def test(model, test_loader, task, device):
model.eval()
test_loss = 0
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
with torch.no_grad():
for batch_idx, (data, target) in enumerate(test_loader):
data = data.to(device)
target = target.to(device)
output = model(data)
# output = F.softmax(output,dim=1)
if task == 'multi-label, binary-class':
loss = F.binary_cross_entropy_with_logits(
output, target.float())
else:
loss = F.cross_entropy(output, target.long().squeeze())
target = target.float()
test_loss += loss.item()
y_true = torch.cat((y_true, target))
y_score = torch.cat((y_score, F.softmax(output, dim=1)))
y_true = y_true.cpu().numpy()
y_score = y_score.cpu().numpy()
auc = getAUC(y_true, y_score, task)
acc = getACC(y_true, y_score, task)
test_loss /= len(test_loader)
print('\nTest set: Average loss: {:.4f}, Accuracy: {:.4f}\n'.format(
test_loss, acc))
return test_loss, auc, acc
def val(model, val_loader, task, device):
model.eval()
val_loss = 0
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
with torch.no_grad():
for batch_idx, (data, target) in enumerate(val_loader):
data = data.to(device)
target = target.to(device)
output = model(data)
if task == 'multi-label, binary-class':
loss = F.binary_cross_entropy_with_logits(
output, target.float())
else:
loss = F.cross_entropy(output, target.long().squeeze())
target = target.float()
val_loss += loss.item()
y_true = torch.cat((y_true, target))
y_score = torch.cat((y_score, F.softmax(output, dim=1)))
y_true = y_true.cpu().numpy()
y_score = y_score.cpu().numpy()
auc = getAUC(y_true, y_score, task)
acc = getACC(y_true, y_score, task)
val_loss /= len(val_loader)
return val_loss, auc, acc
def val(model, val_loader, device, task, dir_path, epoch, criterion):
''' validation function
:param model: the model to validate
:param val_loader: DataLoader of validation set
:param device: cpu or cuda
:param val_auc_list: the list to save AUC score of each epoch
:param task: task of current dataset, binary-class/multi-class/multi-label, binary-class
:param dir_path: where to save model and data
:param epoch: current epoch
:param criterion: loss function
'''
model.eval()
val_loss = []
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
with torch.no_grad():
for batch_idx, (inputs, targets) in enumerate(val_loader):
outputs = model(inputs.to(device))
if task == 'multi-label, binary-class':
targets = targets.to(torch.float32).to(device)
loss = criterion(outputs, targets)
m = nn.Sigmoid()
outputs = m(outputs).to(device)
else:
targets = targets.squeeze().long().to(device)
loss = criterion(outputs, targets)
m = nn.Softmax(dim=1)
outputs = m(outputs).to(device)
targets = targets.float().resize_(len(targets), 1)
y_true = torch.cat((y_true, targets), 0)
y_score = torch.cat((y_score, outputs), 0)
val_loss.append(loss.item())
y_true = y_true.cpu().numpy()
y_score = y_score.detach().cpu().numpy()
auc = getAUC(y_true, y_score, task)
acc = getACC(y_true, y_score, task)
state = {
'net': model.state_dict(),
'auc': auc,
'epoch': epoch,
}
path = os.path.join(dir_path, 'ckpt_%d_auc_%.5f.pth' % (epoch, auc))
torch.save(state, path)
valloss = open(os.path.join(dir_path, 'val_loss.txt'), 'a')
valloss.write(str(np.mean(val_loss)) + "\n")
valloss.close()
data_file = open(os.path.join(dir_path, 'save_data.txt'), 'a')
data_file.write(str(epoch) + ' ' + str(auc) + ' ' + str(acc) + "\n")
data_file.close()
def val(model, val_loader, device, val_auc_list, task, dir_path, epoch):
''' validation function
:param model: the model to validate
:param val_loader: DataLoader of validation set
:param device: cpu or cuda
:param val_auc_list: the list to save AUC score of each epoch
:param task: task of current dataset, binary-class/multi-class/multi-label, binary-class
:param dir_path: where to save model
:param epoch: current epoch
'''
model.eval()
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
with torch.no_grad():
for batch_idx, (inputs, targets) in enumerate(val_loader):
outputs = model(inputs.to(device))
if task == 'multi-label, binary-class':
targets = targets.to(torch.float32).to(device)
m = nn.Sigmoid()
outputs = m(outputs).to(device)
else:
targets = targets.squeeze().long().to(device)
m = nn.Softmax(dim=1)
outputs = m(outputs).to(device)
targets = targets.float().resize_(len(targets), 1)
y_true = torch.cat((y_true, targets), 0)
y_score = torch.cat((y_score, outputs), 0)
y_true = y_true.cpu().numpy()
y_score = y_score.detach().cpu().numpy()
auc = getAUC(y_true, y_score, task)
val_auc_list.append(auc)
state = {
'net': model.state_dict(),
'auc': auc,
'epoch': epoch,
}
path = os.path.join(dir_path, 'ckpt_%d_auc_%.5f.pth' % (epoch, auc))
torch.save(state, path)
def test(model, split, data_loader, device, task, dir_path):
''' testing function
:param model: the model to test
:param split: the data to test, 'train/val/test'
:param data_loader: DataLoader of data
:param device: cpu or cuda
:param task: task of current dataset, binary-class/multi-class/multi-label, binary-class
:param dir_path: where to save data
'''
model.eval()
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
with torch.no_grad():
for batch_idx, (inputs, targets) in enumerate(data_loader):
outputs = model(inputs.to(device))
if task == 'multi-label, binary-class':
targets = targets.to(torch.float32).to(device)
m = nn.Sigmoid()
outputs = m(outputs).to(device)
else:
targets = targets.squeeze().long().to(device)
m = nn.Softmax(dim=1)
outputs = m(outputs).to(device)
targets = targets.float().resize_(len(targets), 1)
y_true = torch.cat((y_true, targets), 0)
y_score = torch.cat((y_score, outputs), 0)
y_true = y_true.cpu().numpy()
y_score = y_score.detach().cpu().numpy()
auc = getAUC(y_true, y_score, task)
acc = getACC(y_true, y_score, task)
print('%s AUC: %.5f ACC: %.5f' % (split, auc, acc))
# if args.output_root is not None:
# output_dir = os.path.join(args.output_root, args.data_name)
# if not os.path.exists(output_dir):
# os.mkdir(output_dir)
# output_path = os.path.join(output_dir, '%s.csv' % (split))
output_path = os.path.join(dir_path, '%s.csv' % (split))
save_results(y_true, y_score, output_path)
def test(model, split, data_loader, device, flag, task, output_root=None):
"""
testing function
:param model: the model to test
:param split: the data to test, 'train/val/test'
:param data_loader: DataLoader of data
:param device: cpu or cuda
:param flag: subset name
:param task: task of current dataset, binary-class/multi-class/multi-label, binary-class
:param data_name: data name
"""
configuration = {
"pathmnist": {
"classes": ['0', '1', '2', '3', '4', '5', '6', '7', '8']
},
"chestmnist": {
"classes": [
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11',
'12', '13'
]
},
"dermamnist": {
"classes": ['0', '1', '2', '3', '4', '5', '6']
},
"octmnist": {
"classes": ['0', '1', '2', '3']
},
"retinamnist": {
"classes": ['0', '1', '2', '3', '4']
},
"pneumoniamnist": {
"classes": ['0', '1']
},
"breastmnist": {
"classes": ['0', '1']
},
"organmnist_axial": {
"classes":
['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
},
"organmnist_coronal": {
"classes":
['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
},
"organmnist_sagittal": {
"classes":
['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
}
}
args = configuration[flag]
model.eval()
y_true = torch.tensor([]).to(device)
y_score = torch.tensor([]).to(device)
pred_labels = []
true_labels = []
scores = []
with torch.no_grad():
for batch_idx, (inputs, targets) in enumerate(data_loader):
outputs = model(inputs.to(device))
if task == 'multi-label, binary-class':
targets = targets.to(torch.float32).to(device)
m = nn.Sigmoid()
outputs = m(outputs).to(device)
else:
targets = targets.squeeze().long().to(device)
m = nn.Softmax(dim=1)
outputs = m(outputs).to(device)
targets = targets.float().resize_(len(targets), 1)
predict_label = outputs.data.max(1)[1].cpu().numpy()
pred_labels.extend(predict_label)
true_label = targets.data.cpu().numpy()
true_labels.extend(true_label)
scores.extend(outputs.data.cpu().numpy().tolist())
y_true = torch.cat((y_true, targets), 0)
y_score = torch.cat((y_score, outputs), 0)
y_true = y_true.cpu().numpy()
y_score = y_score.detach().cpu().numpy()
if split == 'test' and flag != 'chestmnist':
result = metric_results(pred_labels, true_labels)
printMetricResults(result)
plot_confusion_matrix(result['confusion_matrix'],
classes=args["classes"],
normalize=False,
title=flag)
confusion_matrixPath = os.path.join(config.confusionMatrixPath,
flag)
plt.savefig(confusion_matrixPath, dpi=600)
plt.clf()
rocPicName = flag
plotRocCurve(flag, true_labels, scores, config.rocPic_path,
rocPicName)
auc = getAUC(y_true, y_score, task)
acc = getACC(y_true, y_score, task)
print('%s AUC: %.5f ACC: %.5f' % (split, auc, acc))
if output_root is not None:
output_dir = os.path.join(output_root, flag)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
output_path = os.path.join(output_dir, '%s.csv' % (split))
save_results(y_true, y_score, output_path)
