Keras give input to intermediate layer and get final output

First you must learn that in Keras when you apply a layer on an input, a new node is created inside this layer which connects the input and output tensors. Each layer may have multiple nodes connecting different input tensors to their corresponding output tensors. To build a model, these nodes are traversed and a new graph of the model is created which consists all the nodes needed to reach output tensors from input tensors (i.e. which you specify when creating a model: model = Model(inputs=[...], outputs=[...]).

Now you would like to feed an intermediate layer of a model and get the output of the model. Since this is a new data-flow path, we need to create new nodes for each layer corresponding to this new computational graph. We can do it like this:

idx = 3  # index of desired layer
input_shape = model.layers[idx].get_input_shape_at(0) # get the input shape of desired layer
layer_input = Input(shape=input_shape) # a new input tensor to be able to feed the desired layer

# create the new nodes for each layer in the path
x = layer_input
for layer in model.layers[idx:]:
    x = layer(x)

# create the model
new_model = Model(layer_input, x)

Fortunately, your model consists of one-branch and we could simply use a for loop to construct the new model. However, for more complex models it may not be easy to do so and you may need to write more codes to construct the new model.

Here is another method for achieving the same result. Initially create a new input layer and then connect it to the lower layers(with weights).

For this purpose, first re-initialize these layers(with same name) and reload the corresponding weights from the parent model using

new_model.load_weights("parent_model.hdf5", by_name=True)

This will load the required weights from the parent model.Just make sure you name your layers properly beforehand.

idx = 3  
input_shape = model.layers[idx].get_input_shape_at(0) layer

new_input = Input(shape=input_shape)

d=Dense(256,activation='relu', name='layer_3')(new_input)
d=Dense(512,activation='relu', name='layer_4'))(d)
d=Dense(1024,activation='relu', name='layer_5'))(d)
d=Dense(128,activation='linear', name='layer_6'))(d)

new_model = Model(new_input, d)
new_model.load_weights("parent_model.hdf5", by_name=True)

This method will work for complex models with multiple inputs or branches.You just need to copy the same code for required layers, connect the new inputs and finally load the corresponding weights.