.. _pygadkerasga-module:

``pygad.kerasga`` Module
========================

This section of the PyGAD's library documentation discusses the
`pygad.kerasga <https://pygad.readthedocs.io/en/latest/kerasga.html>`__
module.

The ``pygad.kerarsga`` module has helper a class and 2 functions to
train Keras models using the genetic algorithm (PyGAD). The Keras model
can be built either using the `Sequential
Model <https://keras.io/guides/sequential_model>`__ or the `Functional
API <https://keras.io/guides/functional_api>`__.

The contents of this module are:

1. ``KerasGA``: A class for creating an initial population of all
   parameters in the Keras model.

2. ``model_weights_as_vector()``: A function to reshape the Keras model
   weights to a single vector.

3. ``model_weights_as_matrix()``: A function to restore the Keras model
   weights from a vector.

4. ``predict()``: A function to make predictions based on the Keras
   model and a solution.

More details are given in the next sections.

Steps Summary
=============

The summary of the steps used to train a Keras model using PyGAD is as
follows:

1. Create a Keras model.

2. Create an instance of the ``pygad.kerasga.KerasGA`` class.

3. Prepare the training data.

4. Build the fitness function.

5. Create an instance of the ``pygad.GA`` class.

6. Run the genetic algorithm.

Create Keras Model
==================

Before discussing training a Keras model using PyGAD, the first thing to
do is to create the Keras model.

According to the `Keras library
documentation <https://keras.io/api/models>`__, there are 3 ways to
build a Keras model:

1. `Sequential Model <https://keras.io/guides/sequential_model>`__

2. `Functional API <https://keras.io/guides/functional_api>`__

3. `Model Subclassing <https://keras.io/guides/model_subclassing>`__

PyGAD supports training the models created either using the Sequential
Model or the Functional API.

Here is an example of a model created using the Sequential Model.

.. code:: python

   import tensorflow.keras

   input_layer  = tensorflow.keras.layers.Input(3)
   dense_layer1 = tensorflow.keras.layers.Dense(5, activation="relu")
   output_layer = tensorflow.keras.layers.Dense(1, activation="linear")

   model = tensorflow.keras.Sequential()
   model.add(input_layer)
   model.add(dense_layer1)
   model.add(output_layer)

This is the same model created using the Functional API.

.. code:: python

   input_layer  = tensorflow.keras.layers.Input(3)
   dense_layer1 = tensorflow.keras.layers.Dense(5, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(1, activation="linear")(dense_layer1)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

Feel free to add the layers of your choice.

.. _pygadkerasgakerasga-class:

``pygad.kerasga.KerasGA`` Class
===============================

The ``pygad.kerasga`` module has a class named ``KerasGA`` for creating
an initial population for the genetic algorithm based on a Keras model.
The constructor, methods, and attributes within the class are discussed
in this section.

.. _init:

``__init__()``
--------------

The ``pygad.kerasga.KerasGA`` class constructor accepts the following
parameters:

-  ``model``: An instance of the Keras model.

-  ``num_solutions``: Number of solutions in the population. Each
   solution has different parameters of the model.

Instance Attributes
-------------------

All parameters in the ``pygad.kerasga.KerasGA`` class constructor are
used as instance attributes in addition to adding a new attribute called
``population_weights``.

Here is a list of all instance attributes:

-  ``model``

-  ``num_solutions``

-  ``population_weights``: A nested list holding the weights of all
   solutions in the population.

Methods in the ``KerasGA`` Class
--------------------------------

This section discusses the methods available for instances of the
``pygad.kerasga.KerasGA`` class.

.. _createpopulation:

``create_population()``
~~~~~~~~~~~~~~~~~~~~~~~

The ``create_population()`` method creates the initial population of the
genetic algorithm as a list of solutions where each solution represents
different model parameters. The list of networks is assigned to the
``population_weights`` attribute of the instance.

.. _functions-in-the-pygadkerasga-module:

Functions in the ``pygad.kerasga`` Module
=========================================

This section discusses the functions in the ``pygad.kerasga`` module.

.. _pygadkerasgamodelweightsasvector:

``pygad.kerasga.model_weights_as_vector()`` 
--------------------------------------------

The ``model_weights_as_vector()`` function accepts a single parameter
named ``model`` representing the Keras model. It returns a vector
holding all model weights. The reason for representing the model weights
as a vector is that the genetic algorithm expects all parameters of any
solution to be in a 1D vector form.

This function filters the layers based on the ``trainable`` attribute to
see whether the layer weights are trained or not. For each layer, if its
``trainable=False``, then its weights will not be evolved using the
genetic algorithm. Otherwise, it will be represented in the chromosome
and evolved.

The function accepts the following parameters:

-  ``model``: The Keras model.

It returns a 1D vector holding the model weights.

.. _pygadkerasgamodelweightsasmatrix:

``pygad.kerasga.model_weights_as_matrix()``
-------------------------------------------

The ``model_weights_as_matrix()`` function accepts the following
parameters:

1. ``model``: The Keras model.

2. ``weights_vector``: The model parameters as a vector.

It returns the restored model weights after reshaping the vector.

.. _pygadkerasgapredict:

``pygad.kerasga.predict()``
---------------------------

The ``predict()`` function makes a prediction based on a solution. It
accepts the following parameters:

1. ``model``: The Keras model.

2. ``solution``: The solution evolved.

3. ``data``: The test data inputs.

4. ``batch_size=None``: The batch size (i.e. number of samples per step
   or batch).

5. ``verbose=None``: Verbosity mode.

6. ``steps=None``: The total number of steps (batches of samples).

Check documentation of the `Keras
Model.predict() <https://keras.io/api/models/model_training_apis>`__
method for more information about the ``batch_size``, ``verbose``, and
``steps`` parameters.

It returns the predictions of the data samples.

Examples
========

This section gives the complete code of some examples that build and
train a Keras model using PyGAD. Each subsection builds a different
network.

Example 1: Regression Example
-----------------------------

The next code builds a simple Keras model for regression. The next
subsections discuss each part in the code.

.. code:: python

   import tensorflow.keras
   import pygad.kerasga
   import numpy
   import pygad

   def fitness_func(ga_instance, solution, sol_idx):
       global data_inputs, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=data_inputs)

       mae = tensorflow.keras.losses.MeanAbsoluteError()
       abs_error = mae(data_outputs, predictions).numpy() + 0.00000001
       solution_fitness = 1.0/abs_error

       return solution_fitness

   def on_generation(ga_instance):
       print("Generation = {generation}".format(generation=ga_instance.generations_completed))
       print("Fitness    = {fitness}".format(fitness=ga_instance.best_solution()[1]))

   input_layer  = tensorflow.keras.layers.Input(3)
   dense_layer1 = tensorflow.keras.layers.Dense(5, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(1, activation="linear")(dense_layer1)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

   keras_ga = pygad.kerasga.KerasGA(model=model,
                                    num_solutions=10)

   # Data inputs
   data_inputs = numpy.array([[0.02, 0.1, 0.15],
                              [0.7, 0.6, 0.8],
                              [1.5, 1.2, 1.7],
                              [3.2, 2.9, 3.1]])

   # Data outputs
   data_outputs = numpy.array([[0.1],
                               [0.6],
                               [1.3],
                               [2.5]])

   # Prepare the PyGAD parameters. Check the documentation for more information: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   num_generations = 250 # Number of generations.
   num_parents_mating = 5 # Number of solutions to be selected as parents in the mating pool.
   initial_population = keras_ga.population_weights # Initial population of network weights

   ga_instance = pygad.GA(num_generations=num_generations, 
                          num_parents_mating=num_parents_mating, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

   ga_instance.run()

   # After the generations complete, some plots are showed that summarize how the outputs/fitness values evolve over generations.
   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution()
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

   # Make prediction based on the best solution.
   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=data_inputs)
   print("Predictions : \n", predictions)

   mae = tensorflow.keras.losses.MeanAbsoluteError()
   abs_error = mae(data_outputs, predictions).numpy()
   print("Absolute Error : ", abs_error)

Create a Keras Model
~~~~~~~~~~~~~~~~~~~~

According to the steps mentioned previously, the first step is to create
a Keras model. Here is the code that builds the model using the
Functional API.

.. code:: python

   import tensorflow.keras

   input_layer  = tensorflow.keras.layers.Input(3)
   dense_layer1 = tensorflow.keras.layers.Dense(5, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(1, activation="linear")(dense_layer1)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

The model can also be build using the Keras Sequential Model API.

.. code:: python

   input_layer  = tensorflow.keras.layers.Input(3)
   dense_layer1 = tensorflow.keras.layers.Dense(5, activation="relu")
   output_layer = tensorflow.keras.layers.Dense(1, activation="linear")

   model = tensorflow.keras.Sequential()
   model.add(input_layer)
   model.add(dense_layer1)
   model.add(output_layer)

.. _create-an-instance-of-the-pygadkerasgakerasga-class:

Create an Instance of the ``pygad.kerasga.KerasGA`` Class
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The second step is to create an instance of the
``pygad.kerasga.KerasGA`` class. There are 10 solutions per population.
Change this number according to your needs.

.. code:: python

   import pygad.kerasga

   keras_ga = pygad.kerasga.KerasGA(model=model,
                                    num_solutions=10)

Prepare the Training Data
~~~~~~~~~~~~~~~~~~~~~~~~~

The third step is to prepare the training data inputs and outputs. Here
is an example where there are 4 samples. Each sample has 3 inputs and 1
output.

.. code:: python

   import numpy

   # Data inputs
   data_inputs = numpy.array([[0.02, 0.1, 0.15],
                              [0.7, 0.6, 0.8],
                              [1.5, 1.2, 1.7],
                              [3.2, 2.9, 3.1]])

   # Data outputs
   data_outputs = numpy.array([[0.1],
                               [0.6],
                               [1.3],
                               [2.5]])

Build the Fitness Function
~~~~~~~~~~~~~~~~~~~~~~~~~~

The fourth step is to build the fitness function. This function must
accept 2 parameters representing the solution and its index within the
population.

The next fitness function returns the model predictions based on the
current solution using the ``predict()`` function. Then, it calculates
the mean absolute error (MAE) of the Keras model based on the parameters
in the solution. The reciprocal of the MAE is used as the fitness value.
Feel free to use any other loss function to calculate the fitness value.

.. code:: python

   def fitness_func(ga_instance, solution, sol_idx):
       global data_inputs, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=data_inputs)

       mae = tensorflow.keras.losses.MeanAbsoluteError()
       abs_error = mae(data_outputs, predictions).numpy() + 0.00000001
       solution_fitness = 1.0/abs_error

       return solution_fitness

.. _create-an-instance-of-the-pygadga-class:

Create an Instance of the ``pygad.GA`` Class
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The fifth step is to instantiate the ``pygad.GA`` class. Note how the
``initial_population`` parameter is assigned to the initial weights of
the Keras models.

For more information, please check the `parameters this class
accepts <https://pygad.readthedocs.io/en/latest/pygad.html#init>`__.

.. code:: python

   # Prepare the PyGAD parameters. Check the documentation for more information: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   num_generations = 250 # Number of generations.
   num_parents_mating = 5 # Number of solutions to be selected as parents in the mating pool.
   initial_population = keras_ga.population_weights # Initial population of network weights

   ga_instance = pygad.GA(num_generations=num_generations, 
                          num_parents_mating=num_parents_mating, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

Run the Genetic Algorithm
~~~~~~~~~~~~~~~~~~~~~~~~~

The sixth and last step is to run the genetic algorithm by calling the
``run()`` method.

.. code:: python

   ga_instance.run()

After the PyGAD completes its execution, then there is a figure that
shows how the fitness value changes by generation. Call the
``plot_fitness()`` method to show the figure.

.. code:: python

   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

Here is the figure.

.. image:: https://user-images.githubusercontent.com/16560492/93722638-ac261880-fb98-11ea-95d3-e773deb034f4.png
   :alt: 

To get information about the best solution found by PyGAD, use the
``best_solution()`` method.

.. code:: python

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution()
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

.. code:: python

   Fitness value of the best solution = 72.77768757825352
   Index of the best solution : 0

The next code makes prediction using the ``predict()`` function to
return the model predictions based on the best solution.

.. code:: python

   # Fetch the parameters of the best solution.
   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=data_inputs)
   print("Predictions : \n", predictions)

.. code:: python

   Predictions : 
   [[0.09935353]
    [0.63082725]
    [1.2765523 ]
    [2.4999595 ]]

The next code measures the trained model error.

.. code:: python

   mae = tensorflow.keras.losses.MeanAbsoluteError()
   abs_error = mae(data_outputs, predictions).numpy()
   print("Absolute Error : ", abs_error)

.. code:: 

   Absolute Error :  0.013740465

Example 2: XOR Binary Classification
------------------------------------

The next code creates a Keras model to build the XOR binary
classification problem. Let's highlight the changes compared to the
previous example.

.. code:: python

   import tensorflow.keras
   import pygad.kerasga
   import numpy
   import pygad

   def fitness_func(ga_instance, solution, sol_idx):
       global data_inputs, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=data_inputs)

       bce = tensorflow.keras.losses.BinaryCrossentropy()
       solution_fitness = 1.0 / (bce(data_outputs, predictions).numpy() + 0.00000001)

       return solution_fitness

   def on_generation(ga_instance):
       print("Generation = {generation}".format(generation=ga_instance.generations_completed))
       print("Fitness    = {fitness}".format(fitness=ga_instance.best_solution()[1]))

   # Build the keras model using the functional API.
   input_layer  = tensorflow.keras.layers.Input(2)
   dense_layer = tensorflow.keras.layers.Dense(4, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(2, activation="softmax")(dense_layer)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

   # Create an instance of the pygad.kerasga.KerasGA class to build the initial population.
   keras_ga = pygad.kerasga.KerasGA(model=model,
                                    num_solutions=10)

   # XOR problem inputs
   data_inputs = numpy.array([[0, 0],
                              [0, 1],
                              [1, 0],
                              [1, 1]])

   # XOR problem outputs
   data_outputs = numpy.array([[1, 0],
                               [0, 1],
                               [0, 1],
                               [1, 0]])

   # Prepare the PyGAD parameters. Check the documentation for more information: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   num_generations = 250 # Number of generations.
   num_parents_mating = 5 # Number of solutions to be selected as parents in the mating pool.
   initial_population = keras_ga.population_weights # Initial population of network weights.

   # Create an instance of the pygad.GA class
   ga_instance = pygad.GA(num_generations=num_generations, 
                          num_parents_mating=num_parents_mating, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

   # Start the genetic algorithm evolution.
   ga_instance.run()

   # After the generations complete, some plots are showed that summarize how the outputs/fitness values evolve over generations.
   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution()
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

   # Make predictions based on the best solution.
   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=data_inputs)
   print("Predictions : \n", predictions)

   # Calculate the binary crossentropy for the trained model.
   bce = tensorflow.keras.losses.BinaryCrossentropy()
   print("Binary Crossentropy : ", bce(data_outputs, predictions).numpy())

   # Calculate the classification accuracy for the trained model.
   ba = tensorflow.keras.metrics.BinaryAccuracy()
   ba.update_state(data_outputs, predictions)
   accuracy = ba.result().numpy()
   print("Accuracy : ", accuracy)

Compared to the previous regression example, here are the changes:

-  The Keras model is changed according to the nature of the problem.
   Now, it has 2 inputs and 2 outputs with an in-between hidden layer of
   4 neurons.

.. code:: python

   # Build the keras model using the functional API.
   input_layer  = tensorflow.keras.layers.Input(2)
   dense_layer = tensorflow.keras.layers.Dense(4, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(2, activation="softmax")(dense_layer)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

-  The train data is changed. Note that the output of each sample is a
   1D vector of 2 values, 1 for each class.

.. code:: python

   # XOR problem inputs
   data_inputs = numpy.array([[0, 0],
                              [0, 1],
                              [1, 0],
                              [1, 1]])

   # XOR problem outputs
   data_outputs = numpy.array([[1, 0],
                               [0, 1],
                               [0, 1],
                               [1, 0]])

-  The fitness value is calculated based on the binary cross entropy.

.. code:: python

   bce = tensorflow.keras.losses.BinaryCrossentropy()
   solution_fitness = 1.0 / (bce(data_outputs, predictions).numpy() + 0.00000001)

After the previous code completes, the next figure shows how the fitness
value change by generation.

.. image:: https://user-images.githubusercontent.com/16560492/93722639-b811da80-fb98-11ea-8951-f13a7a266c04.png
   :alt: 

Here is some information about the trained model. Its fitness value is
``739.24``, loss is ``0.0013527311`` and accuracy is 100%.

.. code:: python

   Fitness value of the best solution = 739.2397344644013
   Index of the best solution : 7

   Predictions : 
   [[9.9694413e-01 3.0558957e-03]
    [5.0176249e-04 9.9949825e-01]
    [1.8470541e-03 9.9815291e-01]
    [9.9999976e-01 2.0538971e-07]]

   Binary Crossentropy :  0.0013527311

   Accuracy :  1.0

Example 3: Image Multi-Class Classification (Dense Layers)
----------------------------------------------------------

Here is the code.

.. code:: python

   import tensorflow.keras
   import pygad.kerasga
   import numpy
   import pygad

   def fitness_func(ga_instance, solution, sol_idx):
       global data_inputs, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=data_inputs)

       cce = tensorflow.keras.losses.CategoricalCrossentropy()
       solution_fitness = 1.0 / (cce(data_outputs, predictions).numpy() + 0.00000001)

       return solution_fitness

   def on_generation(ga_instance):
       print("Generation = {generation}".format(generation=ga_instance.generations_completed))
       print("Fitness    = {fitness}".format(fitness=ga_instance.best_solution()[1]))

   # Build the keras model using the functional API.
   input_layer  = tensorflow.keras.layers.Input(360)
   dense_layer = tensorflow.keras.layers.Dense(50, activation="relu")(input_layer)
   output_layer = tensorflow.keras.layers.Dense(4, activation="softmax")(dense_layer)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

   # Create an instance of the pygad.kerasga.KerasGA class to build the initial population.
   keras_ga = pygad.kerasga.KerasGA(model=model,
                                      num_solutions=10)

   # Data inputs
   data_inputs = numpy.load("../data/dataset_features.npy")

   # Data outputs
   data_outputs = numpy.load("../data/outputs.npy")
   data_outputs = tensorflow.keras.utils.to_categorical(data_outputs)

   # Prepare the PyGAD parameters. Check the documentation for more information: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   num_generations = 100 # Number of generations.
   num_parents_mating = 5 # Number of solutions to be selected as parents in the mating pool.
   initial_population = keras_ga.population_weights # Initial population of network weights.

   # Create an instance of the pygad.GA class
   ga_instance = pygad.GA(num_generations=num_generations, 
                          num_parents_mating=num_parents_mating, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

   # Start the genetic algorithm evolution.
   ga_instance.run()

   # After the generations complete, some plots are showed that summarize how the outputs/fitness values evolve over generations.
   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution()
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

   # Make predictions based on the best solution.
   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=data_inputs)
   # print("Predictions : \n", predictions)

   # Calculate the categorical crossentropy for the trained model.
   cce = tensorflow.keras.losses.CategoricalCrossentropy()
   print("Categorical Crossentropy : ", cce(data_outputs, predictions).numpy())

   # Calculate the classification accuracy for the trained model.
   ca = tensorflow.keras.metrics.CategoricalAccuracy()
   ca.update_state(data_outputs, predictions)
   accuracy = ca.result().numpy()
   print("Accuracy : ", accuracy)

Compared to the previous binary classification example, this example has
multiple classes (4) and thus the loss is measured using categorical
cross entropy.

.. code:: python

   cce = tensorflow.keras.losses.CategoricalCrossentropy()
   solution_fitness = 1.0 / (cce(data_outputs, predictions).numpy() + 0.00000001)

.. _prepare-the-training-data-2:

Prepare the Training Data
~~~~~~~~~~~~~~~~~~~~~~~~~

Before building and training neural networks, the training data (input
and output) needs to be prepared. The inputs and the outputs of the
training data are NumPy arrays.

The data used in this example is available as 2 files:

1. `dataset_features.npy <https://github.com/ahmedfgad/NumPyANN/blob/master/dataset_features.npy>`__:
   Data inputs.
   https://github.com/ahmedfgad/NumPyANN/blob/master/dataset_features.npy

2. `outputs.npy <https://github.com/ahmedfgad/NumPyANN/blob/master/outputs.npy>`__:
   Class labels.
   https://github.com/ahmedfgad/NumPyANN/blob/master/outputs.npy

The data consists of 4 classes of images. The image shape is
``(100, 100, 3)``. The number of training samples is 1962. The feature
vector extracted from each image has a length 360.

Simply download these 2 files and read them according to the next code.
Note that the class labels are one-hot encoded using the
``tensorflow.keras.utils.to_categorical()`` function.

.. code:: python

   import numpy

   data_inputs = numpy.load("../data/dataset_features.npy")

   data_outputs = numpy.load("../data/outputs.npy")
   data_outputs = tensorflow.keras.utils.to_categorical(data_outputs)

The next figure shows how the fitness value changes.

.. image:: https://user-images.githubusercontent.com/16560492/93722649-c2cc6f80-fb98-11ea-96e7-3f6ce3cfe1cf.png
   :alt: 

Here are some statistics about the trained model.

.. code:: 

   Fitness value of the best solution = 4.197464252185969
   Index of the best solution : 0
   Categorical Crossentropy :  0.23823906
   Accuracy :  0.9852192

Example 4: Image Multi-Class Classification (Conv Layers)
---------------------------------------------------------

Compared to the previous example that uses only dense layers, this
example uses convolutional layers to classify the same dataset.

Here is the complete code.

.. code:: python

   import tensorflow.keras
   import pygad.kerasga
   import numpy
   import pygad

   def fitness_func(ga_instance, solution, sol_idx):
       global data_inputs, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=data_inputs)

       cce = tensorflow.keras.losses.CategoricalCrossentropy()
       solution_fitness = 1.0 / (cce(data_outputs, predictions).numpy() + 0.00000001)

       return solution_fitness

   def on_generation(ga_instance):
       print("Generation = {generation}".format(generation=ga_instance.generations_completed))
       print("Fitness    = {fitness}".format(fitness=ga_instance.best_solution()[1]))

   # Build the keras model using the functional API.
   input_layer = tensorflow.keras.layers.Input(shape=(100, 100, 3))
   conv_layer1 = tensorflow.keras.layers.Conv2D(filters=5,
                                                kernel_size=7,
                                                activation="relu")(input_layer)
   max_pool1 = tensorflow.keras.layers.MaxPooling2D(pool_size=(5,5),
                                                    strides=5)(conv_layer1)
   conv_layer2 = tensorflow.keras.layers.Conv2D(filters=3,
                                                kernel_size=3,
                                                activation="relu")(max_pool1)
   flatten_layer  = tensorflow.keras.layers.Flatten()(conv_layer2)
   dense_layer = tensorflow.keras.layers.Dense(15, activation="relu")(flatten_layer)
   output_layer = tensorflow.keras.layers.Dense(4, activation="softmax")(dense_layer)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

   # Create an instance of the pygad.kerasga.KerasGA class to build the initial population.
   keras_ga = pygad.kerasga.KerasGA(model=model,
                                    num_solutions=10)

   # Data inputs
   data_inputs = numpy.load("../data/dataset_inputs.npy")

   # Data outputs
   data_outputs = numpy.load("../data/dataset_outputs.npy")
   data_outputs = tensorflow.keras.utils.to_categorical(data_outputs)

   # Prepare the PyGAD parameters. Check the documentation for more information: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   num_generations = 200 # Number of generations.
   num_parents_mating = 5 # Number of solutions to be selected as parents in the mating pool.
   initial_population = keras_ga.population_weights # Initial population of network weights.

   # Create an instance of the pygad.GA class
   ga_instance = pygad.GA(num_generations=num_generations, 
                          num_parents_mating=num_parents_mating, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

   # Start the genetic algorithm evolution.
   ga_instance.run()

   # After the generations complete, some plots are showed that summarize how the outputs/fitness values evolve over generations.
   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution()
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

   # Make predictions based on the best solution.
   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=data_inputs)
   # print("Predictions : \n", predictions)

   # Calculate the categorical crossentropy for the trained model.
   cce = tensorflow.keras.losses.CategoricalCrossentropy()
   print("Categorical Crossentropy : ", cce(data_outputs, predictions).numpy())

   # Calculate the classification accuracy for the trained model.
   ca = tensorflow.keras.metrics.CategoricalAccuracy()
   ca.update_state(data_outputs, predictions)
   accuracy = ca.result().numpy()
   print("Accuracy : ", accuracy)

Compared to the previous example, the only change is that the
architecture uses convolutional and max-pooling layers. The shape of
each input sample is 100x100x3.

.. code:: python

   # Build the keras model using the functional API.
   input_layer = tensorflow.keras.layers.Input(shape=(100, 100, 3))
   conv_layer1 = tensorflow.keras.layers.Conv2D(filters=5,
                                                kernel_size=7,
                                                activation="relu")(input_layer)
   max_pool1 = tensorflow.keras.layers.MaxPooling2D(pool_size=(5,5),
                                                    strides=5)(conv_layer1)
   conv_layer2 = tensorflow.keras.layers.Conv2D(filters=3,
                                                kernel_size=3,
                                                activation="relu")(max_pool1)
   flatten_layer  = tensorflow.keras.layers.Flatten()(conv_layer2)
   dense_layer = tensorflow.keras.layers.Dense(15, activation="relu")(flatten_layer)
   output_layer = tensorflow.keras.layers.Dense(4, activation="softmax")(dense_layer)

   model = tensorflow.keras.Model(inputs=input_layer, outputs=output_layer)

.. _prepare-the-training-data-3:

Prepare the Training Data
~~~~~~~~~~~~~~~~~~~~~~~~~

The data used in this example is available as 2 files:

1. `dataset_inputs.npy <https://github.com/ahmedfgad/NumPyCNN/blob/master/dataset_inputs.npy>`__:
   Data inputs.
   https://github.com/ahmedfgad/NumPyCNN/blob/master/dataset_inputs.npy

2. `dataset_outputs.npy <https://github.com/ahmedfgad/NumPyCNN/blob/master/dataset_outputs.npy>`__:
   Class labels.
   https://github.com/ahmedfgad/NumPyCNN/blob/master/dataset_outputs.npy

The data consists of 4 classes of images. The image shape is
``(100, 100, 3)`` and there are 20 images per class for a total of 80
training samples. For more information about the dataset, check the
`Reading the
Data <https://pygad.readthedocs.io/en/latest/cnn.html#reading-the-data>`__
section of the ``pygad.cnn`` module.

Simply download these 2 files and read them according to the next code.
Note that the class labels are one-hot encoded using the
``tensorflow.keras.utils.to_categorical()`` function.

.. code:: python

   import numpy

   data_inputs = numpy.load("../data/dataset_inputs.npy")

   data_outputs = numpy.load("../data/dataset_outputs.npy")
   data_outputs = tensorflow.keras.utils.to_categorical(data_outputs)

The next figure shows how the fitness value changes.

.. image:: https://user-images.githubusercontent.com/16560492/93722654-cc55d780-fb98-11ea-8f95-7b65dc67f5c8.png
   :alt: 

Here are some statistics about the trained model. The model accuracy is
75% after the 200 generations. Note that just running the code again may
give different results.

.. code:: 

   Fitness value of the best solution = 2.7462310258668805
   Index of the best solution : 0
   Categorical Crossentropy :  0.3641354
   Accuracy :  0.75

To improve the model performance, you can do the following:

-  Add more layers

-  Modify the existing layers.

-  Use different parameters for the layers.

-  Use different parameters for the genetic algorithm (e.g. number of
   solution, number of generations, etc)

Example 5: Image Classification using Data Generator
----------------------------------------------------

This example uses the image data generator
``tensorflow.keras.preprocessing.image.ImageDataGenerator`` to feed data
to the model. Instead of reading all the data in the memory, the data
generator generates the data needed by the model and only save it in the
memory instead of saving all the data. This frees the memory but adds
more computational time.

.. code:: python

   import tensorflow as tf
   import tensorflow.keras
   import pygad.kerasga
   import pygad

   def fitness_func(ga_instanse, solution, sol_idx):
       global train_generator, data_outputs, keras_ga, model

       predictions = pygad.kerasga.predict(model=model,
                                           solution=solution,
                                           data=train_generator)

       cce = tensorflow.keras.losses.CategoricalCrossentropy()
       solution_fitness = 1.0 / (cce(data_outputs, predictions).numpy() + 0.00000001)

       return solution_fitness

   def on_generation(ga_instance):
       print("Generation = {generation}".format(generation=ga_instance.generations_completed))
       print("Fitness    = {fitness}".format(fitness=ga_instance.best_solution(ga_instance.last_generation_fitness)[1]))

   # The dataset path.
   dataset_path = r'../data/Skin_Cancer_Dataset' 

   num_classes = 2
   img_size = 224

   # Create a simple CNN. This does not gurantee high classification accuracy.
   model = tf.keras.models.Sequential()
   model.add(tf.keras.layers.Input(shape=(img_size, img_size, 3)))
   model.add(tf.keras.layers.Conv2D(32, (3,3), activation="relu", padding="same"))
   model.add(tf.keras.layers.MaxPooling2D((2, 2)))
   model.add(tf.keras.layers.Flatten())
   model.add(tf.keras.layers.Dropout(rate=0.2))
   model.add(tf.keras.layers.Dense(num_classes, activation="softmax"))

   # Create an instance of the pygad.kerasga.KerasGA class to build the initial population.
   keras_ga = pygad.kerasga.KerasGA(model=model,
                                    num_solutions=10)

   data_generator = tf.keras.preprocessing.image.ImageDataGenerator()
   train_generator = data_generator.flow_from_directory(dataset_path, 
                                                        class_mode='categorical',
                                                        target_size=(224, 224),
                                                        batch_size=32,
                                                        shuffle=False)
   # train_generator.class_indices
   data_outputs = tf.keras.utils.to_categorical(train_generator.labels)

   # Check the documentation for more information about the parameters: https://pygad.readthedocs.io/en/latest/pygad.html#pygad-ga-class
   initial_population = keras_ga.population_weights # Initial population of network weights.

   # Create an instance of the pygad.GA class
   ga_instance = pygad.GA(num_generations=10, 
                          num_parents_mating=5, 
                          initial_population=initial_population,
                          fitness_func=fitness_func,
                          on_generation=on_generation)

   # Start the genetic algorithm evolution.
   ga_instance.run()

   # After the generations complete, some plots are showed that summarize how the outputs/fitness values evolve over generations.
   ga_instance.plot_fitness(title="PyGAD & Keras - Iteration vs. Fitness", linewidth=4)

   # Returning the details of the best solution.
   solution, solution_fitness, solution_idx = ga_instance.best_solution(ga_instance.last_generation_fitness)
   print("Fitness value of the best solution = {solution_fitness}".format(solution_fitness=solution_fitness))
   print("Index of the best solution : {solution_idx}".format(solution_idx=solution_idx))

   predictions = pygad.kerasga.predict(model=model,
                                       solution=solution,
                                       data=train_generator)
   # print("Predictions : \n", predictions)

   # Calculate the categorical crossentropy for the trained model.
   cce = tensorflow.keras.losses.CategoricalCrossentropy()
   print("Categorical Crossentropy : ", cce(data_outputs, predictions).numpy())

   # Calculate the classification accuracy for the trained model.
   ca = tensorflow.keras.metrics.CategoricalAccuracy()
   ca.update_state(data_outputs, predictions)
   accuracy = ca.result().numpy()
   print("Accuracy : ", accuracy)
