def main():
args = parse_args()
model_path = Path(args.model_path)
if args.network_conf_path is not None:
train_conf = ConfigFactory.parse_file(str(Path(
args.network_conf_path)))
conf_path = Path(args.network_conf_path)
else:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
data_config = DataConfig.from_conf(conf_path)
dataset_config = DatasetConfig.from_conf(
name=data_config.training_datasets[0],
mount_prefix=data_config.mount_prefix,
mode=data_config.data_mode)
input_path = Path(args.input_dir).joinpath(
dataset_config.image_label_format.image.format(phase=args.phase))
output_dir = Path(args.output_dir)
checkpoint = torch.load(str(model_path),
map_location=torch.device(args.device))
get_conf(train_conf, group="network", key="experiment_dir")
network = UNet(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
)
network.load_state_dict(checkpoint)
network.cuda(device=args.device)
# image = nib.load(str(input_path)).get_data()
# if image.ndim == 4:
# image = np.squeeze(image, axis=-1).astype(np.int16)
# image = image.astype(np.int16)
# image = np.transpose(image, (2, 0, 1))
dataset = Torch2DSegmentationDataset(
name=dataset_config.name,
image_paths=[input_path],
label_paths=[
input_path.parent.joinpath(
dataset_config.image_label_format.label.format(
phase=args.phase))
],
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
is_3d=True,
)
image = dataset.get_image_tensor_from_index(0)
image = torch.unsqueeze(image, 0)
image = prepare_tensors(image, True, args.device)
label = dataset.get_label_tensor_from_index(0)
inference(
image=image,
label=label,
image_path=input_path,
network=network,
output_dir=output_dir,
)
def main():
args = parse_args()
if args.conf_path is None:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
else:
train_conf = ConfigFactory.parse_file(str(Path(args.conf_path)))
conf_path = Path(args.conf_path)
if get_conf(train_conf, group="experiment", key="experiment_dir") is not None:
experiment_dir = Path(get_conf(train_conf, group="experiment", key="experiment_dir"))
else:
experiment_dir = None
config = ExperimentConfig(
experiment_dir=experiment_dir,
batch_size=get_conf(train_conf, group="experiment", key="batch_size"),
num_epochs=get_conf(train_conf, group="experiment", key="num_epochs"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
num_workers=get_conf(train_conf, group="experiment", key="num_workers"),
pin_memory=get_conf(train_conf, group="experiment", key="pin_memory"),
n_inference=get_conf(train_conf, group="experiment", key="n_inference"),
seed=get_conf(train_conf, group="experiment", key="seed"),
)
augmentation_config = AugmentationConfig.from_conf(conf_path)
shutil.copy(str(conf_path), str(config.experiment_dir.joinpath("train.conf")))
network = DefSegNet(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
int_downsize=get_conf(train_conf, group="network", key="integrate_downsize"),
bidir=True,
)
checkpoint = torch.load(
str(get_conf(train_conf, group="network", key="checkpoint_path")),
map_location=torch.device(get_conf(train_conf, group="experiment", key="device"))
)
network.load_state_dict(checkpoint)
network.cuda(device=get_conf(train_conf, group="experiment", key="device"))
network.freeze_vxm()
training_sets, validation_sets, extra_validation_sets = construct_training_validation_dataset(
DataConfig.from_conf(conf_path), feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"), is_3d=True, seed=config.seed,
augmentation_config=augmentation_config, output_dir=config.experiment_dir,
template_path=Path(get_conf(train_conf, group="network", key="template_path")),
template_image_path=Path(get_conf(train_conf, group="network", key="template_image_path")),
)
for train in training_sets:
train.export(config.experiment_dir.joinpath("training_set_{}.csv".format(train.name)))
for val in validation_sets:
val.export(config.experiment_dir.joinpath("validation_set_{}.csv".format(val.name)))
for val in extra_validation_sets:
val.export(config.experiment_dir.joinpath("extra_validation_set_{}.csv".format(val.name)))
if get_conf(train_conf, group="optimizer", key="type") == "SGD":
optimizer = torch.optim.SGD(
network.parameters(),
lr=get_conf(train_conf, group="optimizer", key="learning_rate"),
momentum=get_conf(train_conf, group="optimizer", key="momentum"),
)
else:
optimizer = torch.optim.Adam(
network.parameters(), lr=get_conf(train_conf, group="optimizer", key="learning_rate")
)
loss = UDADefSegLoss(
penalty="l2",
loss_mult=get_conf(train_conf, group="network", key="integrate_downsize"),
weights=get_conf(train_conf, group="loss", key="weights"),
)
experiment = DefSegExperiment(
config=config,
network=network,
training_sets=training_sets,
validation_sets=validation_sets,
extra_validation_sets=extra_validation_sets,
optimizer=optimizer,
loss=loss,
other_validation_metrics=[
DefSegWarpedTemplateDice(), DefSegPredDice(), DefSegWarpedMapsDice()
],
inference_func=inference
)
experiment.train()
def main():
args = parse_args()
if args.conf_path is None:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
else:
train_conf = ConfigFactory.parse_file(str(Path(args.conf_path)))
if get_conf(train_conf, group="experiment",
key="experiment_dir") is not None:
experiment_dir = Path(
get_conf(train_conf, group="experiment", key="experiment_dir"))
else:
experiment_dir = None
config = ExperimentConfig(
experiment_dir=experiment_dir,
batch_size=get_conf(train_conf, group="experiment", key="batch_size"),
num_epochs=get_conf(train_conf, group="experiment", key="num_epochs"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
num_workers=get_conf(train_conf, group="experiment",
key="num_workers"),
pin_memory=get_conf(train_conf, group="experiment", key="pin_memory"),
)
shutil.copy(str(TRAIN_CONF_PATH),
str(config.experiment_dir.joinpath("train.conf")))
network = FCN2DSegmentationModel(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
up_conv_filter=get_conf(train_conf,
group="network",
key="up_conv_filter"),
final_conv_filter=get_conf(train_conf,
group="network",
key="final_conv_filter"),
feature_size=get_conf(train_conf, group="network", key="feature_size"))
training_set, validation_set = construct_training_validation_dataset(
DataConfig.from_conf(TRAIN_CONF_PATH),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="in_channels"))
training_set.export(config.experiment_dir.joinpath("training_set.csv"))
validation_set.export(config.experiment_dir.joinpath("validation_set.csv"))
if get_conf(train_conf, group="optimizer", key="type") == "SGD":
optimizer = torch.optim.SGD(
network.parameters(),
lr=get_conf(train_conf, group="optimizer", key="learning_rate"),
momentum=get_conf(train_conf, group="optimizer", key="momentum"),
)
else:
optimizer = torch.optim.Adam(network.parameters(),
lr=get_conf(train_conf,
group="optimizer",
key="learning_rate"))
if get_conf(train_conf, group="loss", key="type") == "FocalLoss":
loss = FocalLoss(
alpha=get_conf(train_conf, group="loss", key="alpha"),
gamma=get_conf(train_conf, group="loss", key="gamma"),
logits=True,
)
else:
loss = BCELoss()
experiment = Experiment(
config=config,
network=network,
training_set=training_set,
validation_set=validation_set,
optimizer=optimizer,
loss=loss,
other_validation_metrics=[DiceCoeffWithLogits()],
)
experiment.train()
def main():
args = parse_args()
if args.starting_epoch > 0:
assert args.exp_dir is not None
exp_dir = Path(args.exp_dir)
if args.conf_path is None:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
else:
train_conf = ConfigFactory.parse_file(str(Path(args.conf_path)))
conf_path = Path(args.conf_path)
if get_conf(train_conf, group="experiment",
key="experiment_dir") is not None:
experiment_dir = Path(
get_conf(train_conf, group="experiment", key="experiment_dir"))
else:
experiment_dir = None
config = ExperimentConfig(
experiment_dir=experiment_dir,
batch_size=get_conf(train_conf, group="experiment", key="batch_size"),
num_epochs=get_conf(train_conf, group="experiment", key="num_epochs"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
num_workers=get_conf(train_conf, group="experiment",
key="num_workers"),
pin_memory=get_conf(train_conf, group="experiment", key="pin_memory"),
n_inference=get_conf(train_conf, group="experiment",
key="n_inference"),
seed=get_conf(train_conf, group="experiment", key="seed"),
)
augmentation_config = AugmentationConfig.from_conf(conf_path)
shutil.copy(str(conf_path),
str(config.experiment_dir.joinpath("train.conf")))
if get_conf(train_conf, group="network", key="name") == "encodedecode":
network = ImgTemplateEncoderNet(
feature_size=get_conf(train_conf,
group="network",
key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
batch_norm=get_conf(train_conf, group="network", key="batch_norm"),
group_norm=get_conf(train_conf, group="network", key="group_norm"),
int_downsize=get_conf(train_conf,
group="network",
key="integrate_downsize"),
bidir=True,
in_channels=get_conf(train_conf,
group="network",
key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
batch_size=get_conf(train_conf,
group="experiment",
key="batch_size"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
)
elif get_conf(train_conf, group="network", key="name") == "istn":
network = ISTNNet(
feature_size=get_conf(train_conf,
group="network",
key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
batch_norm=get_conf(train_conf, group="network", key="batch_norm"),
group_norm=get_conf(train_conf, group="network", key="group_norm"),
int_downsize=get_conf(train_conf,
group="network",
key="integrate_downsize"),
bidir=True,
in_channels=get_conf(train_conf,
group="network",
key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
batch_size=get_conf(train_conf,
group="experiment",
key="batch_size"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
)
else:
raise ValueError("network name not supported. istn or encodedecode")
if args.starting_epoch > 0:
print(
exp_dir.joinpath("checkpoints",
"CP_{}.pth".format(args.starting_epoch - 1)))
checkpoint = torch.load(
str(
exp_dir.joinpath("checkpoints",
"CP_{}.pth".format(args.starting_epoch - 1))),
map_location=torch.device(
get_conf(train_conf, group="experiment", key="device")),
)
network.load_state_dict(checkpoint)
network.cuda(
device=get_conf(train_conf, group="experiment", key="device"))
image = DefSegDataset.read_image(
image_path=exp_dir.joinpath(
"atlas", "epoch_{}".format(args.starting_epoch - 1),
"image.nii.gz"),
feature_size=None,
n_slices=None,
)
label = DefSegDataset.read_label(
label_path=exp_dir.joinpath(
"atlas", "epoch_{}".format(args.starting_epoch - 1),
"label.nii.gz"),
feature_size=None,
n_slices=None,
)
atlas = Atlas(image=image, label=label)
else:
atlas = None
training_sets, validation_sets, extra_validation_sets = construct_training_validation_dataset(
DataConfig.from_conf(conf_path),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
is_3d=True,
seed=config.seed,
augmentation_config=augmentation_config,
output_dir=config.experiment_dir,
)
for train in training_sets:
train.export(
config.experiment_dir.joinpath("training_set_{}.csv".format(
train.name)))
for val in validation_sets:
val.export(
config.experiment_dir.joinpath("validation_set_{}.csv".format(
val.name)))
for val in extra_validation_sets:
val.export(
config.experiment_dir.joinpath(
"extra_validation_set_{}.csv".format(val.name)))
if get_conf(train_conf, group="optimizer", key="type") == "SGD":
optimizer = torch.optim.SGD(
network.parameters(),
lr=get_conf(train_conf, group="optimizer", key="learning_rate"),
momentum=get_conf(train_conf, group="optimizer", key="momentum"),
)
else:
optimizer = torch.optim.Adam(network.parameters(),
lr=get_conf(train_conf,
group="optimizer",
key="learning_rate"))
loss = DefLoss(
penalty="l2",
loss_mult=get_conf(train_conf,
group="network",
key="integrate_downsize"),
weights=get_conf(train_conf, group="loss", key="weights"),
)
experiment = DefSegExperiment(
config=config,
network=network,
training_sets=training_sets,
validation_sets=validation_sets,
extra_validation_sets=extra_validation_sets,
optimizer=optimizer,
loss=loss,
other_validation_metrics=[
DefAffineWarpedTemplateDice(),
DefWarpedTemplateDice(),
DefPredDice(),
],
inference_func=inference,
)
experiment.train(
starting_epoch=args.starting_epoch,
atlas=atlas,
atlas_eta=get_conf(train_conf, group="network", key="atlas_eta"),
)
def main():
args = parse_args()
if args.conf_path is None:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
else:
train_conf = ConfigFactory.parse_file(str(Path(args.conf_path)))
conf_path = Path(args.conf_path)
if get_conf(train_conf, group="experiment",
key="experiment_dir") is not None:
experiment_dir = Path(
get_conf(train_conf, group="experiment", key="experiment_dir"))
else:
experiment_dir = None
config = ExperimentConfig(
experiment_dir=experiment_dir,
batch_size=get_conf(train_conf, group="experiment", key="batch_size"),
num_epochs=get_conf(train_conf, group="experiment", key="num_epochs"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
num_workers=get_conf(train_conf, group="experiment",
key="num_workers"),
pin_memory=get_conf(train_conf, group="experiment", key="pin_memory"),
n_inference=get_conf(train_conf, group="experiment",
key="n_inference"),
seed=get_conf(train_conf, group="experiment", key="seed"),
)
augmentation_config = AugmentationConfig.from_conf(conf_path)
shutil.copy(str(conf_path),
str(config.experiment_dir.joinpath("train.conf")))
network = UNet(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
)
training_sets, validation_sets, extra_validation_sets = construct_training_validation_dataset(
DataConfig.from_conf(conf_path),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
is_3d=True,
seed=config.seed,
augmentation_config=augmentation_config,
output_dir=config.experiment_dir,
)
for train in training_sets:
train.export(
config.experiment_dir.joinpath("training_set_{}.csv".format(
train.name)))
for val in validation_sets:
val.export(
config.experiment_dir.joinpath("validation_set_{}.csv".format(
val.name)))
for val in extra_validation_sets:
val.export(
config.experiment_dir.joinpath(
"extra_validation_set_{}.csv".format(val.name)))
if get_conf(train_conf, group="optimizer", key="type") == "SGD":
optimizer = torch.optim.SGD(
network.parameters(),
lr=get_conf(train_conf, group="optimizer", key="learning_rate"),
momentum=get_conf(train_conf, group="optimizer", key="momentum"),
)
else:
optimizer = torch.optim.Adam(network.parameters(),
lr=get_conf(train_conf,
group="optimizer",
key="learning_rate"))
if get_conf(train_conf, group="loss", key="type") == "FocalLoss":
loss = FocalLoss(
alpha=get_conf(train_conf, group="loss", key="alpha"),
gamma=get_conf(train_conf, group="loss", key="gamma"),
logits=True,
)
else:
loss = BCELoss()
experiment = FCN3DExperiment(
config=config,
network=network,
training_sets=training_sets,
validation_sets=validation_sets,
extra_validation_sets=extra_validation_sets,
optimizer=optimizer,
loss=loss,
other_validation_metrics=[DiceCoeffWithLogits()],
inference_func=inference)
experiment.train()
def main():
args = parse_args()
model_path = Path(args.model_path)
if args.network_conf_path is not None:
train_conf = ConfigFactory.parse_file(str(Path(
args.network_conf_path)))
conf_path = Path(args.network_conf_path)
else:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
data_config = DataConfig.from_conf(conf_path)
dataset_config = DatasetConfig.from_conf(
name=data_config.dataset_names[0],
mount_prefix=data_config.mount_prefix,
mode=data_config.data_mode)
input_path = Path(args.input_dir).joinpath(
dataset_config.image_label_format.image.format(phase=args.phase))
output_dir = Path(args.output_dir)
checkpoint = torch.load(str(model_path),
map_location=torch.device(args.device))
get_conf(train_conf, group="network", key="experiment_dir")
network = FCN2DSegmentationModel(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
up_conv_filter=get_conf(train_conf,
group="network",
key="up_conv_filter"),
final_conv_filter=get_conf(train_conf,
group="network",
key="final_conv_filter"),
feature_size=get_conf(train_conf, group="network", key="feature_size"))
network.load_state_dict(checkpoint)
network.cuda(device=args.device)
# image = nib.load(str(input_path)).get_data()
# if image.ndim == 4:
# image = np.squeeze(image, axis=-1).astype(np.int16)
# image = image.astype(np.int16)
# image = np.transpose(image, (2, 0, 1))
image = Torch2DSegmentationDataset.read_image(
input_path,
get_conf(train_conf, group="network", key="feature_size"),
get_conf(train_conf, group="network", key="in_channels"),
crop=args.crop_image,
)
image = np.expand_dims(image, 0)
image = torch.from_numpy(image).float()
image = prepare_tensors(image, gpu=True, device=args.device)
predicted = network(image)
predicted = torch.sigmoid(predicted)
print("sigmoid", torch.mean(predicted).item(), torch.max(predicted).item())
predicted = (predicted > 0.5).float()
print("0.5", torch.mean(predicted).item(), torch.max(predicted).item())
predicted = predicted.cpu().detach().numpy()
nim = nib.load(str(input_path))
# Transpose and crop the segmentation to recover the original size
predicted = np.squeeze(predicted, axis=0)
print(predicted.shape)
# map back to original size
final_predicted = np.zeros(
(image.shape[1], image.shape[2], image.shape[3]))
print(predicted.shape, final_predicted.shape)
for i in range(predicted.shape[0]):
a = predicted[i, :, :, :] > 0.5
print(a.shape)
final_predicted[predicted[i, :, :, :] > 0.5] = i + 1
# image = nim.get_data()
final_predicted = np.transpose(final_predicted, [1, 2, 0])
print(predicted.shape, final_predicted.shape)
# final_predicted = np.resize(final_predicted, (image.shape[0], image.shape[1], image.shape[2]))
print(predicted.shape, final_predicted.shape, np.max(final_predicted),
np.mean(final_predicted), np.min(final_predicted))
# if Z < 64:
# pred_segt = pred_segt[x_pre:x_pre + X, y_pre:y_pre + Y, z1_ - z1:z1_ - z1 + Z]
# else:
# pred_segt = pred_segt[x_pre:x_pre + X, y_pre:y_pre + Y, :]
# pred_segt = np.pad(pred_segt, ((0, 0), (0, 0), (z_pre, z_post)), 'constant')
nim2 = nib.Nifti1Image(final_predicted, nim.affine)
nim2.header['pixdim'] = nim.header['pixdim']
output_dir.mkdir(parents=True, exist_ok=True)
nib.save(nim2, '{0}/seg.nii.gz'.format(str(output_dir)))
final_image = image.cpu().detach().numpy()
final_image = np.squeeze(final_image, 0)
final_image = np.transpose(final_image, [1, 2, 0])
print(final_image.shape)
nim2 = nib.Nifti1Image(final_image, nim.affine)
nim2.header['pixdim'] = nim.header['pixdim']
nib.save(nim2, '{0}/image.nii.gz'.format(str(output_dir)))
# shutil.copy(str(input_path), str(output_dir.joinpath("image.nii.gz")))
label = Torch2DSegmentationDataset.read_label(
input_path.parent.joinpath(
dataset_config.image_label_format.label.format(phase=args.phase)),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="in_channels"),
crop=args.crop_image,
)
final_label = np.zeros((image.shape[1], image.shape[2], image.shape[3]))
for i in range(label.shape[0]):
final_label[label[i, :, :, :] == 1.0] = i + 1
final_label = np.transpose(final_label, [1, 2, 0])
print(final_label.shape)
nim2 = nib.Nifti1Image(final_label, nim.affine)
nim2.header['pixdim'] = nim.header['pixdim']
output_dir.mkdir(parents=True, exist_ok=True)
nib.save(nim2, '{0}/label.nii.gz'.format(str(output_dir)))
def main():
args = parse_args()
if args.conf_path is None:
train_conf = ConfigFactory.parse_file(str(TRAIN_CONF_PATH))
conf_path = TRAIN_CONF_PATH
else:
train_conf = ConfigFactory.parse_file(str(Path(args.conf_path)))
conf_path = Path(args.conf_path)
if get_conf(train_conf, group="experiment",
key="experiment_dir") is not None:
experiment_dir = Path(
get_conf(train_conf, group="experiment", key="experiment_dir"))
else:
experiment_dir = None
config = ExperimentConfig(
experiment_dir=experiment_dir,
batch_size=get_conf(train_conf, group="experiment", key="batch_size"),
num_epochs=get_conf(train_conf, group="experiment", key="num_epochs"),
gpu=get_conf(train_conf, group="experiment", key="gpu"),
device=get_conf(train_conf, group="experiment", key="device"),
num_workers=get_conf(train_conf, group="experiment",
key="num_workers"),
pin_memory=get_conf(train_conf, group="experiment", key="pin_memory"),
n_inference=get_conf(train_conf, group="experiment",
key="n_inference"),
seed=get_conf(train_conf, group="experiment", key="seed"),
)
augmentation_config = AugmentationConfig.from_conf(conf_path)
shutil.copy(str(conf_path),
str(config.experiment_dir.joinpath("train.conf")))
atlas_path = "D:\surui\\rbh\cardiac\DL_segmentation\RBH_3D_atlases\IHD586_10RZ04876_RBH_IHD_201410241040_MRC25598\seg_lvsa_SR_ED.nii.gz"
atlas = Torch2DSegmentationDataset.read_label(
label_path=Path(atlas_path),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
)
network = DefSegNet(
in_channels=get_conf(train_conf, group="network", key="in_channels"),
n_classes=get_conf(train_conf, group="network", key="n_classes"),
n_filters=get_conf(train_conf, group="network", key="n_filters"),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
template=atlas,
int_downsize=2,
)
training_sets, validation_sets, extra_validation_sets = construct_training_validation_dataset(
DataConfig.from_conf(conf_path),
feature_size=get_conf(train_conf, group="network", key="feature_size"),
n_slices=get_conf(train_conf, group="network", key="n_slices"),
is_3d=True,
seed=config.seed,
augmentation_config=augmentation_config,
output_dir=config.experiment_dir,
)
for train in training_sets:
train.export(
config.experiment_dir.joinpath("training_set_{}.csv".format(
train.name)))
for val in validation_sets:
val.export(
config.experiment_dir.joinpath("validation_set_{}.csv".format(
val.name)))
for val in extra_validation_sets:
val.export(
config.experiment_dir.joinpath(
"extra_validation_set_{}.csv".format(val.name)))
if get_conf(train_conf, group="optimizer", key="type") == "SGD":
optimizer = torch.optim.SGD(
network.parameters(),
lr=get_conf(train_conf, group="optimizer", key="learning_rate"),
momentum=get_conf(train_conf, group="optimizer", key="momentum"),
)
else:
optimizer = torch.optim.Adam(network.parameters(),
lr=get_conf(train_conf,
group="optimizer",
key="learning_rate"))
if get_conf(train_conf, group="loss", key="type") == "FocalLoss":
loss = FocalLoss(
alpha=get_conf(train_conf, group="loss", key="alpha"),
gamma=get_conf(train_conf, group="loss", key="gamma"),
logits=True,
)
else:
loss = DefSegLoss(penalty="l2", loss_mult=2, template=atlas)
experiment = Experiment(config=config,
network=network,
training_sets=training_sets,
validation_sets=validation_sets,
extra_validation_sets=extra_validation_sets,
optimizer=optimizer,
loss=loss,
other_validation_metrics=[
DefSegWarpedDice(template=atlas),
DefSegPredDice()
],
inference_func=inference)
experiment.train()