def run_inference_test(root_dir, test_x, test_y,
device=torch.device("cuda:0")):
# define transforms for image and classification
val_transforms = Compose(
[LoadPNG(image_only=True),
AddChannel(),
ScaleIntensity(),
ToTensor()])
val_ds = MedNISTDataset(test_x, test_y, val_transforms)
val_loader = DataLoader(val_ds, batch_size=300, num_workers=10)
model = densenet121(
spatial_dims=2,
in_channels=1,
out_channels=len(np.unique(test_y)),
).to(device)
model_filename = os.path.join(root_dir, "best_metric_model.pth")
model.load_state_dict(torch.load(model_filename))
model.eval()
y_true = list()
y_pred = list()
with torch.no_grad():
for test_data in val_loader:
test_images, test_labels = test_data[0].to(
device), test_data[1].to(device)
pred = model(test_images).argmax(dim=1)
for i in range(len(pred)):
y_true.append(test_labels[i].item())
y_pred.append(pred[i].item())
tps = [
np.sum((np.asarray(y_true) == idx) & (np.asarray(y_pred) == idx))
for idx in np.unique(test_y)
]
return tps
def test_shape(self, data_shape, filenames, expected_shape, meta_shape):
test_image = np.random.randint(0, 256, size=data_shape)
tempdir = tempfile.mkdtemp()
with tempfile.TemporaryDirectory() as tempdir:
for i, name in enumerate(filenames):
filenames[i] = os.path.join(tempdir, name)
Image.fromarray(test_image.astype("uint8")).save(filenames[i])
result = LoadPNG()(filenames)
self.assertTupleEqual(result[1]["spatial_shape"], meta_shape)
self.assertTupleEqual(result[0].shape, expected_shape)
def test_shape(self, data_shape, filenames, expected_shape, meta_shape):
test_image = np.random.randint(0, 256, size=data_shape)
with tempfile.TemporaryDirectory() as tempdir:
for i, name in enumerate(filenames):
filenames[i] = os.path.join(tempdir, name)
Image.fromarray(test_image.astype("uint8")).save(filenames[i])
result = LoadPNG()(filenames)
self.assertTupleEqual(result[1]["spatial_shape"], meta_shape)
self.assertTupleEqual(result[0].shape, expected_shape)
if result[0].shape == test_image.shape:
np.testing.assert_allclose(result[0], test_image)
else:
np.testing.assert_allclose(result[0], np.tile(test_image, [result[0].shape[0], 1, 1]))
def run_training_test(root_dir,
train_x,
train_y,
val_x,
val_y,
device="cuda:0",
num_workers=10):
monai.config.print_config()
# define transforms for image and classification
train_transforms = Compose([
LoadPNG(image_only=True),
AddChannel(),
ScaleIntensity(),
RandRotate(range_x=np.pi / 12, prob=0.5, keep_size=True),
RandFlip(spatial_axis=0, prob=0.5),
RandZoom(min_zoom=0.9, max_zoom=1.1, prob=0.5),
ToTensor(),
])
train_transforms.set_random_state(1234)
val_transforms = Compose(
[LoadPNG(image_only=True),
AddChannel(),
ScaleIntensity(),
ToTensor()])
# create train, val data loaders
train_ds = MedNISTDataset(train_x, train_y, train_transforms)
train_loader = DataLoader(train_ds,
batch_size=300,
shuffle=True,
num_workers=num_workers)
val_ds = MedNISTDataset(val_x, val_y, val_transforms)
val_loader = DataLoader(val_ds, batch_size=300, num_workers=num_workers)
model = densenet121(spatial_dims=2,
in_channels=1,
out_channels=len(np.unique(train_y))).to(device)
loss_function = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(), 1e-5)
epoch_num = 4
val_interval = 1
# start training validation
best_metric = -1
best_metric_epoch = -1
epoch_loss_values = list()
metric_values = list()
model_filename = os.path.join(root_dir, "best_metric_model.pth")
for epoch in range(epoch_num):
print("-" * 10)
print(f"Epoch {epoch + 1}/{epoch_num}")
model.train()
epoch_loss = 0
step = 0
for batch_data in train_loader:
step += 1
inputs, labels = batch_data[0].to(device), batch_data[1].to(device)
optimizer.zero_grad()
outputs = model(inputs)
loss = loss_function(outputs, labels)
loss.backward()
optimizer.step()
epoch_loss += loss.item()
epoch_loss /= step
epoch_loss_values.append(epoch_loss)
print(f"epoch {epoch + 1} average loss:{epoch_loss:0.4f}")
if (epoch + 1) % val_interval == 0:
model.eval()
with torch.no_grad():
y_pred = torch.tensor([], dtype=torch.float32, device=device)
y = torch.tensor([], dtype=torch.long, device=device)
for val_data in val_loader:
val_images, val_labels = val_data[0].to(
device), val_data[1].to(device)
y_pred = torch.cat([y_pred, model(val_images)], dim=0)
y = torch.cat([y, val_labels], dim=0)
auc_metric = compute_roc_auc(y_pred,
y,
to_onehot_y=True,
softmax=True)
metric_values.append(auc_metric)
acc_value = torch.eq(y_pred.argmax(dim=1), y)
acc_metric = acc_value.sum().item() / len(acc_value)
if auc_metric > best_metric:
best_metric = auc_metric
best_metric_epoch = epoch + 1
torch.save(model.state_dict(), model_filename)
print("saved new best metric model")
print(
f"current epoch {epoch +1} current AUC: {auc_metric:0.4f} "
f"current accuracy: {acc_metric:0.4f} best AUC: {best_metric:0.4f} at epoch {best_metric_epoch}"
)
print(
f"train completed, best_metric: {best_metric:0.4f} at epoch: {best_metric_epoch}"
)
return epoch_loss_values, best_metric, best_metric_epoch
params['rotate_prob'] = 0.5
params['min_zoom'] = 0.9
params['max_zoom'] = 1.1
params['zoom_prob'] = 0.5
monai.config.print_config()
train_data, val_data, test_data, raw_data = get_train_val_test_data(
params['data_dir'], params['test_val_split'])
size_n = 3
sample_data = train_data.sample(size_n**2)
#show_sample_dataframe(sample_data, size_n=size_n, title="Training samples")
train_transforms = Compose([
LoadPNG(image_only=True),
AddChannel(),
ScaleIntensity(),
RandRotate(range_x=params['rotate_range_x'],
prob=params['rotate_prob'],
keep_size=True),
# RandFlip(spatial_axis=0, prob=0.5),
RandZoom(min_zoom=params['min_zoom'],
max_zoom=params['max_zoom'],
prob=params['zoom_prob'],
keep_size=True),
ToTensor()
])
val_transforms = Compose(
[LoadPNG(image_only=True),
