EMG_Biometrics_2021/Neural_Network_Analysis.py

import json
from python_speech_features.python_speech_features.base import mfcc
import numpy as np
from sklearn.model_selection import train_test_split
import tensorflow as tf
import tensorflow.keras as keras
from pathlib import Path
import pandas as pd
import matplotlib.pyplot as plt

# path to json file that stores MFCCs and subject labels for each processed sample
DATA_PATH = str(Path.cwd()) + "/mfcc_data.json"

def load_data_from_json(data_path): 

    with open(data_path, "r") as fp:
        data = json.load(fp)

    # convert lists to numpy arraysls
    X = np.array(data['mfcc'])
    X = X.reshape(X.shape[0], 1, X.shape[1])
    #print(X.shape)
    
    y = np.array(data["labels"])
    y = y.reshape(y.shape[0], 1)
    #print(y.shape)
    

    print("Data succesfully loaded!")

    return X, y


def plot_history(history):
    """Plots accuracy/loss for training/validation set as a function of the epochs
        :param history: Training history of model
        :return:
    """

    fig, axs = plt.subplots(2)

    # create accuracy sublpot
    axs[0].plot(history.history["accuracy"], label="train accuracy")
    axs[0].plot(history.history["val_accuracy"], label="test accuracy")
    axs[0].set_ylabel("Accuracy")
    axs[0].legend(loc="lower right")
    axs[0].set_title("Accuracy eval")

    # create error sublpot
    axs[1].plot(history.history["loss"], label="train error")
    axs[1].plot(history.history["val_loss"], label="test error")
    axs[1].set_ylabel("Error")
    axs[1].set_xlabel("Epoch")
    axs[1].legend(loc="upper right")
    axs[1].set_title("Error eval")

    plt.show()


def prepare_datasets(test_size=0.25, validation_size=0.2):
    """Loads data and splits it into train, validation and test sets.
    :param test_size (float): Value in [0, 1] indicating percentage of data set to allocate to test split
    :param validation_size (float): Value in [0, 1] indicating percentage of train set to allocate to validation split
    :return X_train (ndarray): Input training set
    :return X_validation (ndarray): Input validation set
    :return X_test (ndarray): Input test set
    :return y_train (ndarray): Target training set
    :return y_validation (ndarray): Target validation set
    :return y_test (ndarray): Target test set
    """

    # load data
    X, y = load_data(DATA_PATH)

    # create train, validation and test split
    X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=test_size)
    X_train, X_validation, y_train, y_validation = train_test_split(X_train, y_train, test_size=validation_size)

    return X_train, X_validation, X_test, y_train, y_validation, y_test


def build_model(input_shape, nr_classes=5):
    """Generates RNN-LSTM model
    :param input_shape (tuple): Shape of input set
    :return model: RNN-LSTM model
    """

    # build network topology
    model = keras.Sequential()

    # 2 LSTM layers
    model.add(keras.layers.LSTM(64, input_shape=input_shape, return_sequences=True))
    model.add(keras.layers.LSTM(64))

    # dense layer
    model.add(keras.layers.Dense(64, activation='relu'))
    model.add(keras.layers.Dropout(0.3))

    # output layer
    model.add(keras.layers.Dense(nr_classes, activation='softmax'))

    return model


if __name__ == "__main__":

    # get train, validation, test splits
    X_train, X_validation, X_test, y_train, y_validation, y_test = prepare_datasets(0.25, 0.2)

    print(X_train.shape[1], X_train.shape[2])
    # create network
    
    input_shape = (X_train.shape[1], X_train.shape[2])  # (~2800), 1, 208
    model = build_model(input_shape)

    # compile model
    optimiser = keras.optimizers.Adam(learning_rate=0.0001)
    model.compile(optimizer=optimiser,
                  loss='sparse_categorical_crossentropy',
                  metrics=['accuracy'])

    model.summary()

    # train model
    history = model.fit(X_train, y_train, validation_data=(X_validation, y_validation), batch_size=64, epochs=30)

    # plot accuracy/error for training and validation
    plot_history(history)

    # evaluate model on test set
    test_loss, test_acc = model.evaluate(X_test, y_test, verbose=2)
    print('\nTest accuracy:', test_acc)