def __init__(self):
super(AffinityDisplacementLoss, self).__init__()
self.path_index = indexing.PathIndex(radius=10,
default_size=(irn_crop_size // 4,
irn_crop_size // 4))
path_index = self.path_index
self.n_path_lengths = len(path_index.path_indices)
for i, pi in enumerate(path_index.path_indices):
self.register_buffer(
AffinityDisplacementLoss.path_indices_prefix + str(i),
torch.from_numpy(pi))
self.register_buffer(
'disp_target',
torch.unsqueeze(
torch.unsqueeze(
torch.from_numpy(path_index.search_dst).transpose(1, 0),
0), -1).float())
self.params = [
tuple(self.edge_layers.parameters()),
tuple(self.dp_layers.parameters())
]
def run(args):
path_index = indexing.PathIndex(radius=10,
default_size=(args.irn_crop_size // 4,
args.irn_crop_size // 4))
model = getattr(importlib.import_module(args.irn_network),
'AffinityDisplacementLoss')(path_index)
train_dataset = voc12.dataloader.VOC12AffinityDataset(
args.train_list,
label_dir=args.ir_label_out_dir,
voc12_root=args.voc12_root,
indices_from=path_index.src_indices,
indices_to=path_index.dst_indices,
hor_flip=True,
crop_size=args.irn_crop_size,
crop_method="random",
rescale=(0.5, 1.5))
train_data_loader = DataLoader(train_dataset,
batch_size=args.irn_batch_size,
shuffle=True,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
max_step = (len(train_dataset) //
args.irn_batch_size) * args.irn_num_epoches
param_groups = model.trainable_parameters()
optimizer = torchutils.PolyOptimizer([{
'params': param_groups[0],
'lr': 1 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}, {
'params': param_groups[1],
'lr': 10 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}],
lr=args.irn_learning_rate,
weight_decay=args.irn_weight_decay,
max_step=max_step)
model = torch.nn.DataParallel(model).cuda()
model.train()
avg_meter = pyutils.AverageMeter()
timer = pyutils.Timer()
for ep in range(args.irn_num_epoches):
print('Epoch %d/%d' % (ep + 1, args.irn_num_epoches))
for iter, pack in enumerate(train_data_loader):
img = pack['img'].cuda(non_blocking=True)
bg_pos_label = pack['aff_bg_pos_label'].cuda(non_blocking=True)
fg_pos_label = pack['aff_fg_pos_label'].cuda(non_blocking=True)
neg_label = pack['aff_neg_label'].cuda(non_blocking=True)
pos_aff_loss, neg_aff_loss, dp_fg_loss, dp_bg_loss = model(
img, True)
bg_pos_aff_loss = torch.sum(
bg_pos_label * pos_aff_loss) / (torch.sum(bg_pos_label) + 1e-5)
fg_pos_aff_loss = torch.sum(
fg_pos_label * pos_aff_loss) / (torch.sum(fg_pos_label) + 1e-5)
pos_aff_loss = bg_pos_aff_loss / 2 + fg_pos_aff_loss / 2
neg_aff_loss = torch.sum(
neg_label * neg_aff_loss) / (torch.sum(neg_label) + 1e-5)
dp_fg_loss = torch.sum(dp_fg_loss * torch.unsqueeze(
fg_pos_label, 1)) / (2 * torch.sum(fg_pos_label) + 1e-5)
dp_bg_loss = torch.sum(dp_bg_loss * torch.unsqueeze(
bg_pos_label, 1)) / (2 * torch.sum(bg_pos_label) + 1e-5)
avg_meter.add({
'loss1': pos_aff_loss.item(),
'loss2': neg_aff_loss.item(),
'loss3': dp_fg_loss.item(),
'loss4': dp_bg_loss.item()
})
total_loss = (pos_aff_loss + neg_aff_loss) / 2 + (dp_fg_loss +
dp_bg_loss) / 2
optimizer.zero_grad()
total_loss.backward()
optimizer.step()
if (optimizer.global_step - 1) % 50 == 0:
timer.update_progress(optimizer.global_step / max_step)
print('step:%5d/%5d' % (optimizer.global_step - 1, max_step),
'loss:%.4f %.4f %.4f %.4f' %
(avg_meter.pop('loss1'), avg_meter.pop('loss2'),
avg_meter.pop('loss3'), avg_meter.pop('loss4')),
'imps:%.1f' % ((iter + 1) * args.irn_batch_size /
timer.get_stage_elapsed()),
'lr: %.4f' % (optimizer.param_groups[0]['lr']),
'etc:%s' % (timer.str_estimated_complete()),
flush=True)
else:
timer.reset_stage()
infer_dataset = voc12.dataloader.VOC12ImageDataset(
args.infer_list,
voc12_root=args.voc12_root,
crop_size=args.irn_crop_size,
crop_method="top_left")
infer_data_loader = DataLoader(infer_dataset,
batch_size=args.irn_batch_size,
shuffle=False,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
model.eval()
print('Analyzing displacements mean ... ', end='')
dp_mean_list = []
with torch.no_grad():
for iter, pack in enumerate(infer_data_loader):
img = pack['img'].cuda(non_blocking=True)
aff, dp = model(img, False)
dp_mean_list.append(torch.mean(dp, dim=(0, 2, 3)).cpu())
model.module.mean_shift.running_mean = torch.mean(
torch.stack(dp_mean_list), dim=0)
print('done.')
torch.save(model.module.state_dict(), args.irn_weights_name)
torch.cuda.empty_cache()
def run(args):
path_index = indexing.PathIndex(radius=10,
default_size=(args.irn_crop_size // 4,
args.irn_crop_size // 4))
model = getattr(importlib.import_module(args.irn_network),
'AffinityDisplacementLoss')(path_index, args.model_dir,
args.dataset, args.tag,
args.num_classes, args.use_cls)
if args.dataset == 'voc12':
train_dataset = voc12.dataloader.VOC12AffinityDataset(
args.train_list,
label_dir=args.ir_label_out_dir,
dev_root=args.dev_root,
indices_from=path_index.src_indices,
indices_to=path_index.dst_indices,
hor_flip=True,
crop_size=args.irn_crop_size,
crop_method=args.crop_method,
rescale=args.rescale_range,
outsize=args.outsize,
norm_mode=args.norm_mode)
infer_dataset = voc12.dataloader.VOC12ImageDataset(
args.infer_list,
dev_root=args.dev_root,
crop_size=args.irn_crop_size,
crop_method="top_left")
elif args.dataset in ['adp_morph', 'adp_func']:
train_dataset = adp.dataloader.ADPAffinityDataset(
args.train_list,
is_eval=args.dataset == 'evaluation',
label_dir=args.ir_label_out_dir,
dev_root=args.dev_root,
htt_type=args.dataset.split('_')[-1],
indices_from=path_index.src_indices,
indices_to=path_index.dst_indices,
hor_flip=True,
crop_size=args.irn_crop_size,
crop_method=args.crop_method,
rescale=args.rescale_range,
outsize=args.outsize,
norm_mode=args.norm_mode)
infer_dataset = adp.dataloader.ADPImageDataset(
args.infer_list,
dev_root=args.dev_root,
htt_type=args.dataset.split('_')[-1],
is_eval=args.dataset == 'evaluation',
crop_size=args.irn_crop_size,
crop_method="top_left")
elif args.dataset in ['deepglobe', 'deepglobe_balanced']:
train_dataset = deepglobe.dataloader.DeepGlobeAffinityDataset(
args.train_list,
is_balanced=args.dataset == 'deepglobe_balanced',
label_dir=args.ir_label_out_dir,
dev_root=args.dev_root,
indices_from=path_index.src_indices,
indices_to=path_index.dst_indices,
hor_flip=True,
crop_size=args.irn_crop_size,
crop_method=args.crop_method,
rescale=args.rescale_range,
outsize=args.outsize,
norm_mode=args.norm_mode)
infer_dataset = deepglobe.dataloader.DeepGlobeImageDataset(
args.infer_list,
dev_root=args.dev_root,
is_balanced=args.dataset == 'deepglobe_balanced',
crop_size=args.irn_crop_size,
crop_method="top_left")
else:
raise KeyError('Dataset %s not yet implemented' % args.dataset)
train_data_loader = DataLoader(train_dataset,
batch_size=args.irn_batch_size,
shuffle=True,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
max_step = (len(train_dataset) //
args.irn_batch_size) * args.irn_num_epoches
param_groups = model.trainable_parameters()
optimizer = torchutils.PolyOptimizer([{
'params': param_groups[0],
'lr': 1 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}, {
'params': param_groups[1],
'lr': 10 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}],
lr=args.irn_learning_rate,
weight_decay=args.irn_weight_decay,
max_step=max_step)
model = torch.nn.DataParallel(model).cuda()
model.train()
# writer = SummaryWriter('log_tb/' + args.run_name)
avg_meter = pyutils.AverageMeter()
timer = pyutils.Timer()
for ep in range(args.irn_num_epoches):
print('Epoch %d/%d' % (ep + 1, args.irn_num_epoches))
for iter, pack in enumerate(train_data_loader):
img = pack['img'].cuda(non_blocking=True)
bg_pos_label = pack['aff_bg_pos_label'].cuda(non_blocking=True)
fg_pos_label = pack['aff_fg_pos_label'].cuda(non_blocking=True)
neg_label = pack['aff_neg_label'].cuda(non_blocking=True)
pos_aff_loss, neg_aff_loss, dp_fg_loss, dp_bg_loss = model(
img, True)
bg_pos_aff_loss = torch.sum(
bg_pos_label * pos_aff_loss) / (torch.sum(bg_pos_label) + 1e-5)
fg_pos_aff_loss = torch.sum(
fg_pos_label * pos_aff_loss) / (torch.sum(fg_pos_label) + 1e-5)
pos_aff_loss = bg_pos_aff_loss / 2 + fg_pos_aff_loss / 2
neg_aff_loss = torch.sum(
neg_label * neg_aff_loss) / (torch.sum(neg_label) + 1e-5)
dp_fg_loss = torch.sum(dp_fg_loss * torch.unsqueeze(
fg_pos_label, 1)) / (2 * torch.sum(fg_pos_label) + 1e-5)
dp_bg_loss = torch.sum(dp_bg_loss * torch.unsqueeze(
bg_pos_label, 1)) / (2 * torch.sum(bg_pos_label) + 1e-5)
avg_meter.add({
'loss1': pos_aff_loss.item(),
'loss2': neg_aff_loss.item(),
'loss3': dp_fg_loss.item(),
'loss4': dp_bg_loss.item()
})
total_loss = (pos_aff_loss + neg_aff_loss) / 2 + (dp_fg_loss +
dp_bg_loss) / 2
optimizer.zero_grad()
total_loss.backward()
optimizer.step()
if (optimizer.global_step - 1) % 50 == 0:
timer.update_progress(optimizer.global_step / max_step)
losses = {}
for i in range(1, 5):
losses[str(i)] = avg_meter.pop('loss' + str(i))
print('step:%5d/%5d' % (optimizer.global_step - 1, max_step),
'loss:%.4f %.4f %.4f %.4f' %
(losses['1'], losses['2'], losses['3'], losses['4']),
'imps:%.1f' % ((iter + 1) * args.irn_batch_size /
timer.get_stage_elapsed()),
'lr: %.4f' % (optimizer.param_groups[0]['lr']),
'etc:%s' % (timer.str_estimated_complete()),
flush=True)
# writer.add_scalar('step', optimizer.global_step, ep * len(train_data_loader) + iter)
# writer.add_scalar('loss', losses['1']+losses['2']+losses['3']+losses['4'],
# ep * len(train_data_loader) + iter)
# writer.add_scalar('lr', optimizer.param_groups[0]['lr'], ep * len(train_data_loader) + iter)
else:
timer.reset_stage()
infer_data_loader = DataLoader(infer_dataset,
batch_size=args.irn_batch_size,
shuffle=False,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
model.eval()
print('Analyzing displacements mean ... ', end='')
dp_mean_list = []
with torch.no_grad():
for iter, pack in enumerate(infer_data_loader):
img = pack['img'].cuda(non_blocking=True)
aff, dp = model(img, False)
dp_mean_list.append(torch.mean(dp, dim=(0, 2, 3)).cpu())
model.module.mean_shift.running_mean = torch.mean(
torch.stack(dp_mean_list), dim=0)
print('done.')
torch.save(model.module.state_dict(), args.irn_weights_name)
torch.cuda.empty_cache()
def run(args):
path_index = indexing.PathIndex(radius=10,
default_size=(args.irn_crop_size // 4,
args.irn_crop_size // 4))
model = getattr(importlib.import_module(args.irn_network),
'AffinityDisplacementLoss')(path_index)
transform_config = {
'augmentation_scope': 'horizontal_flip',
'images_normalization': 'default',
'images_output_format_type': 'float',
'masks_normalization': 'none',
'masks_output_format_type': 'byte',
'size': 512,
'size_transform': 'resize'
}
transform = get_transforms(transform_config)
train_dataset = voc12.dataloader.PneumothoraxAffinityDataset(
'/datasets/LID/Pneumothorax/train/train_all_positive.csv',
transform=transform,
indices_from=path_index.src_indices,
indices_to=path_index.dst_indices,
)
train_data_loader = DataLoader(train_dataset,
batch_size=args.irn_batch_size,
shuffle=True,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
max_step = (len(train_dataset) //
args.irn_batch_size) * args.irn_num_epoches
param_groups = model.trainable_parameters()
optimizer = torchutils.PolyOptimizer([{
'params': param_groups[0],
'lr': 1 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}, {
'params': param_groups[1],
'lr': 10 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}],
lr=args.irn_learning_rate,
weight_decay=args.irn_weight_decay,
max_step=max_step)
model = torch.nn.DataParallel(model.cuda(1),
device_ids=['cuda:1', 'cuda:2'])
model.train()
avg_meter = pyutils.AverageMeter()
timer = pyutils.Timer()
for ep in range(args.irn_num_epoches):
print('Epoch %d/%d' % (ep + 1, args.irn_num_epoches))
for iter, pack in enumerate(train_data_loader):
img = pack['img']
bg_pos_label = pack['aff_bg_pos_label'].cuda(1, non_blocking=True)
fg_pos_label = pack['aff_fg_pos_label'].cuda(1, non_blocking=True)
neg_label = pack['aff_neg_label'].cuda(1, non_blocking=True)
pos_aff_loss, neg_aff_loss, dp_fg_loss, dp_bg_loss = model(
img, True)
bg_pos_aff_loss = torch.sum(
bg_pos_label * pos_aff_loss) / (torch.sum(bg_pos_label) + 1e-5)
fg_pos_aff_loss = torch.sum(
fg_pos_label * pos_aff_loss) / (torch.sum(fg_pos_label) + 1e-5)
pos_aff_loss = bg_pos_aff_loss / 2 + fg_pos_aff_loss / 2
neg_aff_loss = torch.sum(
neg_label * neg_aff_loss) / (torch.sum(neg_label) + 1e-5)
dp_fg_loss = torch.sum(dp_fg_loss * torch.unsqueeze(
fg_pos_label, 1)) / (2 * torch.sum(fg_pos_label) + 1e-5)
dp_bg_loss = torch.sum(dp_bg_loss * torch.unsqueeze(
bg_pos_label, 1)) / (2 * torch.sum(bg_pos_label) + 1e-5)
avg_meter.add({
'loss1': pos_aff_loss.item(),
'loss2': neg_aff_loss.item(),
'loss3': dp_fg_loss.item(),
'loss4': dp_bg_loss.item()
})
total_loss = (pos_aff_loss + neg_aff_loss) / 2 + (dp_fg_loss +
dp_bg_loss) / 2
optimizer.zero_grad()
total_loss.backward()
optimizer.step()
if (optimizer.global_step - 1) % 50 == 0:
timer.update_progress(optimizer.global_step / max_step)
print('step:%5d/%5d' % (optimizer.global_step - 1, max_step),
'loss:%.4f %.4f %.4f %.4f' %
(avg_meter.pop('loss1'), avg_meter.pop('loss2'),
avg_meter.pop('loss3'), avg_meter.pop('loss4')),
'imps:%.1f' % ((iter + 1) * args.irn_batch_size /
timer.get_stage_elapsed()),
'lr: %.4f' % (optimizer.param_groups[0]['lr']),
'etc:%s' % (timer.str_estimated_complete()),
flush=True)
else:
timer.reset_stage()
transform_config = {
'augmentation_scope': 'none',
'images_normalization': 'default',
'images_output_format_type': 'float',
'size': 512,
'size_transform': 'resize'
}
transform = get_transforms(transform_config)
infer_dataset = voc12.dataloader.PneumothoraxImageDataset(
'/datasets/LID/Pneumothorax/train/train_all_positive.csv',
transform=transform)
infer_data_loader = DataLoader(infer_dataset,
batch_size=args.irn_batch_size,
shuffle=False,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
model.eval()
print('Analyzing displacements mean ... ', end='')
dp_mean_list = []
with torch.no_grad():
for iter, pack in enumerate(infer_data_loader):
img = pack['img']
aff, dp = model(img, False)
dp_mean_list.append(torch.mean(dp, dim=(0, 2, 3)).cpu())
model.module.mean_shift.running_mean = torch.mean(
torch.stack(dp_mean_list), dim=0)
print('done.')
torch.save(model.module.state_dict(), args.irn_weights_name)
torch.cuda.empty_cache()
def run(args):
path_index = indexing.PathIndex(radius=10,
default_size=(args.irn_crop_size // 4,
args.irn_crop_size // 4))
model = getattr(importlib.import_module(args.irn_network),
'AffinityDisplacement')(
path_index.default_path_indices,
torch.from_numpy(path_index.default_src_indices),
torch.from_numpy(path_index.default_dst_indices))
train_dataset = voc12.dataloader.VOC12AffinityDataset(
args.train_list,
label_dir=args.ir_label_out_dir,
voc12_root=args.voc12_root,
indices_from=path_index.default_src_indices,
indices_to=path_index.default_dst_indices,
hor_flip=True,
crop_size=args.irn_crop_size,
crop_method="random",
rescale=(0.5, 1.5))
train_data_loader = DataLoader(train_dataset,
batch_size=args.irn_batch_size,
shuffle=True,
num_workers=args.num_workers,
pin_memory=True,
drop_last=True)
max_step = (len(train_dataset) //
args.irn_batch_size) * args.irn_num_epoches
param_groups = model.trainable_parameters()
optimizer = torchutils.PolyOptimizer([{
'params': param_groups[0],
'lr': 1 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}, {
'params': param_groups[1],
'lr': 10 * args.irn_learning_rate,
'weight_decay': args.irn_weight_decay
}],
lr=args.irn_learning_rate,
weight_decay=args.irn_weight_decay,
max_step=max_step)
model = model.cuda()
model.train()
avg_meter = pyutils.AverageMeter()
timer = pyutils.Timer()
for ep in range(args.irn_num_epoches):
print('Epoch %d/%d' % (ep + 1, args.irn_num_epoches))
for iter, pack in enumerate(train_data_loader):
img = pack['img'].cuda(non_blocking=True)
bg_pos_label = pack['aff_bg_pos_label'].cuda(non_blocking=True)
fg_pos_label = pack['aff_fg_pos_label'].cuda(non_blocking=True)
neg_label = pack['aff_neg_label'].cuda(non_blocking=True)
aff, dp = model(img)
dp = path_index.to_displacement(dp)
bg_pos_aff_loss = torch.sum(
-bg_pos_label *
torch.log(aff + 1e-5)) / (torch.sum(bg_pos_label) + 1e-5)
fg_pos_aff_loss = torch.sum(
-fg_pos_label *
torch.log(aff + 1e-5)) / (torch.sum(fg_pos_label) + 1e-5)
pos_aff_loss = bg_pos_aff_loss / 2 + fg_pos_aff_loss / 2
neg_aff_loss = torch.sum(
-neg_label *
torch.log(1. + 1e-5 - aff)) / (torch.sum(neg_label) + 1e-5)
dp_fg_loss = torch.sum(
path_index.to_displacement_loss(dp) * torch.unsqueeze(
fg_pos_label, 1)) / (2 * torch.sum(fg_pos_label) + 1e-5)
dp_bg_loss = torch.sum(
torch.abs(dp) * torch.unsqueeze(bg_pos_label, 1)) / (
2 * torch.sum(bg_pos_label) + 1e-5)
avg_meter.add({
'loss1': pos_aff_loss,
'loss2': neg_aff_loss,
'loss3': dp_fg_loss.item(),
'loss4': dp_bg_loss.item()
})
total_loss = (pos_aff_loss + neg_aff_loss) / 2 + (dp_fg_loss +
dp_bg_loss) / 2
optimizer.zero_grad()
total_loss.backward()
optimizer.step()
if (optimizer.global_step - 1) % 100 == 0:
timer.update_progress(optimizer.global_step / max_step)
print('step:%5d/%5d' % (optimizer.global_step - 1, max_step),
'loss:%.4f %.4f %.4f %.4f' %
(avg_meter.pop('loss1'), avg_meter.pop('loss2'),
avg_meter.pop('loss3'), avg_meter.pop('loss4')),
'imps:%.1f' % ((iter + 1) * args.irn_batch_size /
timer.get_stage_elapsed()),
'lr: %.4f' % (optimizer.param_groups[0]['lr']),
'etc:%s' % (timer.str_estimated_complete()),
flush=True)
else:
timer.reset_stage()
torch.save(model.state_dict(), args.irn_weights_name)
torch.cuda.empty_cache()