def run_masking(self, data_type: str) -> None:
"""
Mask all bids scans in self.data_selection with data type "data_type".
Parameters
----------
data_type : either anat or func
"""
masking_opts = get_masking_opts(self.masking_config_path, data_type)
if 'model_folder_path' not in masking_opts or not masking_opts[
'model_folder_path']:
# if no model_folder_path is given in the config, the default models are selected.
masking_opts['model_folder_path'] = get_mlebe_models(data_type)
model_config = get_model_config(masking_opts)
# load model
model = get_model(model_config.model)
df = self.data_selection.loc[self.data_selection.datatype == data_type]
for _, elem in tqdm(df.iterrows(), total=len(df)):
bids_path = str(elem.path if data_type ==
'anat' else elem.tmean_path)
mask_path, masked_path = self.mask_one(bids_path, elem,
masking_opts, model,
model_config)
self.data_selection.loc[self.data_selection.path == elem.path,
'mask_path'] = mask_path
self.data_selection.loc[self.data_selection.path == elem.path,
'masked_path'] = masked_path
def get_mask(json_opts, in_file_data, ori_shape, use_cuda: bool, model=None):
"""Predict segmentation mask on in_file_data with mlebe model."""
if not model:
from mlebe.training.models import get_model
# To make sure that the GPU is not used for the predictions: (might be unnecessary)
if not use_cuda:
os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
model = get_model(json_opts.model)
ds_transform = get_dataset_transformation(
'mlebe',
opts=json_opts.augmentation,
max_output_channels=json_opts.model.output_nc)
transformer = ds_transform['bids']()
# preprocess data for compatibility with model
model_input = transformer(np.expand_dims(in_file_data, -1))
# add dimension for batches
model_input = model_input.unsqueeze(0)
model.set_input(model_input)
model.test()
# predict
mask_pred = np.squeeze(model.pred_seg.cpu().byte().numpy()).astype(
np.int16)
# switching to z,x,y
mask_pred = np.moveaxis(mask_pred, 2, 0)
in_file_data = np.moveaxis(in_file_data, 2, 0)
model_input = np.moveaxis(np.squeeze(model_input.cpu().numpy()), 2, 0)
# need to un-pad on the z-axis to the original shape:
diff = int(np.ceil(mask_pred.shape[0] - ori_shape[0]))
mask_pred = mask_pred[int(np.ceil(diff / 2.)):ori_shape[0] +
int(np.ceil(diff / 2.)), :, :]
model_input = model_input[int(np.ceil(diff / 2.)):ori_shape[0] +
int(np.ceil(diff / 2.)), :, :]
return in_file_data, mask_pred, model_input
def tester(json_opts, test_dataset, save_directory):
model = get_model(json_opts.model)
train_opts = json_opts.training
test_loader = DataLoader(dataset=test_dataset,
num_workers=0,
batch_size=train_opts.batchSize,
shuffle=False)
error_logger = ErrorLogger()
# test
x_test = []
y_test = []
y_pred = []
for iteration, (images, labels, indices) in tqdm(enumerate(test_loader, 1),
total=len(test_loader)):
model.set_input(images, labels)
model.test()
ids = test_dataset.get_ids(indices)
stats = model.get_segmentation_stats()
error_logger.update(stats, split='test')
for batch_iter in range(len(ids)):
input_arr = np.squeeze(images[batch_iter].cpu().numpy()).astype(
np.float32)
label_arr = np.squeeze(labels[batch_iter].cpu().numpy()).astype(
np.int16)
if len(ids) != 1:
output_arr = np.squeeze(
model.pred_seg.cpu().byte().numpy()).astype(
np.int16)[batch_iter]
else:
output_arr = np.squeeze(
model.pred_seg.cpu().byte().numpy()).astype(np.int16)
y = input_arr.shape[2]
for slice in range(y):
if not np.max(label_arr[..., slice]) <= 0:
x_img = cv2.normalize(input_arr[..., slice],
None,
alpha=0,
beta=1,
norm_type=cv2.NORM_MINMAX,
dtype=cv2.CV_32F)
assert x_img.shape == output_arr[
..., slice].shape == label_arr[..., slice].shape == (
json_opts.augmentation.mlebe.scale_size[0],
json_opts.augmentation.mlebe.scale_size[1])
x_test.append(x_img)
y_test.append(label_arr[..., slice])
y_pred.append(output_arr[..., slice])
with open(os.path.join(save_directory, 'x_test.npy'), 'wb') as file1:
np.save(file1, x_test)
with open(os.path.join(save_directory, 'y_test.npy'), 'wb') as file2:
np.save(file2, y_test)
with open(os.path.join(save_directory, 'y_pred.npy'), 'wb') as file3:
np.save(file3, y_pred)
def tester(json_opts, test_dataset, save_directory):
model = get_model(json_opts.model)
train_opts = json_opts.training
test_loader = DataLoader(dataset=test_dataset,
num_workers=16,
batch_size=train_opts.batchSize,
shuffle=False)
# test
x_test = []
y_test = []
y_pred = []
for iteration, (images, labels, indices) in tqdm(enumerate(test_loader, 1),
total=len(test_loader)):
model.set_input(images, labels)
model.test()
ids = test_dataset.get_ids(indices)
for batch_iter in range(len(ids)):
input_arr = np.squeeze(images[batch_iter].cpu().numpy()).astype(
np.float32)
label_arr = np.squeeze(labels[batch_iter].cpu().numpy()).astype(
np.int16)
output_arr = np.squeeze(
model.pred_seg.cpu().byte().numpy()).astype(
np.int16)[batch_iter]
input_img, target = remove_black_images(input_arr, label_arr)
_, output_img = remove_black_images(input_arr, output_arr)
y = input_img.shape[2]
for slice in range(y):
x_test.append(input_img[..., slice])
y_test.append(target[..., slice])
y_pred.append(output_img[..., slice])
with open(os.path.join(save_directory, 'x_test.npy'), 'wb') as file1:
np.save(file1, x_test)
with open(os.path.join(save_directory, 'y_test.npy'), 'wb') as file2:
np.save(file2, y_test)
with open(os.path.join(save_directory, 'y_pred.npy'), 'wb') as file3:
np.save(file3, y_pred)
def evaluate(config_path):
json_opts = json_file_to_pyobj(config_path)
template_dir = json_opts.data.template_dir
model = get_model(json_opts.model)
save_path = os.path.join(model.save_dir, 'irsabi_test')
mkdir(save_path)
data_type = json_opts.data.data_type
print(save_path)
# shape of the images on which the classifier was trained:
training_shape = json_opts.augmentation.mlebe.scale_size[:3]
ds_class = get_dataset('mlebe_dataset')
# define preprocessing transformations for model
ds_transform = get_dataset_transformation('mlebe', opts=json_opts.augmentation,
max_output_channels=json_opts.model.output_nc)
test_dataset = ds_class(template_dir, json_opts.data.data_dir, json_opts.data, split='test',
transform=ds_transform['valid'],
train_size=None, training_shape=training_shape)
data_selection = test_dataset.data_selection
transformer = ds_transform['valid']()
temp = load_mask(template_dir)
mask_data = [copy.deepcopy(temp) for _ in range(len(data_selection))]
dice_scores_df = pd.DataFrame(columns=['volume_name', 'slice', 'dice_score', 'idx'])
predictions = []
for volume in tqdm(range(len(data_selection))): # volume is an index
# get volume
volume_name = data_selection.iloc[volume]['uid']
img = nib.load(data_selection.iloc[volume]['path']).get_data()
target = mask_data[volume].get_data()
if json_opts.data.with_arranged_mask:
# set the mask to zero where the image is zero
target = arrange_mask(img, target)
# img = preprocess(img, training_shape[:2], 'coronal')
# target = preprocess(target, training_shape[:2], 'coronal')
#
# # set image shape to x,y,z
# img = np.moveaxis(img, 0, 2)
# target = np.moveaxis(target, 0, 2)
# preprocess data for compatibility with model
network_input = transformer(np.expand_dims(img, -1))
target = np.squeeze(transformer(np.expand_dims(target, -1)).cpu().byte().numpy()).astype(np.int16)
# add dimension for batches
network_input = network_input.unsqueeze(0)
model.set_input(network_input)
model.test()
# predict
mask_pred = np.squeeze(model.pred_seg.cpu().numpy())
img = np.squeeze(network_input.numpy())
# set image shape to z,x,y
mask_pred = np.moveaxis(mask_pred, 2, 0)
img = np.moveaxis(img, 2, 0)
target = np.moveaxis(target, 2, 0)
for slice in range(img.shape[0]):
dice_score = dice(target[slice], mask_pred[slice])
# see if this is a black slice (want to skip those for visualisation)
black_slice = np.max(img[slice]) <= 0
dice_scores_df = dice_scores_df.append(
{'volume_name': volume_name, 'slice': slice, 'dice_score': dice_score, 'idx': volume,
'black_slice': black_slice},
ignore_index=True)
predictions.append(mask_pred)
min_df = dice_scores_df.loc[dice_scores_df['black_slice'] == False].sort_values(by=['dice_score']).head(
sum(IMG_NBRs) // 2)
min_df = pd.concat([min_df,
dice_scores_df.loc[dice_scores_df['black_slice'] == False].sort_values(by=['dice_score']).tail(
sum(IMG_NBRs) - sum(IMG_NBRs) // 2)],
ignore_index=True)
with PdfPages(os.path.join(save_path, 'irsabi_test_{}.pdf'.format(data_type))) as pdf:
df_idx = 0
for IMG_NBR in IMG_NBRs:
plt.figure(figsize=(40, IMG_NBR * 10))
plt.figtext(.5, .9, 'Mean dice score of {}'.format(np.round(dice_scores_df['dice_score'].mean(), 4)),
fontsize=100, ha='center')
i = 1
while i <= IMG_NBR * 2 and df_idx < len(min_df):
volume = min_df.iloc[df_idx]['idx']
slice = min_df.iloc[df_idx]['slice']
dice_score = min_df.iloc[df_idx]['dice_score']
plt.subplot(IMG_NBR, 2, i)
plt.imshow(img[slice], cmap='gray')
plt.imshow(target[slice], cmap='Blues', alpha=0.6)
plt.axis('off')
i += 1
plt.subplot(IMG_NBR, 2, i)
plt.imshow(img[slice], cmap='gray')
plt.imshow(predictions[volume][slice], cmap='Blues', alpha=0.6)
plt.title('Volume: {}, slice {}, dice {}'.format(volume_name, slice, dice_score))
plt.axis('off')
i += 1
df_idx += 1
pdf.savefig()
plt.close()
plt.title('Dice score = {}'.format(dice_scores_df['dice_score'].mean()))
plt.savefig('{}.pdf'.format(save_path), format='pdf')
return dice_scores_df['dice_score'].mean(), dice_scores_df['dice_score'].std()
def train(json_filename, network_debug=False, experiment_config=None):
"""
Main training function for the model.
Parameters
----------
json_filename : str
Path to the json configuration file
network_debug : bool (optional)
experiment_config : class used for logging (optional)
"""
# Load options
json_opts = json_file_to_pyobj(json_filename)
bigprint(f'New try with parameters: {json_opts}')
train_opts = json_opts.training
# Setup Dataset and Augmentation
ds_class = get_dataset('mlebe_dataset')
ds_path = json_opts.data.data_dir
template_path = json_opts.data.template_dir
ds_transform = get_dataset_transformation(
'mlebe',
opts=json_opts.augmentation,
max_output_channels=json_opts.model.output_nc)
# Setup channels
channels = json_opts.data_opts.channels
if len(channels) != json_opts.model.input_nc \
or len(channels) != getattr(json_opts.augmentation, 'mlebe').scale_size[-1]:
raise Exception(
'Number of data channels must match number of model channels, and patch and scale size dimensions'
)
# Setup the NN Model
model = get_model(json_opts.model)
if json_filename == 'configs/test_config.json':
print('removing dir ', model.save_dir)
shutil.rmtree(model.save_dir)
os.mkdir(model.save_dir)
if network_debug:
print('# of pars: ', model.get_number_parameters())
print('fp time: {0:.3f} sec\tbp time: {1:.3f} sec per sample'.format(
*model.get_fp_bp_time()))
exit()
# Setup Data Loader
split_opts = json_opts.data_split
data_opts = json_opts.data
train_dataset = ds_class(
template_path,
ds_path,
data_opts,
split='train',
save_dir=model.save_dir,
transform=ds_transform['train'],
train_size=split_opts.train_size,
test_size=split_opts.test_size,
valid_size=split_opts.validation_size,
split_seed=split_opts.seed,
training_shape=json_opts.augmentation.mlebe.scale_size[:3])
valid_dataset = ds_class(
template_path,
ds_path,
data_opts,
split='validation',
save_dir=model.save_dir,
transform=ds_transform['valid'],
train_size=split_opts.train_size,
test_size=split_opts.test_size,
valid_size=split_opts.validation_size,
split_seed=split_opts.seed,
training_shape=json_opts.augmentation.mlebe.scale_size[:3])
test_dataset = ds_class(
template_path,
ds_path,
data_opts,
split='test',
save_dir=model.save_dir,
transform=ds_transform['valid'],
train_size=split_opts.train_size,
test_size=split_opts.test_size,
valid_size=split_opts.validation_size,
split_seed=split_opts.seed,
training_shape=json_opts.augmentation.mlebe.scale_size[:3])
train_loader = DataLoader(dataset=train_dataset,
num_workers=1,
batch_size=train_opts.batchSize,
shuffle=True)
valid_loader = DataLoader(dataset=valid_dataset,
num_workers=1,
batch_size=train_opts.batchSize,
shuffle=False)
test_loader = DataLoader(dataset=test_dataset,
num_workers=1,
batch_size=train_opts.batchSize,
shuffle=False)
# Visualisation Parameters
visualizer = Visualiser(json_opts.visualisation, save_dir=model.save_dir)
error_logger = ErrorLogger()
# Training Function
model.set_scheduler(train_opts)
# Setup Early Stopping
early_stopper = EarlyStopper(json_opts.training.early_stopping_patience)
for epoch in range(model.which_epoch, train_opts.n_epochs):
print('(epoch: %d, total # iters: %d)' % (epoch, len(train_loader)))
train_volumes = []
validation_volumes = []
# Training Iterations
for epoch_iter, (images, labels,
indices) in tqdm(enumerate(train_loader, 1),
total=len(train_loader)):
# Make a training update
model.set_input(images, labels)
model.optimize_parameters()
# model.optimize_parameters_accumulate_grd(epoch_iter)
# Error visualisation
errors = model.get_current_errors()
error_logger.update(errors, split='train')
ids = train_dataset.get_ids(indices)
volumes = model.get_current_volumes()
visualizer.display_current_volumes(volumes, ids, 'train', epoch)
train_volumes.append(volumes)
# Validation and Testing Iterations
for loader, split, dataset in zip([valid_loader, test_loader],
['validation', 'test'],
[valid_dataset, test_dataset]):
for epoch_iter, (images, labels,
indices) in tqdm(enumerate(loader, 1),
total=len(loader)):
ids = dataset.get_ids(indices)
# Make a forward pass with the model
model.set_input(images, labels)
model.validate()
# Error visualisation
errors = model.get_current_errors()
stats = model.get_segmentation_stats()
error_logger.update({**errors, **stats}, split=split)
# Visualise predictions
if split == 'validation': # do not look at testing
# Visualise predictions
volumes = model.get_current_volumes()
visualizer.display_current_volumes(volumes, ids, split,
epoch)
validation_volumes.append(volumes)
current_loss = error_logger.get_errors('validation')['Seg_Loss']
# Update best validation loss/epoch values
model.update_validation_state(epoch, current_loss)
early_stopper.update(model, epoch, current_loss)
# Update the plots
for split in ['train', 'validation', 'test']:
visualizer.plot_current_errors(epoch,
error_logger.get_errors(split),
split_name=split)
visualizer.print_current_errors(epoch,
error_logger.get_errors(split),
split_name=split)
visualizer.save_plots(epoch, save_frequency=5)
error_logger.reset()
# saving checkpoint
if model.is_improving:
print('saving model')
# replacing old model with new model
model.save(json_opts.model.model_type, epoch)
# Update the model learning rate
model.update_learning_rate(metric=current_loss)
if early_stopper.should_stop_early:
print('early stopping')
# get validation metrics
val_loss_log = pd.read_excel(os.path.join(
'checkpoints', json_opts.model.experiment_name,
'loss_log.xlsx'),
sheet_name='validation').iloc[:, 1:]
irsabi_dice_mean, irsabi_dice_std = finalize(
json_opts, json_filename, model, experiment_config)
val_loss_log['irsabi_dice_mean'] = irsabi_dice_mean
val_loss_log['irsabi_dice_std'] = irsabi_dice_std
return val_loss_log.loc[val_loss_log['Seg_Loss'] ==
val_loss_log['Seg_Loss'].min()]
# get validation metrics
val_loss_log = pd.read_excel(os.path.join(json_opts.model.checkpoints_dir,
json_opts.model.experiment_name,
'loss_log.xlsx'),
sheet_name='validation').iloc[:, 1:]
irsabi_dice_mean, irsabi_dice_std = finalize(json_opts, json_filename,
model, experiment_config)
val_loss_log['irsabi_dice_mean'] = irsabi_dice_mean
val_loss_log['irsabi_dice_std'] = irsabi_dice_std
return val_loss_log.loc[val_loss_log['Seg_Loss'] ==
val_loss_log['Seg_Loss'].min()]