# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. ############################################################################### # Copyright (C) 2021 Habana Labs, Ltd. an Intel Company ############################################################################### # Changes: # - script migration to Tensorflow 2.x version # - included HPU horovod setup # - added tensorboard logging functionality # - added TumorCore, PeritumoralEdema and EnhancingTumor metrics to evaluation results # - debug_train and debug_predict options have been removed # - added tensor dumping possibility for training with dump_callback function # - added TimeToTrain estimator for dumping evaluation timestamps import os import logging import numpy as np import tensorflow as tf from dataset.data_loader import Dataset, CLASSES from runtime.hooks import get_hooks from runtime.arguments import parse_args from runtime.setup import prepare_model_dir, build_estimator, setup_horovod, set_flags, get_logger from TensorFlow.common.debug import dump_callback def parse_evaluation_results(result): data = {CLASSES[i]: result[CLASSES[i]] for i in range(len(CLASSES))} data['MeanDice'] = str(sum([result[CLASSES[i]] for i in range(len(CLASSES))]) / len(CLASSES)) data['WholeTumor'] = str(result['WholeTumor']) data['TumorCore'] = str(data['TumorCore']) data['PeritumoralEdema'] = str(data['PeritumoralEdema']) data['EnhancingTumor'] = str(data['EnhancingTumor']) return data def main(): params = parse_args() tf.random.set_seed(params.seed) tf.get_logger().setLevel(logging.ERROR) params = setup_horovod(params) set_flags(params) model_dir = prepare_model_dir(params) logger = get_logger(params) dataset = Dataset(data_dir=params.data_dir, batch_size=params.batch_size, fold_idx=params.fold, n_folds=params.num_folds, params=params, seed=params.seed) estimator = build_estimator(params, model_dir) if params.tensorboard_logging and (params.worker_id == 0 or params.log_all_workers): from TensorFlow.common.tb_utils import write_hparams_v1 write_hparams_v1(params.log_dir, vars(params)) if params.tensorboard_logging: from TensorFlow.common.tb_utils import TimeToTrainEstimatorHook ttt = TimeToTrainEstimatorHook(train_or_eval ='eval', output_dir=params.log_dir) if not params.benchmark: params.max_steps = params.max_steps // params.num_workers if 'train' in params.exec_mode: with dump_callback(params.dump_config): training_hooks = get_hooks(params, logger) dataset_fn = dataset.synth_train_fn if params.synth_data else dataset.train_fn estimator.train( input_fn=dataset_fn, steps=params.max_steps, hooks=training_hooks) if 'evaluate' in params.exec_mode: if params.tensorboard_logging: ttt.begin() result = estimator.evaluate(input_fn=dataset.eval_fn, steps=dataset.eval_size) if params.tensorboard_logging: ttt.end(session=None) data = parse_evaluation_results(result) if params.worker_id == 0: logger.log(step=(), data=data) if 'predict' == params.exec_mode: inference_hooks = get_hooks(params, logger) if params.worker_id == 0: count = 1 if not params.benchmark else 2 * params.warmup_steps * params.batch_size // dataset.test_size predictions = estimator.predict( input_fn=lambda: dataset.test_fn(count=count, drop_remainder=params.benchmark), hooks=inference_hooks) for idx, p in enumerate(predictions): volume = p['predictions'] if not params.benchmark: np.save(os.path.join(params.model_dir, "vol_{}.npy".format(idx)), volume) if __name__ == '__main__': tf.compat.v1.disable_eager_execution() main()