def test(test_dataset, model, mapping, args, filename):
"""
Produces a csv on predictions of the test dataset
"""
batch_time = AverageMeter('Time', ':6.3f')
test_loader = torch.utils.data.DataLoader(test_dataset,
batch_size=args.batch_size,
shuffle=False,
num_workers=args.workers,
pin_memory=True)
progress = ProgressMeter(len(test_loader), [batch_time], prefix='Test: ')
# switch to evaluate mode
model.eval()
print(mapping)
idx_to_class = dict()
for k, v in mapping.items():
idx_to_class[v] = k
# Append results to csv
results = open(filename, 'a')
image = 0
with torch.no_grad():
end = time.time()
for i, (images, target) in enumerate(test_loader):
if args.gpu is not None:
images = images.cuda(args.gpu, non_blocking=True)
# compute output
output = model(images)
_, pred = output.topk(1, 1, True, True)
pred = pred.t()
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % args.print_freq == 0:
progress.display(i)
# write classifications
predictions = pred.cpu().detach().numpy()[0]
result = ""
for prediction in predictions:
test = 'test_{}.JPEG'.format(image)
classification = idx_to_class[prediction]
result += '{} {}\n'.format(test, classification)
image += 1
results.write(result)
results.close()
def validate(val_loader, model, criterion, args, filename, epoch=-1):
"""
Validate model accuracy on val_loader data.
### Arguments:
val_loader - torch.utils.data.DataLoader: validation dataset wrapped in a dataloader.
model - PyTorch Model: the model to validate.
criterion - torch.nn: Loss Function to use.
args - dict: arguments passed.
filename - str: file to write results to.
### Return:
float- top1 average accuracy.
"""
batch_time = AverageMeter('Time', ':6.3f')
losses = AverageMeter('Loss', ':.4e')
top1 = AverageMeter('Acc@1', ':6.2f')
top5 = AverageMeter('Acc@5', ':6.2f')
progress = ProgressMeter(len(val_loader), [batch_time, losses, top1, top5],
prefix='Test: ')
# switch to evaluate mode
model.eval()
with torch.no_grad():
end = time.time()
for i, (images, target) in enumerate(val_loader):
if args.gpu is not None:
images = images.cuda(args.gpu, non_blocking=True)
target = target.cuda(args.gpu, non_blocking=True)
# compute output
output = model(images)
loss = criterion(output, target)
# measure accuracy and record loss
acc1, acc5 = accuracy(output, target, topk=(1, 5))
losses.update(loss.item(), images.size(0))
top1.update(acc1[0], images.size(0))
top5.update(acc5[0], images.size(0))
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % args.print_freq == 0:
progress.display(i)
print(' * Acc@1 {top1.avg:.3f} Acc@5 {top5.avg:.3f}'.format(top1=top1,
top5=top5))
# Append results to csv
results = open(filename, 'a')
result = '{},{},{}\n'.format(epoch, top1.avg, top5.avg)
results.write(result)
results.close()
return top1.avg
def train(train_loader, model, criterion, optimizer, epoch, args, writer=None):
# TODO: get writer from locals()
# writer = locals()['writer']
batch_time = CumMeter('Time(s)', ':.2f')
data_time = CumMeter('Data(s)', ':.2f')
losses = AverageMeter('bce', ':.3e')
dices = AverageMeter('dice', ':.3f')
progress = ProgressMeter(
len(train_loader),
[batch_time, data_time, losses, dices],
prefix="Epoch: [{}][trn]".format(epoch),
)
model.train()
train_loader.shuffle()
end = time.time()
# for batch, (x, y1, y2) in enumerate(train_loader):
# BUG: RuntimeError: cuDNN error: CUDNN_STATUS_BAD_PARAM
for batch in range(0, len(train_loader) // args.batch_size):
x, y1, y2 = train_loader.get_batch(
range(batch * args.batch_size, (batch + 1) * args.batch_size))
data_time.update(time.time() - end)
x, y1, y2 = x.cuda(), y1.cuda(), y2.cuda()
out1, out2 = model(x)
loss1 = criterion(out1, y1)
loss2 = criterion(out2, y2)
loss = loss1 + loss2
optimizer.zero_grad()
loss.backward()
optimizer.step()
out_pred = (out1 > out2).float() * out1 + (out2 > out1).float() * out2
out_gt = y1 + y2
dice = binary_dice(out_pred, out_gt)
losses.update(loss.item(), 2)
dices.update(dice.item(), 2)
batch_time.update(time.time() - end)
end = time.time()
if batch % args.print_freq == 0:
progress.display(batch, logging.DEBUG)
writer.add_scalar('train_loss', loss.item(),
epoch * len(train_loader) + batch)
output_grid = select_rand(out_pred[:, 1, ...].detach(),
out_gt[:, 1, ...].detach())
writer.add_image('out_pred',
output_grid,
epoch * len(train_loader) + batch,
dataformats='CHW')
progress.display(batch, logging.INFO, reduce=True)
def train(train_loader, model, criterion, optimizer, epoch, args):
"""
Train model on train_loader data.
### Arguments:
train_loader - torch.utils.data.DataLoader: training dataset wrapped in a dataloader.
model - PyTorch Model: the model to train.
criterion - torch.nn: Loss Function to use.
optimizer - torch.optim: optimizer to use
epoch - int: current training epoch.
args - dict: arguments passed.
"""
batch_time = AverageMeter('Time', ':6.3f')
data_time = AverageMeter('Data', ':6.3f')
losses = AverageMeter('Loss', ':.4e')
top1 = AverageMeter('Acc@1', ':6.2f')
top5 = AverageMeter('Acc@5', ':6.2f')
progress = ProgressMeter(len(train_loader),
[batch_time, data_time, losses, top1, top5],
prefix="Epoch: [{}]".format(epoch))
# switch to train mode
model.train()
end = time.time()
for i, (images, target) in enumerate(train_loader):
# measure data loading time
data_time.update(time.time() - end)
if args.gpu is not None:
images = images.cuda(args.gpu, non_blocking=True)
target = target.cuda(args.gpu, non_blocking=True)
# compute output
output = model(images)
loss = criterion(output, target)
# measure accuracy and record loss
acc1, acc5 = accuracy(output, target, topk=(1, 5))
losses.update(loss.item(), images.size(0))
top1.update(acc1[0], images.size(0))
top5.update(acc5[0], images.size(0))
# compute gradient and do SGD step
optimizer.zero_grad()
loss.backward()
optimizer.step()
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % args.print_freq == 0:
progress.display(i)
def validate(val_loader, model, criterion, epoch, args, writer=None):
batch_time = CumMeter('Time(s)', ':.2f')
data_time = CumMeter('Data(s)', ':.2f')
losses = AverageMeter('bce', ':.3e')
dices = AverageMeter('dice', ':.3f')
progress = ProgressMeter(
len(val_loader),
[batch_time, data_time, losses, dices],
prefix="Epoch: [{}][val]".format(epoch),
)
model.eval()
end = time.time()
with torch.no_grad():
# for batch, (x, y1, y2) in enumerate(val_loader):
for batch in range(0, len(val_loader) // args.batch_size):
x, y1, y2 = val_loader.get_batch(
range(batch * args.batch_size, (batch + 1) * args.batch_size))
data_time.update(time.time() - end)
x, y1, y2 = x.cuda(), y1.cuda(), y2.cuda()
out1, out2 = model(x)
loss1 = criterion(out1, y1)
loss2 = criterion(out2, y2)
loss = loss1 + loss2
out_pred = (out1 > out2).float() * out1 + (out2 >
out1).float() * out2
out_gt = y1 + y2
dice = binary_dice(out_pred, out_gt)
losses.update(loss.item(), 2)
dices.update(dice.item(), 2)
batch_time.update(time.time() - end)
end = time.time()
if batch % args.print_freq == 0:
progress.display(batch, logging.DEBUG)
writer.add_scalar('valid loss', loss.item(),
epoch * len(val_loader) + batch)
progress.display(batch, logging.INFO, reduce=True)
return dice.cpu().data
def validate(val_loader, model, criterion, epoch, args, writer=None):
batch_time = CumMeter('Time(s)', ':.2f')
data_time = CumMeter('Data(s)', ':.2f')
losses = AverageMeter('bce', ':.3e')
dices = AverageMeter('dice', ':.3f')
progress = ProgressMeter(
len(val_loader),
[batch_time, data_time, losses, dices],
prefix="Epoch: [{}][val]".format(epoch),
)
model.eval()
end = time.time()
with torch.no_grad():
for batch, (volumes, label_masks) in enumerate(val_loader):
data_time.update(time.time() - end)
volumes, label_masks = volumes.to(args.device), label_masks.to(
args.device)
out_masks = model(volumes)
[n, _, d, h, w] = out_masks.shape
new_label_masks = nn.functional.interpolate(
label_masks, size=(d, h, w)) #.to(torch.int64)
loss = criterion(out_masks,
new_label_masks.squeeze(1).to(torch.int64))
pred_masks = F.softmax(out_masks, dim=1).permute(0, 2, 3, 4, 1)
pred_masks = pred_masks.reshape(-1, pred_masks.shape[-1])
new_label_masks_onehot = to_one_hot(new_label_masks, 3)
dice = multi_dice(pred_masks, new_label_masks_onehot)
losses.update(loss.item(), 2)
dices.update(dice.item(), 2)
batch_time.update(time.time() - end)
end = time.time()
if batch % args.print_freq == 0:
progress.display(batch, logging.DEBUG)
writer.add_scalar('Loss/val', loss.item(),
epoch * len(val_loader) + batch)
writer.add_scalar('Dice/val', dice.item(),
epoch * len(val_loader) + batch)
if batch % 10 * args.print_freq == 0:
pred_masks = F.softmax(out_masks, dim=1).argmax(dim=1)
output_grid = select_rand(pred_masks.detach(),
new_label_masks[:, 0, ...].detach())
writer.add_image('out_pred/val',
output_grid,
epoch * len(val_loader) + batch,
dataformats='CHW')
progress.display(batch, logging.INFO, reduce=True)
writer.add_scalar('Epoch/val_loss', losses.avg, epoch)
writer.add_scalar('Epoch/val_dice', dices.avg, epoch)
return losses.avg, dices.avg
def train(train_loader, model, criterion, optimizer, epoch, args, writer=None):
# TODO: get writer from locals()
# writer = locals()['writer']
batch_time = CumMeter('Time(s)', ':.2f')
data_time = CumMeter('Data(s)', ':.2f')
losses = AverageMeter('bce', ':.3e')
dices = AverageMeter('dice', ':.3f')
progress = ProgressMeter(
len(train_loader),
[batch_time, data_time, losses, dices],
prefix="Epoch: [{}][trn]".format(epoch),
)
model.train()
end = time.time()
for batch, (volumes, label_masks) in enumerate(train_loader):
data_time.update(time.time() - end)
volumes, label_masks = volumes.to(args.device), label_masks.to(
args.device)
out_masks = model(volumes)
# resize label
[n, _, d, h, w] = out_masks.shape
new_label_masks = F.interpolate(label_masks,
size=(d, h, w)) #.to(torch.int64)
loss = criterion(out_masks, new_label_masks.squeeze(1).to(torch.int64))
optimizer.zero_grad()
loss.backward()
optimizer.step()
# TODO: check multi dice
pred_masks = F.softmax(out_masks, dim=1).permute(0, 2, 3, 4, 1)
pred_masks = pred_masks.reshape(-1, pred_masks.shape[-1])
new_label_masks_onehot = to_one_hot(new_label_masks, 3)
dice = multi_dice(pred_masks, new_label_masks_onehot)
losses.update(loss.item(), 2)
dices.update(dice.item(), 2)
batch_time.update(time.time() - end)
end = time.time()
if batch % args.print_freq == 0:
progress.display(batch, logging.DEBUG)
writer.add_scalar('Loss/train', loss.item(),
epoch * len(train_loader) + batch)
writer.add_scalar('Dice/train', dice.item(),
epoch * len(train_loader) + batch)
# pdb.set_trace()
if batch % 10 * args.print_freq == 0:
output_grid = select_rand(volumes[:, 0, ...].detach(),
label_masks[:, 0, ...].detach())
writer.add_image('Dataset/train',
output_grid,
epoch * len(train_loader) + batch,
dataformats='CHW')
pred_masks = F.softmax(out_masks, dim=1).argmax(dim=1)
output_grid = select_rand(pred_masks.detach(),
new_label_masks[:, 0, ...].detach())
writer.add_image('out_pred/train',
output_grid,
epoch * len(train_loader) + batch,
dataformats='CHW')
progress.display(batch, logging.INFO, reduce=True)
writer.add_scalar('Epoch/train_loss', losses.avg, epoch)
writer.add_scalar('Epoch/train_dice', dices.avg, epoch)