Deep supervision

[twentyfiveYang]

Hi @MrGiovanni ,thank you for sharing your code. I have a question about the implement of the Deep supervision structure. In the paper, you said that the final output of the model is the average of the 4 outputs of the branches. I calculate the average output feature map in this way but got the error below:

nestnet_output_1 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_1',  kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_2)
    nestnet_output_2 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_2', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_3)
    nestnet_output_3 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_3', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_4)
    nestnet_output_4 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_4', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_5)
    nestnet_output_all = (nestnet_output_1+nestnet_output_2+nestnet_output_3+nestnet_output_4)/4

if deep_supervision:
    # model = Model(input=img_input, output=[nestnet_output_1,
    #                                        nestnet_output_2,
    #                                        nestnet_output_3,
    #                                        nestnet_output_4])
    model = Model(input=img_input, output=[nestnet_output_all])
else:
    model = Model(input=img_input, output=[nestnet_output_4])

`

Using TensorFlow backend. D:\code\unet-master\revisedModel.py:116: UserWarning: Update your Model call to the Keras 2 API: Model(outputs=[<tf.Tenso..., inputs=Tensor("ma...) model = Model(input=img_input, output=[nestnet_output_all]) Traceback (most recent call last): File "D:/code/unet-master/revisedModelTrain.py", line 16, in model = Nest_Net(256,256,1) File "D:\code\unet-master\revisedModel.py", line 116, in Nest_Net model = Model(input=img_input, output=[nestnet_output_all]) File "C:\Users\Administrator\Anaconda3\envs\tensorflow-gpu\lib\site-packages\keras\legacy\interfaces.py", line 91, in wrapper return func(*args, *kwargs) File "C:\Users\Administrator\Anaconda3\envs\tensorflow-gpu\lib\site-packages\keras\engine\network.py", line 93, in init self._init_graph_network(args, **kwargs) File "C:\Users\Administrator\Anaconda3\envs\tensorflow-gpu\lib\site-packages\keras\engine\network.py", line 188, in _init_graph_network 'Found: ' + str(x)) ValueError: Output tensors to a Model must be the output of a Keras Layer (thus holding past layer metadata). Found: Tensor("truediv:0", shape=(?, 256, 256, 1), dtype=float32)

Can you help about this, thanks!

[DHW-Master]

Hello, I have the same problem as you. How did you solve it? @twentyfiveYang

[kevinkwshin]

Try this. `

nestnet_output_all = keras.layers.Average()([nestnet_output_1,nestnet_output_2,nestnet_output_3,nestnet_output_4])

if deep_supervision:
    model = Model(inputs=[img_input], outputs=[nestnet_output_all])

else:
    model = Model(inputs=img_input, outputs=[nestnet_output_4])`

[zsk-tech]

In helper_functions.py : He writes as this:

if deep_supervision: model = Model(input=img_input, output=[nestnet_output_1, nestnet_output_2, nestnet_output_3, nestnet_output_4])

else: model = Model(input=img_input, output=[nestnet_output_4])

[Einshowstank]

I have the same question.

[MrGiovanni]

Hi @Einshowstank

The deep supervision code is as below (you don't need to average outputs before computing loss):

% Architecture definition
def UNetPlusPlus(img_rows, img_cols, color_type=1, num_class=1, connection='concatenation', deep_supervision=False):

    ... ...

    nestnet_output_1 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_1', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_2)
    nestnet_output_2 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_2', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_3)
    nestnet_output_3 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_3', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_4)
    nestnet_output_4 = Conv2D(num_class, (1, 1), activation='sigmoid', name='output_4', kernel_initializer = 'he_normal', padding='same', kernel_regularizer=l2(1e-4))(conv1_5)

    if deep_supervision:
        model = Model(input=img_input, output=[nestnet_output_1,
                                               nestnet_output_2,
                                               nestnet_output_3,
                                               nestnet_output_4])
    else:
        model = Model(input=img_input, output=[nestnet_output_4])

    return model

% Model compiling
if config.deep_supervision:
    model.compile(optimizer='Adam', 
                  loss={'output_1': bce_dice_loss, 'output_2': bce_dice_loss, 'output_3': bce_dice_loss, 'output_4': bce_dice_loss},
                  metrics={'output_1': dice_coef, 'output_2': dice_coef,
                           'output_3': dice_coef, 'output_4': dice_coef},
                  loss_weights={'output_1': 1., 'output_2': 1., 'output_3': 1., 'output_4': 1.})
else:
    model.compile(optimizer='Adam', 
                  loss=bce_dice_loss, 
                  metrics=['binary_crossentropy', mean_iou, dice_coef])

Thanks,

Zongwei