pytorch_SUT.py

# coding=utf-8
# Copyright (c) 2020 NVIDIA CORPORATION. All rights reserved.
# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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.

import array
import json
import os
import sys
sys.path.insert(0, os.getcwd())

import mlperf_loadgen as lg
import numpy as np
import torch
import torch.nn.functional as F
from brats_QSL import get_brats_QSL

sys.path.insert(0, os.path.join(os.getcwd(), "nnUnet"))
from nnunet.training.model_restore import load_model_and_checkpoint_files

class _3DUNET_PyTorch_SUT():
    def __init__(self, model_dir, preprocessed_data_dir, performance_count, folds, checkpoint_name):

        print("Loading PyTorch model...")
        model_path = os.path.join(model_dir, "plans.pkl")
        assert os.path.isfile(model_path), "Cannot find the model file {:}!".format(model_path)
        self.trainer, params = load_model_and_checkpoint_files(model_dir, folds, fp16=False, checkpoint_name=checkpoint_name)
        self.trainer.load_checkpoint_ram(params[0], False)
        self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")

        print("Constructing SUT...")
        self.sut = lg.ConstructSUT(self.issue_queries, self.flush_queries, self.process_latencies)
        print("Finished constructing SUT.")
        self.qsl = get_brats_QSL(preprocessed_data_dir, performance_count)

    def issue_queries(self, query_samples):
        with torch.no_grad():
            for i in range(len(query_samples)):
                data = self.qsl.get_features(query_samples[i].index)

                print("Processing sample id {:d} with shape = {:}".format(query_samples[i].index, data.shape))

                image = torch.from_numpy(data[np.newaxis,...]).float().to(self.device)
                output = self.trainer.network(image)[0].cpu().numpy().astype(np.float16)

                transpose_forward = self.trainer.plans.get("transpose_forward")
                transpose_backward = self.trainer.plans.get("transpose_backward")
                assert transpose_forward == [0, 1, 2], "Unexpected transpose_forward {:}".format(transpose_forward)
                assert transpose_backward == [0, 1, 2], "Unexpected transpose_backward {:}".format(transpose_backward)

                response_array = array.array("B", output.tobytes())
                bi = response_array.buffer_info()
                response = lg.QuerySampleResponse(query_samples[i].id, bi[0], bi[1])
                lg.QuerySamplesComplete([response])

    def flush_queries(self):
        pass

    def process_latencies(self, latencies_ns):
        pass

def get_pytorch_sut(model_dir, preprocessed_data_dir, performance_count, folds=1, checkpoint_name="model_final_checkpoint"):
    return _3DUNET_PyTorch_SUT(model_dir, preprocessed_data_dir, performance_count, folds, checkpoint_name)