diff --git a/model_zoo/official/cv/unet/postprocess.py b/model_zoo/official/cv/unet/postprocess.py index ce6485be436..67def617c84 100644 --- a/model_zoo/official/cv/unet/postprocess.py +++ b/model_zoo/official/cv/unet/postprocess.py @@ -18,75 +18,24 @@ import cv2 import numpy as np from src.model_utils.config import config - -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 config.eval_activate.lower() == "softmax": - y_softmax = np.squeeze(inputs[0][0], axis=0) - if config.eval_resize: - y_pred = [] - for m in range(config.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 config.eval_activate.lower() == "argmax": - y_argmax = np.squeeze(inputs[0][1], axis=0) - y_pred = [] - for n in range(config.num_classes): - if config.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)) - +from src.utils import dice_coeff if __name__ == '__main__': rst_path = config.rst_path metrics = dice_coeff() + eval_activate = config.eval_activate.lower() + if eval_activate not in ("softmax", "argmax"): + raise ValueError("eval_activate only support 'softmax' or 'argmax'") if hasattr(config, "dataset") and config.dataset == "Cell_nuclei": img_size = tuple(config.image_size) for i, bin_name in enumerate(os.listdir('./preprocess_Result/')): f = bin_name.replace(".png", "") - bin_name_softmax = f + "_0.bin" - bin_name_argmax = f + "_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) + file_name = rst_path + f + "_0.bin" + if eval_activate == "softmax": + rst_out = np.fromfile(file_name, np.float32).reshape(1, 96, 96, 2) + else: + rst_out = np.fromfile(file_name, np.int32).reshape(1, 96, 96) mask = cv2.imread(os.path.join(config.data_path, f, "mask.png"), cv2.IMREAD_GRAYSCALE) mask = cv2.resize(mask, img_size) mask = mask.astype(np.float32) / 255 @@ -94,16 +43,17 @@ if __name__ == '__main__': mask = (np.arange(2) == mask[..., None]).astype(int) mask = mask.transpose(2, 0, 1).astype(np.float32) label = mask.reshape(1, 2, 96, 96) - metrics.update((softmax_out, argmax_out), label) + metrics.update(rst_out, label) else: label_list = np.load('label.npy') 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) + file_name = rst_path + "ISBI_test_bs_1_" + str(j) + "_0" + ".bin" + if eval_activate == "softmax": + rst_out = np.fromfile(file_name, np.float32).reshape(1, 576, 576, 2) + else: + rst_out = np.fromfile(file_name, np.int32).reshape(1, 576, 576) label = label_list[j] - metrics.update((softmax_out, argmax_out), label) + metrics.update(rst_out, label) eval_score = metrics.eval() print("============== Cross valid dice coeff is:", eval_score[0]) diff --git a/model_zoo/official/cv/unet/preprocess.py b/model_zoo/official/cv/unet/preprocess.py index 77fec76db3c..90c81e26715 100644 --- a/model_zoo/official/cv/unet/preprocess.py +++ b/model_zoo/official/cv/unet/preprocess.py @@ -44,7 +44,6 @@ class CellNucleiDataset: self.data_dir = data_dir self.img_ids = sorted(next(os.walk(self.data_dir))[1]) self.train_ids = self.img_ids[:int(len(self.img_ids) * split)] * repeat - np.random.shuffle(self.train_ids) self.val_ids = self.img_ids[int(len(self.img_ids) * split):] self.is_train = is_train self.result_path = result_path