ASSR.py

# coding: utf-8

# # ASSR: Automatic Stuttered Speech Recoginition

# In[ ]:


from __future__ import print_function, division, absolute_import
import numpy as np

import matplotlib.pyplot as plt
import matplotlib.style as ms
ms.use('seaborn-muted')
#%matplotlib inline

import librosa
import librosa.display
import IPython.display

import os
import sys
import re
import shutil
import datetime
import logging
import colorlog
import progressbar

import tensorflow as tf
from sklearn.model_selection import train_test_split

# Setting up progressbar and logger
progressbar.streams.wrap_stderr()
logger = colorlog.getLogger("ASSR")
handler = logging.StreamHandler()
handler.setFormatter(colorlog.ColoredFormatter('%(log_color)s%(levelname)-8s| %(message)s'))
logger.addHandler(handler)
logger.setLevel(logging.INFO)


# ## Data Preparation

# In[ ]:


class FeatureExtraction:
    def __init__(self, n_mels=128):
        self.n_mels = n_mels
        self.y = None
        self.sr = None
        self.S = None
        self.log_S = None
        self.mfcc = None
        self.delta_mfcc = None
        self.delta2_mfcc = None
        self.M = None
        self.rmse = None
    
    def loadFile(self, filename):
        self.y, self.sr = librosa.load(filename)
        logger.debug('File loaded: %s', filename)
    
    def load_y_sr(self, y, sr):
        self.y = y
        self.sr = sr
    
    def melspectrogram(self):
        self.S = librosa.feature.melspectrogram(self.y, sr=self.sr, n_mels=self.n_mels)
        self.log_S = librosa.amplitude_to_db(self.S, ref=np.max)
    
    def plotmelspectrogram(self):
        plt.figure(figsize=(12, 4))
        librosa.display.specshow(self.log_S, sr=self.sr, x_axis='time', y_axis='mel')
        plt.title('mel Power Spectrogram')
        plt.colorbar(format='%+02.0f dB')
        plt.tight_layout()
    
    def extractmfcc(self, n_mfcc=13):
        self.mfcc = librosa.feature.mfcc(S=self.log_S, n_mfcc=n_mfcc)
        self.delta_mfcc = librosa.feature.delta(self.mfcc, width=3)
        self.delta2_mfcc = librosa.feature.delta(self.mfcc, order=2, width=3)
        self.M = np.vstack([self.mfcc, self.delta_mfcc, self.delta2_mfcc])
    
    def plotmfcc(self):
        plt.figure(figsize=(12, 6))
        plt.subplot(3, 1, 1)
        librosa.display.specshow(self.mfcc)
        plt.ylabel('MFCC')
        plt.colorbar()
        
        plt.subplot(3, 1, 2)
        librosa.display.specshow(self.delta_mfcc)
        plt.ylabel('MFCC-$\Delta$')
        plt.colorbar()
        
        plt.subplot(3, 1, 3)
        librosa.display.specshow(self.delta2_mfcc, sr=self.sr, x_axis='time')
        plt.ylabel('MFCC-$\Delta^2$')
        plt.colorbar()
        
        plt.tight_layout()
    
    def extractrmse(self):
        self.rmse = librosa.feature.rmse(y=self.y)


# In[ ]:


class Dataset:
    def __init__(self, datasetDir, datasetLabelFilename, datasetArrayFilename):
        self.n_features = 80
        logger.info("Number of features: %s", self.n_features)
        self.X = np.empty(shape=(0, self.n_features))
        self.Y = np.empty(shape=(0, 2))
        
        self.datasetArrayFilename = datasetArrayFilename
        logger.debug("Dataset array filename: %s", self.datasetArrayFilename)
        
        if os.path.isfile(self.datasetArrayFilename):    
            self.__readFromFile()
        else:
            self.datasetDir = datasetDir
            logger.debug("Dataset Directory: %s", self.datasetDir)

            self.datasetLabelFilename = datasetLabelFilename
            logger.debug("Dataset labels filename: %s", self.datasetLabelFilename)

            if not os.path.isdir(self.datasetDir) or not os.path.isfile(self.datasetLabelFilename):
                logger.info("%s or %s does not exists", self.datasetDir, self.datasetLabelFilename)
                self.__buildDatasetAndLabels('wav/release1')
                
            self.__build()
            self.__writeToFile()
    
    def __build(self):
        logger.info("Building dataset from directory: %s", self.datasetDir)
        num_lines = sum(1 for line in open(self.datasetLabelFilename, 'r'))
        with open(self.datasetLabelFilename, 'r') as datasetLabelFile:
            filesProcessed=0
            pbar = progressbar.ProgressBar(redirect_stdout=True)
            for line in pbar(datasetLabelFile, max_value=num_lines):
                lineSplit = line.strip().split(' ')
                audiofilename = lineSplit[0]
                label = lineSplit[1]
                try:
                    features = FeatureExtraction()
                    features.loadFile(os.path.join(self.datasetDir, audiofilename))
                    features.melspectrogram()
                    features.extractmfcc()
                    features.extractrmse()
                except ValueError:
                    logger.warning("Error in extracting features from file %s", audiofilename)
                    continue
                
                featureVector = []
                for feature in features.mfcc:
                    featureVector.append(np.mean(feature))
                    featureVector.append(np.var(feature))
                
                for feature in features.delta_mfcc:
                    featureVector.append(np.mean(feature))
                    featureVector.append(np.var(feature))
                
                for feature in features.delta2_mfcc:
                    featureVector.append(np.mean(feature))
                    featureVector.append(np.var(feature))
                
                featureVector.append(np.mean(features.rmse))
                featureVector.append(np.var(features.rmse))
                
                self.X = np.vstack((self.X, [featureVector]))
                
                if label == "STUTTER":
                    self.Y = np.vstack((self.Y, [0, 1]))
                elif label == "NORMAL":
                    self.Y = np.vstack((self.Y, [1, 0]))
                else:
                    logger.error("Unexpected label: %s", label)
                    sys.exit()
                
                filesProcessed += 1            
            
            logger.info("Total files processed: %d", filesProcessed)
    
    def __buildDatasetAndLabels(self, audioAndChaFilesDirectory):
        logger.info("Rebuilding the dataset directory and labels")
        if os.path.isdir(self.datasetDir):
            shutil.rmtree(self.datasetDir)
        os.makedirs(self.datasetDir)
        
        labelFile = open(self.datasetLabelFilename, 'w')
        
        splitDuration = 300 # milliseconds
        pbar = progressbar.ProgressBar(redirect_stdout=True)
        for chaFileName in pbar(os.listdir(audioAndChaFilesDirectory)):
            if chaFileName.endswith(".cha"):
                subject = chaFileName.split('.')[0]
                wavFileName = subject + ".wav"
                y, sr = librosa.load(os.path.join(audioAndChaFilesDirectory, wavFileName))

                logger.debug("Parsing file: %s", chaFileName)

                with open(os.path.join(audioAndChaFilesDirectory, chaFileName), 'r') as chaFile:
                    sndFound = False
                    phoFound = False
                    startTime = -1
                    endTime = -1
                    label = None
                    for line in chaFile:
                        if not sndFound:
                            if re.search(r"%snd:", line):
                                lineSplit = line.split("_")
                                startTime = int(lineSplit[-2])
                                endTime = lineSplit[-1]
                                endTime = int(re.sub(r"\u0015\n", '', endTime))
                                sndFound = True
                        else:
                            if re.search(r"%pho:", line):
                                if re.search(r'[A-Z]', line):
                                    label = "STUTTER"
                                else:
                                    label = "NORMAL"
                                phoFound = True
                        if sndFound and phoFound:
                            n_splits = int(np.round((endTime - startTime) / splitDuration))
                            
                            startingSample = int(startTime * sr / 1000)
                            for i in range(1, n_splits):
                                endingSample = int(startingSample + (splitDuration * sr / 1000))
                                audiofilename = subject + ":" + str(startTime) + ":" + str(int(startTime) + splitDuration) + ".wav"
                                labelFile.write(audiofilename + " " + label + "\n")
                                audio = y[startingSample:endingSample]
                                librosa.output.write_wav(os.path.join(self.datasetDir, audiofilename), audio, sr)
                                
                                startingSample = endingSample
                                startTime = int(startTime) + splitDuration
                            
                            endingSample = int(endTime * sr / 1000)
                            audiofilename = subject + ":" + str(startTime) + ":" + str(endTime) + ".wav"
                            labelFile.write(audiofilename + " " + label + "\n")
                            audio = y[startingSample:endingSample]
                            librosa.output.write_wav(os.path.join(self.datasetDir, audiofilename), audio, sr)
                            
                            
                            sndFound = False
                            phoFound = False
                            startTime = -1
                            endTime = -1
                            label = None

        labelFile.close()
    
    def __writeToFile(self, filename=None):
        if filename == None:
            filename = self.datasetArrayFilename
            
        if os.path.exists(filename):
            os.remove(filename)
        np.savetxt(filename, np.hstack((self.X, self.Y)))
        logger.info("Array stored in file %s", filename)
    
    def __readFromFile(self, filename=None):
        if filename == None:
            filename = self.datasetArrayFilename
            
        if not os.path.isfile(filename):
            logger.error("%s does not exists or is not a file", filename)
            sys.exit()
        matrix = np.loadtxt(filename)
        self.X = matrix[:, 0:self.n_features]
        self.Y = matrix[:, self.n_features:]
        logger.info("Array read from file %s", filename)


# ## Tensorflow binary classification

# In[ ]:


class NeuralNetwork:
    def __init__(self, X_train=None, Y_train=None, X_test=None, Y_test=None):
        # Data
        self.X_train = X_train
        self.Y_train = Y_train
        self.X_test = X_test
        self.Y_test = Y_test
        
        # Learning Parameters
        self.learning_rate = 0.001
        self.training_epochs = 1200
        self.batch_size = 100
        self.display_step = 100

        # Model Parameters
        self.n_hidden = [10, 10, 10]
        self.hiddenLayers = len(self.n_hidden)
        self.n_input = 80
        self.n_classes = 2

        logger.debug("Neural network of depth %d", self.hiddenLayers)
        for i in range(self.hiddenLayers):
            logger.debug("Depth of layer %d is %d", (i + 1), self.n_hidden[i])

        self.x = tf.placeholder("float", [None, self.n_input])
        self.y = tf.placeholder("float", [None, self.n_classes])
        self.layer = None
        self.weights = None
        self.biases = None
        # Model
        self.model = self.__network(self.x)
        self.save_path = None

        # Loss function and optimizer
        self.cost = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits_v2(logits=self.model, labels=self.y))
        self.optimizer = tf.train.AdamOptimizer(learning_rate=self.learning_rate).minimize(self.cost)

        # Initialize the variables
        self.init = tf.global_variables_initializer()
    
    def setTrainData(self, X, Y):
        self.X_train = X
        self.Y_train = Y
        
    def setTestData(self, X, Y):
        self.X_test = X
        self.Y_test = Y
        
    def __network(self, x):
        self.layer = []
        self.weights = []
        self.biases = []

        for n_layer in range(self.hiddenLayers):
            if n_layer == 0:
                self.weights.append(tf.Variable(tf.random_normal([self.n_input, self.n_hidden[n_layer]])))
                self.biases.append(tf.Variable(tf.random_normal([self.n_hidden[n_layer]])))
                self.layer.append(tf.nn.relu(tf.add(tf.matmul(x, self.weights[n_layer]), self.biases[n_layer])))
            else:
                self.weights.append(tf.Variable(tf.random_normal([self.n_hidden[n_layer - 1], self.n_hidden[n_layer]])))
                self.biases.append(tf.Variable(tf.random_normal([self.n_hidden[n_layer]])))
                self.layer.append(tf.nn.relu(tf.add(tf.matmul(self.layer[n_layer - 1], self.weights[n_layer]), self.biases[n_layer])))


        # Output layer
        self.weights.append(tf.Variable(tf.random_normal([self.n_hidden[self.hiddenLayers - 1], self.n_classes])))
        self.biases.append(tf.Variable(tf.random_normal([self.n_classes])))
        self.layer.append(tf.matmul(self.layer[self.hiddenLayers - 1], self.weights[self.hiddenLayers]) + self.biases[self.hiddenLayers])

        return self.layer[self.hiddenLayers]
    
    def train(self):
        logger.info("Training the neural network")
        saver = tf.train.Saver()
        with tf.Session() as sess:
            sess.run(self.init)
            pbarWidgets = [
                progressbar.Percentage(),
                ' (',
                progressbar.SimpleProgress(),
                ') ',
                progressbar.Bar(),
                ' ',
                progressbar.Timer(),
                ' ',
                progressbar.ETA(),
                ' ',
                progressbar.DynamicMessage('Cost'),
            ]
            with progressbar.ProgressBar(max_value=self.training_epochs, redirect_stdout=True, widgets=pbarWidgets) as pbar:
                for epoch in range(self.training_epochs):
                    avg_cost = 0
                    total_batch = int(len(self.X_train) / self.batch_size)
                    X_batches = np.array_split(self.X_train, total_batch)
                    Y_batches = np.array_split(self.Y_train, total_batch)

                    for i in range(total_batch):
                        batch_x, batch_y = X_batches[i], Y_batches[i]
                        # Run optimization op (backprop) and cost op (to get loss value)
                        _, c = sess.run([self.optimizer, self.cost], feed_dict={self.x: batch_x, self.y: batch_y})

                        # Compute average loss
                        avg_cost += c / total_batch

                    pbar.update(epoch + 1, Cost=avg_cost)
                
            logger.info("Optimization Finished!")

            evalAccuracy = self.__getAccuracy()
            
            global result 
            result = tf.argmax(self.model, 1).eval({self.x: self.X_test, self.y: self.Y_test})
            
            tfSessionsDir = "tfSessions"
            if not os.path.isdir(tfSessionsDir):
                os.makedirs(tfSessionsDir)
            timestamp = '{:%Y-%m-%d-%H:%M:%S}'.format(datetime.datetime.now()) + '-' + str(evalAccuracy)
            os.makedirs(os.path.join(tfSessionsDir, timestamp))
            modelfilename =  os.path.join(os.path.join(tfSessionsDir, timestamp), 'session.ckpt')
            self.save_path = saver.save(sess, modelfilename)
            
            with open(os.path.join(os.path.join(tfSessionsDir, timestamp), 'details.txt'), 'w') as details:
                details.write("learning_rate = " + str(self.learning_rate) + "\n")
                details.write("training_epochs = " + str(self.training_epochs) + "\n")
                details.write("batch_size = " + str(self.batch_size) + "\n")
                details.write("display_step = " + str(self.display_step) + "\n")
                details.write("n_hidden = " + str(self.n_hidden) + "\n")
                details.write("hiddenLayers = " + str(self.hiddenLayers) + "\n")
                details.write("n_input = " + str(self.n_input) + "\n")
                details.write("n_classes = " + str(self.n_classes) + "\n")
                
            logger.info("Model saved in file: %s" % self.save_path)
    
    def getModelPath(self):
        return self.save_path
        
    def __getAccuracy(self):
        # Test model
        correct_prediction = tf.equal(tf.argmax(self.model, 1), tf.argmax(self.y, 1))
        # Calculate accuracy
        accuracy = tf.reduce_mean(tf.cast(correct_prediction, "float"))
        evalAccuracy = accuracy.eval({self.x: self.X_test, self.y: self.Y_test})
        logger.info("Accuracy: %f", evalAccuracy)
        return evalAccuracy
        
    def loadAndClassify(self, filename, X):            
        saver = tf.train.Saver()
        with tf.Session() as sess:
            saver.restore(sess, filename)
            prediction_model = tf.argmax(self.model, 1)
            return prediction_model.eval({self.x: X})
            


# ## Using the NN model for classification

# In[ ]:


class AudioCorrection():
    def __init__(self, audiofile, tfSessionFile, segmentLength=300, segmentHop=100, n_features=80, correctionsDir='corrections'):
        self.tfSessionFile = tfSessionFile
        self.segmentLength = segmentLength
        self.segmentHop = segmentHop
        self.n_features = n_features
        self.correctionsDir = correctionsDir
        self.samplesPerSegment = None
        self.samplesToSkipPerHop = None
        self.upperLimit = None
        self.inputFilename = None
        self.y = None
        self.sr = None
        self.target_sr = 16000
        NORMAL = 0
        STUTTER = 1
        self.speech = {NORMAL: [], STUTTER: []}
        self.smoothingSamples = 1000
        self.__loadfile(audiofile)
    
    def __loadfile(self, inputFilename):
        if not os.path.isfile(inputFilename):
            logger.error("%s does not exists or is not a file", inputFilename)
            sys.exit()
        self.inputFilename = inputFilename
        logger.info("Loading file %s", self.inputFilename)
        self.y, self.sr = librosa.load(self.inputFilename)
        self.samplesPerSegment = int(self.segmentLength * self.sr / 1000)
        self.samplesToSkipPerHop = int(self.segmentHop * self.sr / 1000)
        self.upperLimit = len(self.y) - self.samplesPerSegment

    def process(self):
        logger.info("Attempting to correct %s", self.inputFilename)
        X = np.empty(shape=(0, self.n_features))
        durations = np.empty(shape=(0, 2))

        pbar = progressbar.ProgressBar()
        start = 0
        end = 0
        for start in pbar(range(0, self.upperLimit, self.samplesToSkipPerHop)):
            end = start + self.samplesPerSegment
            audio = self.y[start:end]

            featureVector = self.__getFeatureVector(audio, self.sr)
            if featureVector != None:
                X = np.vstack((X, [featureVector]))
                durations = np.vstack((durations, [start, end]))
        
        audio = self.y[end:]
        featureVector = self.__getFeatureVector(audio, self.sr)
        if featureVector != None:
            X = np.vstack((X, [featureVector]))
            durations = np.vstack((durations, [end, self.upperLimit + self.samplesPerSegment]))
        logger.debug("Finished extracting features")

        tf.reset_default_graph()
        nn = NeuralNetwork()
        classificationResult = nn.loadAndClassify(self.tfSessionFile, X)
        logger.debug("Finished classification of segments")
        
        currentSegment = {'type': classificationResult[0], 'start': durations[0][0], 'end': durations[0][1]}
        for (label, [start, end]) in zip(classificationResult[1:], durations[1:]):
            if currentSegment['type'] == label:
                currentSegment['end'] = end
            else:
                self.speech[currentSegment['type']].append((currentSegment['start'], currentSegment['end']))
                currentSegment['type'] = label
                currentSegment['start'] = start
                currentSegment['end'] = end
    
    def __getFeatureVector(self, y, sr):
        try:
            features = FeatureExtraction()
            features.load_y_sr(y, sr)
            features.melspectrogram()
            features.extractmfcc()
            features.extractrmse()
        except ValueError:
            logger.warning("Error extracting features")
            return None

        featureVector = []
        for feature in features.mfcc:
            featureVector.append(np.mean(feature))
            featureVector.append(np.var(feature))

        for feature in features.delta_mfcc:
            featureVector.append(np.mean(feature))
            featureVector.append(np.var(feature))

        for feature in features.delta2_mfcc:
            featureVector.append(np.mean(feature))
            featureVector.append(np.var(feature))

        featureVector.append(np.mean(features.rmse))
        featureVector.append(np.var(features.rmse))
        
        return featureVector
    
    def saveCorrectedAudio(self):
        NORMAL = 0
        STUTTER = 1
        if not os.path.isdir(self.correctionsDir):
            os.makedirs(self.correctionsDir)
        outputFilenamePrefix = os.path.join(self.correctionsDir, os.path.splitext(os.path.basename(self.inputFilename))[0])
        
        normalSpeech = np.ndarray(shape=(1, 0))
        (start, end) = self.speech[NORMAL][0]
        normalSpeech = np.append(normalSpeech, self.y[int(start):int(end)])
        for (start, end) in self.speech[NORMAL][1:]:
            # Smoothing
            previousSample = normalSpeech[-1]
            nextSample = self.y[int(start)]
            if nextSample > previousSample:
                low, high = previousSample, nextSample
            else:
                low, high = nextSample, previousSample
            
            step = (high - low) / self.smoothingSamples
            
            normalSpeech = np.append(normalSpeech, np.arange(low, high, step))
            normalSpeech = np.append(normalSpeech, self.y[int(start):int(end)])

        stutteredSpeech = np.ndarray(shape=(1, 0))
        for (start, end) in self.speech[STUTTER]:
            stutteredSpeech = np.append(stutteredSpeech, self.y[int(start):int(end)])

        # Resampling the audio
        logger.debug("Resampling corrected audio from %d to %d", self.sr, self.target_sr)
        resampledNormalSpeech = librosa.resample(normalSpeech, self.sr, self.target_sr)
        resampledStutteredSpeech = librosa.resample(stutteredSpeech, self.sr, self.target_sr)
        librosa.output.write_wav(outputFilenamePrefix + "-corrected.wav", normalSpeech, self.sr)
        librosa.output.write_wav(outputFilenamePrefix + "-stuttered.wav", stutteredSpeech, self.sr)
        logger.info("Corrected audio saved as %s", outputFilenamePrefix + "-corrected.wav") 
	


# In[ ]:


def run(train=False, correct=False):
    if train:
        dataset = Dataset('dataset', 'datasetLabels.txt', 'datasetArray80.gz')
        X_train, X_test, Y_train, Y_test = train_test_split(dataset.X, dataset.Y)

        tf.reset_default_graph()
        nn = NeuralNetwork(X_train, Y_train, X_test, Y_test)
        nn.train()

    if correct:
        audiofile = 'M_0219_11y2m_1.wav'
        if train:
            tfSessionFile = nn.getModelPath()
        else:
            tfSessionFile = 'tfSessions/2017-11-26-20:08:45-0.870725/session.ckpt'

        correction = AudioCorrection(audiofile, tfSessionFile)
        correction.process()
        correction.saveCorrectedAudio()


# In[ ]:


if __name__ == "__main__":
    run(True, True)