def train_model(train_loader, model, criterion, optimizer, epoch, print_freq):
train_loader = load_dataset(find_csv(args.data, 'train'))
batch_time = AverageMeter()
data_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
# switch to train mode
model.train()
end = time.time()
for i, (target, cont_input, cat_input,
identification) in enumerate(train_loader):
# measure data loading timepil_resize
data_time.update(time.time() - end)
target = target.cuda(non_blocking=True)
target = target.squeeze()
# compute output
output = model(cont_input, cat_input)
# loss = criterion(output, target)
loss = criterion_smoothing(output, target)
# measure accuracy and record loss
prec1 = accuracy(output, target, topk=(1, ))
losses.update(loss.item(), target.size(0))
top1.update(prec1[0].cpu().data.numpy()[0], target.size(0))
# compute gradient and do SGD step
optimizer.zero_grad()
loss.backward()
# nothing line
gradClamp(model.parameters(), grad_clip)
optimizer.step()
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % print_freq == 0:
message = ('Epoch: [{0}][{1}/{2}]\t' +
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t' +
'Data {data_time.val:.3f} ({data_time.avg:.3f})\t' +
'Loss {loss.val:.4f} ({loss.avg:.4f})\t' +
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})').format(
epoch,
i,
len(train_loader),
batch_time=batch_time,
data_time=data_time,
loss=losses,
top1=top1)
log(message)
def train_model(train_loader, model, criterion, optimizer, epoch, print_freq):
batch_time = AverageMeter()
data_time = AverageMeter()
losses = AverageMeter()
psnrs = AverageMeter()
# switch to train mode
model.train()
end = time.time()
for i, (input, target, target_seg, filename) in enumerate(train_loader):
# measure data loading time
data_time.update(time.time() - end)
target = target.cuda(non_blocking=True)
target_seg = target_seg.cuda(non_blocking=True)
# compute output
output_seg = model(input)
# compute loss
if args.unet:
loss = criterionCros(output_seg, target_seg)
else:
loss = criterionMSE(output_seg, target_seg)
# compute psnr
psnr = compute_psnr(loss)
psnrs.update(psnr)
# measure accuracy and record loss
losses.update(loss.item(), input.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 % print_freq == 0:
print('Epoch: [{0}][{1}/{2}]\t'
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
'Data {data_time.val:.3f} ({data_time.avg:.3f})\t'
'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
'Psnr {psnr:.4f} ({psnr:.4f})'.format(epoch,
i,
len(train_loader),
batch_time=batch_time,
data_time=data_time,
loss=losses,
psnr=psnr))
def train_model(train_loader, model, criterion, optimizer, epoch, print_freq):
batch_time = AverageMeter()
data_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
# switch to train mode
model.train()
end = time.time()
for i, (input, target, input_path) in enumerate(train_loader):
# measure data loading timepil_resize
data_time.update(time.time() - end)
target = target.cuda(non_blocking=True)
#check agumentation
if args.save_tensor_image:
save_tensor_image(input, input_path, args.agumetation_check)
# compute output
output = model(input)
loss = criterion(output, target)
# measure accuracy and record loss
prec1 = accuracy(output, target, topk=(1, ))
losses.update(loss.item(), input.size(0))
top1.update(prec1[0].cpu().data.numpy()[0], input.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 % print_freq == 0:
message = ('Epoch: [{0}][{1}/{2}]\t' +
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t' +
'Data {data_time.val:.3f} ({data_time.avg:.3f})\t' +
'Loss {loss.val:.4f} ({loss.avg:.4f})\t' +
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})').format(
epoch,
i,
len(train_loader),
batch_time=batch_time,
data_time=data_time,
loss=losses,
top1=top1)
log(message)
def train_model(train_loader, model, criterion, optimizer, epoch, print_freq):
batch_time = AverageMeter()
data_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
# switch to train mode
model.train()
end = time.time()
for i, (input, target, input2, target2) in enumerate(train_loader):
# measure data loading time
data_time.update(time.time() - end)
target = target.cuda(non_blocking=True)
target2 = target2.cuda(non_blocking=True) # for multi task
# compute output
output, output2 = model(input) # for multi task
loss = criterion(output, target)
loss2 = criterion(output2, target2) # for multi task
loss = loss + loss2 # for multi task
# measure accuracy and record loss
prec1 = accuracy(output, target, topk=(1,))
losses.update(loss.item(), input.size(0))
top1.update(prec1[0].cpu().data.numpy()[0], input.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 % print_freq == 0:
print('Epoch: [{0}][{1}/{2}]\t'
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
'Data {data_time.val:.3f} ({data_time.avg:.3f})\t'
'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})'.format(epoch,
i,
len(train_loader),
batch_time=batch_time,
data_time=data_time,
loss=losses,
top1=top1))
def validate_model(val_loader, model, criterion, epoch, print_freq):
batch_time = AverageMeter()
top1 = AverageMeter()
# switch to evaluate mode
model.eval()
with torch.no_grad():
end = time.time()
target_index_output = []
target_index_target = []
for i, (input, target) in enumerate(val_loader):
target = target.cuda(non_blocking=True)
# compute output
output, output_seg = model(input)
if args.acc_classify:
prec1 = accuracy(output, target, topk=(1, ))
prec1 = prec1[0].cpu().data.numpy()[0]
# for auroc
output_cpu = output.squeeze().cpu().data.numpy()
output_cpu = np.array([
softmax(out)[args.target_index] for out in output_cpu
]) # convert to probability
else:
output_max = F.max_pool2d(
output_seg,
(args.avg_pooling_height, args.avg_pooling_width))
output_max_cpu = output_max.cpu().data.numpy()
target_cpu = target.cpu().data.numpy()
output_max_cpu = [
1.0 if o > 0.5 else 0.0 for o in output_max_cpu
]
prec1 = np.average(
np.equal(output_max_cpu, target_cpu).astype(
np.float)) * 100
# for auroc
output_cpu = output_max.squeeze().cpu().data.numpy()
# --------------------------------------
# for auroc get value from target index
target_index_output.extend(output_cpu.astype(np.float))
target_index_target.extend(
np.equal(target.cpu().data.numpy(),
args.target_index).astype(np.int))
# --------------------------------------
# measure accuracy and record loss
top1.update(prec1, input.size(0))
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % print_freq == 0:
print('Test: [{0}/{1}]\t'
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})'.format(
i, len(val_loader), batch_time=batch_time,
top1=top1))
auc, roc = compute_auroc(target_index_output, target_index_target)
save_auroc(auc, roc, os.path.join(args.result, str(epoch) + '.png'))
print(' * Prec@1 {top1.avg:.3f} at Epoch {epoch:0}'.format(top1=top1,
epoch=epoch))
print(' * auc@1 {auc:.3f}'.format(auc=auc))
return top1.avg
def train_model(train_loader, model, criterion, optimizer, epoch, print_freq):
batch_time = AverageMeter()
data_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
# switch to train mode
model.train()
end = time.time()
for i, (input, target, target_seg) in enumerate(train_loader):
# measure data loading time
data_time.update(time.time() - end)
target = target.cuda(non_blocking=True)
target_seg = target_seg.cuda(non_blocking=True)
# compute output
output, output_seg = model(input)
# compute loss
loss1 = criterion(output, target)
loss2 = criterionMSE(output_seg, target_seg)
# compose loss
if args.do_classify and args.do_seg:
loss = loss1 + loss2
elif args.do_classify:
loss = loss1
elif args.do_seg:
loss = loss2
if args.acc_classify:
prec1 = accuracy(output, target, topk=(1, ))
prec1 = prec1[0].cpu().data.numpy()[0]
else:
output_max = F.max_pool2d(
output_seg, (args.avg_pooling_height, args.avg_pooling_width))
output_max = output_max.cpu().data.numpy()
target = target.cpu().data.numpy()
output_max = [1.0 if o > 0.5 else 0.0 for o in output_max]
prec1 = np.average(np.equal(output_max, target).astype(
np.float)) * 100
# measure accuracy and record loss
losses.update(loss.item(), input.size(0))
top1.update(prec1, input.size(0))
# compute gradient and do SGD step
if args.train_per_loss and args.do_classify and args.do_seg:
if args.do_classify:
optimizer.zero_grad()
loss2.backward(retain_graph=True)
optimizer.step()
optimizer.zero_grad()
loss1.backward()
optimizer.step()
elif args.do_seg:
optimizer.zero_grad()
loss1.backward(retain_graph=True)
optimizer.step()
optimizer.zero_grad()
loss2.backward()
optimizer.step()
else:
optimizer.zero_grad()
loss.backward()
optimizer.step()
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
if i % print_freq == 0:
print('Epoch: [{0}][{1}/{2}]\t'
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
'Data {data_time.val:.3f} ({data_time.avg:.3f})\t'
'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})'.format(
epoch,
i,
len(train_loader),
batch_time=batch_time,
data_time=data_time,
loss=losses,
top1=top1))
def validate_model(val_loader, model, criterion, epoch, print_freq):
batch_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
cnt_cnt_label = [0] * args.num_classes
cnt_exact_pred = [0] * args.num_classes
# switch to evaluate mode
model.eval()
if args.evaluate:
evaluate_csv_file = os.path.join(args.result, 'evaluate.csv')
feval = open(evaluate_csv_file, 'wt')
with torch.no_grad():
end = time.time()
target_index_output, target_index_target = list(), list()
for i, (input, target, input_path) in enumerate(val_loader):
target = target.cuda(non_blocking=True)
# compute output
output = model(input)
loss = criterion(output, target)
# --------------------------------------
# for auroc get value from target index
output_cpu = output.squeeze().cpu().data.numpy()
output_cpu = np.array([softmax(out)[args.target_index] for out in output_cpu])
target_index_output.extend(output_cpu.astype(np.float))
target_index_target.extend(np.equal(target.cpu().data.numpy(), args.target_index).astype(np.int))
# --------------------------------------
if args.evaluate:
output_softmax = np.array([softmax(out) for out in output.cpu().numpy()])
for file_path, pred_values in zip(input_path, output_softmax):
_, file = os.path.split(file_path)
name, _ = os.path.splitext(file)
line = ','.join([name] + [str(v) for v in pred_values])
feval.write(line + '\n')
# measure accuracy and record loss
prec1 = accuracy(output, target, topk=(1,))
losses.update(loss.item(), input.size(0))
top1.update(prec1[0].cpu().data.numpy()[0], input.size(0))
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
# put together for acc per label
pred_list = pred(output).cpu().numpy().squeeze()
target_list = target.cpu().numpy().squeeze()
for (p, t) in zip(pred_list, target_list):
cnt_cnt_label[t] += 1
if p == t:
cnt_exact_pred[t] += 1
pred_list = pred(output).cpu().numpy().squeeze()
for pred_idx, pred_item in enumerate(pred_list):
dst = os.path.join(args.classification_result, 'kidney' if pred_item == 1 else 'no_kidney')
if not os.path.exists(dst):
os.makedirs(dst)
seg_img = input_path[pred_idx]
shutil.copy(seg_img, dst)
if i % print_freq == 0:
log(('Test: [{0}/{1}]\t' +
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t' +
'Loss {loss.val:.4f} ({loss.avg:.4f})\t' +
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})').format(i,
len(val_loader),
batch_time=batch_time,
loss=losses,
top1=top1))
auc, roc = compute_auroc(target_index_output, target_index_target)
# save_auroc(auc, roc, os.path.join(args.result, str(epoch) + '.png'))
log(' * Prec@1 {top1.avg:.3f} at Epoch {epoch:0}'.format(top1=top1, epoch=epoch))
log(' * auc@1 {auc:.3f}'.format(auc=auc))
for (i, (n_label, n_exact)) in enumerate(zip(cnt_cnt_label, cnt_exact_pred)):
acc_label = (n_exact / n_label * 100) if n_label > 0 else 0
log('acc of label {:0d}: {:0.3f}%'.format(i, acc_label))
return auc
def validate_model(val_loader, model, criterion, epoch, print_freq):
if args.evaluate:
print('eval check')
val_loader = load_dataset(find_csv(args.data, ''))
else:
val_loader = load_dataset(find_csv(args.data, 'val'))
batch_time = AverageMeter()
losses = AverageMeter()
top1 = AverageMeter()
cnt_cnt_label = [0] * args.num_classes
cnt_exact_pred = [0] * args.num_classes
# switch to evaluate mode
model.eval()
if args.evaluate:
evaluate_csv_file = os.path.join(args.result, 'evaluate.csv')
feval = open(evaluate_csv_file, 'wt')
with torch.no_grad():
end = time.time()
target_index_output, target_index_target = list(), list()
for i, (target, cont_input, cat_input,
identification) in enumerate(val_loader):
target = target.cuda(non_blocking=True)
target = target.squeeze()
# compute output
output = model(cont_input, cat_input)
# loss = criterion(output, target)
loss = criterion_smoothing(output, target)
# --------------------------------------
# for auroc get value from target index
output_cpu = output.cpu().data.numpy()
output_cpu = np.array(
[softmax(out)[args.target_index] for out in output_cpu])
target_index_output.extend(output_cpu.astype(np.float))
target_index_target.extend(
np.equal(target.cpu().data.numpy(),
args.target_index).astype(np.int))
# --------------------------------------
if args.evaluate:
output_softmax = np.array(
[softmax(out) for out in output.cpu().numpy()])
for ident, pred_values in zip(identification, output_softmax):
ident = str(np.squeeze(ident.data.numpy()))
idx_biger = np.argmax(pred_values)
diag = 'CKD' if idx_biger == 1 else 'AKI or NOR'
line = ','.join([ident, diag])
feval.write(line + '\n')
# measure accuracy and record loss
prec1 = accuracy(output, target, topk=(1, ))
losses.update(loss.item(), target.size(0))
top1.update(prec1[0].cpu().data.numpy()[0], target.size(0))
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
# put together for acc per label
pred_list = pred(output).cpu().numpy()[0]
target_list = target.cpu().numpy()
for (p, t) in zip(pred_list, target_list):
cnt_cnt_label[t] += 1
if p == t:
cnt_exact_pred[t] += 1
if i % print_freq == 0 and False:
log(('Test: [{0}/{1}]\t' +
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t' +
'Loss {loss.val:.4f} ({loss.avg:.4f})\t' +
'Prec@1 {top1.val:.3f} ({top1.avg:.3f})').format(
i,
len(val_loader),
batch_time=batch_time,
loss=losses,
top1=top1))
auc, roc = compute_auroc(target_index_output, target_index_target)
global best_acc
global best_auc
# if auc > best_auc:
if top1.avg > best_acc:
log(' * Prec@1 {top1.avg:.3f} at Epoch {epoch:0}'.format(
top1=top1, epoch=epoch))
log(' * auc@1 {auc:.3f}'.format(auc=auc))
best_acc = top1.avg
best_auc = auc
acc_label_list = []
for (i, (n_label,
n_exact)) in enumerate(zip(cnt_cnt_label,
cnt_exact_pred)):
acc_label = (n_exact / n_label * 100) if n_label > 0 else 0
acc_label_list.append(acc_label)
log('acc of label {:0d}: {:0.3f}%'.format(i, acc_label))
save_values(epoch, losses.avg, top1.avg, auc, acc_label_list)
print("=" * 50)
return auc
def validate_model(val_loader, model, criterion, epoch, print_freq):
batch_time = AverageMeter()
losses = AverageMeter()
psnrs = AverageMeter()
# switch to evaluate mode
model.eval()
with torch.no_grad():
end = time.time()
for i, (input, target, target_seg, filename) in enumerate(val_loader):
target = target.cuda(non_blocking=True)
target_seg = target_seg.cuda(non_blocking=True)
# compute output
output_seg = model(input)
# compute loss
# add crossentropy
if args.unet:
loss = criterionCros(output_seg, target_seg)
else:
loss = criterionMSE(output_seg, target_seg)
# measure accuracy and record loss
psnrs.update(compute_psnr(loss))
losses.update(loss.item(), input.size(0))
# measure elapsed time
batch_time.update(time.time() - end)
end = time.time()
# save segmentation result
if args.seg_result != '':
name = [os.path.split(f)[1] for f in filename]
save_tensor_image(output_seg, name, args.seg_result)
if i % print_freq == 0:
print('Test: [{0}/{1}]\t'
'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
'Psnr {psnr.val:.4f} ({psnr.avg:.4f})'.format(
i,
len(val_loader),
batch_time=batch_time,
loss=losses,
psnr=psnrs))
print(' * Loss@1 {loss.avg:.4f} Psnr@1 {psnr.avg:.4f} at Epoch {epoch:0}'.
format(loss=losses, psnr=psnrs, epoch=epoch))
# save log graph
# It's not a good location, but it's practical.
# save_log_graph(log=os.path.join(args.result, 'log.txt'))
# do post process seg_result
if args.post_processing:
for filename in os.listdir(args.seg_result):
filename = os.path.join(args.seg_result, filename)
with open(filename, 'rb') as f:
with Image.open(f) as img:
# do post processing
img = np.array(img)
img = post_processing(img)
#add resize
img = cv2.resize(img, dsize=(512, 512))
img = Image.fromarray(img)
# save post processed result
img.save(filename)
return psnrs.avg