def get_longitudinal_preprocess(is_label: bool) -> List[Transform]:
# only without cropping, somehow, there is not much left to crop in this dataset...
if not is_label:
return [
NormalizeIntensity(nonzero=True),
Unsqueeze(),
SpatialPad(spatial_size=[215, 215, 215],
method="symmetric",
mode="constant"),
Resize((IMAGESIZE, IMAGESIZE, IMAGESIZE)),
]
else:
return [
NormalizeIntensity(nonzero=True),
Unsqueeze(),
SpatialPad(spatial_size=[215, 215, 215],
method="symmetric",
mode="constant"),
Resize((IMAGESIZE, IMAGESIZE, IMAGESIZE)),
]
def test_pad_kwargs(self):
for p in TEST_NDARRAYS:
input_data = p(np.zeros((3, 8, 4)))
if isinstance(input_data, torch.Tensor):
result = (SpatialPad(spatial_size=[15, 8],
method="end",
mode="constant",
value=2)(img=input_data).cpu().numpy())
else:
result = SpatialPad(spatial_size=[15, 8],
method="end",
mode="constant",
constant_values=((0, 0), (1, 1),
(2, 2)))(img=input_data)
torch.testing.assert_allclose(result[:, 8:, :4],
np.ones((3, 7, 4)),
rtol=1e-7,
atol=0)
torch.testing.assert_allclose(result[:, :, 4:],
np.ones((3, 15, 4)) + 1,
rtol=1e-7,
atol=0)
def get_preprocess(is_label: bool) -> List[Transform]:
if not is_label:
return [
Crop(),
NormalizeIntensity(nonzero=True),
# Channel
Unsqueeze(),
SpatialPad(spatial_size=[193, 193, 193],
method="symmetric",
mode="constant"),
Resize((IMAGESIZE, IMAGESIZE, IMAGESIZE)),
]
else:
return [
Crop(),
NormalizeIntensity(nonzero=True),
Unsqueeze(),
SpatialPad(spatial_size=[193, 193, 193],
method="symmetric",
mode="constant"),
Resize((IMAGESIZE, IMAGESIZE, IMAGESIZE)),
]
def __call__(self, data):
d = dict(data)
centroid = d[
self.
centroid_key] # create mask based on centroid (select nuclei based on centroid)
roi_size = (self.patch_size, self.patch_size)
for key in self.keys:
img = d[key]
x_start, x_end, y_start, y_end = self.bbox(self.patch_size,
centroid,
img.shape[-2:])
cropped = img[:, x_start:x_end, y_start:y_end]
d[key] = SpatialPad(spatial_size=roi_size, **self.kwargs)(cropped)
return d
def test_pad_shape(self, input_param, input_shape, expected_shape):
results_1 = []
results_2 = []
input_data = self.get_arr(input_shape)
# check result is the same regardless of input type
for p in TEST_NDARRAYS:
padder = SpatialPad(**input_param)
r1 = padder(p(input_data))
r2 = padder(p(input_data), mode=input_param["mode"])
results_1.append(r1.cpu() if isinstance(r1, torch.Tensor) else r1)
results_2.append(r2.cpu() if isinstance(r2, torch.Tensor) else r2)
for results in (results_1, results_2):
np.testing.assert_allclose(results[-1].shape, expected_shape)
if input_param["mode"] not in ("empty", NumpyPadMode.EMPTY):
torch.testing.assert_allclose(results[0],
results[-1],
atol=0,
rtol=1e-5)
from monai.transforms.spatial.dictionary import RandAffined, RandRotate90d
from monai.utils import optional_import, set_determinism
from monai.utils.enums import InverseKeys
from tests.utils import make_nifti_image
_, has_nib = optional_import("nibabel")
KEYS = ["image"]
TESTS_DICT: List[Tuple] = []
TESTS_DICT.append((SpatialPadd(KEYS, 150), RandFlipd(KEYS, prob=1.0, spatial_axis=1)))
TESTS_DICT.append((RandRotate90d(KEYS, prob=0.0, max_k=1),))
TESTS_DICT.append((RandAffined(KEYS, prob=0.0, translate_range=10),))
TESTS_LIST: List[Tuple] = []
TESTS_LIST.append((SpatialPad(150), RandFlip(prob=1.0, spatial_axis=1)))
TESTS_LIST.append((RandRotate90(prob=0.0, max_k=1),))
TESTS_LIST.append((RandAffine(prob=0.0, translate_range=10),))
TEST_BASIC = [
[("channel", "channel"), ["channel", "channel"]],
[torch.Tensor([1, 2, 3]), [torch.tensor(1.0), torch.tensor(2.0), torch.tensor(3.0)]],
[
[[torch.Tensor((1.0, 2.0, 3.0)), torch.Tensor((2.0, 3.0, 1.0))]],
[
[[torch.tensor(1.0), torch.tensor(2.0)]],
[[torch.tensor(2.0), torch.tensor(3.0)]],
[[torch.tensor(3.0), torch.tensor(1.0)]],
],
],
def test_array_transform(self):
for t in [SpatialPad(10), Compose([SpatialPad(10)])]:
with self.assertRaises(TypeError):
with allow_missing_keys_mode(t):
pass
def test_pad_shape(self, input_param, input_data, expected_val):
padder = SpatialPad(**input_param)
result = padder(input_data)
np.testing.assert_allclose(result.shape, expected_val.shape)
result = padder(input_data, mode=input_param["mode"])
np.testing.assert_allclose(result.shape, expected_val.shape)
def test_pad_shape(self, input_param, input_data, expected_val):
padder = SpatialPad(**input_param)
result = padder(input_data)
self.assertAlmostEqual(result.shape, expected_val.shape)
result = padder(input_data, mode=input_param["mode"])
self.assertAlmostEqual(result.shape, expected_val.shape)
def main():
monai.config.print_config()
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
data_dir = '/home/marafath/scratch/eu_data'
labels = np.load('eu_labels.npy')
train_images = []
train_labels = []
val_images = []
val_labels = []
n_count = 0
p_count = 0
idx = 0
for case in os.listdir(data_dir):
if p_count < 13 and labels[idx] == 1:
val_images.append(
os.path.join(data_dir, case, 'image_masked.nii.gz'))
val_labels.append(labels[idx])
p_count += 1
idx += 1
elif n_count < 11 and labels[idx] == 0:
val_images.append(
os.path.join(data_dir, case, 'image_masked.nii.gz'))
val_labels.append(labels[idx])
n_count += 1
idx += 1
else:
train_images.append(
os.path.join(data_dir, case, 'image_masked.nii.gz'))
train_labels.append(labels[idx])
idx += 1
# Define transforms
train_transforms = Compose([
ScaleIntensity(),
AddChannel(),
RandZoom(min_zoom=0.9, max_zoom=1.1, prob=0.5),
SpatialPad((256, 256, 92), mode='constant'),
Resize((256, 256, 92)),
ToTensor()
])
val_transforms = Compose([
ScaleIntensity(),
AddChannel(),
SpatialPad((256, 256, 92), mode='constant'),
Resize((256, 256, 92)),
ToTensor()
])
# create a training data loader
train_ds = NiftiDataset(image_files=train_images,
labels=train_labels,
transform=train_transforms)
train_loader = DataLoader(train_ds,
batch_size=2,
shuffle=True,
num_workers=2,
pin_memory=torch.cuda.is_available())
# create a validation data loader
val_ds = NiftiDataset(image_files=val_images,
labels=val_labels,
transform=val_transforms)
val_loader = DataLoader(val_ds,
batch_size=2,
num_workers=2,
pin_memory=torch.cuda.is_available())
# Create DenseNet121, CrossEntropyLoss and Adam optimizer
device = torch.device('cuda:0')
model = monai.networks.nets.densenet.densenet121(
spatial_dims=3,
in_channels=1,
out_channels=2,
).to(device)
loss_function = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(), 1e-3)
# finetuning
#model.load_state_dict(torch.load('best_metric_model_d121.pth'))
# start a typical PyTorch training
val_interval = 1
best_metric = -1
best_metric_epoch = -1
epoch_loss_values = list()
metric_values = list()
writer = SummaryWriter()
epc = 100 # Number of epoch
for epoch in range(epc):
print('-' * 10)
print('epoch {}/{}'.format(epoch + 1, epc))
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=device, dtype=torch.int64)
optimizer.zero_grad()
outputs = model(inputs)
loss = loss_function(outputs, labels)
loss.backward()
optimizer.step()
epoch_loss += loss.item()
epoch_len = len(train_ds) // train_loader.batch_size
print('{}/{}, train_loss: {:.4f}'.format(step, epoch_len,
loss.item()))
writer.add_scalar('train_loss', loss.item(),
epoch_len * epoch + step)
epoch_loss /= step
epoch_loss_values.append(epoch_loss)
print('epoch {} average loss: {:.4f}'.format(epoch + 1, epoch_loss))
if (epoch + 1) % val_interval == 0:
model.eval()
with torch.no_grad():
num_correct = 0.
metric_count = 0
for val_data in val_loader:
val_images, val_labels = val_data[0].to(
device), val_data[1].to(device)
val_outputs = model(val_images)
value = torch.eq(val_outputs.argmax(dim=1), val_labels)
metric_count += len(value)
num_correct += value.sum().item()
metric = num_correct / metric_count
metric_values.append(metric)
#torch.save(model.state_dict(), 'model_d121_epoch_{}.pth'.format(epoch + 1))
if metric > best_metric:
best_metric = metric
best_metric_epoch = epoch + 1
torch.save(
model.state_dict(),
'/home/marafath/scratch/saved_models/best_metric_model_d121.pth'
)
print('saved new best metric model')
print(
'current epoch: {} current accuracy: {:.4f} best accuracy: {:.4f} at epoch {}'
.format(epoch + 1, metric, best_metric, best_metric_epoch))
writer.add_scalar('val_accuracy', metric, epoch + 1)
print('train completed, best_metric: {:.4f} at epoch: {}'.format(
best_metric, best_metric_epoch))
writer.close()