Note

This documentation is for a development version. Click here for the latest stable release (v3.3.0).

Migration guide

The goal of this section is to help with upgrading code that was written for an older version of NengoDL. Note that this is not a list of all the new features available in newer versions. Here we will only look at features that were present in older versions, and how they have changed.

See the release history for complete details on what has changed in each version.

NengoDL 2 to 3

NengoDL 3 makes some significant changes to the API, mainly motivated by the release of TensorFlow 2.0. TensorFlow 2.0 adopts the Keras API as the standard high-level interface, so in NengoDL 3 we make the same change, modifying the API to better integrate with Keras.

Simulator changes

  1. Use Simulator.fit instead of Simulator.train. Simulator.fit is the new access point for optimizing a NengoDL model. It is closely based on the Keras Model.fit function. One important difference between fit and train is that the optimizer and loss functions are specified in a separate Simulator.compile step (analogous to Keras’ Model.compile) rather than directly in Simulator.train. Another difference is that input and target data are specified in separate x and y arguments, rather than a single data argument.

    Also note that you should use the updated TensorFlow 2.0 optimizers/loss functions in tf.optimizers and tf.losses, rather than the deprecated optimizers in tf.compat.v1.train.

    with nengo.Network() as example_net:
        node = nengo.Node([0])
        ens = nengo.Ensemble(10, 1)
        nengo.Connection(node, ens, synapse=None)
        probe = nengo.Probe(ens)
    

    NengoDL 2:

    with nengo_dl.Simulator(example_net) as sim:
        sim.train(
            data={node: np.zeros((1, 1, 1)), probe: np.zeros((1, 1, 1))},
            optimizer=tf.train.AdamOptimizer(0.01),
            objective=nengo_dl.objectives.mse,
            n_epochs=10,
        )
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net) as sim:
        sim.compile(optimizer=tf.optimizers.Adam(0.01), loss=tf.losses.mse)
        sim.fit(
            x={node: np.zeros((1, 1, 1))},
            y={probe: np.zeros((1, 1, 1))},
            epochs=10
        )
    
  2. Use Simulator.evaluate instead of Simulator.loss. In the same way as train is replaced by fit, loss is replaced by evaluate, which is equivalent to the Keras Model.evaluate function. It differs from loss in all the same ways (separate compile step and independently specified inputs and targets).

    NengoDL 2:

    with nengo_dl.Simulator(example_net) as sim:
        sim.loss(
            data={node: np.zeros((1, 1, 1)), probe: np.zeros((1, 1, 1))},
            objective=nengo_dl.objectives.mse,
        )
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net) as sim:
        sim.compile(loss=tf.losses.mse)
        sim.evaluate(
            x={node: np.zeros((1, 1, 1))}, y={probe: np.zeros((1, 1, 1))})
    
  3. Extra simulator steps will no longer be hidden. When simulating a number of timesteps that is not evenly divisible by Simulator.unroll_simulation, extra simulation steps will be executed (this is true in both 2 and 3). In NengoDL 2 these extra steps and any data associated with them were hidden from the user. In NengoDL 3 the number of steps executed is unchanged, but the simulation is now updated to reflect the number of steps that were actually executed (rather than the number the user requested).

    NengoDL 2:

    with nengo_dl.Simulator(example_net, unroll_simulation=5) as sim:
        sim.run_steps(18)
        assert sim.n_steps == 18
        assert len(sim.data[probe]) == 18
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net, unroll_simulation=5) as sim:
        sim.run_steps(18)
        assert sim.n_steps == 20
        assert len(sim.data[probe]) == 20
    
  4. Simulator.save_params and Simulator.load_params arguments include_global and include_local replaced with include_non_trainable. TensorFlow 2.0 removed the division of Variables into “global” and “local” collections. Instead, Keras organizes Variables according to whether they are trainable or not. Generally speaking, in NengoDL 2 global variables were trainable and local variables were not, so the two organization schemes are roughly equivalent. However, it is possible for users to manually create non-trainable global variables or trainable local variables, in which case these two organization schemes would not be equivalent.

    NengoDL 2:

    with nengo_dl.Simulator(example_net) as sim:
        sim.save_params("trainable", include_global=True, include_local=False)
        sim.save_params("non_trainable", include_global=False, include_local=True)
        sim.save_params("both", include_global=True, include_local=True)
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net) as sim:
        sim.save_params("trainable", include_non_trainable=False)
        sim.save_params("both", include_non_trainable=True)
    

    Note that with the simplified single argument it is no longer possible to save only the non-trainable parameters. However, it is still possible to save these parameters manually if it is critical that trainable parameters not be included.

    with nengo_dl.Simulator(example_net) as sim:
        np.savez_compressed(
            "non_trainable",
            *tf.keras.backend.batch_get_value(sim.keras_model.non_trainable_weights)
        )
    
  5. Rate/spiking neuron swapping is controlled by Keras learning_phase. In NengoDL 2 and 3 spiking neuron models are automatically swapped for rate mode equivalents during training. However, sometimes it is useful to manually enable this swapping in other functions (for example, in order to evaluate the loss function on test data but with the swapped rate neuron models). There were a couple ways to do this in NengoDL 2; in NengoDL 3 it is all controlled through the learning_phase configuration option.

    NengoDL 2:

    with nengo_dl.Simulator(example_net) as sim:
        sim.loss(
            data={node: np.zeros((1, 1, 1)), probe: np.zeros((1, 1, 1))},
            objective=nengo_dl.objectives.mse,
            training=True,
        )
    
        sim.run(1.0, extra_feeds={sim.tensor_graph.signals.training: True})
    

    NengoDL 3:

    with example_net:
        nengo_dl.configure_settings(learning_phase=True)
    
    with nengo_dl.Simulator(example_net) as sim:
        sim.compile(loss=tf.losses.mse)
        sim.evaluate(
            x={node: np.zeros((1, 1, 1))}, y={probe: np.zeros((1, 1, 1))})
    
        sim.run(1.0)
    
  6. TensorBoard functionality replaced by Keras TensorBoard callback. NengoDL allows data about training metrics or model parameters to be output and displayed in TensorBoard. In TensorFlow 2.0 the recommended way of doing this is through Keras callbacks, and NengoDL 3 adopts the same API.

    NengoDL 2:

    with nengo_dl.Simulator(example_net, tensorboard="results") as sim:
        sim.train(
            data={node: np.zeros((1, 1, 1)), probe: np.zeros((1, 1, 1))},
            optimizer=tf.train.AdamOptimizer(0.01),
            objective=nengo_dl.objectives.mse,
            n_epochs=10,
            summaries=["loss", ens],
        )
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net) as sim:
        sim.compile(optimizer=tf.optimizers.Adam(0.01), loss=tf.losses.mse)
        sim.fit(
            x={node: np.zeros((1, 1, 1))},
            y={probe: np.zeros((1, 1, 1))},
            epochs=10,
            callbacks=[
                tf.keras.callbacks.TensorBoard(log_dir="results"),
                nengo_dl.callbacks.NengoSummaries("results", sim, [ens]),
            ]
        )
    

TensorNode changes

  1. Use nengo_dl.Layer instead of nengo_dl.tensor_layer. nengo_dl.tensor_layer was designed to mimic the tf.layers API. In TensorFlow 2.0 tf.layers has been deprecated in favour of tf.keras.layers. nengo_dl.Layer has the same functionality as nengo_dl.tensor_layer, but mimics the Keras Layer API instead.

    NengoDL 2:

    with nengo.Network():
        layer = nengo_dl.tensor_layer(node, tf.layers.dense, units=10)
    

    NengoDL 3:

    with nengo.Network():
        layer = nengo_dl.Layer(tf.keras.layers.Dense(units=10))(node)
    
  2. Use custom Keras Layers instead of callable classes. When making more complicated TensorNodes we sometimes need to separate the layer logic into separate preparation and execution steps. In NengoDL 2 this was done by creating a callable class that defined pre_build, __call__, and post_build functions. In NengoDL 3 this is done by creating a custom Keras Layer subclass instead, which can define build and call methods. There is no longer a post_build step, as this was used for TensorNodes that needed access to the TensorFlow Session object (which is no longer used in TensorFlow 2.0).

    NengoDL 2:

    class MyLayer:
        def pre_build(self, shape_in, shape_out):
            self.w = tf.Variable(tf.ones((1,)))
    
        def __call__(self, t):
            return t * self.weights
    
    with nengo.Network():
        tensor_node = nengo_dl.TensorNode(MyLayer())
    

    NengoDL 3:

    class MyLayer(tf.keras.layers.Layer):
        def build(self, input_shapes):
            self.w = self.add_weight(
                shape=(1,), initializer=tf.initializers.ones(),
            )
    
        def call(self, inputs):
            return inputs * self.weights
    
    with nengo.Network():
        tensor_node = nengo_dl.TensorNode(MyLayer())
    
  3. TensorNodes define multidimensional shape_in/shape_out rather than scalar size_in/size_out. In core Nengo all inputs and outputs are vectors, and in NengoDL 2 this was also true for TensorNodes. However, often when working with TensorNodes it is useful to have multidimensional inputs and outputs, so in NengoDL 3 TensorNodes are defined with a full shape. Note that these shapes do not include the batch dimension (which is defined when the Simulator is created).

    NengoDL 2:

    def my_func(t, x):
        assert t.shape == ()
        assert x.shape == (1, 24)
        return tf.reshape(x, (1, 2, 3, 4))
    
    with nengo.Network():
        tensor_node = nengo_dl.TensorNode(my_func, size_in=24, size_out=24)
    

    NengoDL 3:

    def my_func(t, x):
        assert t.shape == ()
        assert x.shape == (1, 2, 12)
        return tf.reshape(x, (1, 2, 3, 4))
    
    with nengo.Network():
        tensor_node = nengo_dl.TensorNode(
            my_func, shape_in=(2, 12), shape_out=(2, 3, 4))
    
  4. Connections created by nengo_dl.Layer are non-trainable by default. We usually don’t want these Connections to contain trainable weights (since any weights we want would be built into the TensorNode). In NengoDL 2 they needed to be manually marked as non-trainable, but that is the default behaviour in NengoDL 3.

    NengoDL 2:

    with nengo.Network() as net:
        nengo_dl.configure_settings(trainable=None)
        layer, conn = nengo_dl.tensor_layer(
            node, tf.layers.dense, units=10, return_conn=True)
        net.config[conn].trainable = False
    

    NengoDL 3:

    with nengo.Network() as net:
        layer = nengo_dl.Layer(tf.keras.layers.Dense(units=10))(node)
    

    The connection can still be manually marked as trainable if desired:

    with nengo.Network() as net:
        nengo_dl.configure_settings(trainable=None)
        layer, conn = nengo_dl.Layer(tf.keras.layers.Dense(units=10))(
            node, return_conn=True)
        net.config[conn].trainable = True
    

nengo_dl.objectives changes

  1. nengo_dl.objectives renamed to nengo_dl.losses. This is for consistency with tf.losses/tf.keras.losses.

  2. Loss functions take two arguments (y_true, y_pred) instead of (outputs, targets). Again this is for consistency with tf.losses. Note that this swaps the order of the two arguments (so the ground truth now comes first).

    NengoDL 2:

    def my_loss(outputs, targets):
        return outputs - targets
    

    NengoDL 3:

    def my_loss(y_true, y_pred):
        return y_pred - y_true
    
  3. nengo_dl.losses.Regularize accepts two arguments (y_true and y_pred) instead of just outputs. y_true is not used, but Keras requires all loss functions to accept two arguments regardless.

    NengoDL 2:

    nengo_dl.objectives.Regularize()(tf.ones((1, 2, 3)))
    

    NengoDL 3:

    nengo_dl.losses.Regularize()(None, tf.ones((1, 2, 3)))
    
  4. Use loss_weights parameter in Simulator.compile instead of weight parameter in nengo_dl.losses.Regularize.

    with example_net:
        p0 = nengo.Probe(node)
        p1 = nengo.Probe(ens)
    

    NengoDL 2:

    with nengo_dl.Simulator(example_net) as sim:
        sim.train(
            data={node: np.zeros((1, 1, 1)), probe: np.zeros((1, 1, 1))},
            optimizer=tf.train.AdamOptimizer(0.01),
            objective={
                probe: nengo_dl.objectives.mse,
                p0: nengo_dl.objectives.Regularize(weight=0.5),
                p1: nengo_dl.objectives.Regularize(weight=0.5),
            },
            n_epochs=10,
        )
    

    NengoDL 3:

    with nengo_dl.Simulator(example_net) as sim:
        sim.compile(
            optimizer=tf.optimizers.Adam(0.01),
            loss={
                probe: tf.losses.mse,
                p0: nengo_dl.losses.Regularize(),
                p1: nengo_dl.losses.Regularize(),
            },
            loss_weights={probe: 1, p0: 0.5, p1: 0.5},
        )
        sim.fit(
            x={node: np.zeros((1, 1, 1))},
            y={
                probe: np.zeros((1, 1, 1)),
                p0: np.zeros((1, 1, 1)),
                p1: np.zeros((1, 1, 1)),
            },
            epochs=10,
        )
    
  5. nengo_dl.objectives.mse renamed to nengo_dl.losses.nan_mse. This is to distinguish it from the standard tf.losses.mse, and emphasize the special treatment of nan targets.

    NengoDL 2:

    assert nengo_dl.objectives.mse(np.zeros((2, 3)), np.ones((2, 3)) * np.nan) == 0
    

    NengoDL 3:

    assert nengo_dl.losses.nan_mse(np.ones((2, 3)) * np.nan, np.zeros((2, 3))) == 0
    

configure_settings changes

  1. Specify dtype as string instead of tf.Dtype.

    NengoDL 2:

    with nengo.Network():
        nengo_dl.configure_settings(dtype=tf.float32)
    

    NengoDL 3:

    with nengo.Network():
        nengo_dl.configure_settings(dtype="float32")
    
  2. Configure trainability separately within subnetworks, rather than marking networks as trainable.

    NengoDL 2:

    with nengo.Network() as net:
        nengo_dl.configure_settings(trainable=None)
    
        with nengo.Network() as subnet:
            ens = nengo.Ensemble(10, 1)
    
        net.config[subnet].trainable = False
    

    NengoDL 3:

    with nengo.Network() as net:
        with nengo.Network() as subnet:
            nengo_dl.configure_settings(trainable=False)
    
            ens = nengo.Ensemble(10, 1)
    
  3. Use tf.config instead of session_config. TensorFlow 2.0 uses functions in the tf.config namespace to control settings that used to be controlled through the SessionConfig object (which no longer exists). So we no longer need the session_config option, and can instead just directly use those tf.config functions.

    NengoDL 2:

    with nengo.Network():
        nengo_dl.configure_settings(session_config={"allow_soft_placement": True})
    

    NengoDL 3:

    tf.config.set_soft_device_placement(True)