def __init__(self, minibatch_size, image_moving, image_fixed):
self.minibatch_size = minibatch_size
self.image_size = image_fixed.shape.as_list()[1:4]
self.grid_ref = util.get_reference_grid(self.image_size)
self.grid_warped = tf.zeros_like(
self.grid_ref) # initial zeros are safer for debug
self.image_moving = image_moving
self.image_fixed = image_fixed
self.input_layer = tf.concat(
[layer.resize_volume(image_moving, self.image_size), image_fixed],
axis=4)
def warp_volumes_by_ddf(input_, ddf):
grid_warped = util.get_reference_grid(ddf.shape[1:4]) + ddf
warped = util.resample_linear(tf.convert_to_tensor(input_, dtype=tf.float32), grid_warped)
with tf.Session() as sess:
return sess.run(warped)
def build_network(self):
self.global_step = tf.Variable(0, trainable=False)
self.learning_rate = tf.train.exponential_decay(self.args.lr,
self.global_step,
self.args.decay_freq,
0.96,
staircase=True)
self.grid_ref = util.get_reference_grid(self.image_size)
self.grid_warped_MV_FIX = tf.zeros_like(
self.grid_ref) # initial zeros are safer for debug
self.grid_warped_FIX_MV = tf.zeros_like(
self.grid_ref) # initial zeros are safer for debug
self.ph_MV_image = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_FIX_image = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_moving_affine = tf.placeholder(
tf.float32, [self.args.batch_size] +
[1, 12]) # 数据进行augment,4x4矩阵，但是最后四个参数为0001，所以一共12个参数
self.ph_fixed_affine = tf.placeholder(tf.float32,
[self.args.batch_size] + [1, 12])
self.ph_random_ddf = tf.placeholder(
tf.float32, [self.args.batch_size] + self.image_size + [3])
self.ph_MV_label = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_FIX_label = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.input_MV_image, self.input_MV_label = util.augment_3Ddata_by_affine(
self.ph_MV_image, self.ph_MV_label, self.ph_moving_affine)
self.input_FIX_image, self.input_FIX_label = util.augment_3Ddata_by_affine(
self.ph_FIX_image, self.ph_FIX_label, self.ph_fixed_affine)
self.input_layer = tf.concat([
layer.resize_volume(self.input_MV_image, self.image_size),
self.input_FIX_image
],
axis=4)
self.transform_initial = [
1., 0., 0., 0., 0., 1., 0., 0., 0., 0., 1., 0.
]
nc = [int(self.args.num_channel_initial * (2**i)) for i in range(5)]
h0, hc0 = layer.downsample_resnet_block(self.is_train,
self.input_layer,
2,
nc[0],
k_conv0=[7, 7, 7],
name='global_down_0')
h1, hc1 = layer.downsample_resnet_block(self.is_train,
h0,
nc[0],
nc[1],
name='global_down_1')
h2, hc2 = layer.downsample_resnet_block(self.is_train,
h1,
nc[1],
nc[2],
name='global_down_2')
h3, hc3 = layer.downsample_resnet_block(self.is_train,
h2,
nc[2],
nc[3],
name='global_down_3')
h4 = layer.conv3_block(self.is_train,
h3,
nc[3],
nc[4],
name='global_deep_4')
self.theta_fw = layer.fully_connected(h4,
12,
self.transform_initial,
name='global_project_0')
self.theta_bw = layer.fully_connected(h4,
12,
self.transform_initial,
name='global_project_1')
# out=tf.layers.flatten(h4)
# out=tf.layers.dense(out,1024)
# out=tf.layers.dense(out,256)
# xyz=tf.layers.dense(out,3)
# angles=tf.nn.tanh(tf.layers.dense(out,3))
self.grid_warped_fw = util.warp_grid(self.grid_ref, self.theta_fw)
# 这个地方为啥又减去,
self.ddf_fw = self.grid_warped_fw - self.grid_ref
self.grid_warped_bw = util.warp_grid(self.grid_ref, self.theta_bw)
# 这个地方为啥又减去,
self.ddf_bw = self.grid_warped_bw - self.grid_ref
self.warped_MV_image = self.warp_image(
self.input_MV_image, self.grid_warped_fw
) # warp the moving label with the predicted ddf
self.warped_FIX_image = self.warp_image(
self.input_FIX_image, self.grid_warped_bw
) # warp the moving label with the predicted ddf
# self.resotre_MV_label=self.warp_image(self.warped_MV_label,self.grid_warped_bw)
self.restore_MV_image = self.warp_image(self.warped_MV_image,
self.grid_warped_bw)
# self.resotre_FIX_label=self.warp_image(self.warped_FIX_label,self.grid_warped_fw)
self.restore_FIX_image = self.warp_image(self.warped_FIX_image,
self.grid_warped_fw)
#这里可以让restore_fix_image* restore_fix_label，因为在形变的时候，图像四周容易生成空白，
self.ddf_regularisation1 = self.args.lambda_consis * restore_loss2(
self.input_FIX_image, self.restore_FIX_image)
self.ddf_regularisation2 = self.args.lambda_consis * restore_loss2(
self.input_MV_image, self.restore_MV_image)
self.ddf_regularisation = self.ddf_regularisation1 + self.ddf_regularisation2
# self.restore_MV_label= self.warp_image(self.warped_MV_label,self.grid_warped_bw) # warp the moving label with the predicted ddf
# self.warped_MV_image = self.warp_MV_image(self.input_MV_image)
# self.warped_MV_label = self.warp_MV_image(self.input_MV_label) # warp the moving label with the predicted ddf
self.warped_MV_label = self.warp_image(
self.input_MV_label, self.grid_warped_fw
) # warp the moving label with the predicted ddf
self.warped_FIX_label = self.warp_image(
self.input_FIX_label, self.grid_warped_bw
) # warp the moving label with the predicted ddf
self.grad_loss_fw = tf.reduce_mean(
loss.multi_scale_loss(self.input_FIX_label, self.warped_MV_label,
'dice', [0, 1, 2, 4, 8]))
self.grad_loss_bw = tf.reduce_mean(
loss.multi_scale_loss(self.input_MV_label, self.warped_FIX_label,
'dice', [0, 1, 2, 4, 8]))
self.grad_loss = self.grad_loss_fw + self.grad_loss_bw
self.train_op = tf.train.AdamOptimizer(
self.args.lr).minimize(self.grad_loss + self.ddf_regularisation)
def build_network(self):
self.global_step = tf.Variable(0, trainable=False)
self.learning_rate = tf.train.exponential_decay(self.args.lr,
self.global_step,
self.args.decay_freq,
0.96,
staircase=True)
self.grid_ref = util.get_reference_grid(self.image_size)
self.grid_warped_MV_FIX = tf.zeros_like(
self.grid_ref) # initial zeros are safer for debug
self.grid_warped_FIX_MV = tf.zeros_like(
self.grid_ref) # initial zeros are safer for debug
self.ph_MV_image = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_FIX_image = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_moving_affine = tf.placeholder(
tf.float32, [self.args.batch_size] +
[1, 12]) # 数据进行augment,4x4矩阵，但是最后四个参数为0001，所以一共12个参数
self.ph_fixed_affine = tf.placeholder(tf.float32,
[self.args.batch_size] + [1, 12])
self.ph_random_ddf = tf.placeholder(
tf.float32, [self.args.batch_size] + self.image_size + [3])
self.ph_MV_label = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.ph_FIX_label = tf.placeholder(tf.float32, [self.args.batch_size] +
self.image_size + [1])
self.input_MV_image, self.input_MV_label = util.augment_3Ddata_by_affine(
self.ph_MV_image, self.ph_MV_label, self.ph_moving_affine)
self.input_FIX_image, self.input_FIX_label = util.augment_3Ddata_by_affine(
self.ph_FIX_image, self.ph_FIX_label, self.ph_fixed_affine)
# self.input_FIX_image,self.input_FIX_label=util.augment_3Ddata_by_DDF(self.ph_FIX_image,self.ph_FIX_label,self.ph_random_ddf)
self.input_layer = tf.concat([
layer.resize_volume(self.input_MV_image, self.image_size),
self.input_FIX_image
],
axis=4)
self.lambda_bend = self.args.lambda_ben
self.lambda_consis = self.args.lambda_consis
self.ddf_levels = [0, 1, 2, 3, 4]
self.num_channel_initial = self.args.num_channel_initial
# 32,64,128,256,512
nc = [int(self.num_channel_initial * (2**i)) for i in range(5)]
h0, hc0 = layer.downsample_resnet_block(self.is_train,
self.input_layer,
2,
nc[0],
k_conv0=[7, 7, 7],
name='local_down_0')
h1, hc1 = layer.downsample_resnet_block(self.is_train,
h0,
nc[0],
nc[1],
name='local_down_1')
h2, hc2 = layer.downsample_resnet_block(self.is_train,
h1,
nc[1],
nc[2],
name='local_down_2')
h3, hc3 = layer.downsample_resnet_block(self.is_train,
h2,
nc[2],
nc[3],
name='local_down_3')
# 这个代码是对应文章中 fig.4 中的哪个卷积块？
hm = [
layer.conv3_block(self.is_train,
h3,
nc[3],
nc[4],
name='local_deep_4')
]
min_level = min(self.ddf_levels)
gated_h1, self.gated1 = layer.att_upsample_resnet_block(
self.is_train, hm[0], hc3, nc[4], nc[3],
name='local_up_3') # if min_level < 4 else None,None
hm += [gated_h1]
gated_h2, self.gated2 = layer.att_upsample_resnet_block(
self.is_train, hm[1], hc2, nc[3], nc[2],
name='local_up_2') # if min_level < 3 else None,None
hm += [gated_h2]
gated_h3, self.gated3 = layer.att_upsample_resnet_block(
self.is_train, hm[2], hc1, nc[2], nc[1],
name='local_up_1') # if min_level < 2 else None,None
hm += [gated_h3]
gated_h4, self.gated4 = layer.att_upsample_resnet_block(
self.is_train, hm[3], hc0, nc[1], nc[0],
name='local_up_0') # if min_level < 1 else None,None
hm += [gated_h4]
ddf_list = [
layer.ddf_summand(hm[4 - idx],
nc[idx],
self.image_size,
name='ddf1_sum_%d' % idx)
for idx in self.ddf_levels
]
ddf_list = tf.stack(ddf_list, axis=5)
self.ddf_MV_FIX = tf.reduce_sum(ddf_list, axis=5)
self.grid_warped_MV_FIX = self.grid_ref + self.ddf_MV_FIX
# self.grid_warped_FIX_MV = self.grid_ref + self.ddf_FIX_MV
#create loss
self.warped_MV_image = self.warp_MV_image(self.input_MV_image)
self.warped_MV_label = self.warp_MV_image(
self.input_MV_label
) # warp the moving label with the predicted ddf
self.loss_warp_mv_fix = tf.reduce_mean(
loss.multi_scale_loss(self.input_FIX_label, self.warped_MV_label,
'dice', [0, 1, 2, 4]))
self.ddf_regu_MV = self.args.lambda_ben * tf.reduce_mean(
loss.local_displacement_energy(self.ddf_MV_FIX, 'bending', 1))
self.train_op = tf.train.AdamOptimizer(self.learning_rate).minimize(
self.loss_warp_mv_fix + self.ddf_regu_MV,
global_step=self.global_step)
self.logger.debug("build network finish")
