# Copyright 2021 Huawei Technologies Co., Ltd # # 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. # ============================================================================ """unet 310 infer.""" import os import argparse import cv2 import numpy as np from src.data_loader import create_dataset, create_cell_nuclei_dataset from src.config import cfg_unet class dice_coeff(): def __init__(self): self.clear() def clear(self): self._dice_coeff_sum = 0 self._iou_sum = 0 self._samples_num = 0 def update(self, *inputs): if len(inputs) != 2: raise ValueError('Need 2 inputs ((y_softmax, y_argmax), y), but got {}'.format(len(inputs))) y = np.array(inputs[1]) self._samples_num += y.shape[0] y = y.transpose(0, 2, 3, 1) b, h, w, c = y.shape if b != 1: raise ValueError('Batch size should be 1 when in evaluation.') y = y.reshape((h, w, c)) if cfg_unet["eval_activate"].lower() == "softmax": y_softmax = np.squeeze(inputs[0][0], axis=0) if cfg_unet["eval_resize"]: y_pred = [] for m in range(cfg_unet["num_classes"]): y_pred.append(cv2.resize(np.uint8(y_softmax[:, :, m] * 255), (w, h)) / 255) y_pred = np.stack(y_pred, axis=-1) else: y_pred = y_softmax elif cfg_unet["eval_activate"].lower() == "argmax": y_argmax = np.squeeze(inputs[0][1], axis=0) y_pred = [] for n in range(cfg_unet["num_classes"]): if cfg_unet["eval_resize"]: y_pred.append(cv2.resize(np.uint8(y_argmax == n), (w, h), interpolation=cv2.INTER_NEAREST)) else: y_pred.append(np.float32(y_argmax == n)) y_pred = np.stack(y_pred, axis=-1) else: raise ValueError('config eval_activate should be softmax or argmax.') y_pred = y_pred.astype(np.float32) inter = np.dot(y_pred.flatten(), y.flatten()) union = np.dot(y_pred.flatten(), y_pred.flatten()) + np.dot(y.flatten(), y.flatten()) single_dice_coeff = 2*float(inter)/float(union+1e-6) single_iou = single_dice_coeff / (2 - single_dice_coeff) print("single dice coeff is: {}, IOU is: {}".format(single_dice_coeff, single_iou)) self._dice_coeff_sum += single_dice_coeff self._iou_sum += single_iou def eval(self): if self._samples_num == 0: raise RuntimeError('Total samples num must not be 0.') return (self._dice_coeff_sum / float(self._samples_num), self._iou_sum / float(self._samples_num)) def test_net(data_dir, cross_valid_ind=1, cfg=None): if 'dataset' in cfg and cfg['dataset'] == "Cell_nuclei": valid_dataset = create_cell_nuclei_dataset(data_dir, cfg['img_size'], 1, 1, is_train=False, eval_resize=cfg["eval_resize"], split=0.8) else: _, valid_dataset = create_dataset(data_dir, 1, 1, False, cross_valid_ind, False, do_crop=cfg['crop'], img_size=cfg['img_size']) labels_list = [] for data in valid_dataset: labels_list.append(data[1].asnumpy()) return labels_list def get_args(): parser = argparse.ArgumentParser(description='Test the UNet on images and target masks', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d', '--data_url', dest='data_url', type=str, default='data/', help='data directory') parser.add_argument('-p', '--rst_path', dest='rst_path', type=str, default='./result_Files/', help='infer result path') return parser.parse_args() if __name__ == '__main__': args = get_args() label_list = test_net(data_dir=args.data_url, cross_valid_ind=cfg_unet['cross_valid_ind'], cfg=cfg_unet) rst_path = args.rst_path metrics = dice_coeff() if 'dataset' in cfg_unet and cfg_unet['dataset'] == "Cell_nuclei": for i, bin_name in enumerate(os.listdir('./preprocess_Result/')): bin_name_softmax = bin_name.replace(".png", "") + "_0.bin" bin_name_argmax = bin_name.replace(".png", "") + "_1.bin" file_name_sof = rst_path + bin_name_softmax file_name_arg = rst_path + bin_name_argmax softmax_out = np.fromfile(file_name_sof, np.float32).reshape(1, 96, 96, 2) argmax_out = np.fromfile(file_name_arg, np.float32).reshape(1, 96, 96) label = label_list[i] metrics.update((softmax_out, argmax_out), label) else: for j in range(len(os.listdir('./preprocess_Result/'))): file_name_sof = rst_path + "ISBI_test_bs_1_" + str(j) + "_0" + ".bin" file_name_arg = rst_path + "ISBI_test_bs_1_" + str(j) + "_1" + ".bin" softmax_out = np.fromfile(file_name_sof, np.float32).reshape(1, 576, 576, 2) argmax_out = np.fromfile(file_name_arg, np.float32).reshape(1, 576, 576) label = label_list[j] metrics.update((softmax_out, argmax_out), label) eval_score = metrics.eval() print("============== Cross valid dice coeff is:", eval_score[0]) print("============== Cross valid IOU is:", eval_score[1])