def secondary_prediction(mask, vol, config2, model2_path=None,
preprocess_method2=None, norm_params2=None,
overlap_factor=0.9, augment2=None, num_augment=32, return_all_preds=False):
model2 = load_old_model(get_last_model_path(model2_path), config=config2)
pred = mask
bbox_start, bbox_end = find_bounding_box(pred)
check_bounding_box(pred, bbox_start, bbox_end)
padding = [16, 16, 8]
if padding is not None:
bbox_start = np.maximum(bbox_start - padding, 0)
bbox_end = np.minimum(bbox_end + padding, mask.shape)
data = vol.astype(np.float)[
bbox_start[0]:bbox_end[0],
bbox_start[1]:bbox_end[1],
bbox_start[2]:bbox_end[2]
]
data = preproc_and_norm(data, preprocess_method2, norm_params2)
prediction = get_prediction(data, model2, augment=augment2, num_augments=num_augment, return_all_preds=return_all_preds,
overlap_factor=overlap_factor, config=config2)
padding2 = list(zip(bbox_start, np.array(vol.shape) - bbox_end))
if return_all_preds:
padding2 = [(0, 0)] + padding2
print(padding2)
print(prediction.shape)
prediction = np.pad(prediction, padding2, mode='constant', constant_values=0)
return prediction
def norm_net_model(input_shape=(1, 128, 128, 128),
n_base_filters=16,
depth=5,
dropout_rate=0.3,
n_segmentation_levels=3,
n_labels=1,
optimizer=Adam,
initial_learning_rate=5e-4,
loss_function=dice_coefficient_loss,
old_model_path=None):
inputs = Input(input_shape)
norm_net = isensee2017_model_3d(input_shape,
n_base_filters,
depth,
dropout_rate,
n_segmentation_levels,
n_labels,
optimizer,
initial_learning_rate,
loss_function,
activation_name=None)
norm_inputs = norm_net(inputs)
seg_net = load_old_model(old_model_path)
seg_net.trainable = False
segmentation = seg_net(norm_inputs)
metrics = ['binary_accuracy', vod_coefficient]
if loss_function != dice_coefficient_loss:
metrics += [dice_coefficient]
model = Model(inputs=[inputs], outputs=segmentation, name='NormNetModel')
model.compile(optimizer=optimizer(lr=initial_learning_rate),
loss=loss_function,
metrics=metrics)
return model
def secondary_prediction(mask,
vol,
config2,
model2_path=None,
preprocess_method2=None,
norm_params2=None,
overlap_factor=0.9):
model2 = load_old_model(get_last_model_path(model2_path))
pred = mask
bbox_start, bbox_end = find_bounding_box(pred)
check_bounding_box(pred, bbox_start, bbox_end)
padding = [16, 16, 8]
if padding is not None:
bbox_start = np.maximum(bbox_start - padding, 0)
bbox_end = np.minimum(bbox_end + padding, mask.shape)
data = vol.astype(np.float)[bbox_start[0]:bbox_end[0],
bbox_start[1]:bbox_end[1],
bbox_start[2]:bbox_end[2]]
data = preproc_and_norm(data, preprocess_method2, norm_params2)
prediction = \
patch_wise_prediction(model=model2,
data=np.expand_dims(data, 0),
overlap_factor=overlap_factor,
patch_shape=config2["patch_shape"] + [config2["patch_depth"]])
prediction = prediction.squeeze()
padding2 = list(zip(bbox_start, np.array(vol.shape) - bbox_end))
print(padding2)
print(prediction.shape)
prediction = np.pad(prediction,
padding2,
mode='constant',
constant_values=0)
return prediction
def main(input_path, output_path, overlap_factor,
config, model_path, preprocess_method=None, norm_params=None, augment=None, num_augment=0,
config2=None, model2_path=None, preprocess_method2=None, norm_params2=None, augment2=None, num_augment2=0,
z_scale=None, xy_scale=None, return_all_preds=False):
print(model_path)
model = load_old_model(get_last_model_path(model_path), config=config)
print('Loading nifti from {}...'.format(input_path))
nifti = read_img(input_path)
print('Predicting mask...')
data = nifti.get_fdata().astype(np.float).squeeze()
print('original_shape: ' + str(data.shape))
scan_name = Path(input_path).name.split('.')[0]
if (z_scale is None):
z_scale = 1.0
if (xy_scale is None):
xy_scale = 1.0
if z_scale != 1.0 or xy_scale != 1.0:
data = ndimage.zoom(data, [xy_scale, xy_scale, z_scale])
data = preproc_and_norm(data, preprocess_method, norm_params,
scale=config.get('scale_data', None),
preproc=config.get('preproc', None))
save_nifti(data, os.path.join(output_path, scan_name + '_data.nii.gz'))
data = np.pad(data, 3, 'constant', constant_values=data.min())
print('Shape: ' + str(data.shape))
prediction = get_prediction(data=data, model=model, augment=augment,
num_augments=num_augment, return_all_preds=return_all_preds,
overlap_factor=overlap_factor, config=config)
# unpad
prediction = prediction[3:-3, 3:-3, 3:-3]
# revert to original size
if config.get('scale_data', None) is not None:
prediction = ndimage.zoom(prediction.squeeze(), np.divide([1, 1, 1], config.get('scale_data', None)), order=0)[..., np.newaxis]
save_nifti(prediction, os.path.join(output_path, scan_name + '_pred.nii.gz'))
if z_scale != 1.0 or xy_scale != 1.0:
prediction = ndimage.zoom(prediction.squeeze(), [1.0 / xy_scale, 1.0 / xy_scale, 1.0 / z_scale], order=1)[..., np.newaxis]
# if prediction.shape[-1] > 1:
# prediction = prediction[..., 1]
if config2 is not None:
prediction = prediction.squeeze()
mask = process_pred(prediction, gaussian_std=0.5, threshold=0.5) # .astype(np.uint8)
nifti = read_img(input_path)
prediction = secondary_prediction(mask, vol=nifti.get_fdata().astype(np.float),
config2=config2, model2_path=model2_path,
preprocess_method2=preprocess_method2, norm_params2=norm_params2,
overlap_factor=overlap_factor, augment2=augment2, num_augment=num_augment2,
return_all_preds=return_all_preds)
save_nifti(prediction, os.path.join(output_path, scan_name + 'pred_roi.nii.gz'))
print('Saving to {}'.format(output_path))
print('Finished.')
def main(input_mat_path,
output_mat_path,
overlap_factor,
config,
model_path,
preprocess_method=None,
norm_params=None,
config2=None,
model2_path=None,
preprocess_method2=None,
norm_params2=None):
print(model_path)
model = load_old_model(get_last_model_path(model_path))
print('Loading mat from {}...'.format(input_mat_path))
mat = loadmat(input_mat_path)
print('Predicting mask...')
data = mat['volume'].astype(np.float)
data = preproc_and_norm(data, preprocess_method, norm_params)
prediction = \
patch_wise_prediction(model=model,
data=np.expand_dims(data, 0),
overlap_factor=overlap_factor,
patch_shape=config["patch_shape"] + [config["patch_depth"]])
print('Post-processing mask...')
if prediction.shape[-1] > 1:
prediction = prediction[..., 1]
prediction = prediction.squeeze()
print("Storing prediction in [7-9], 7 should be the best...")
mat['masks'][0, 9] = \
process_pred(prediction, gaussian_std=0, threshold=0.2) # .astype(np.uint8)
mat['masks'][0, 8] = \
process_pred(prediction, gaussian_std=1, threshold=0.5) # .astype(np.uint8)
mat['masks'][0, 7] = \
process_pred(prediction, gaussian_std=0.5, threshold=0.5) # .astype(np.uint8)
if config2 is not None:
print('Making secondary prediction... [6]')
prediction = secondary_prediction(
mat['masks'][0, 7],
vol=mat['volume'].astype(np.float),
config2=config2,
model2_path=model2_path,
preprocess_method2=preprocess_method2,
norm_params2=norm_params2,
overlap_factor=0.9)
mat['masks'][0, 6] = \
process_pred(prediction, gaussian_std=0, threshold=0.2) # .astype(np.uint8)
mat['masks'][0, 5] = \
process_pred(prediction, gaussian_std=1, threshold=0.5) # .astype(np.uint8)
mat['masks'][0, 4] = \
process_pred(prediction, gaussian_std=0.5, threshold=0.5) # .astype(np.uint8)
print('Saving mat to {}'.format(output_mat_path))
savemat(output_mat_path, mat)
print('Finished.')
def main(input_path,
output_path,
overlap_factor,
config,
model_path,
preprocess_method=None,
norm_params=None,
config2=None,
model2_path=None,
preprocess_method2=None,
norm_params2=None):
print(model_path)
model = load_old_model(get_last_model_path(model_path))
print('Loading mat from {}...'.format(input_path))
nifti = read_img(input_path)
print('Predicting mask...')
data = nifti.get_fdata().astype(np.float)
data = preproc_and_norm(data, preprocess_method, norm_params)
prediction = \
patch_wise_prediction(model=model,
data=np.expand_dims(data, 0),
overlap_factor=overlap_factor,
patch_shape=config["patch_shape"] + [config["patch_depth"]])
nib.save(prediction, os.path.join(output_path, 'pred.nii'))
print('Post-processing mask...')
if prediction.shape[-1] > 1:
prediction = prediction[..., 1]
prediction = prediction.squeeze()
print("Storing prediction in [7-9], 7 should be the best...")
mask = process_pred(prediction, gaussian_std=0.5,
threshold=0.5) # .astype(np.uint8)
if config2 is not None:
print('Making secondary prediction... [6]')
prediction = secondary_prediction(
mask,
vol=nifti.get_fdata().astype(np.float),
config2=config2,
model2_path=model2_path,
preprocess_method2=preprocess_method2,
norm_params2=norm_params2,
overlap_factor=0.9)
nib.save(prediction, os.path.join(output_path, 'pred_roi.nii'))
print('Saving to {}'.format(output_path))
print('Finished.')
def main(input_mat_path, output_mat_path, config, overlap_factor, model_path, preprocess_method=None, norm_params=None):
print(model_path)
model = load_old_model(get_last_model_path(model_path))
print('Loading mat from {}...'.format(input_mat_path))
mat = loadmat(input_mat_path)
print('Predicting mask...')
data = mat['volume'].astype(np.float)
if preprocess_method is not None:
print('Applying preprocess by {}...'.format(preprocess_method))
if preprocess_method == 'window_1_99':
data = window_intensities_data(data)
else:
raise Exception('Unknown preprocess: {}'.format(preprocess_method))
if norm_params is not None and any(norm_params.values()):
data = normalize_data(data, mean=norm_params['mean'], std=norm_params['std'])
prediction = \
patch_wise_prediction(model=model,
data=np.expand_dims(data, 0),
overlap_factor=overlap_factor,
patch_shape=config["patch_shape"] + [config["patch_depth"]])
print('Post-processing mask...')
if prediction.shape[-1] > 1:
prediction = prediction[..., 1]
prediction = prediction.squeeze()
mat['masks'][0, 9] = \
process_pred(prediction, gaussian_std=0, threshold=0.2) # .astype(np.uint8)
mat['masks'][0, 8] = \
process_pred(prediction, gaussian_std=1, threshold=0.5) # .astype(np.uint8)
mat['masks'][0, 7] = \
process_pred(prediction, gaussian_std=0.5, threshold=0.5) # .astype(np.uint8)
print('Saving mat to {}'.format(output_mat_path))
savemat(output_mat_path, mat)
print('Finished.')
def get_config_and_model(configs_folder, model_folder):
with open(os.path.join(configs_folder, model_folder,
CONFIG_FILENAME)) as f:
config = json.load(f)
model = load_old_model(get_last_model_path(config["model_file"]))
return config, model
def main(overwrite=False):
# convert input images into an hdf5 file
if overwrite or not os.path.exists(config["data_file"]):
create_data_file(config)
data_file_opened = open_data_file(config["data_file"])
if not overwrite and len(glob.glob(config["model_file"] + '*.h5')) > 0:
model_path = get_last_model_path(config["model_file"])
print('Loading model from: {}'.format(model_path))
model = load_old_model(model_path)
else:
# instantiate new model
loss_func = getattr(fetal_net.metrics, config['loss'])
model_func = getattr(fetal_net.model, config['model_name'])
model = model_func(
input_shape=config["input_shape"],
initial_learning_rate=config["initial_learning_rate"],
**{
'dropout_rate':
config['dropout_rate'],
'loss_function':
loss_func,
'mask_shape':
None
if config["weight_mask"] is None else config["input_shape"],
# TODO: change to output shape
'old_model_path':
config['old_model']
})
if not overwrite and len(glob.glob(config["model_file"] + '*.h5')) > 0:
model_path = get_last_model_path(config["model_file"])
print('Loading model from: {}'.format(model_path))
model.load_weights(model_path)
model.summary()
# get training and testing generators
train_generator, validation_generator, n_train_steps, n_validation_steps = get_training_and_validation_generators(
data_file_opened,
batch_size=config["batch_size"],
data_split=config["validation_split"],
overwrite=overwrite,
validation_keys_file=config["validation_file"],
training_keys_file=config["training_file"],
test_keys_file=config["test_file"],
n_labels=config["n_labels"],
labels=config["labels"],
patch_shape=(*config["patch_shape"], config["patch_depth"]),
validation_batch_size=config["validation_batch_size"],
augment=config["augment"],
skip_blank_train=config["skip_blank_train"],
skip_blank_val=config["skip_blank_val"],
truth_index=config["truth_index"],
truth_size=config["truth_size"],
prev_truth_index=config["prev_truth_index"],
prev_truth_size=config["prev_truth_size"],
truth_downsample=config["truth_downsample"],
truth_crop=config["truth_crop"],
patches_per_epoch=config["patches_per_epoch"],
categorical=config["categorical"],
is3d=config["3D"],
drop_easy_patches_train=config["drop_easy_patches_train"],
drop_easy_patches_val=config["drop_easy_patches_val"])
# run training
train_model(model=model,
model_file=config["model_file"],
training_generator=train_generator,
validation_generator=validation_generator,
steps_per_epoch=n_train_steps,
validation_steps=n_validation_steps,
initial_learning_rate=config["initial_learning_rate"],
learning_rate_drop=config["learning_rate_drop"],
learning_rate_patience=config["patience"],
early_stopping_patience=config["early_stop"],
n_epochs=config["n_epochs"],
output_folder=config["base_dir"])
data_file_opened.close()
def main(pred_dir,
config,
split='test',
overlap_factor=1,
preprocess_method=None):
padding = [16, 16, 8]
prediction2_dir = os.path.abspath(
os.path.join(config['base_dir'], 'predictions2', split))
model = load_old_model(get_last_model_path(config["model_file"]))
with open(os.path.join(opts.config_dir, 'norm_params.json'), 'r') as f:
norm_params = json.load(f)
for sample_folder in glob(os.path.join(pred_dir, split, '*')):
mask_path = os.path.join(sample_folder, 'prediction.nii.gz')
truth_path = os.path.join(sample_folder, 'truth.nii.gz')
subject_id = Path(sample_folder).name
dest_folder = os.path.join(prediction2_dir, subject_id)
Path(dest_folder).mkdir(parents=True, exist_ok=True)
truth = nib.load(truth_path)
nib.save(truth, os.path.join(dest_folder, Path(truth_path).name))
mask = nib.load(mask_path)
mask = process_pred(mask.get_data(), gaussian_std=0.5, threshold=0.5)
bbox_start, bbox_end = find_bounding_box(mask)
check_bounding_box(mask, bbox_start, bbox_end)
if padding is not None:
bbox_start = np.maximum(bbox_start - padding, 0)
bbox_end = np.minimum(bbox_end + padding, mask.shape)
print("BBox: {}-{}".format(bbox_start, bbox_end))
volume = nib.load(
os.path.join(original_data_folder, subject_id, 'volume.nii'))
orig_volume_shape = np.array(volume.get_data().shape)
volume = cut_bounding_box(volume, bbox_start,
bbox_end).get_data().astype(np.float)
if preprocess_method is not None:
print('Applying preprocess by {}...'.format(preprocess_method))
if preprocess_method == 'window_1_99':
volume = window_intensities_data(volume)
else:
raise Exception(
'Unknown preprocess: {}'.format(preprocess_method))
if norm_params is not None and any(norm_params.values()):
volume = normalize_data(volume,
mean=norm_params['mean'],
std=norm_params['std'])
prediction = patch_wise_prediction(model=model,
data=np.expand_dims(volume, 0),
patch_shape=config["patch_shape"] +
[config["patch_depth"]],
overlap_factor=overlap_factor)
prediction = prediction.squeeze()
padding2 = list(zip(bbox_start, orig_volume_shape - bbox_end))
print(padding2)
prediction = np.pad(prediction,
padding2,
mode='constant',
constant_values=0)
assert all(
[s1 == s2 for s1, s2 in zip(prediction.shape, orig_volume_shape)])
prediction = get_image(prediction)
nib.save(prediction, os.path.join(dest_folder, Path(mask_path).name))
step_1_network_experiments_paths = ['/datadrive/configs/...', '/datadrive/configs/...', '/datadrive/configs/...']
step_2_network_experiments_paths = ['/datadrive/configs/...']
output_prediction_dir = r""
if not os.path.exists(output_prediction_dir):
os.mkdir(output_prediction_dir)
#subject_ids = ['40']
subject_index = []
overlap_factor = 0.9
hdf5_file = r""
data_file = tables.open_file(hdf5_file, "a")
filters = tables.Filters(complevel=5, complib='blosc')
pred_storage = data_file.create_vlarray(data_file.root, 'pred', tables.ObjectAtom(), filters=filters,
expectedrows=len(subject_index)) # TODO: needs to be same length as other arrays
step_1_networks = [load_old_model(get_last_model_path(os.path.join(exp_folder, "fetal_net_model")))
for exp_folder in step_1_network_experiments_paths]
step_1_configs = []
n_step_1_models = len(step_1_networks)
for i in range(n_step_1_models):
with open(os.path.join(step_1_network_experiments_paths[i], 'config.json')) as f:
config = json.load(f)
step_1_configs.append(config)
step_2_network = [load_old_model(get_last_model_path(os.path.join(exp_folder, "fetal_net_model")))
for exp_folder in step_2_network_experiments_paths]
with open(os.path.join(step_2_network_experiments_paths[0], 'config.json')) as f:
step_2_config = json.load(f)
########################### Step 1 ###########################
from keras import Model
from fetal_net.training import load_old_model
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--model_path",
help="specifies model path",
type=str,
required=True)
opts = parser.parse_args()
from_metric = 'acc'
to_metric = 'binary_accuracy'
model: Model = load_old_model(opts.model_path)
model.compile(
optimizer=model.optimizer,
loss=model.loss,
metrics=[to_metric if _ == from_metric else _ for _ in model.metrics])
model.save(opts.model_path)
def main_train(config, overwrite=False):
# convert input images into an hdf5 file
if overwrite or not os.path.exists(config["data_file"]):
print("Writing h5 file")
training_files, subject_ids = fetch_training_data_files(
return_subject_ids=True)
_, (mean, std) = write_data_to_file(training_files,
config["data_file"],
subject_ids=subject_ids,
normalize=config['normalization'],
add_pred=config['pred_size'])
with open(os.path.join(config["base_dir"], 'norm_params.json'),
mode='w') as f:
json.dump({'mean': mean, 'std': std}, f)
data_file_opened = open_data_file(config["data_file"])
if not overwrite and len(glob.glob(config["model_file"] + '*.h5')) > 0:
model_path = get_last_model_path(config["model_file"])
print('Loading model from: {}'.format(model_path))
model = load_old_model(model_path)
else:
# instantiate new model
loss_func = getattr(fetal_net.metrics, config['loss'])
model_func = getattr(fetal_net.model, config['model_name'])
model = model_func(
input_shape=config["input_shape"],
initial_learning_rate=config["initial_learning_rate"],
**{
'dropout_rate': config['dropout_rate'],
'loss_function': loss_func,
'depth': config['model_params']['depth'],
'n_base_filters': config['model_params']['n_base_filters'],
'old_model_path': config['old_model'],
'truth_index': config['truth_index'],
'truth_size': config['truth_size']
})
model.summary()
# get training and testing generators
train_generator, validation_generator, n_train_steps, n_validation_steps = get_training_and_validation_generators(
data_file_opened,
batch_size=config["batch_size"],
data_split=config["validation_split"],
overwrite=overwrite,
validation_keys_file=config["validation_file"],
training_keys_file=config["training_file"],
test_keys_file=config["test_file"],
n_labels=config["n_labels"],
labels=config["labels"],
patch_shape=(*config["patch_shape"], config["patch_depth"]),
validation_batch_size=config["validation_batch_size"],
augment=config["augment"],
skip_blank_train=config["skip_blank_train"],
skip_blank_val=config["skip_blank_val"],
truth_index=config["truth_index"],
truth_size=config["truth_size"],
prev_truth_index=config["prev_truth_index"],
prev_truth_size=config["prev_truth_size"],
pred_index=config["pred_index"],
pred_size=config["pred_size"],
truth_downsample=config["truth_downsample"],
truth_crop=config["truth_crop"],
patches_per_epoch=config["patches_per_epoch"],
categorical=config["categorical"],
is3d=config["3D"],
drop_easy_patches_train=config["drop_easy_patches_train"],
drop_easy_patches_val=config["drop_easy_patches_val"])
# run training
train_model(model=model,
model_file=config["model_file"],
training_generator=train_generator,
validation_generator=validation_generator,
steps_per_epoch=n_train_steps,
validation_steps=n_validation_steps,
initial_learning_rate=config["initial_learning_rate"],
learning_rate_drop=config["learning_rate_drop"],
learning_rate_patience=config["patience"],
early_stopping_patience=config["early_stop"],
n_epochs=config["n_epochs"],
output_folder=config["base_dir"])
data_file_opened.close()
