本文采用Unet3d进行BRAST2015数据集的分割

BRAST2015读取

BRAST2015数据集为脑部肿瘤分割的，数据集分为两类，一类为HGG（高分级胶质瘤），另一类为LGG（低分级胶质瘤）

文件夹目录如图所示

包含了MRI Flair T1 T1c T2四种模态，OT为ground Truth（0，1，2，3，4五种标签）

数据文件都为.mha文件，可以直接使用SimpleITK进行读取

def sitk_read(img_path):nda = sitk.ReadImage(img_path)nda = sitk.GetArrayFromImage(nda) #(155,240,240)nda = nda.transpose(1, 2, 0) #(240,240,155)return nda

直接调用SimpleITK.ReadImage得到Image对象，然后转成np，这里读出来的shape是(depth,height,width)

因为BRAST的数据集中只有train数据集有ground truth，val数据集是没有ground truth的，所以要在train数据集上分成train、val、test三部分用于网络，先读入所有train文件名用list存起来，然后用random随机打乱顺序，然后取8份为train，1份为val，1份为test，将三个数据集的文件名用txt存起来，以便于训练的时候直接读取

    def write_train_val_test_name_list(self):data_name_list = os.listdir(self.train_root_path + self.type + "\\")random.shuffle(data_name_list)length = len(data_name_list)n_train_file = int(length / 10 * 8)n_val_file = int(length / 10 * 1)train_name_list = data_name_list[0:n_train_file]val_name_list = data_name_list[n_train_file:(n_train_file + n_val_file)]test_name_list = data_name_list[(n_train_file + n_val_file):len(data_name_list)]self.write_name_list(train_name_list, "train_name_list.txt")self.write_name_list(val_name_list, "val_name_list.txt")self.write_name_list(test_name_list, "test_name_list.txt")def write_name_list(self, name_list, file_name):f = open(self.train_root_path + file_name, 'w')for i in range(len(name_list)):f.write(name_list[i] + "\n")f.close()

完整代码如下：

def make_one_hot_3d(x, n):one_hot = np.zeros([x.shape[0], x.shape[1], x.shape[2], n])for i in range(x.shape[0]):for j in range(x.shape[1]):for v in range(x.shape[2]):one_hot[i, j, v, int(x[i, j, v])] = 1return one_hotclass brast_reader:def __init__(self, train_batch_size, val_batch_size, test_batch_size, type='HGG'):self.train_root_path = "D:\\pyproject\\data\\BRATS2015\\BRATS2015_Training\\BRATS2015_Training\\"self.type = typeself.train_name_list = self.load_file_name_list(self.train_root_path + "train_name_list.txt")self.val_name_list = self.load_file_name_list(self.train_root_path + "val_name_list.txt")self.test_name_list = self.load_file_name_list(self.train_root_path + "test_name_list.txt")self.n_train_file = len(self.train_name_list)self.n_val_file = len(self.val_name_list)self.n_test_file = len(self.test_name_list)self.train_batch_size = train_batch_sizeself.val_batch_size = val_batch_sizeself.test_batch_size = test_batch_sizeself.n_train_steps_per_epoch = self.n_train_file // self.train_batch_sizeself.n_val_steps_per_epoch = self.n_val_file // self.val_batch_sizeself.img_height = 240self.img_width = 240self.img_depth = 160self.n_labels = 5self.train_batch_index = 0self.val_batch_index = 0def load_file_name_list(self, file_path):file_name_list = []with open(file_path, 'r') as file_to_read:while True:lines = file_to_read.readline().strip()  # 整行读取数据if not lines:breakpassfile_name_list.append(lines)passreturn file_name_listdef write_train_val_test_name_list(self):data_name_list = os.listdir(self.train_root_path + self.type + "\\")random.shuffle(data_name_list)length = len(data_name_list)n_train_file = int(length / 10 * 8)n_val_file = int(length / 10 * 1)train_name_list = data_name_list[0:n_train_file]val_name_list = data_name_list[n_train_file:(n_train_file + n_val_file)]test_name_list = data_name_list[(n_train_file + n_val_file):len(data_name_list)]self.write_name_list(train_name_list, "train_name_list.txt")self.write_name_list(val_name_list, "val_name_list.txt")self.write_name_list(test_name_list, "test_name_list.txt")def write_name_list(self, name_list, file_name):f = open(self.train_root_path + file_name, 'w')for i in range(len(name_list)):f.write(name_list[i] + "\n")f.close()def next_train_batch_2d(self):if self.train_batch_index >= self.n_train_file:self.train_batch_index = 0data_path = self.train_root_path + self.type + '\\' + self.train_name_list[self.train_batch_index]# flair, t1, t1c, t2, ot=self.get_np_data(data_path)t1, ot = self.get_np_data_2d(data_path)train_imgs=t1[:,:,:,np.newaxis] #(155,240,240,1)train_labels=make_one_hot_3d(ot,self.n_labels) #(155,240,240,5)self.train_batch_index+=1return train_imgs,train_labelsdef next_val_batch_2d(self):if self.val_batch_index >= self.n_val_file:self.val_batch_index = 0data_path = self.train_root_path + self.type + '\\' + self.val_name_list[self.val_batch_index]# flair, t1, t1c, t2, ot=self.get_np_data(data_path)t1, ot = self.get_np_data_2d(data_path)val_imgs=t1[:,:,:,np.newaxis] #(155,240,240,1)val_labels=make_one_hot_3d(ot,self.n_labels)self.val_batch_index += 1return val_imgs, val_labelsdef next_train_batch_3d(self):train_imgs = np.zeros((self.train_batch_size, self.img_height, self.img_width, self.img_depth, 1))train_labels = np.zeros([self.train_batch_size, self.img_height, self.img_width, self.img_depth, self.n_labels])if self.train_batch_index >= self.n_train_steps_per_epoch:self.train_batch_index = 0for i in range(self.train_batch_size):data_path = self.train_root_path + self.type + '\\' + self.train_name_list[self.train_batch_size * self.train_batch_index + i]# flair, t1, t1c, t2, ot=self.get_np_data(data_path)t1, ot = self.get_np_data_3d(data_path)# flair=flair[:,:,:,np.newaxis]t1 = t1[:, :, :, np.newaxis]# t1c = t1c[:, :, :, np.newaxis]# t2 = t2[:, :, :, np.newaxis]train_imgs[i] = t1one_hot = make_one_hot_3d(ot, self.n_labels)train_labels[i] = one_hotself.train_batch_index += 1return train_imgs, train_labelsdef next_val_batch_3d(self):val_imgs = np.zeros((self.train_batch_size, self.img_height, self.img_width, self.img_depth, 1))val_labels = np.zeros([self.train_batch_size, self.img_height, self.img_width, self.img_depth, self.n_labels])if self.val_batch_index >= self.n_val_steps_per_epoch:self.val_batch_index = 0for i in range(self.val_batch_size):data_path = self.train_root_path + self.type + '\\' + self.val_name_list[self.val_batch_size * self.val_batch_index + i]# flair, t1, t1c, t2, ot=self.get_np_data(data_path)t1, ot = self.get_np_data_3d(data_path)# flair=flair[:,:,:,np.newaxis]t1 = t1[:, :, :, np.newaxis]# t1c = t1c[:, :, :, np.newaxis]# t2 = t2[:, :, :, np.newaxis]val_imgs[i] = t1one_hot = make_one_hot_3d(ot, self.n_labels)val_labels[i] = one_hotself.val_batch_index += 1return val_imgs, val_labelsdef get_np_data_3d(self, data_path):for i in glob.glob(os.path.join(data_path, 'VSD.Brain.XX.O.MR_T1.*\\VSD.Brain.XX.O.MR_T1.*.mha')):t1_file_path = ifor i in glob.glob(os.path.join(data_path, 'VSD.Brain_3more.XX.*\\VSD.Brain_3more.XX.*.mha')):ot_file_path = i'''for i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_Flair.*\\VSD.Brain.XX.O.MR_Flair.*.mha')):flair_file_path=ifor i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_T1c.*\\VSD.Brain.XX.O.MR_T1c.*.mha')):t1c_file_path=ifor i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_T2.*\\VSD.Brain.XX.O.MR_T2.*.mha')):t2_file_path=iflair=sitk_read(flair_file_path)t1c=sitk_read(t1c_file_path)t2=sitk_read(t2_file_path)'''t1 = sitk_read(t1_file_path)ot = sitk_read(ot_file_path)return t1, ot# return flair,t1,t1c,t2,otdef get_np_data_2d(self, data_path):for i in glob.glob(os.path.join(data_path, 'VSD.Brain.XX.O.MR_T1.*\\VSD.Brain.XX.O.MR_T1.*.mha')):t1_file_path = ifor i in glob.glob(os.path.join(data_path, 'VSD.Brain_3more.XX.*\\VSD.Brain_3more.XX.*.mha')):ot_file_path = i'''for i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_Flair.*\\VSD.Brain.XX.O.MR_Flair.*.mha')):flair_file_path=ifor i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_T1c.*\\VSD.Brain.XX.O.MR_T1c.*.mha')):t1c_file_path=ifor i in glob.glob(os.path.join(data_path,'VSD.Brain.XX.O.MR_T2.*\\VSD.Brain.XX.O.MR_T2.*.mha')):t2_file_path=iflair=sitk_read(flair_file_path)t1c=sitk_read(t1c_file_path)t2=sitk_read(t2_file_path)'''t1 = sitk_read_row(t1_file_path)ot = sitk_read_row(ot_file_path)return t1, ot# return flair,t1,t1c,t2,ot

U-Net3D

import keras.backend as K
from keras.engine import Input, Model
import keras
from keras.optimizers import Adam
from keras.layers import BatchNormalization, Activation, Conv3D, Conv3DTranspose, MaxPooling3D
import metrics as m
from keras.layers.core import Lambda
import numpy as npdef up_and_concate_3d(down_layer, layer):in_channel = down_layer.get_shape().as_list()[4]out_channel = in_channel // 2up = Conv3DTranspose(out_channel, [2, 2, 2], strides=[2, 2, 2], padding='valid')(down_layer)print("--------------")print(str(up.get_shape()))print(str(layer.get_shape()))print("--------------")my_concat = Lambda(lambda x: K.concatenate([x[0], x[1]], axis=4))concate = my_concat([up, layer])# must use lambda# concate=K.concatenate([up, layer], 3)return concatedef attention_block_3d(x, g, inter_channel):''':param x: x input from down_sampling same layer output x(?,x_height,x_width,x_depth,x_channel):param g: gate input from up_sampling layer last output g(?,g_height,g_width,g_depth,g_channel)g_height,g_width,g_depth=x_height/2,x_width/2,x_depth/2:return:'''# theta_x(?,g_height,g_width,g_depth,inter_channel)theta_x = Conv3D(inter_channel, [2, 2, 2], strides=[2, 2, 2])(x)# phi_g(?,g_height,g_width,g_depth,inter_channel)phi_g = Conv3D(inter_channel, [1, 1, 1], strides=[1, 1, 1])(g)# f(?,g_height,g_width,g_depth,inter_channel)f = Activation('relu')(keras.layers.add([theta_x, phi_g]))# psi_f(?,g_height,g_width,g_depth,1)psi_f = Conv3D(1, [1, 1, 1], strides=[1, 1, 1])(f)# sigm_psi_f(?,g_height,g_width,g_depth)sigm_psi_f = Activation('sigmoid')(psi_f)# rate(?,x_height,x_width,x_depth)rate = UpSampling3D(size=[2, 2, 2])(sigm_psi_f)# att_x(?,x_height,x_width,x_depth,x_channel)att_x = keras.layers.multiply([x, rate])return att_xdef unet_model_3d(input_shape, n_labels, batch_normalization=False, initial_learning_rate=0.00001,metrics=m.dice_coefficient):"""input_shape:without batch_size,(img_height,img_width,img_depth)metrics:"""inputs = Input(input_shape)down_layer = []layer = inputs# down_layer_1layer = res_block_v2_3d(layer, 64, batch_normalization=batch_normalization)down_layer.append(layer)layer = MaxPooling3D(pool_size=[2, 2, 2], strides=[2, 2, 2],padding='same')(layer)print(str(layer.get_shape()))# down_layer_2layer = res_block_v2_3d(layer, 128, batch_normalization=batch_normalization)down_layer.append(layer)layer = MaxPooling3D(pool_size=[2, 2, 2], strides=[2, 2, 2],padding='same')(layer)print(str(layer.get_shape()))# down_layer_3layer = res_block_v2_3d(layer, 256, batch_normalization=batch_normalization)down_layer.append(layer)layer = MaxPooling3D(pool_size=[2, 2, 2], strides=[2, 2, 2],padding='same')(layer)print(str(layer.get_shape()))# down_layer_4layer = res_block_v2_3d(layer, 512, batch_normalization=batch_normalization)down_layer.append(layer)layer = MaxPooling3D(pool_size=[2, 2, 2], strides=[2, 2, 2],padding='same')(layer)print(str(layer.get_shape()))# bottle_layerlayer = res_block_v2_3d(layer, 1024, batch_normalization=batch_normalization)print(str(layer.get_shape()))# up_layer_4layer = up_and_concate_3d(layer, down_layer[3])layer = res_block_v2_3d(layer, 512, batch_normalization=batch_normalization)print(str(layer.get_shape()))# up_layer_3layer = up_and_concate_3d(layer, down_layer[2])layer = res_block_v2_3d(layer, 256, batch_normalization=batch_normalization)print(str(layer.get_shape()))# up_layer_2layer = up_and_concate_3d(layer, down_layer[1])layer = res_block_v2_3d(layer, 128, batch_normalization=batch_normalization)print(str(layer.get_shape()))# up_layer_1layer = up_and_concate_3d(layer, down_layer[0])layer = res_block_v2_3d(layer, 64, batch_normalization=batch_normalization)print(str(layer.get_shape()))# score_layerlayer = Conv3D(n_labels, [1, 1, 1], strides=[1, 1, 1])(layer)print(str(layer.get_shape()))# softmaxlayer = Activation('softmax')(layer)print(str(layer.get_shape()))outputs = layermodel = Model(inputs=inputs, outputs=outputs)metrics = [metrics]model.compile(optimizer=Adam(lr=initial_learning_rate), loss=m.dice_coefficient_loss, metrics=metrics)return modeldef res_block_v2_3d(input_layer, out_n_filters, batch_normalization=False, kernel_size=[3, 3, 3], stride=[1, 1, 1],padding='same'):input_n_filters = input_layer.get_shape().as_list()[3]print(str(input_layer.get_shape()))layer = input_layerfor i in range(2):if batch_normalization:layer = BatchNormalization()(layer)layer = Activation('relu')(layer)layer = Conv3D(out_n_filters, kernel_size, strides=stride, padding=padding)(layer)if out_n_filters != input_n_filters:skip_layer = Conv3D(out_n_filters, [1, 1, 1], strides=stride, padding=padding)(input_layer)else:skip_layer = input_layerout_layer = keras.layers.add([layer, skip_layer])return out_layer

和之前那篇使用u-net2d进行voc分割的网络结构没有什么区别，只是将卷积、pooling、concate操作都改成了3维操作

在跑的过程中发现了一些bug，最新代码可在git上找到，以最近代码为准：

https://github.com/panxiaobai/brats_keras

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[深度学习从入门到女装]keras实战-Unet3d（BRAST2015）

BRAST2015读取

U-Net3D

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