make_predictions.py

# This is the primary python script used by the inference engine
# This contains all code necessary for the web app

# Common, File Based, and Math Imports
import pandas as pd
import numpy as np
import collections
import os
from os.path import isdir, join
from pathlib import Path
import subprocess
from subprocess import check_output
import sys
import math
import pickle
from glob import glob
import random
from random import sample
import json
from mpl_toolkits.axes_grid1 import make_axes_locatable
from numpy.lib.stride_tricks import as_strided
from tqdm import tqdm
import timeit
import time
import base64
import datetime
import uuid
import wave
import requests
import audioop
from io import BytesIO

# Audio processing imports
from scipy import signal
from scipy.fftpack import dct
import soundfile
from python_speech_features import mfcc
import scipy.io.wavfile as wav
from scipy.fftpack import fft

# Neural Network imports
import keras
from keras import backend as K
from keras.backend.tensorflow_backend import set_session
from keras import regularizers, callbacks, constraints, initializers
from keras.utils.generic_utils import get_custom_objects
from keras.constraints import max_norm
from keras.models import Model, Sequential, load_model
from keras.layers import Input, Lambda, Dense, Dropout, Flatten, Embedding, merge, Activation, GRUCell, LSTMCell,SimpleRNNCell
from keras.layers import Convolution2D, MaxPooling2D, Convolution1D, Conv1D, SimpleRNN, GRU, LSTM, CuDNNLSTM, CuDNNGRU, Conv2D
from keras.layers import LeakyReLU, PReLU, ThresholdedReLU, ELU, BatchNormalization, TimeDistributed, Bidirectional, activations, Wrapper
from keras.regularizers import l2
from keras.layers.advanced_activations import LeakyReLU, PReLU, ThresholdedReLU, ELU
from keras.optimizers import Adam
from keras.callbacks import ModelCheckpoint 
from keras.utils import np_utils
from keras.engine.topology import Layer
import keras.losses
from keras.engine import InputSpec

# Model metric imports
from sklearn.feature_extraction.text import CountVectorizer, TfidfVectorizer
from sklearn.metrics.pairwise import cosine_similarity

# Visualization imports
import matplotlib.pyplot as plt
import seaborn as sns

# Visualization settings
color = sns.color_palette()
sns.set_style('darkgrid')

# Setting Random Seeds
np.random.seed(95)
RNG_SEED = 95

# Function for shuffling data
def shuffle_dataset(audio_paths, durations, texts):
    p = np.random.permutation(len(audio_paths))
    audio_paths = [audio_paths[i] for i in p] 
    durations = [durations[i] for i in p] 
    texts = [texts[i] for i in p]
    return audio_paths, durations, texts

# Function for sorting data by duration
def sort_dataset(audio_paths, durations, texts):
    p = np.argsort(durations).tolist()
    audio_paths = [audio_paths[i] for i in p]
    durations = [durations[i] for i in p] 
    texts = [texts[i] for i in p]
    return audio_paths, durations, texts

# Mapping each character that could be spoken at each time step
char_map_str = """
' 0
<SPACE> 1
a 2
b 3
c 4
d 5
e 6
f 7
g 8
h 9
i 10
j 11
k 12
l 13
m 14
n 15
o 16
p 17
q 18
r 19
s 20
t 21
u 22
v 23
w 24
x 25
y 26
z 27
"""
# This leaves "blank" character mapped to number 28

char_map = {}
index_map = {}
for line in char_map_str.strip().split('\n'):
    ch, index = line.split()
    char_map[ch] = int(index)
    index_map[int(index)+1] = ch
index_map[2] = ' '

# Function for converting text to an integer sequence
def text_to_int_seq(text):
    int_sequence = []
    for c in text:
        if c == ' ':
            ch = char_map['<SPACE>']
        else:
            ch = char_map[c]
        int_sequence.append(ch)
    return int_sequence

# Function for converting an integer sequence to text
def int_seq_to_text(int_sequence):
    text = []
    for c in int_sequence:
        ch = index_map[c]
        text.append(ch)
    return text
# Function for calculating feature dimensions.
def calc_feat_dim(window, max_freq):
    return int(0.001 * window * max_freq) + 1

class AudioGenerator():
    def __init__(self, step=10, window=20, max_freq=8000, mfcc_dim=13,
        minibatch_size=20, desc_file=None, spectrogram=True, max_duration=10.0, 
        sort_by_duration=False):
        # Initializing variables
        self.feat_dim = calc_feat_dim(window, max_freq)
        self.mfcc_dim = mfcc_dim
        self.feats_mean = np.zeros((self.feat_dim,))
        self.feats_std = np.ones((self.feat_dim,))
        self.rng = random.Random(RNG_SEED)
        if desc_file is not None:
            self.load_metadata_from_desc_file(desc_file)
        self.step = step
        self.window = window
        self.max_freq = max_freq
        self.cur_train_index = 0
        self.cur_valid_index = 0
        self.cur_test_index = 0
        self.max_duration=max_duration
        self.minibatch_size = minibatch_size
        self.spectrogram = spectrogram
        self.sort_by_duration = sort_by_duration

    def get_batch(self, partition):
    # Obtain a batch of audio files
        if partition == 'train':
            audio_paths = self.train_audio_paths
            cur_index = self.cur_train_index
            texts = self.train_texts
        elif partition == 'valid':
            audio_paths = self.valid_audio_paths
            cur_index = self.cur_valid_index
            texts = self.valid_texts
        elif partition == 'test':
            audio_paths = self.test_audio_paths
            cur_index = self.test_valid_index
            texts = self.test_texts
        else:
            raise Exception("Invalid partition. "
                "Must be train/val")

        features = [self.normalize(self.featurize(a)) for a in 
            audio_paths[cur_index:cur_index+self.minibatch_size]]

        # Calculate size
        max_length = max([features[i].shape[0] 
            for i in range(0, self.minibatch_size)])
        max_string_length = max([len(texts[cur_index+i]) 
            for i in range(0, self.minibatch_size)])
        
        # Initialize arrays
        X_data = np.zeros([self.minibatch_size, max_length, 
            self.feat_dim*self.spectrogram + self.mfcc_dim*(not self.spectrogram)])
        labels = np.ones([self.minibatch_size, max_string_length]) * 28
        input_length = np.zeros([self.minibatch_size, 1])
        label_length = np.zeros([self.minibatch_size, 1])
        
        for i in range(0, self.minibatch_size):
            # Calculate input_length
            feat = features[i]
            input_length[i] = feat.shape[0]
            X_data[i, :feat.shape[0], :] = feat

            # Calculate label_length
            label = np.array(text_to_int_seq(texts[cur_index+i])) 
            labels[i, :len(label)] = label
            label_length[i] = len(label)

        # Output arrays
        outputs = {'ctc': np.zeros([self.minibatch_size])}
        inputs = {'the_input': X_data, 
                  'the_labels': labels, 
                  'input_length': input_length, 
                  'label_length': label_length 
                 }
        return (inputs, outputs)

    def shuffle_dataset_by_partition(self, partition):
    # Shuffle the data
        if partition == 'train':
            self.train_audio_paths, self.train_durations, self.train_texts = shuffle_dataset(
                self.train_audio_paths, self.train_durations, self.train_texts)
        elif partition == 'valid':
            self.valid_audio_paths, self.valid_durations, self.valid_texts = shuffle_dataset(
                self.valid_audio_paths, self.valid_durations, self.valid_texts)
        else:
            raise Exception("Invalid partition. "
                "Must be train/val")

    def sort_dataset_by_duration(self, partition):
    # Sort the data
        if partition == 'train':
            self.train_audio_paths, self.train_durations, self.train_texts = sort_dataset(
                self.train_audio_paths, self.train_durations, self.train_texts)
        elif partition == 'valid':
            self.valid_audio_paths, self.valid_durations, self.valid_texts = sort_dataset(
                self.valid_audio_paths, self.valid_durations, self.valid_texts)
        else:
            raise Exception("Invalid partition. "
                "Must be train/val")

    def next_train(self):
    # Get a batch of training data
        while True:
            ret = self.get_batch('train')
            self.cur_train_index += self.minibatch_size
            if self.cur_train_index >= len(self.train_texts) - self.minibatch_size:
                self.cur_train_index = 0
                self.shuffle_dataset_by_partition('train')
            yield ret    

    def next_valid(self):
    # Get a batch of validation data
        while True:
            ret = self.get_batch('valid')
            self.cur_valid_index += self.minibatch_size
            if self.cur_valid_index >= len(self.valid_texts) - self.minibatch_size:
                self.cur_valid_index = 0
                self.shuffle_dataset_by_partition('valid')
            yield ret

    def next_test(self):
    # Get a batch of testing data
        while True:
            ret = self.get_batch('test')
            self.cur_test_index += self.minibatch_size
            if self.cur_test_index >= len(self.test_texts) - self.minibatch_size:
                self.cur_test_index = 0
            yield ret
            
    # Load datasets
    def load_train_data(self, desc_file='train_corpus.json'):
        self.load_metadata_from_desc_file(desc_file, 'train')
        self.fit_train()
        if self.sort_by_duration:
            self.sort_dataset_by_duration('train')

    def load_validation_data(self, desc_file='valid_corpus.json'):
        self.load_metadata_from_desc_file(desc_file, 'validation')
        if self.sort_by_duration:
            self.sort_dataset_by_duration('valid')

    def load_test_data(self, desc_file='test_corpus.json'):
        self.load_metadata_from_desc_file(desc_file, 'test')
    
    def load_metadata_from_desc_file(self, desc_file, partition):
    # Get metadata from json corpus
        audio_paths, durations, texts = [], [], []
        with open(desc_file) as json_line_file:
            for line_num, json_line in enumerate(json_line_file):
                try:
                    spec = json.loads(json_line)
                    if float(spec['duration']) > self.max_duration:
                        continue
                    audio_paths.append(spec['key'])
                    durations.append(float(spec['duration']))
                    texts.append(spec['text'])
                except Exception as e:
                    print('Error reading line #{}: {}'
                                .format(line_num, json_line))
        if partition == 'train':
            self.train_audio_paths = audio_paths
            self.train_durations = durations
            self.train_texts = texts
        elif partition == 'validation':
            self.valid_audio_paths = audio_paths
            self.valid_durations = durations
            self.valid_texts = texts
        elif partition == 'test':
            self.test_audio_paths = audio_paths
            self.test_durations = durations
            self.test_texts = texts
        else:
            raise Exception("Invalid partition. "
             "Must be train/val/test")
            
    def fit_train(self, k_samples=100):
    # Estimate descriptive stats for training set based on sample of 100
        k_samples = min(k_samples, len(self.train_audio_paths))
        samples = self.rng.sample(self.train_audio_paths, k_samples)
        feats = [self.featurize(s) for s in samples]
        feats = np.vstack(feats)
        self.feats_mean = np.mean(feats, axis=0)
        self.feats_std = np.std(feats, axis=0)
        
    def featurize(self, audio_clip):
    # Create features from data, either spectrogram or mfcc
        if self.spectrogram:
            return spectrogram_from_file(
                audio_clip, step=self.step, window=self.window,
                max_freq=self.max_freq)
        else:
            (rate, sig) = wav.read(audio_clip)
            return mfcc(sig, rate, numcep=self.mfcc_dim)

    def normalize(self, feature, eps=1e-14):
    # Scale the data
        return (feature - self.feats_mean) / (self.feats_std + eps)

def spectrogram(samples, fft_length=256, sample_rate=2, hop_length=128):
# Create a spectrogram from audio signals
    assert not np.iscomplexobj(samples), "You shall not pass in complex numbers"
    window = np.hanning(fft_length)[:, None]
    window_norm = np.sum(window**2)  
    scale = window_norm * sample_rate
    trunc = (len(samples) - fft_length) % hop_length
    x = samples[:len(samples) - trunc]
    # Reshape to include the overlap
    nshape = (fft_length, (len(x) - fft_length) // hop_length + 1)
    nstrides = (x.strides[0], x.strides[0] * hop_length)
    x = as_strided(x, shape=nshape, strides=nstrides)
    # Window stride sanity check
    assert np.all(x[:, 1] == samples[hop_length:(hop_length + fft_length)])
    # Broadcast window, and then compute fft over columns and square mod
    x = np.fft.rfft(x * window, axis=0)
    x = np.absolute(x)**2
    # Scale 2.0 for everything except dc and fft_length/2
    x[1:-1, :] *= (2.0 / scale)
    x[(0, -1), :] /= scale
    freqs = float(sample_rate) / fft_length * np.arange(x.shape[0])
    return x, freqs

def spectrogram_from_file(filename, step=10, window=20, max_freq=None,
                          eps=1e-14):
# Calculate log(linear spectrogram) from FFT energy
    with soundfile.SoundFile(filename) as sound_file:
        audio = sound_file.read(dtype='float32')
        sample_rate = sound_file.samplerate
        if audio.ndim >= 2:
            audio = np.mean(audio, 1)
        if max_freq is None:
            max_freq = sample_rate / 2
        if max_freq > sample_rate / 2:
            raise ValueError("max_freq can not be > than 0.5 of "
                             " sample rate")
        if step > window:
            raise ValueError("step size can not be > than window size")
        hop_length = int(0.001 * step * sample_rate)
        fft_length = int(0.001 * window * sample_rate)
        pxx, freqs = spectrogram(
            audio, fft_length=fft_length, sample_rate=sample_rate,
            hop_length=hop_length)
        ind = np.where(freqs <= max_freq)[0][-1] + 1
    return np.transpose(np.log(pxx[:ind, :] + eps))

def vis_audio_features(index, partition):
# Function for visualizing a single audio file based on index chosen
    if partition == 'validation':
        audio_gen = AudioGenerator(spectrogram=True)
        audio_gen.load_validation_data()
        vis_audio_path = audio_gen.valid_audio_paths[index]
        vis_spectrogram_feature = audio_gen.normalize(audio_gen.featurize(vis_audio_path))
        vis_text = audio_gen.valid_texts[index]
        sample_rate, samples = wav.read(vis_audio_path)
        return vis_text, vis_spectrogram_feature, vis_audio_path, sample_rate, samples
    
    elif partition == 'test':
        audio_gen = AudioGenerator(spectrogram=True)
        audio_gen.load_test_data()
        vis_audio_path = audio_gen.test_audio_paths[index]
        vis_spectrogram_feature = audio_gen.normalize(audio_gen.featurize(vis_audio_path))
        vis_text = audio_gen.test_texts[index]
        sample_rate, samples = wav.read(vis_audio_path)
        return vis_text, vis_spectrogram_feature, vis_audio_path, sample_rate, samples
    
    elif partition == 'train':
        audio_gen = AudioGenerator(spectrogram=True)
        audio_gen.load_train_data()
        vis_audio_path = audio_gen.train_audio_paths[index]
        vis_spectrogram_feature = audio_gen.normalize(audio_gen.featurize(vis_audio_path))
        vis_text = audio_gen.train_texts[index]
        sample_rate, samples = wav.read(vis_audio_path)
        return vis_text, vis_spectrogram_feature, vis_audio_path, sample_rate, samples

    else:
        raise Exception('Invalid partition!  Must be "train", "test", or "validation"')

# Custom CTC loss function (discussed below)
def ctc_lambda_func(args):
    y_pred, labels, input_length, label_length = args
    return K.ctc_batch_cost(labels, y_pred, input_length, label_length)

def add_ctc_loss(input_to_softmax):
    the_labels = Input(name='the_labels', shape=(None,), dtype='float32')
    input_lengths = Input(name='input_length', shape=(1,), dtype='int64')
    label_lengths = Input(name='label_length', shape=(1,), dtype='int64')
    output_lengths = Lambda(input_to_softmax.output_length)(input_lengths)
    # CTC loss is implemented in a lambda layer
    loss_out = Lambda(ctc_lambda_func, output_shape=(1,), name='ctc')(
        [input_to_softmax.output, the_labels, output_lengths, label_lengths])
    model = Model(
        inputs=[input_to_softmax.input, the_labels, input_lengths, label_lengths], 
        outputs=loss_out)
    return model

# Functions for modifying CNN layers for sequence problems 
def cnn_output_length(input_length, filter_size, border_mode, stride, dilation=1):
# Compute the length of cnn output seq after 1D convolution across time
    if input_length is None:
        return None
    assert border_mode in {'same', 'valid', 'causal'}
    dilated_filter_size = filter_size + (filter_size - 1) * (dilation - 1)
    if border_mode == 'same':
        output_length = input_length
    elif border_mode == 'valid':
        output_length = input_length - dilated_filter_size + 1
    elif border_mode == 'causal':
        output_length = input_length
    return (output_length + stride - 1) // stride

# Class for attention mechanism
class Attention(keras.layers.Layer):

    ATTENTION_TYPE_ADD = 'additive'
    ATTENTION_TYPE_MUL = 'multiplicative'

    def __init__(self,
                 units=512,
                 attention_width=None,
                 attention_type=ATTENTION_TYPE_MUL,
                 return_attention=False,
                 history_only=False,
                 kernel_initializer='glorot_normal',
                 bias_initializer='zeros',
                 kernel_regularizer=None,
                 bias_regularizer=None,
                 kernel_constraint=None,
                 bias_constraint=None,
                 use_additive_bias=True,
                 use_attention_bias=True,
                 attention_activation=None,
                 attention_regularizer_weight=0.0,
                 **kwargs):
        """Layer initialization.

        For additive attention, see: https://arxiv.org/pdf/1806.01264.pdf

        :param units: The dimension of the vectors that used to calculate the attention weights.
        :param attention_width: The width of local attention.
        :param attention_type: 'additive' or 'multiplicative'.
        :param return_attention: Whether to return the attention weights for visualization.
        :param history_only: Only use historical pieces of data.
        :param kernel_initializer: The initializer for weight matrices.
        :param bias_initializer: The initializer for biases.
        :param kernel_regularizer: The regularization for weight matrices.
        :param bias_regularizer: The regularization for biases.
        :param kernel_constraint: The constraint for weight matrices.
        :param bias_constraint: The constraint for biases.
        :param use_additive_bias: Whether to use bias while calculating the relevance of inputs features
                                  in additive mode.
        :param use_attention_bias: Whether to use bias while calculating the weights of attention.
        :param attention_activation: The activation used for calculating the weights of attention.
        :param attention_regularizer_weight: The weights of attention regularizer.
        :param kwargs: Parameters for parent class.
        """
        super(Attention, self).__init__(**kwargs)
        self.supports_masking = True
        self.units = units
        self.attention_width = attention_width
        self.attention_type = attention_type
        self.return_attention = return_attention
        self.history_only = history_only
        if history_only and attention_width is None:
            self.attention_width = int(1e9)

        self.use_additive_bias = use_additive_bias
        self.use_attention_bias = use_attention_bias
        self.kernel_initializer = keras.initializers.get(kernel_initializer)
        self.bias_initializer = keras.initializers.get(bias_initializer)
        self.kernel_regularizer = keras.regularizers.get(kernel_regularizer)
        self.bias_regularizer = keras.regularizers.get(bias_regularizer)
        self.kernel_constraint = keras.constraints.get(kernel_constraint)
        self.bias_constraint = keras.constraints.get(bias_constraint)
        self.attention_activation = keras.activations.get(attention_activation)
        self.attention_regularizer_weight = attention_regularizer_weight
        self._backend = keras.backend.backend()

        if attention_type == Attention.ATTENTION_TYPE_ADD:
            self.Wx, self.Wt, self.bh = None, None, None
            self.Wa, self.ba = None, None
        elif attention_type == Attention.ATTENTION_TYPE_MUL:
            self.Wa, self.ba = None, None
        else:
            raise NotImplementedError('No implementation for attention type : ' + attention_type)

    def get_config(self):
        config = {
            'units': self.units,
            'attention_width': self.attention_width,
            'attention_type': self.attention_type,
            'return_attention': self.return_attention,
            'history_only': self.history_only,
            'use_additive_bias': self.use_additive_bias,
            'use_attention_bias': self.use_attention_bias,
            'kernel_initializer': keras.regularizers.serialize(self.kernel_initializer),
            'bias_initializer': keras.regularizers.serialize(self.bias_initializer),
            'kernel_regularizer': keras.regularizers.serialize(self.kernel_regularizer),
            'bias_regularizer': keras.regularizers.serialize(self.bias_regularizer),
            'kernel_constraint': keras.constraints.serialize(self.kernel_constraint),
            'bias_constraint': keras.constraints.serialize(self.bias_constraint),
            'attention_activation': keras.activations.serialize(self.attention_activation),
            'attention_regularizer_weight': self.attention_regularizer_weight,
        }
        base_config = super(Attention, self).get_config()
        return dict(list(base_config.items()) + list(config.items()))

    def build(self, input_shape):
        if self.attention_type == Attention.ATTENTION_TYPE_ADD:
            self._build_additive_attention(input_shape)
        elif self.attention_type == Attention.ATTENTION_TYPE_MUL:
            self._build_multiplicative_attention(input_shape)
        super(Attention, self).build(input_shape)

    def _build_additive_attention(self, input_shape):
        feature_dim = int(input_shape[2])

        self.Wt = self.add_weight(shape=(feature_dim, self.units),
                                  name='{}_Add_Wt'.format(self.name),
                                  initializer=self.kernel_initializer,
                                  regularizer=self.kernel_regularizer,
                                  constraint=self.kernel_constraint)
        self.Wx = self.add_weight(shape=(feature_dim, self.units),
                                  name='{}_Add_Wx'.format(self.name),
                                  initializer=self.kernel_initializer,
                                  regularizer=self.kernel_regularizer,
                                  constraint=self.kernel_constraint)
        if self.use_additive_bias:
            self.bh = self.add_weight(shape=(self.units,),
                                      name='{}_Add_bh'.format(self.name),
                                      initializer=self.bias_initializer,
                                      regularizer=self.bias_regularizer,
                                      constraint=self.bias_constraint)

        self.Wa = self.add_weight(shape=(self.units, 1),
                                  name='{}_Add_Wa'.format(self.name),
                                  initializer=self.kernel_initializer,
                                  regularizer=self.kernel_regularizer,
                                  constraint=self.kernel_constraint)
        if self.use_attention_bias:
            self.ba = self.add_weight(shape=(1,),
                                      name='{}_Add_ba'.format(self.name),
                                      initializer=self.bias_initializer,
                                      regularizer=self.bias_regularizer,
                                      constraint=self.bias_constraint)

    def _build_multiplicative_attention(self, input_shape):
        feature_dim = int(input_shape[2])

        self.Wa = self.add_weight(shape=(feature_dim, feature_dim),
                                  name='{}_Mul_Wa'.format(self.name),
                                  initializer=self.kernel_initializer,
                                  regularizer=self.kernel_regularizer,
                                  constraint=self.kernel_constraint)
        if self.use_attention_bias:
            self.ba = self.add_weight(shape=(1,),
                                      name='{}_Mul_ba'.format(self.name),
                                      initializer=self.bias_initializer,
                                      regularizer=self.bias_regularizer,
                                      constraint=self.bias_constraint)

    def call(self, inputs, mask=None, **kwargs):
        input_len = K.shape(inputs)[1]

        if self.attention_type == Attention.ATTENTION_TYPE_ADD:
            e = self._call_additive_emission(inputs)
        elif self.attention_type == Attention.ATTENTION_TYPE_MUL:
            e = self._call_multiplicative_emission(inputs)

        if self.attention_activation is not None:
            e = self.attention_activation(e)
        e = K.exp(e - K.max(e, axis=-1, keepdims=True))
        if self.attention_width is not None:
            if self.history_only:
                lower = K.arange(0, input_len) - (self.attention_width - 1)
            else:
                lower = K.arange(0, input_len) - self.attention_width // 2
            lower = K.expand_dims(lower, axis=-1)
            upper = lower + self.attention_width
            indices = K.expand_dims(K.arange(0, input_len), axis=0)
            e = e * K.cast(lower <= indices, K.floatx()) * K.cast(indices < upper, K.floatx())
        if mask is not None:
            mask = K.cast(mask, K.floatx())
            mask = K.expand_dims(mask)
            e = K.permute_dimensions(K.permute_dimensions(e * mask, (0, 2, 1)) * mask, (0, 2, 1))

        # a_{t} = \text{softmax}(e_t)
        s = K.sum(e, axis=-1, keepdims=True)
        a = e / (s + K.epsilon())

        # l_t = \sum_{t'} a_{t, t'} x_{t'}
        v = K.batch_dot(a, inputs)
        if self.attention_regularizer_weight > 0.0:
            self.add_loss(self._attention_regularizer(a))

        if self.return_attention:
            return [v, a]
        return v

    def _call_additive_emission(self, inputs):
        input_shape = K.shape(inputs)
        batch_size, input_len = input_shape[0], input_shape[1]

        # h_{t, t'} = \tanh(x_t^T W_t + x_{t'}^T W_x + b_h)
        q = K.expand_dims(K.dot(inputs, self.Wt), 2)
        k = K.expand_dims(K.dot(inputs, self.Wx), 1)
        if self.use_additive_bias:
            h = K.tanh(q + k + self.bh)
        else:
            h = K.tanh(q + k)

        # e_{t, t'} = W_a h_{t, t'} + b_a
        if self.use_attention_bias:
            e = K.reshape(K.dot(h, self.Wa) + self.ba, (batch_size, input_len, input_len))
        else:
            e = K.reshape(K.dot(h, self.Wa), (batch_size, input_len, input_len))
        return e

    def _call_multiplicative_emission(self, inputs):
        # e_{t, t'} = x_t^T W_a x_{t'} + b_a
        e = K.batch_dot(K.dot(inputs, self.Wa), K.permute_dimensions(inputs, (0, 2, 1)))
        if self.use_attention_bias:
            e += self.ba[0]
        return e

    def compute_output_shape(self, input_shape):
        output_shape = input_shape
        if self.return_attention:
            attention_shape = (input_shape[0], output_shape[1], input_shape[1])
            return [output_shape, attention_shape]
        return output_shape

    def compute_mask(self, inputs, mask=None):
        if self.return_attention:
            return [mask, None]
        return mask

    def _attention_regularizer(self, attention):
        batch_size = K.cast(K.shape(attention)[0], K.floatx())
        input_len = K.shape(attention)[-1]
        indices = K.expand_dims(K.arange(0, input_len), axis=0)
        diagonal = K.expand_dims(K.arange(0, input_len), axis=-1)
        eye = K.cast(K.equal(indices, diagonal), K.floatx())
        return self.attention_regularizer_weight * K.sum(K.square(K.batch_dot(
            attention,
            K.permute_dimensions(attention, (0, 2, 1))) - eye)) / batch_size

def train_model(input_to_softmax, 
                pickle_path,
                save_model_path,
                train_json='train_corpus.json',
                valid_json='valid_corpus.json',
                minibatch_size=16, # You will want to change this depending on the GPU you are training on
                spectrogram=True,
                mfcc_dim=13,
                optimizer=Adam(lr=0.0001, beta_1=0.9, beta_2=0.999, epsilon=None, decay=0.0, amsgrad=False, clipnorm=1, clipvalue=.5),
                epochs=30, # You will want to change this depending on the model you are training and data you are using
                verbose=1,
                sort_by_duration=False,
                max_duration=10.0):
    
    # Obtain batches of data
    audio_gen = AudioGenerator(minibatch_size=minibatch_size, 
        spectrogram=spectrogram, mfcc_dim=mfcc_dim, max_duration=max_duration,
        sort_by_duration=sort_by_duration)
    # Load the datasets
    audio_gen.load_train_data(train_json)
    audio_gen.load_validation_data(valid_json)  
    # Calculate steps per epoch
    num_train_examples=len(audio_gen.train_audio_paths)
    steps_per_epoch = num_train_examples//minibatch_size
    # Calculate validation steps
    num_valid_samples = len(audio_gen.valid_audio_paths) 
    validation_steps = num_valid_samples//minibatch_size    
    # Add custom CTC loss function to the nn
    model = add_ctc_loss(input_to_softmax)
    # Dummy lambda function for loss since CTC loss is implemented above
    model.compile(loss={'ctc': lambda y_true, y_pred: y_pred}, optimizer=optimizer)
    # Make  initial results/ directory for saving model pickles
    if not os.path.exists('results'):
        os.makedirs('results')
    # Add callbacks
    checkpointer = ModelCheckpoint(filepath='results/'+save_model_path, verbose=0)
    terminator = callbacks.TerminateOnNaN()
    time_machiner = callbacks.History()
    logger = callbacks.CSVLogger('training.log')
    stopper = callbacks.EarlyStopping(monitor='val_loss', patience=2, verbose=1, mode='auto')
    reducer = callbacks.ReduceLROnPlateau(monitor='val_loss', factor=0.1, patience=10, verbose=0, mode='auto', min_delta=0.0001, cooldown=0, min_lr=0)
    tensor_boarder = callbacks.TensorBoard(log_dir='./logs', batch_size=16,
                                          write_graph=True, write_grads=True, write_images=True,)
    # Fit/train model
    hist = model.fit_generator(generator=audio_gen.next_train(), steps_per_epoch=steps_per_epoch,
        epochs=epochs, validation_data=audio_gen.next_valid(), validation_steps=validation_steps,
        callbacks=[checkpointer, terminator, logger, time_machiner, tensor_boarder, stopper, reducer], verbose=verbose)
    # Save model loss
    with open('results/'+pickle_path, 'wb') as f:
        pickle.dump(hist.history, f)

def keras_model(input_dim, filters, activation, kernel_size, conv_stride,
    conv_border_mode, recur_layers, dilation_rate, units, conv_layers, output_dim=29):
    # Input
    input_data = Input(name='the_input', shape=(None, input_dim))
    # Inital Convolutional layer
    conv_1d = Conv1D(filters, kernel_size, 
                     strides=conv_stride, 
                     padding=conv_border_mode,
                     activation=activation,
                     name='conv1d')(input_data)
    # Batch normalization
    bn_cnn = BatchNormalization()(conv_1d)
    # Loop for additional layers
    for i in range(conv_layers - 1):
        conv_1d = Conv1D(filters, kernel_size,
                         padding=conv_border_mode,
                         activation=activation,
                         dilation_rate=2**i,
                         name="conv_1d_"+str(i))(bn_cnn)
        bn_cnn = BatchNormalization()(conv_1d)
    # Initial Bidirectional recurrent layer
    brnn = Bidirectional(GRU(units, activation=activation, 
        return_sequences=True, implementation=2, recurrent_dropout=0.02, name='brnn'))(bn_cnn)
    # Batch normalization 
    bn_rnn = BatchNormalization()(brnn)
    # Loop for additional layers
    for i in range(recur_layers - 1):
        name = 'brnn_' + str(i + 1)
        brnn = Bidirectional(GRU(units, activation=activation, 
        return_sequences=True, implementation=2, name=name))(bn_rnn)
        bn_rnn = BatchNormalization()(brnn)
    # Attention layer
    attentive = Attention()(bn_rnn)
    # TimeDistributed Dense layers
    time_distributed_dense = TimeDistributed(Dense(1024))(attentive)
    time_dense = TimeDistributed(Dense(output_dim))(time_distributed_dense)
    # Softmax activation layer
    y_pred = Activation('softmax', name='softmax')(time_dense)
    # Specifying the model
    model = Model(inputs=input_data, outputs=y_pred)
    model.output_length = lambda x: cnn_output_length(
        x, kernel_size, conv_border_mode, conv_stride)
    print(model.summary())
    return model

def get_ground_truth(index, partition):
    # Load the train, validation, and test data
    data_gen = AudioGenerator(spectrogram = spectrogram)
    data_gen.load_validation_data()
    data_gen.load_test_data()
    
    # Obtain ground truth transcriptions and audio features 
    if partition == 'validation':
        transcription = data_gen.valid_texts[index]
    elif partition == 'test':
        transcription = data_gen.test_texts[index]
    else:
        raise Exception('Invalid partition!  Must be "test", or "validation"')
    
    # Display ground truth transcription
    return transcription

def get_prediction(index, partition):
    # Load the train, validation, and test data
    data_gen = AudioGenerator(spectrogram = spectrogram)
    data_gen.load_validation_data()
    data_gen.load_test_data()
    
    # Obtain ground truth transcriptions and audio features 
    if partition == 'validation':
        audio_path = data_gen.valid_audio_paths[index]
        data_point = data_gen.normalize(data_gen.featurize(audio_path))
    elif partition == 'test':
        audio_path = data_gen.test_audio_paths[index]
        data_point = data_gen.normalize(data_gen.featurize(audio_path))
    else:
        raise Exception('Invalid partition!  Must be "test", or "validation"')
    # Clear tensorflow graph
    K.clear_session()
    # Define model
    hey_jetson = keras_model(input_dim=161, # 161 for Spectrogram/13 for MFCC
                         filters=256,
                         activation='relu',
                         kernel_size=5, 
                         conv_stride=2,
                         recur_layers=7,
                         conv_border_mode='causal',
                         conv_layers=3,
                         dilation_rate=2,
                         units=256)
    # Load model
    hey_jetson.load_weights('./results/model_11.h5')
    # hey_jetson = load_model('./results/model_11.h5', custom_objects={'Attention': Attention, cnn_output_length': cnn_output_length, '<lambda>': lambda y_true, y_pred: y_pred})
    # Obtain Predictions
    prediction = hey_jetson.predict(np.expand_dims(data_point, axis=0))
    output_length = [hey_jetson.output_length(data_point.shape[0])] 
    pred_ints = (K.eval(K.ctc_decode(
                prediction, output_length)[0][0])+1).flatten().tolist()
    
    # Display predicted transcripted.
    prediction_transcription = ''.join(int_seq_to_text(pred_ints))
    # Clear tensorflow graph
    K.clear_session()
    return prediction_transcription

def run_inference(audio_path):
    # Load the audio
    data_gen = AudioGenerator(spectrogram = spectrogram)
    data_gen.load_validation_data()
    data_gen.load_test_data()
    data_point = data_gen.normalize(data_gen.featurize(audio_path))
        
    # Clear tensorflow graph
    K.clear_session()
    # Define model
    hey_jetson = keras_model(input_dim=161, # 161 for Spectrogram/13 for MFCC
                         filters=256,
                         activation='relu',
                         kernel_size=5, 
                         conv_stride=2,
                         recur_layers=7,
                         conv_border_mode='causal',
                         conv_layers=3,
                         dilation_rate=2,
                         units=256)
    # Load model
    hey_jetson.load_weights('./results/model_11.h5')
    # hey_jetson = load_model('./results/model_11.h5', custom_objects={'Attention': Attention, cnn_output_length': cnn_output_length, '<lambda>': lambda y_true, y_pred: y_pred})
    # Obtain Predictions
    prediction = hey_jetson.predict(np.expand_dims(data_point, axis=0))
    output_length = [hey_jetson.output_length(data_point.shape[0])] 
    pred_ints = (K.eval(K.ctc_decode(
                prediction, output_length)[0][0])+1).flatten().tolist()
    
    # Display predicted transcripted.
    prediction_transcription = ''.join(int_seq_to_text(pred_ints))
    # Clear tensorflow graph
    K.clear_session()
    return prediction_transcription

def inference_vis_audio_features(index):
# Function for visualizing a single audio file based on index chosen
    audio_gen = AudioGenerator(spectrogram=True)
    vis_audio_path = index
    vis_spectrogram_feature = audio_gen.normalize(audio_gen.featurize(vis_audio_path))
    sample_rate, samples = wav.read(vis_audio_path)
    return vis_spectrogram_feature, sample_rate, samples

def azure_inference(index, partition):
    # Load the audio
    data_gen = AudioGenerator(spectrogram=True)
    data_gen.load_train_data()
    data_gen.load_validation_data()
    data_gen.load_test_data()
    # Identify the path for the audio file
    if partition == 'validation':
        audio_path = data_gen.valid_audio_paths[index]
    elif partition == 'test':
        audio_path = data_gen.test_audio_paths[index]
    elif partition == 'train':
        audio_path = data_gen.train_audio_paths[index]
    # Return the file path
    return audio_path

# Plot for the raw audio signal
def plot_raw_audio(sample_rate, samples):
    time = np.arange(0, float(samples.shape[0]), 1) / sample_rate
    fig = plt.figure(figsize=(6,3))
    ax = fig.add_subplot(111)
    ax.plot(time, samples, linewidth=1, alpha=0.7, color='#512da8')
    plt.title('Raw Audio Signal')
    plt.xlabel('Time')
    plt.ylabel('Amplitude')
    figfile1 = BytesIO()
    plt.savefig(figfile1, format='png')
    figfile1.seek(0)
    raw_plot = base64.b64encode(figfile1.getvalue())
    return raw_plot.decode('utf8')

# Plot for normalized spectrogram
def plot_spectrogram_feature(vis_spectrogram_feature):
    fig = plt.figure(figsize=(6,3))
    ax1 = fig.add_subplot(111)
    im = ax1.imshow(vis_spectrogram_feature.T, cmap=plt.cm.viridis, aspect='auto', origin='lower')
    plt.title('Log Spectrogram')
    plt.ylabel('Frequency')
    plt.xlabel('Time (s)')
    divider = make_axes_locatable(ax1)
    cax = divider.append_axes("right", size="5%", pad=0.05)
    plt.colorbar(im, cax=cax)
    figfile2 = BytesIO()
    plt.savefig(figfile2, format='png')
    figfile2.seek(0)
    spectrogram_plot = base64.b64encode(figfile2.getvalue())
    return spectrogram_plot.decode('utf8')

def log_spectrogram_feature(samples, sample_rate, window_size=20, step_size=10, eps=1e-14):
    nperseg = int(round(window_size * sample_rate / 1e3))
    noverlap = int(round(step_size * sample_rate / 1e3))
    freqs, times, spec = signal.spectrogram(samples,
                                    fs=sample_rate,
                                    window='hann',
                                    nperseg=nperseg,
                                    noverlap=noverlap,
                                    detrend=False)
    freqs = (freqs*2)
    return freqs, times, np.log(spec.T.astype(np.float64) + eps)

# 2nd plot for normalized spectrogram
def plot_log_spectrogram_feature(freqs, times, log_spectrogram):
    fig = plt.figure(figsize=(6,3))
    ax2 = fig.add_subplot(111)
    ax2.imshow(log_spectrogram.T, aspect='auto', origin='lower', cmap=plt.cm.viridis, 
               extent=[times.min(), times.max(), freqs.min(), freqs.max()])
    ax2.set_yticks(freqs[::20])
    ax2.set_xticks(times[::20])
    ax2.set_title('Normalized Log Spectrogram')
    ax2.set_ylabel('Frequency')
    ax2.set_xlabel('Time (s)')
    figfile3 = BytesIO()
    plt.savefig(figfile3, format='png')
    figfile3.seek(0)
    log_spectrogram_plot = base64.b64encode(figfile3.getvalue())
    return log_spectrogram_plot.decode('utf8')

# Plot a normalized MFCC feature
def plot_mfcc_feature(vis_mfcc_feature):
    fig = plt.figure(figsize=(6,3))
    ax = fig.add_subplot(111)
    im = ax.imshow(vis_mfcc_feature, cmap=plt.cm.viridis, aspect='auto')
    plt.title('Normalized MFCC')
    plt.ylabel('Time')
    plt.xlabel('MFCC Coefficient')
    divider = make_axes_locatable(ax)
    cax = divider.append_axes("right", size="5%", pad=0.05)
    plt.colorbar(im, cax=cax)
    ax.set_xticks(np.arange(0, 13, 2), minor=False)
    figfile4 = BytesIO()
    plt.savefig(figfile4, format='png')
    figfile4.seek(0)
    mfcc_plot = base64.b64encode(figfile4.getvalue())
    return mfcc_plot.decode('utf8')

# Function to calcualte word error rate
def wer_calc(ref, pred):
    d = np.zeros((len(ref) + 1) * (len(pred) + 1), dtype=np.uint16)
    d = d.reshape((len(ref) + 1, len(pred) + 1))
    for i in range(len(ref) + 1):
        for j in range(len(pred) + 1):
            if i == 0:
                d[0][j] = j
            elif j == 0:
                d[i][0] = i
    for i in range(1, len(ref) + 1):
        for j in range(1, len(pred) + 1):
            if ref[i - 1] == pred[j - 1]:
                d[i][j] = d[i - 1][j - 1]
            else:
                substitution = d[i - 1][j - 1] + 1
                insertion = d[i][j - 1] + 1
                deletion = d[i - 1][j] + 1
                d[i][j] = min(substitution, insertion, deletion)
    result = float(d[len(ref)][len(pred)]) / len(ref) * 100
    return result

# Generator to read a file piece by piece. Default chunk size: 1k
def read_in_chunks(file_object, blocksize=1024, chunks=-1):
    while chunks:
        data = file_object.read(blocksize)
        if not data:
            break
        yield data
        chunks -= 1