def train(args):
if not os.path.exists('checkpoints'):
os.mkdir('checkpoints')
# Setup Augmentations
data_aug = transforms.Compose([
transforms.ToPILImage(),
transforms.RandomHorizontalFlip(p=0.5),
transforms.RandomAffine(degrees=10,
translate=(0.05, 0.05),
scale=(0.95, 1.05)),
])
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
t_loader = data_loader(data_path,
is_transform=True,
split='train',
version='simplified',
img_size=(args.img_rows, args.img_cols),
augmentations=data_aug,
train_fold_num=args.train_fold_num,
num_train_folds=args.num_train_folds,
seed=args.seed)
v_loader = data_loader(data_path,
is_transform=True,
split='val',
version='simplified',
img_size=(args.img_rows, args.img_cols),
num_val=args.num_val,
seed=args.seed)
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
n_classes = t_loader.n_classes
trainloader = data.DataLoader(t_loader,
batch_size=args.batch_size,
num_workers=2,
shuffle=True,
pin_memory=True,
drop_last=True)
valloader = data.DataLoader(v_loader,
batch_size=args.batch_size,
num_workers=2,
pin_memory=True)
# Setup Metrics
running_metrics = runningScore(n_classes)
# Setup Model
v_demision = 300
model = get_model(args.arch, v_demision, use_cbam=args.use_cbam)
model.cuda()
optimizer = torch.optim.Adam(filter(lambda p: p.requires_grad,
model.parameters()),
lr=args.l_rate,
weight_decay=args.weight_decay)
if args.num_cycles > 0:
len_trainloader = int(5e6) # 4960414
scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
optimizer,
T_max=args.num_train_folds * len_trainloader // args.num_cycles,
eta_min=args.l_rate * 1e-1)
else:
scheduler = torch.optim.lr_scheduler.MultiStepLR(
optimizer, milestones=[2, 4, 6, 8], gamma=0.5)
start_epoch = 0
if args.resume is not None:
if os.path.isfile(args.resume):
print("Loading model and optimizer from checkpoint '{}'".format(
args.resume))
checkpoint = torch.load(args.resume)
model_dict = model.state_dict()
if checkpoint.get('model_state', -1) == -1:
model_dict.update(
convert_state_dict(checkpoint,
load_classifier=args.load_classifier))
else:
model_dict.update(
convert_state_dict(checkpoint['model_state'],
load_classifier=args.load_classifier))
print(
"Loaded checkpoint '{}' (epoch {}, mapk {:.5f}, top1_acc {:7.3f}, top2_acc {:7.3f} top3_acc {:7.3f})"
.format(args.resume, checkpoint['epoch'],
checkpoint['mapk'], checkpoint['top1_acc'],
checkpoint['top2_acc'], checkpoint['top3_acc']))
model.load_state_dict(model_dict)
if checkpoint.get('optimizer_state', None) is not None:
optimizer.load_state_dict(checkpoint['optimizer_state'])
start_epoch = checkpoint['epoch']
else:
print("No checkpoint found at '{}'".format(args.resume))
loss_sum = 0.0
for epoch in range(start_epoch, args.n_epoch):
start_train_time = timeit.default_timer()
if args.num_cycles == 0:
scheduler.step(epoch)
model.train()
optimizer.zero_grad()
for i, (images, labels, recognized, _) in enumerate(trainloader):
if args.num_cycles > 0:
iter_num = i + epoch * len_trainloader
scheduler.step(
iter_num %
(args.num_train_folds * len_trainloader //
args.num_cycles)) # Cosine Annealing with Restarts
images = images.cuda()
labels = labels.cuda()
outputs = model(images)
a_loss = Adptive_loss().cuda()
loss = a_loss(outputs, labels)
loss = loss / float(args.iter_size) # Accumulated gradients
loss_sum = loss_sum + loss
loss.backward()
if (i + 1) % args.print_train_freq == 0:
print("Epoch [%d/%d] Iter [%6d/%6d] Loss: %.4f" %
(epoch + 1, args.n_epoch, i + 1, len(trainloader),
loss_sum))
if (i + 1) % args.iter_size == 0 or i == len(trainloader) - 1:
optimizer.step()
optimizer.zero_grad()
loss_sum = 0.0
elapsed_train_time = timeit.default_timer() - start_train_time
print('Training time (epoch {0:5d}): {1:10.5f} seconds'.format(
epoch + 1, elapsed_train_time))
def train(args):
if not os.path.exists('checkpoints'):
os.mkdir('checkpoints')
# Setup Augmentations
data_aug = transforms.Compose([
transforms.ToPILImage(),
transforms.RandomHorizontalFlip(p=0.5),
transforms.RandomAffine(degrees=10, translate=(0.05, 0.05), scale=(0.95, 1.05)),
])
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
t_loader = data_loader(data_path, is_transform=True, split='train', version='simplified', img_size=(args.img_rows, args.img_cols), augmentations=data_aug, train_fold_num=args.train_fold_num, num_train_folds=args.num_train_folds, seed=args.seed)
v_loader = data_loader(data_path, is_transform=True, split='val', version='simplified', img_size=(args.img_rows, args.img_cols), num_val=args.num_val, seed=args.seed)
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
n_classes = t_loader.n_classes
trainloader = data.DataLoader(t_loader, batch_size=args.batch_size, num_workers=2, shuffle=True, pin_memory=True, drop_last=True)
valloader = data.DataLoader(v_loader, batch_size=args.batch_size, num_workers=2, pin_memory=True)
# Setup Metrics
running_metrics = runningScore(n_classes)
# Setup Model
# model = get_model(args.arch, n_classes, use_cbam=args.use_cbam)
model = torchvision.models.mobilenet_v2(pretrained=True)
num_ftrs = model.last_channel
model.classifier = nn.Sequential(
nn.Dropout(0.2),
nn.Linear(num_ftrs, n_classes),
)
model.cuda()
# Check if model has custom optimizer / loss
if hasattr(model, 'optimizer'):
optimizer = model.optimizer
else:
##optimizer = torch.optim.SGD(filter(lambda p: p.requires_grad, model.parameters()), lr=args.l_rate, momentum=args.momentum, weight_decay=args.weight_decay)
optimizer = torch.optim.Adam(model.parameters(), lr=args.l_rate, weight_decay=args.weight_decay)
# if args.num_cycles > 0:
# len_trainloader = int(5e6) # 4960414
# scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=args.num_train_folds*len_trainloader//args.num_cycles, eta_min=args.l_rate*1e-1)
# else:
# scheduler = torch.optim.lr_scheduler.MultiStepLR(optimizer, milestones=[2, 4, 6, 8], gamma=0.5)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer,mode='min',factor=0.5,patience=5,cooldown=5,min_lr=1e-7)
if hasattr(model, 'loss'):
print('Using custom loss')
loss_fn = model.loss
else:
loss_fn = F.cross_entropy
start_epoch = 0
if args.resume is not None:
if os.path.isfile(args.resume):
print("Loading model and optimizer from checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
model_dict = model.state_dict()
if checkpoint.get('model_state', -1) == -1:
model_dict.update(convert_state_dict(checkpoint, load_classifier=args.load_classifier))
else:
model_dict.update(convert_state_dict(checkpoint['model_state'], load_classifier=args.load_classifier))
print("Loaded checkpoint '{}' (epoch {}, mapk {:.5f}, top1_acc {:7.3f}, top2_acc {:7.3f} top3_acc {:7.3f})"
.format(args.resume, checkpoint['epoch'], checkpoint['mapk'], checkpoint['top1_acc'], checkpoint['top2_acc'], checkpoint['top3_acc']))
model.load_state_dict(model_dict)
if checkpoint.get('optimizer_state', None) is not None:
optimizer.load_state_dict(checkpoint['optimizer_state'])
start_epoch = checkpoint['epoch']
else:
print("No checkpoint found at '{}'".format(args.resume))
loss_sum = 0.0
for epoch in range(start_epoch, args.n_epoch):
start_train_time = timeit.default_timer()
model.train()
optimizer.zero_grad()
for i, (images, labels, recognized, _) in enumerate(trainloader):
images = images.cuda()
labels = labels.cuda()
recognized = recognized.cuda()
outputs = model(images)
loss = (loss_fn(outputs, labels.view(-1), ignore_index=t_loader.ignore_index, reduction='none') * recognized.view(-1)).mean()
# loss = loss / float(args.iter_size) # Accumulated gradients
loss_sum = loss_sum + loss
loss.backward()
if (i+1) % args.print_train_freq == 0:
print("Epoch [%d/%d] Iter [%6d/%6d] Loss: %.4f" % (epoch+1, args.n_epoch, i+1, len(trainloader), loss_sum))
if (i+1) % args.iter_size == 0 or i == len(trainloader) - 1:
optimizer.step()
optimizer.zero_grad()
loss_sum = 0.0
mapk_val = AverageMeter()
top1_acc_val = AverageMeter()
top2_acc_val = AverageMeter()
top3_acc_val = AverageMeter()
mean_loss_val = AverageMeter()
model.eval()
with torch.no_grad():
for i_val, (images_val, labels_val, recognized_val, _) in tqdm(enumerate(valloader)):
images_val = images_val.cuda()
labels_val = labels_val.cuda()
recognized_val = recognized_val.cuda()
outputs_val = model(images_val)
loss_val = (loss_fn(outputs_val, labels_val.view(-1), ignore_index=v_loader.ignore_index, reduction='none') * recognized_val.view(-1)).mean()
mean_loss_val.update(loss_val, n=images_val.size(0))
_, pred = outputs_val.topk(k=3, dim=1, largest=True, sorted=True)
running_metrics.update(labels_val, pred[:, 0])
acc1, acc2, acc3 = accuracy(outputs_val, labels_val, topk=(1, 2, 3))
top1_acc_val.update(acc1, n=images_val.size(0))
top2_acc_val.update(acc2, n=images_val.size(0))
top3_acc_val.update(acc3, n=images_val.size(0))
mapk_v = mapk(labels_val, pred, k=3)
mapk_val.update(mapk_v, n=images_val.size(0))
print('Mean Average Precision (MAP) @ 3: {:.5f}'.format(mapk_val.avg))
print('Top 3 accuracy: {:7.3f} / {:7.3f} / {:7.3f}'.format(top1_acc_val.avg, top2_acc_val.avg, top3_acc_val.avg))
print('Mean val loss: {:.4f}'.format(mean_loss_val.avg))
score, class_iou = running_metrics.get_scores()
for k, v in score.items():
print(k, v)
#for i in range(n_classes):
# print(i, class_iou[i])
scheduler.step(mean_loss_val.avg)
state = {'epoch': epoch+1,
'model_state': model.state_dict(),
'optimizer_state': optimizer.state_dict(),
'mapk': mapk_val.avg,
'top1_acc': top1_acc_val.avg,
'top2_acc': top2_acc_val.avg,
'top3_acc': top3_acc_val.avg,}
torch.save(state, "checkpoints/{}_{}_{}_{}x{}_{}-{}-{}_model.pth".format(args.arch, args.dataset, epoch+1, args.img_rows, args.img_cols, args.train_fold_num, args.num_train_folds, args.num_val))
running_metrics.reset()
mapk_val.reset()
top1_acc_val.reset()
top2_acc_val.reset()
top3_acc_val.reset()
mean_loss_val.reset()
elapsed_train_time = timeit.default_timer() - start_train_time
print('Training time (epoch {0:5d}): {1:10.5f} seconds'.format(epoch+1, elapsed_train_time))
def merge(args):
if not os.path.exists(args.root_results):
os.makedirs(args.root_results)
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
loader = data_loader(data_path, split=args.split, transforms=None, fold_num=0, num_folds=1, no_gt=args.no_gt, seed=args.seed, no_load_images=True)
n_classes = loader.n_classes
testloader = data.DataLoader(loader, batch_size=args.batch_size)#, num_workers=2, pin_memory=True)
avg_y_prob = np.zeros((loader.__len__(), 1, 1024, 1024), dtype=np.float32)
avg_y_pred_sum = np.zeros((loader.__len__(),), dtype=np.int32)
fold_list = []
for prob_file_name in glob.glob(os.path.join(args.root_results, '*.npy')):
prob = np.load(prob_file_name, mmap_mode='r')
for i in range(loader.__len__()):
avg_y_prob[i, :, :, :] += prob[i, :, :, :]
fold_list.append(prob_file_name)
print(prob_file_name)
avg_y_prob = avg_y_prob / len(fold_list)
##avgprob_file_name = 'prob_{}_avg'.format(len(fold_list))
##np.save(os.path.join(args.root_results, '{}.npy'.format(avgprob_file_name)), avg_y_prob)
avg_y_pred = (avg_y_prob > args.thresh).astype(np.int)
avg_y_pred_sum = avg_y_pred.sum(3).sum(2).sum(1)
avg_y_pred_sum_argsorted = np.argsort(avg_y_pred_sum)[::-1]
pruned_idx = int(avg_y_pred_sum_argsorted.shape[0]*args.non_empty_ratio)
mask_sum_thresh = int(avg_y_pred_sum[avg_y_pred_sum_argsorted[pruned_idx]]) if pruned_idx < avg_y_pred_sum_argsorted.shape[0] else 0
running_metrics = runningScore(n_classes=2, weight_acc_non_empty=args.weight_acc_non_empty)
pred_dict = collections.OrderedDict()
num_non_empty_masks = 0
for i, (_, labels, names) in tqdm(enumerate(testloader)):
labels = labels.cuda()
prob = avg_y_prob[i*args.batch_size:i*args.batch_size+labels.size(0), :, :, :]
pred = (prob > args.thresh).astype(np.int)
pred = torch.from_numpy(pred).long().cuda()
pred_sum = pred.sum(3).sum(2).sum(1)
for k in range(labels.size(0)):
if pred_sum[k] > mask_sum_thresh:
num_non_empty_masks += 1
else:
pred[k, :, :, :] = torch.zeros_like(pred[k, :, :, :])
if args.only_non_empty:
pred[k, :, 0, 0] = 1
if not args.no_gt:
running_metrics.update(labels.long(), pred.long())
for k in range(labels.size(0)):
name = names[0][k]
if pred_dict.get(name, None) is None:
mask = pred[k, 0, :, :].cpu().numpy()
rle = loader.mask2rle(mask)
pred_dict[name] = rle
print('# non-empty masks: {:5d} (non_empty_ratio: {:.5f} / mask_sum_thresh: {:6d})'.format(num_non_empty_masks, args.non_empty_ratio, mask_sum_thresh))
if not args.no_gt:
dice, dice_empty, dice_non_empty, miou, acc, acc_empty, acc_non_empty = running_metrics.get_scores()
print('Dice (per image): {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.format(dice, dice_empty, dice_non_empty))
print('Classification accuracy: {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.format(acc, acc_empty, acc_non_empty))
print('Overall mIoU: {:.5f}'.format(miou))
running_metrics.reset()
# Create submission
csv_file_name = 'merged_{}_{}_{}_{}'.format(args.split, len(fold_list), args.thresh, args.non_empty_ratio)
sub = pd.DataFrame.from_dict(pred_dict, orient='index')
sub.index.names = ['ImageId']
sub.columns = ['EncodedPixels']
sub.to_csv(os.path.join(args.root_results, '{}.csv'.format(csv_file_name)))
def test(args):
model_file_name = os.path.split(args.model_path)[1]
model_name = model_file_name[:model_file_name.find('_')]
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
loader = data_loader(data_path,
split=args.split,
is_transform=True,
img_size=(args.img_rows, args.img_cols),
no_gt=args.no_gt,
seed=args.seed)
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
n_classes = loader.n_classes
testloader = data.DataLoader(loader,
batch_size=args.batch_size,
num_workers=4,
pin_memory=True)
# Setup Model
model = torchvision.models.mobilenet_v2(pretrained=True)
num_ftrs = model.last_channel
model.classifier = nn.Sequential(
nn.Dropout(0.2),
nn.Linear(num_ftrs, n_classes),
)
model.cuda()
checkpoint = torch.load(args.model_path)
state = convert_state_dict(checkpoint['model_state'])
model_dict = model.state_dict()
model_dict.update(state)
model.load_state_dict(model_dict)
print(
"Loaded checkpoint '{}' (epoch {}, mapk {:.5f}, top1_acc {:7.3f}, top2_acc {:7.3f} top3_acc {:7.3f})"
.format(args.model_path, checkpoint['epoch'], checkpoint['mapk'],
checkpoint['top1_acc'], checkpoint['top2_acc'],
checkpoint['top3_acc']))
running_metrics = runningScore(n_classes)
pred_dict = collections.OrderedDict()
mapk = AverageMeter()
model.eval()
with torch.no_grad():
for i, (images, labels, _, names) in tqdm(enumerate(testloader)):
plt.imshow((images[0].numpy().transpose(1, 2, 0) -
np.min(images[0].numpy().transpose(1, 2, 0))) /
(np.max(images[0].numpy().transpose(1, 2, 0) -
np.min(images[0].numpy().transpose(1, 2, 0)))))
plt.show()
images = images.cuda()
if args.tta:
images_flip = flip(images, dim=3)
outputs = model(images)
if args.tta:
outputs_flip = model(images_flip)
prob = F.softmax(outputs, dim=1)
if args.tta:
prob_flip = F.softmax(outputs_flip, dim=1)
prob = (prob + prob_flip) / 2.0
_, pred = prob.topk(k=3, dim=1, largest=True, sorted=True)
for k in range(images.size(0)):
pred_dict[int(names[0][k])] = loader.encode_pred_name(
pred[k, :])
if not args.no_gt:
running_metrics.update(labels, pred)
mapk_val = mapk(labels, pred, k=3)
mapk.update(mapk_val, n=images.size(0))
print('Mean Average Precision (MAP) @ 3: {:.5f}'.format(mapk.avg))
if not args.no_gt:
print('Mean Average Precision (MAP) @ 3: {:.5f}'.format(mapk.avg))
score, class_iou = running_metrics.get_scores()
for k, v in score.items():
print(k, v)
#for i in range(n_classes):
# print(i, class_iou[i])
running_metrics.reset()
mapk.reset()
# Create submission
sub = pd.DataFrame.from_dict(pred_dict, orient='index')
sub.index.names = ['key_id']
sub.columns = ['word']
sub.to_csv('{}_{}x{}.csv'.format(args.split, args.img_rows, args.img_cols))
def train(args):
if not os.path.exists('checkpoints'):
os.mkdir('checkpoints')
# Setup Augmentations & Transforms
rgb_mean = [122.7717 / 255., 115.9465 / 255., 102.9801 /
255.] if args.norm_type == 'gn' and args.load_pretrained else [
0.485, 0.456, 0.406
]
rgb_std = [1. / 255., 1. / 255., 1. /
255.] if args.norm_type == 'gn' and args.load_pretrained else [
0.229, 0.224, 0.225
]
data_trans = transforms.Compose([
transforms.ToPILImage(),
transforms.Resize(size=(args.img_rows, args.img_cols)),
transforms.ToTensor(),
transforms.Normalize(mean=rgb_mean, std=rgb_std),
])
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
t_loader = data_loader(data_path,
transforms=data_trans,
in_channels=args.in_channels,
split='train',
augmentations=True,
fold_num=args.fold_num,
num_folds=args.num_folds,
only_non_empty=args.only_non_empty,
seed=args.seed,
mask_dilation_size=args.mask_dilation_size)
v_loader = data_loader(data_path,
transforms=data_trans,
in_channels=args.in_channels,
split='val',
fold_num=args.fold_num,
num_folds=args.num_folds,
only_non_empty=args.only_non_empty,
seed=args.seed)
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
trainloader = data.DataLoader(t_loader,
batch_size=args.batch_size,
num_workers=2,
pin_memory=True,
shuffle=args.only_non_empty,
drop_last=args.only_non_empty)
valloader = data.DataLoader(v_loader,
batch_size=args.batch_size,
num_workers=2,
pin_memory=True)
# Setup Model
model = get_model(args.arch,
n_classes=1,
in_channels=args.in_channels,
norm_type=args.norm_type,
load_pretrained=args.load_pretrained,
use_cbam=args.use_cbam)
model.to(torch.device(args.device))
running_metrics = runningScore(
n_classes=2,
weight_acc_non_empty=args.weight_acc_non_empty,
device=args.device)
# Check if model has custom optimizer / loss
if hasattr(model, 'optimizer'):
optimizer = model.optimizer
else:
warmup_iter = int(args.n_iter * 5. / 100.)
milestones = [
int(args.n_iter * 30. / 100.) - warmup_iter,
int(args.n_iter * 60. / 100.) - warmup_iter,
int(args.n_iter * 90. / 100.) - warmup_iter
] # [30, 60, 90]
gamma = 0.5 #0.1
if args.optimizer_type == 'sgd':
optimizer = torch.optim.SGD(group_weight(model),
lr=args.l_rate,
momentum=args.momentum,
weight_decay=args.weight_decay)
elif args.optimizer_type == 'adam':
optimizer = torch.optim.Adam(group_weight(model),
lr=args.l_rate,
weight_decay=args.weight_decay)
else: #if args.optimizer_type == 'radam':
optimizer = RAdam(group_weight(model),
lr=args.l_rate,
weight_decay=args.weight_decay)
if args.num_cycles > 0:
scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
optimizer,
T_max=(args.n_iter - warmup_iter) // args.num_cycles,
eta_min=args.l_rate * 0.1)
else:
scheduler = torch.optim.lr_scheduler.MultiStepLR(
optimizer, milestones=milestones, gamma=gamma)
scheduler_warmup = GradualWarmupScheduler(optimizer,
total_epoch=warmup_iter,
min_lr_mul=0.1,
after_scheduler=scheduler)
start_iter = 0
if args.resume is not None:
if os.path.isfile(args.resume):
print("Loading model and optimizer from checkpoint '{}'".format(
args.resume))
checkpoint = torch.load(args.resume,
map_location=torch.device(
args.device)) #, encoding="latin1")
model_dict = model.state_dict()
if checkpoint.get('model_state', None) is not None:
model_dict.update(convert_state_dict(
checkpoint['model_state']))
else:
model_dict.update(convert_state_dict(checkpoint))
start_iter = checkpoint.get('iter', -1)
dice_val = checkpoint.get('dice', -1)
wacc_val = checkpoint.get('wacc', -1)
print("Loaded checkpoint '{}' (iter {}, dice {:.5f}, wAcc {:.5f})".
format(args.resume, start_iter, dice_val, wacc_val))
model.load_state_dict(model_dict)
if checkpoint.get('optimizer_state', None) is not None:
optimizer.load_state_dict(checkpoint['optimizer_state'])
del model_dict
del checkpoint
torch.cuda.empty_cache()
else:
print("No checkpoint found at '{}'".format(args.resume))
start_iter = args.start_iter if args.start_iter >= 0 else start_iter
scale_weight = torch.tensor([1.0, 0.4, 0.4,
0.4]).to(torch.device(args.device))
dice_weight = [args.dice_weight0, args.dice_weight1]
lv_margin = [args.lv_margin0, args.lv_margin1]
total_loss_sum = 0.0
ms_loss_sum = 0.0
cls_loss_sum = 0.0
t_loader.__gen_batchs__(args.batch_size, ratio=args.ratio)
trainloader_iter = iter(trainloader)
optimizer.zero_grad()
start_train_time = timeit.default_timer()
elapsed_train_time = 0.0
best_dice = -100.0
best_wacc = -100.0
for i in range(start_iter, args.n_iter):
#"""
model.train()
if i % args.iter_size == 0:
if args.num_cycles == 0:
scheduler_warmup.step(i)
else:
scheduler_warmup.step(i // args.num_cycles)
try:
images, labels, _ = next(trainloader_iter)
except:
t_loader.__gen_batchs__(args.batch_size, ratio=args.ratio)
trainloader_iter = iter(trainloader)
images, labels, _ = next(trainloader_iter)
images = images.to(torch.device(args.device))
labels = labels.to(torch.device(args.device))
outputs, outputs_gap = model(images)
labels_gap = torch.where(
labels.sum(3, keepdim=True).sum(2, keepdim=True) > 0,
torch.ones(labels.size(0), 1, 1, 1).to(torch.device(args.device)),
torch.zeros(labels.size(0), 1, 1, 1).to(torch.device(args.device)))
cls_loss = F.binary_cross_entropy_with_logits(
outputs_gap,
labels_gap) if args.lambda_cls > 0 else torch.tensor(0.0).to(
labels.device)
ms_loss = multi_scale_loss(outputs,
labels,
scale_weight=scale_weight,
reduction='mean',
alpha=args.alpha,
gamma=args.gamma,
dice_weight=dice_weight,
lv_margin=lv_margin,
lambda_fl=args.lambda_fl,
lambda_dc=args.lambda_dc,
lambda_lv=args.lambda_lv)
total_loss = ms_loss + args.lambda_cls * cls_loss
total_loss = total_loss / float(args.iter_size)
total_loss.backward()
total_loss_sum = total_loss_sum + total_loss.item()
ms_loss_sum = ms_loss_sum + ms_loss.item()
cls_loss_sum = cls_loss_sum + cls_loss.item()
if (i + 1) % args.print_train_freq == 0:
print("Iter [%7d/%7d] Loss: %7.4f (MS: %7.4f / CLS: %7.4f)" %
(i + 1, args.n_iter, total_loss_sum, ms_loss_sum,
cls_loss_sum))
if (i + 1) % args.iter_size == 0:
optimizer.step()
optimizer.zero_grad()
total_loss_sum = 0.0
ms_loss_sum = 0.0
cls_loss_sum = 0.0
#"""
if args.eval_freq > 0 and (i + 1) % args.eval_freq == 0:
state = {
'iter': i + 1,
'model_state': model.state_dict(),
}
#'optimizer_state': optimizer.state_dict(),}
if (i + 1) % int(args.eval_freq / args.save_freq) == 0:
torch.save(
state, "checkpoints/{}_{}_{}_{}x{}_{}-{}_model.pth".format(
args.arch, args.dataset, i + 1, args.img_rows,
args.img_cols, args.fold_num, args.num_folds))
dice_val = 0.0
thresh = 0.5
mask_sum_thresh = 0
mean_loss_val = AverageMeter()
model.eval()
with torch.no_grad():
for i_val, (images_val, labels_val, _) in enumerate(valloader):
images_val = images_val.to(torch.device(args.device))
labels_val = labels_val.to(torch.device(args.device))
outputs_val, outputs_gap_val = model(images_val)
pred_val = (F.sigmoid(outputs_val if not isinstance(
outputs_val, tuple) else outputs_val[0]) >
thresh).long() #outputs_val.max(1)[1]
pred_val_sum = pred_val.sum(3).sum(2).sum(1)
for k in range(labels_val.size(0)):
if pred_val_sum[k] < mask_sum_thresh:
pred_val[k, :, :, :] = torch.zeros_like(
pred_val[k, :, :, :])
labels_gap_val = torch.where(
labels_val.sum(3, keepdim=True).sum(2, keepdim=True) >
0,
torch.ones(labels_val.size(0), 1, 1,
1).to(torch.device(args.device)),
torch.zeros(labels_val.size(0), 1, 1,
1).to(torch.device(args.device)))
cls_loss_val = F.binary_cross_entropy_with_logits(
outputs_gap_val, labels_gap_val
) if args.lambda_cls > 0 else torch.tensor(0.0).to(
labels_val.device)
ms_loss_val = multi_scale_loss(outputs_val,
labels_val,
scale_weight=scale_weight,
reduction='mean',
alpha=args.alpha,
gamma=args.gamma,
dice_weight=dice_weight,
lv_margin=lv_margin,
lambda_fl=args.lambda_fl,
lambda_dc=args.lambda_dc,
lambda_lv=args.lambda_lv)
loss_val = ms_loss_val + args.lambda_cls * cls_loss_val
mean_loss_val.update(loss_val.item(), n=labels_val.size(0))
running_metrics.update(labels_val.long(), pred_val.long())
dice_val, dice_empty_val, dice_non_empty_val, miou_val, wacc_val, acc_empty_val, acc_non_empty_val = running_metrics.get_scores(
)
print(
'Dice (per image): {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.
format(dice_val, dice_empty_val, dice_non_empty_val))
print('wAcc: {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.format(
wacc_val, acc_empty_val, acc_non_empty_val))
print('Overall mIoU: {:.5f}'.format(miou_val))
print('Mean val loss: {:.4f}'.format(mean_loss_val.avg))
state['dice'] = dice_val
state['wacc'] = wacc_val
state['miou'] = miou_val
running_metrics.reset()
mean_loss_val.reset()
if (i + 1) % int(args.eval_freq / args.save_freq) == 0:
torch.save(
state, "checkpoints/{}_{}_{}_{}x{}_{}-{}_model.pth".format(
args.arch, args.dataset, i + 1, args.img_rows,
args.img_cols, args.fold_num, args.num_folds))
if best_dice <= dice_val:
best_dice = dice_val
torch.save(
state, "checkpoints/{}_{}_{}_{}x{}_{}-{}_model.pth".format(
args.arch, args.dataset, 'best-dice', args.img_rows,
args.img_cols, args.fold_num, args.num_folds))
if best_wacc <= wacc_val:
best_wacc = wacc_val
torch.save(
state, "checkpoints/{}_{}_{}_{}x{}_{}-{}_model.pth".format(
args.arch, args.dataset, 'best-wacc', args.img_rows,
args.img_cols, args.fold_num, args.num_folds))
elapsed_train_time = timeit.default_timer() - start_train_time
print('Training time (iter {0:5d}): {1:10.5f} seconds'.format(
i + 1, elapsed_train_time))
if args.saving_last_time > 0 and (i + 1) % args.iter_size == 0 and (
timeit.default_timer() -
start_train_time) > args.saving_last_time:
state = {
'iter': i + 1,
'model_state': model.state_dict(), #}
'optimizer_state': optimizer.state_dict(),
}
torch.save(
state, "checkpoints/{}_{}_{}_{}x{}_{}-{}_model.pth".format(
args.arch, args.dataset, i + 1, args.img_rows,
args.img_cols, args.fold_num, args.num_folds))
return
print('best_dice: {:.5f}; best_wacc: {:.5f}'.format(best_dice, best_wacc))
def test(args):
if not os.path.exists(args.root_results):
os.makedirs(args.root_results)
model_file_name = os.path.split(args.model_path)[1]
model_name = model_file_name[:model_file_name.find('_')]
# Setup Transforms
rgb_mean = [122.7717 / 255., 115.9465 / 255., 102.9801 /
255.] if args.norm_type == 'gn' and args.load_pretrained else [
0.485, 0.456, 0.406
]
rgb_std = [1. / 255., 1. / 255., 1. /
255.] if args.norm_type == 'gn' and args.load_pretrained else [
0.229, 0.224, 0.225
]
data_trans = transforms.Compose([
transforms.ToPILImage(),
transforms.Resize(size=(args.img_rows, args.img_cols)),
transforms.ToTensor(),
transforms.Normalize(mean=rgb_mean, std=rgb_std),
])
# Setup Dataloader
data_loader = get_loader(args.dataset)
data_path = get_data_path(args.dataset)
loader = data_loader(data_path,
split=args.split,
in_channels=args.in_channels,
transforms=data_trans,
fold_num=args.fold_num,
num_folds=args.num_folds,
no_gt=args.no_gt,
seed=args.seed)
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
torch.cuda.manual_seed(args.seed)
n_classes = loader.n_classes
testloader = data.DataLoader(
loader, batch_size=args.batch_size) #, num_workers=2, pin_memory=True)
# Setup Model
model = get_model(model_name,
n_classes=1,
in_channels=args.in_channels,
norm_type=args.norm_type,
use_cbam=args.use_cbam)
model.cuda()
checkpoint = torch.load(args.model_path) #, encoding="latin1")
state = convert_state_dict(checkpoint['model_state'])
model_dict = model.state_dict()
model_dict.update(state)
model.load_state_dict(model_dict)
saved_iter = checkpoint.get('iter', -1)
dice_val = checkpoint.get('dice', -1)
wacc_val = checkpoint.get('wacc', -1)
print("Loaded checkpoint '{}' (iter {}, dice {:.5f}, wAcc {:.5f})".format(
args.model_path, saved_iter, dice_val, wacc_val))
running_metrics = runningScore(
n_classes=2, weight_acc_non_empty=args.weight_acc_non_empty)
y_prob = np.zeros((loader.__len__(), 1, 1024, 1024), dtype=np.float32)
y_pred_sum = np.zeros((loader.__len__(), ), dtype=np.int32)
pred_dict = collections.OrderedDict()
num_non_empty_masks = 0
model.eval()
with torch.no_grad():
for i, (images, labels, _) in tqdm(enumerate(testloader)):
images = images.cuda()
labels = labels.cuda()
if args.tta:
bs, c, h, w = images.size()
images = torch.cat(
[images, torch.flip(images, dims=[3])], dim=0) # hflip
outputs = model(images, return_aux=False)
prob = F.sigmoid(outputs)
if args.tta:
prob = prob.view(-1, bs, 1, h, w)
prob[1, :, :, :, :] = torch.flip(prob[1, :, :, :, :], dims=[3])
prob = prob.mean(0)
pred = (prob > args.thresh).long()
pred_sum = pred.sum(3).sum(2).sum(1)
y_prob[i * args.batch_size:i * args.batch_size +
labels.size(0), :, :, :] = prob.cpu().numpy()
y_pred_sum[i * args.batch_size:i * args.batch_size +
labels.size(0)] = pred_sum.cpu().numpy()
y_pred_sum_argsorted = np.argsort(y_pred_sum)[::-1]
pruned_idx = int(y_pred_sum_argsorted.shape[0] * args.non_empty_ratio)
mask_sum_thresh = int(
y_pred_sum[y_pred_sum_argsorted[pruned_idx]]
) if pruned_idx < y_pred_sum_argsorted.shape[0] else 0
for i, (_, labels, names) in tqdm(enumerate(testloader)):
labels = labels.cuda()
prob = torch.from_numpy(
y_prob[i * args.batch_size:i * args.batch_size +
labels.size(0), :, :, :]).float().cuda()
pred = (prob > args.thresh).long()
pred_sum = pred.sum(3).sum(2).sum(1)
for k in range(labels.size(0)):
if pred_sum[k] > mask_sum_thresh:
num_non_empty_masks += 1
else:
pred[k, :, :, :] = torch.zeros_like(pred[k, :, :, :])
if args.only_non_empty:
pred[k, :, 0, 0] = 1
if not args.no_gt:
running_metrics.update(labels.long(), pred.long())
"""
if args.split == 'test':
for k in range(labels.size(0)):
name = names[0][k]
if pred_dict.get(name, None) is None:
mask = pred[k, 0, :, :].cpu().numpy()
rle = loader.mask2rle(mask)
pred_dict[name] = rle
#"""
print(
'# non-empty masks: {:5d} (non_empty_ratio: {:.5f} / mask_sum_thresh: {:6d})'
.format(num_non_empty_masks, args.non_empty_ratio, mask_sum_thresh))
if not args.no_gt:
dice, dice_empty, dice_non_empty, miou, wacc, acc_empty, acc_non_empty = running_metrics.get_scores(
)
print('Dice (per image): {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.
format(dice, dice_empty, dice_non_empty))
print('wAcc: {:.5f} (empty: {:.5f} / non-empty: {:.5f})'.format(
wacc, acc_empty, acc_non_empty))
print('Overall mIoU: {:.5f}'.format(miou))
running_metrics.reset()
if args.split == 'test':
fold_num, num_folds = model_file_name.split('_')[4].split('-')
prob_file_name = 'prob-{}_{}x{}_{}_{}_{}-{}'.format(
args.split, args.img_rows, args.img_cols, model_name, saved_iter,
fold_num, num_folds)
np.save(
os.path.join(args.root_results, '{}.npy'.format(prob_file_name)),
y_prob)
"""
