimal AUC: %.4f" %
(AP, AUC, AUC_val))
# log images
if opt.log_images:
print('\nlog images ...\n')
I_train = utils.make_grid(inputs[0:16, :, :, :],
nrow=4,
normalize=True,
scale_each=True)
I_seg_1 = utils.make_grid(seg_1[0:16, :, :, :],
nrow=4,
normalize=True,
scale_each=True)
I_seg_2 = utils.make_grid(seg_2[0:16, :, :, :],
nrow=4,
normalize=True,
scale_each=True)
writer.add_image('train/image', I_train, epoch)
writer.add_image('train/seg1', I_seg_1, epoch)
writer.add_image('train/seg2', I_seg_2, epoch)
if epoch == 0:
I_val = utils.make_grid(fixed_batch,
nrow=4,
normalize=True,
scale_each=True)
writer.add_image('val/image', I_val, epoch)
if opt.log_images and (not opt.no_attention):
print('\nlog attention maps ...\n')
# training data
__, a1, a2 = model(inputs[0:16, :, :, :])
if a1 is not None:
attn1 = visualize_attn(I_train,
a1,
up_factor=opt.base_up_factor,
nrow=4)
writer.add_image('train/attention_map_1', attn1, epoch)
if a2 is not None:
attn2 = visualize_attn(I_train,
a2,
up_factor=2 * opt.base_up_factor,
nrow=4)
writer.add_image('train/attention_map_2', attn2, epoch)
# val data
__, a1, a2 = model(fixed_batch)
if a1 is not None:
attn1 = visualize_attn(I_val,
a1,
up_factor=opt.base_up_factor,
nrow=4)
writer.add_image('val/attention_map_1', attn1, epoch)
if a2 is not None:
attn2 = visualize_attn(I_val,
a2,
up_factor=2 * opt.base_up_factor,
nrow=4)
writer.add_image('val/attention_map_2', attn2, epoch)
def main():
# load the config
config = parse_train_config()
# load the model
model = Unet3d(in_channels=config.in_channels,
out_channels=config.out_channels,
interpolate=config.interpolate,
concatenate=config.concatenate,
norm_type=config.norm_type,
init_channels=config.init_channels,
scale_factor=(2, 2, 2))
if config.init_weight:
model.apply(init_weight)
# get the device to train on
gpu_all = tuple(config.gpu_index)
gpu_main = gpu_all[0]
device = torch.device(
'cuda:' + str(gpu_main) if torch.cuda.is_available() else 'cpu')
model = nn.DataParallel(model, device_ids=gpu_all)
model.to(device)
# load the saved checkpoint - update model parameters
utils.load_checkpoint(config.model_path, device, model)
for params in model.parameters():
params.requires_grad = False
model2 = smallmodel(out_channels=config.out_channels,
interpolate=config.interpolate,
norm_type=config.norm_type,
init_channels=config.init_channels)
if config.init_weight:
model2.apply(init_weight)
model2 = nn.DataParallel(model2, device_ids=gpu_all)
model2.to(device)
# load data
phase = 'train'
train_dataset = Hdf5Dataset(config.data_path, phase,
config.train_sub_index)
train_loader = DataLoader(dataset=train_dataset,
batch_size=config.train_batch_size,
shuffle=True,
num_workers=8,
pin_memory=True,
drop_last=True)
val_dataset = Hdf5Dataset(config.data_path, phase, config.val_sub_index)
val_loader = DataLoader(dataset=val_dataset,
batch_size=config.val_batch_size,
shuffle=False,
num_workers=8,
pin_memory=True,
drop_last=True)
# define accuracy
accuracy_criterion = DiceAccuracy()
# define loss
if config.loss_weight is None:
loss_criterion = DiceLoss()
else:
loss_criterion = DiceLoss(weight=config.loss_weight)
# define optimizer
optimizer = torch.optim.Adam(model2.parameters(),
lr=config.learning_rate,
weight_decay=config.weight_decay)
trainer = Trainer(config, model, model2, device, train_loader, val_loader,
accuracy_criterion, loss_criterion, optimizer)
trainer.main()
def display_dataset_details(dataset, train_set, val_set):
x = 'Total Images :'+str(len(dataset))
y = 'Total Training Images :'+str(len(train_set))
z = 'Total Validation Images :'+str(len(val_set))
return x,y,z
if(add_selectbox == 'Training'):
st.header(add_selectbox)
st.markdown('Device Detected : '+str(device))
st.write('Select Training Parameters')
epochs = st.number_input('Epochs', min_value = 1, value = 2)
lr = st.number_input('Learning Rate', min_value = 0.0001, max_value = None, value = 0.0010, step = 0.001, format = '%f')
if st.button('Load Data'):
dsc_loss = DiceLoss()
dataset = SyntheticCellDataset('dataset')
indices = torch.randperm(len(dataset)).tolist()
sr = int(0.2 * len(dataset))
train_set = torch.utils.data.Subset(dataset, indices[:-sr])
val_set = torch.utils.data.Subset(dataset, indices[-sr:])
train_loader = torch.utils.data.DataLoader(train_set, batch_size=2, shuffle=True, pin_memory=True)
val_loader = torch.utils.data.DataLoader(val_set, batch_size=2, shuffle=False, pin_memory=True)
st.write('Data Loaded')
x,y,z = display_dataset_details(dataset, train_set, val_set)
st.write(x)
st.write(y)
st.write(z)
#if st.button('Start Training'):
model = UNet()
model.to(device)
def train(args, model, optimizer, dataloader_train, dataloader_val_train,
dataloader_test):
writer = SummaryWriter(log_dir='runs_50_adadelta',
comment=''.format(args.optimizer,
args.context_path))
if args.loss == 'dice':
loss_func = DiceLoss()
elif args.loss == 'crossentropy':
loss_func = torch.nn.CrossEntropyLoss()
max_miou = 0
step = 0
for epoch in range(args.epoch_start_i, args.num_epochs):
lr = poly_lr_scheduler(optimizer,
args.learning_rate,
iter=epoch,
max_iter=args.num_epochs)
model.train()
tq = tqdm.tqdm(total=len(dataloader_train) * args.batch_size)
tq.set_description('epoch %d, lr %f' % (epoch, lr))
loss_record = []
for i, (data, label) in enumerate(dataloader_train):
if torch.cuda.is_available() and args.use_gpu:
data = data.cuda()
label = label.cuda()
output, output_sup1, output_sup2 = model(data)
loss1 = loss_func(output, label)
loss2 = loss_func(output_sup1, label)
loss3 = loss_func(output_sup2, label)
loss = loss1 + loss2 + loss3
tq.update(args.batch_size)
tq.set_postfix(loss='%.6f' % loss)
optimizer.zero_grad()
loss.backward()
optimizer.step()
step += 1
writer.add_scalar('loss_step', loss, step)
loss_record.append(loss.item())
tq.close()
loss_train_mean = np.mean(loss_record)
writer.add_scalar('epoch/loss_epoch_train', float(loss_train_mean),
epoch)
print('loss for train : %f' % (loss_train_mean))
if epoch % args.checkpoint_step == 0 and epoch != 0:
if not os.path.isdir(args.save_model_path):
os.mkdir(args.save_model_path)
torch.save(
model.module.state_dict(),
os.path.join(args.save_model_path, 'latest_dice_loss.pth'))
if epoch % args.validation_step == 0:
#precision, miou = val(args, model, dataloader_val)
oa, miou, cm, cks, f1 = val(args, model, dataloader_val_train,
'train')
oa_test, miou_test, cm_test, cks_test, f1_test = val(
args, model, dataloader_test, 'test')
if miou > max_miou:
max_miou = miou
torch.save(
model.module.state_dict(),
os.path.join(args.save_model_path, 'best_dice_loss.pth'))
#writer.add_scalar('epoch/precision_val', precision, epoch)
writer.add_scalar('epoch/oa_train', oa, epoch)
writer.add_scalar('epoch/oa_test', oa_test, epoch)
#writer.add_scalar('epoch/miou val', miou, epoch)
writer.add_scalar('epoch/miou_train', miou, epoch)
writer.add_scalar('epoch/miou_test', miou_test, epoch)
writer.add_scalar('epoch/cks_train', cks, epoch)
writer.add_scalar('epoch/cks_test', cks_test, epoch)
writer.add_scalar('epoch/f1_train', f1, epoch)
writer.add_scalar('epoch/f1_test', f1_test, epoch)
with open(os.path.join(args.save_model_path,
'classification_results.txt'),
mode='a') as f:
f.write('epoch: ' + str(epoch) + '\n')
# f.write('train time:\t' + str(train_time))
# f.write('\ntest time:\t' + str(test_time))
f.write('\nmiou:\t' + str(miou))
f.write('\noverall accuracy:\t' + str(oa))
f.write('\ncohen kappa:\t' + str(cks))
f.write('\nconfusion matrix:\n')
f.write(str(cm))
f.write('\nf1:\t' + str(f1))
f.write('\n\n')
data_dir = './data'
train_csv_path = os.path.join(data_dir, 'train.csv')
test_csv_path = os.path.join(data_dir, 'test.csv')
train_images_dir = os.path.join(data_dir, 'stage_1_train_images/')
test_images_dir = os.path.join(data_dir, 'stage_1_test_images/')
train_df, train_loader, dev_pids, dev_loader, dev_dataset_for_predict, dev_loader_for_predict, test_loader, test_df, test_pids, boxes_by_pid_dict, min_box_area = load_data(
train_csv_path, test_csv_path, train_images_dir, test_images_dir,
batch_size, validation_prop, rescale_factor)
min_box_area = int(round(min_box_area / float(rescale_factor**2)))
# model = torch.nn.DataParallel(LeakyUNET().cuda(), device_ids=[0, 1, 2, 3, 4, 5, 6, 7])
model = torch.nn.DataParallel(LeakyUNET().cuda(), device_ids=[0, 1, 2, 3])
loss_fn = DiceLoss().cuda()
init_learning_rate = 0.5
num_epochs = 1 if debug else 5
num_train_steps = 5 if debug else len(train_loader)
num_dev_steps = 5 if debug else len(dev_loader)
img_dim = int(round(original_dim / rescale_factor))
print("Training for {} epochs".format(num_epochs))
histories, best_models = train_and_evaluate(model,
train_loader,
dev_loader,
init_learning_rate,
loss_fn,
parser.add_argument('--restart', type=int, default=50,
help='restart learning rate every <restart> epochs')
parser.add_argument('--resume_model',
type=str,
default=None,
help='path to load previously saved model')
args = parser.parse_args(argv)
print(args)
is_cuda = torch.cuda.is_available()
net = UNet3D(1, 1, use_bias=True, inplanes=16)
if args.resume_model is not None:
transfer_weights(net, args.resume_model)
bce_crit = nn.BCELoss()
dice_crit = DiceLoss()
last_bce_loss = 0
last_dice_loss = 0
def criterion(pred, labels, weights=[0.1, 0.9]):
_bce_loss = bce_crit(pred, labels)
_dice_loss = dice_crit(pred, labels)
global last_bce_loss, last_dice_loss
last_bce_loss = _bce_loss.item()
last_dice_loss = _dice_loss.item()
return weights[0] * _bce_loss + weights[1] * _dice_loss
size = args.volume_size * 3 if len(args.volume_size) == 1 else args.volume_size
assert len(size) == 3
def main():
args = parser.parse_args()
save_path = 'Trainid_' + args.id
writer = SummaryWriter(log_dir='runs/' + args.tag + str(time.time()))
if not os.path.isdir(save_path):
os.mkdir(save_path)
os.mkdir(save_path + '/Checkpoint')
train_dataset_path = 'data/train'
val_dataset_path = 'data/valid'
train_transform = transforms.Compose([ToTensor()])
val_transform = transforms.Compose([ToTensor()])
train_dataset = TrainDataset(path=train_dataset_path,
transform=train_transform)
val_dataset = TrainDataset(path=val_dataset_path, transform=val_transform)
train_dataloader = DataLoader(train_dataset,
batch_size=args.batch_size,
shuffle=True,
pin_memory=True,
num_workers=4)
val_dataloader = DataLoader(val_dataset,
batch_size=args.batch_size,
shuffle=False,
pin_memory=True,
num_workers=4)
size_train = len(train_dataloader)
size_val = len(val_dataloader)
print('Number of Training Images: {}'.format(size_train))
print('Number of Validation Images: {}'.format(size_val))
start_epoch = 0
model = Res(n_ch=4, n_classes=9)
class_weights = torch.Tensor([1, 1, 1, 1, 1, 1, 1, 1, 0]).cuda()
criterion = DiceLoss()
criterion1 = torch.nn.CrossEntropyLoss(weight=class_weights)
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
if args.gpu:
model = model.cuda()
criterion = criterion.cuda()
criterion1 = criterion1.cuda()
if args.resume is not None:
weight_path = sorted(os.listdir(save_path + '/Checkpoint/'),
key=lambda x: float(x[:-8]))[0]
checkpoint = torch.load(save_path + '/Checkpoint/' + weight_path)
start_epoch = checkpoint['epoch']
model.load_state_dict(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
print('Loaded Checkpoint of Epoch: {}'.format(args.resume))
for epoch in range(start_epoch, int(args.epoch) + start_epoch):
adjust_learning_rate(optimizer, epoch)
train(model, train_dataloader, criterion, criterion1, optimizer, epoch,
writer, size_train)
print('')
val_loss = val(model, val_dataloader, criterion, criterion1, epoch,
writer, size_val)
print('')
save_checkpoint(
{
'epoch': epoch + 1,
'state_dict': model.state_dict(),
'optimizer': optimizer.state_dict(),
},
filename=save_path + '/Checkpoint/' + str(val_loss) + '.pth.tar')
writer.export_scalars_to_json(save_path + '/log.json')
def train_net(image_size, batch_size, num_epochs, lr, num_workers, checkpoint):
train_loader, val_loader = data_loaders(image_size=(image_size,
image_size),
batch_size=batch_size)
device = torch.device('cuda') if torch.cuda.is_available() else 'cpu'
model = Unet().to(device)
if checkpoint:
model.load_state_dict(torch.load(checkpoint))
criterion = DiceLoss().to(device)
optimizer = Adam(model.parameters(), lr=lr)
logging.info(f'Start training:\n'
f'Num epochs: {num_epochs}\n'
f'Batch size: {batch_size}\n'
f'Learning rate: {lr}\n'
f'Num workers: {num_workers}\n'
f'Scale image size: {image_size}\n'
f'Device: {device}\n'
f'Checkpoint: {checkpoint}\n')
train_losses = []
val_losses = []
for epoch in range(num_epochs):
print(f'Epoch {epoch+1}: ')
train_batch_losses = []
val_batch_losses = []
best_val_loss = 9999
for x_train, y_train in tqdm(train_loader):
x_train = x_train.to(device)
y_train = y_train.to(device)
y_pred = model(x_train)
optimizer.zero_grad()
loss = criterion(y_pred, y_train)
train_batch_losses.append(loss.item())
loss.backward()
optimizer.step()
train_losses.append(sum(train_batch_losses) / len(train_batch_losses))
print(
f'-----------------------Train loss: {train_losses[-1]} -------------------------------'
)
for x_val, y_val in tqdm(val_loader):
x_val = x_val.to(device)
y_val = y_val.to(device)
y_pred = model(x_val)
loss = criterion(y_pred, y_val)
val_batch_losses.append(loss.item())
val_losses.append(sum(val_batch_losses) / len(val_batch_losses))
print(
f'-----------------------Val loss: {val_losses[-1]} -------------------------------'
)
if val_losses[-1] < best_val_loss:
best_val_loss = val_losses[-1]
if not os.path.isdir('weights/'):
os.mkdir('weights/')
torch.save(model.state_dict(), f'weights/checkpoint{epoch+1}.pth')
print(f'Save checkpoint in: weights/checkpoint{epoch+1}.pth')
# optimizer = torch.optim.RMSprop(params, lr=config.lr, alpha = 0.95)
# optimizer = RAdam(params, lr=1e-3, betas=(0.9, 0.999), eps=1e-8, weight_decay=0)
# optimizer = PlainRAdam(params, lr=1e-3, betas=(0.9, 0.999), eps=1e-8, weight_decay=0)
if os.path.exists(config.init_optimizer):
ckpt = torch.load(config.init_optimizer)
optimizer.load_state_dict(ckpt['optimizer'])
# lr_scheduler
# lr_scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=4, gamma=0.3)
scheduler_cosine = torch.optim.lr_scheduler.CosineAnnealingLR(optimizer, config.num_epochs*len(data_loader))
lr_scheduler = GradualWarmupScheduler(optimizer, multiplier=100,
total_epoch=min(1000, len(data_loader)-1),
after_scheduler=scheduler_cosine)
# loss function
criterion = DiceLoss()
# criterion = Weight_Soft_Dice_Loss(weight=[0.1, 0.9])
# criterion = BCELoss()
# criterion = MixedLoss(10.0, 2.0)
# criterion = Weight_BCELoss(weight_pos=0.25, weight_neg=0.75)
# criterion = Lovasz_Loss(margin=[1, 5]
print('start training...')
train_start = time.time()
for epoch in range(config.num_epochs):
epoch_start = time.time()
model_ft, optimizer = train_one_epoch(model_ft, data_loader, criterion,
optimizer, lr_scheduler=lr_scheduler, device=device,
epoch=epoch, vis=vis)
do_valid(model_ft, dataloader_val, criterion, epoch, device, vis=vis)
print('Epoch time: {:.3f}min\n'.format((time.time()-epoch_start)/60/60))
def __init__(self, args, logger):
"""Constructor for training algorithm.
Args:
args: From command line, picked up by `argparse`.
Initializes:
- Data: train, val and test.
- Model: shared and controller.
- Inference: optimizers for shared and controller parameters.
- Criticism: cross-entropy loss for training the shared model.
"""
self.args = args
self.controller_step = 0
self.cuda = args.cuda
self.epoch = 0
self.shared_step = 0
self.start_epoch = 0
self.logger = logger
self.baseline = None
"""Load dataset"""
self.load_dataset()
if args.mode == 'train':
self.train_data_loader.restart()
if args.use_tensorboard:
self.tb = TensorBoard(args.model_dir)
else:
self.tb = None
self.build_model()
if self.args.load_path:
self.load_model()
shared_optimizer = _get_optimizer(self.args.shared_optim)
controller_optimizer = _get_optimizer(self.args.controller_optim)
self.shared_optim = shared_optimizer(
self.shared.parameters(),
lr=self.shared_lr,
)
self.controller_optim = controller_optimizer(
self.controller.parameters(), lr=self.args.controller_lr)
self.ce = nn.CrossEntropyLoss()
if self.args.loss == 'MulticlassDiceLoss':
self.model_loss = MulticlassDiceLoss()
else:
self.model_loss = DiceLoss()
self.time = time.time()
self.dag_file = open(
self.args.model_dir + '/' + self.args.mode + '_dag.log', 'a')
cnn_type_index = {}
for i, action in enumerate(self.args.shared_cnn_types):
cnn_type_index[action] = i
if self.args.use_ref:
self.ref_arch_num = []
ip = []
action = []
for i, block in enumerate(self.args.ref_arch):
ip.append(block[0])
action.append(cnn_type_index[block[1]])
for i in range(len(ip) / 2):
self.ref_arch_num.append(
[ip[i], ip[i + 1], action[i], action[i + 1]])
self.ref_arch_num = np.array(self.ref_arch_num)
self.ref_arch_num = self.ref_arch_num.reshape(
1, 2 * len(self.ref_arch_num))
"""