def setUp(self):
brats_db = Loader.create(config_dict=DB.BRATS2017)
subject_list = brats_db.load_subjects()
self.subject = subject_list[0]
loss_name=params[p.LOSS])
else:
model = BraTS_models.compile(model,
lr=params[p.LR],
model_type=params[p.MODEL_TYPE],
loss_name=params[p.LOSS])
# plot_file = join(dir_path, filename +'.png')
# plot_model(model, to_file=plot_file)
json_string = model.to_json()
open(join(dir_path, filename + '_model.json'), 'w').write(json_string)
print("Architecture defined ...")
""" DATA LOADING """
brats_db = Loader.create(config_dict=DB.BRATS2017)
subject_list = brats_db.load_subjects()
dataset = Dataset_train(
input_shape=tuple(params[p.INPUT_DIM]),
output_shape=tuple(params[p.INPUT_DIM]),
n_classes=params[p.N_CLASSES],
n_subepochs=params[p.N_SUBEPOCHS],
batch_size=params[p.BATCH_SIZE],
sampling_scheme=params[p.SAMPLING_SCHEME],
sampling_weights=params[p.SAMPLING_WEIGHTS],
n_subjects_per_epoch_train=params[p.N_SUBJECTS_TRAIN],
n_segments_per_epoch_train=params[p.N_SEGMENTS_TRAIN],
n_subjects_per_epoch_validation=params[p.N_SUBJECTS_VALIDATION],
n_segments_per_epoch_validation=params[p.N_SEGMENTS_VALIDATION],
train_size=params[p.TRAIN_SIZE],
model_type=params[p.MODEL_TYPE][1],
l1=0.00001,
l2=0.001,
momentum=0.99,
mode='test')
weights_filepath_2 = '/imatge/acasamitjana/work/segmentation/BraTS/mask_seg/20170815/LR_0.0005_mask_seg_dice_momentum0.99_brainmask/model_weights/brats2017_epoch32.h5'
model2.load_weights(weights_filepath_2)
model2 = BraTS_models.compile(model2,
lr=params[p.LR],
model_type=params[p.MODEL_TYPE][1],
loss_name=params[p.LOSS])
print("Architecture defined ...")
""" DATA LOADING """
brats_db = Loader.create(config_dict=DB.BRATS2017_Validation)
subject_list = brats_db.load_subjects()
dataset = Dataset_train(
input_shape=tuple(params[p.INPUT_DIM]),
output_shape=tuple(params[p.INPUT_DIM]),
n_classes=params[p.N_CLASSES],
n_subepochs=params[p.N_SUBEPOCHS],
batch_size=params[p.BATCH_SIZE],
sampling_scheme=params[p.SAMPLING_SCHEME],
sampling_weights=params[p.SAMPLING_WEIGHTS],
n_subjects_per_epoch_train=params[p.N_SUBJECTS_TRAIN],
n_segments_per_epoch_train=params[p.N_SEGMENTS_TRAIN],
n_subjects_per_epoch_validation=params[p.N_SUBJECTS_VALIDATION],
n_segments_per_epoch_validation=params[p.N_SEGMENTS_VALIDATION],
train_size=params[p.TRAIN_SIZE],