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Feature caching

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This commit is contained in:
Reuben Morais 2018-09-10 22:41:14 -03:00
parent 5ff3b31bbd
commit 44e502e236
6 changed files with 179 additions and 169 deletions
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34
DeepSpeech.py
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@ -25,6 +25,7 @@ from tensorflow.python.tools import freeze_graph
from threading import Thread, Lock
from util.audio import audiofile_to_input_vector
from util.feeding import DataSet, ModelFeeder
from util.preprocess import preprocess
from util.gpu import get_available_gpus
from util.shared_lib import check_cupti
from util.text import sparse_tensor_value_to_texts, wer, levenshtein, Alphabet, ndarray_to_text
@ -40,6 +41,10 @@ def create_flags():
tf.app.flags.DEFINE_string ('test_files', '', 'comma separated list of files specifying the dataset used for testing. multiple files will get merged')
tf.app.flags.DEFINE_boolean ('fulltrace', False, 'if full trace debug info should be generated during training')
tf.app.flags.DEFINE_string ('train_cached_features_path', '', 'comma separated list of files specifying the dataset used for training. multiple files will get merged')
tf.app.flags.DEFINE_string ('dev_cached_features_path', '', 'comma separated list of files specifying the dataset used for validation. multiple files will get merged')
tf.app.flags.DEFINE_string ('test_cached_features_path', '', 'comma separated list of files specifying the dataset used for testing. multiple files will get merged')
# Cluster configuration
# =====================
@ -402,7 +407,7 @@ def BiRNN(batch_x, seq_length, dropout, reuse=False, batch_size=None, n_steps=-1
# This is done to prepare the batch for input into the first layer which expects a tensor of rank `2`.
# Permute n_steps and batch_size
batch_x = tf.transpose(batch_x, [1, 0, 2])
batch_x = tf.transpose(batch_x, [1, 0, 2, 3])
# Reshape to prepare input for first layer
batch_x = tf.reshape(batch_x, [-1, n_input + 2*n_input*n_context]) # (n_steps*batch_size, n_input + 2*n_input*n_context)
layers['input_reshaped'] = batch_x
@ -1459,19 +1464,40 @@ def train(server=None):
global_step = tf.Variable(0, trainable=False, name='global_step')
# Reading training set
train_set = DataSet(FLAGS.train_files.split(','),
train_data = preprocess(FLAGS.train_files.split(','),
FLAGS.train_batch_size,
n_input,
n_context,
alphabet,
hdf5_cache_path=FLAGS.train_cached_features_path)
train_set = DataSet(train_data,
FLAGS.train_batch_size,
limit=FLAGS.limit_train,
next_index=lambda i: COORD.get_next_index('train'))
# Reading validation set
dev_set = DataSet(FLAGS.dev_files.split(','),
dev_data = preprocess(FLAGS.dev_files.split(','),
FLAGS.dev_batch_size,
n_input,
n_context,
alphabet,
hdf5_cache_path=FLAGS.dev_cached_features_path)
dev_set = DataSet(dev_data,
FLAGS.dev_batch_size,
limit=FLAGS.limit_dev,
next_index=lambda i: COORD.get_next_index('dev'))
# Reading test set
test_set = DataSet(FLAGS.test_files.split(','),
test_data = preprocess(FLAGS.test_files.split(','),
FLAGS.test_batch_size,
n_input,
n_context,
alphabet,
hdf5_cache_path=FLAGS.test_cached_features_path)
test_set = DataSet(test_data,
FLAGS.test_batch_size,
limit=FLAGS.limit_test,
next_index=lambda i: COORD.get_next_index('test'))

83
evaluate.py
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@ -19,6 +19,7 @@ from multiprocessing import Pool
from six.moves import zip, range
from util.audio import audiofile_to_input_vector
from util.text import sparse_tensor_value_to_texts, text_to_char_array, Alphabet, ctc_label_dense_to_sparse, wer, levenshtein
from util.preprocess import pmap, preprocess
FLAGS = tf.app.flags.FLAGS
@ -28,88 +29,6 @@ N_FEATURES = 26
N_CONTEXT = 9
def pmap(fun, iterable, threads=8):
pool = Pool(threads)
results = pool.map(fun, iterable)
pool.close()
return results
def process_single_file(row):
# row = index, Series
_, file = row
features = audiofile_to_input_vector(file.wav_filename, N_FEATURES, N_CONTEXT)
transcript = text_to_char_array(file.transcript, alphabet)
return features, len(features), transcript, len(transcript)
# load samples from CSV, compute features, optionally cache results on disk
def preprocess(dataset_files, batch_size, hdf5_dest_path=None):
COLUMNS = ('features', 'features_len', 'transcript', 'transcript_len')
if hdf5_dest_path and os.path.exists(hdf5_dest_path):
with tables.open_file(hdf5_dest_path, 'r') as file:
features = file.root.features[:]
features_len = file.root.features_len[:]
transcript = file.root.transcript[:]
transcript_len = file.root.transcript_len[:]
# features are stored flattened, so reshape into
# [n_steps, (n_input + 2*n_context*n_input)]
for i in range(len(features)):
features[i] = np.reshape(features[i], [features_len[i], -1])
in_data = list(zip(features, features_len,
transcript, transcript_len))
return pandas.DataFrame(data=in_data, columns=COLUMNS)
csv_files = dataset_files.split(',')
source_data = None
for csv in csv_files:
file = pandas.read_csv(csv, encoding='utf-8', na_filter=False)
if source_data is None:
source_data = file
else:
source_data = source_data.append(file)
# discard last samples if dataset does not divide batch size evenly
if len(source_data) % batch_size != 0:
source_data = source_data[:-(len(source_data) % batch_size)]
out_data = pmap(process_single_file, source_data.iterrows())
if hdf5_dest_path:
# list of tuples -> tuple of lists
features, features_len, transcript, transcript_len = zip(*out_data)
with tables.open_file(hdf5_dest_path, 'w') as file:
features_dset = file.create_vlarray(file.root,
'features',
tables.Float32Atom(),
filters=tables.Filters(complevel=1))
# VLArray atoms need to be 1D, so flatten feature array
for f in features:
features_dset.append(np.reshape(f, -1))
features_len_dset = file.create_array(file.root,
'features_len',
features_len)
transcript_dset = file.create_vlarray(file.root,
'transcript',
tables.Int32Atom(),
filters=tables.Filters(complevel=1))
for t in transcript:
transcript_dset.append(t)
transcript_len_dset = file.create_array(file.root,
'transcript_len',
transcript_len)
return pandas.DataFrame(data=out_data, columns=COLUMNS)
def split_data(dataset, batch_size):
remainder = len(dataset) % batch_size
if remainder != 0:

1
requirements.txt
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@ -13,3 +13,4 @@ pyxdg
bs4
six
requests
tables

62
util/audio.py
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@ -1,53 +1,7 @@
from __future__ import absolute_import, print_function
import numpy as np
import scipy.io.wavfile as wav
import sys
import warnings
class DeepSpeechDeprecationWarning(DeprecationWarning):
pass
warnings.simplefilter('once', category=DeepSpeechDeprecationWarning)
try:
from deepspeech import audioToInputVector
except ImportError:
warnings.warn('DeepSpeech Python bindings could not be imported, resorting to slower code to compute audio features. '
'Refer to README.md for instructions on how to install (or build) the DeepSpeech Python bindings.',
category=DeepSpeechDeprecationWarning)
import numpy as np
from python_speech_features import mfcc
from six.moves import range
def audioToInputVector(audio, fs, numcep, numcontext):
# Get mfcc coefficients
features = mfcc(audio, samplerate=fs, numcep=numcep)
# We only keep every second feature (BiRNN stride = 2)
features = features[::2]
# One stride per time step in the input
num_strides = len(features)
# Add empty initial and final contexts
empty_context = np.zeros((numcontext, numcep), dtype=features.dtype)
features = np.concatenate((empty_context, features, empty_context))
# Create a view into the array with overlapping strides of size
# numcontext (past) + 1 (present) + numcontext (future)
window_size = 2*numcontext+1
train_inputs = np.lib.stride_tricks.as_strided(
features,
(num_strides, window_size, numcep),
(features.strides[0], features.strides[0], features.strides[1]),
writeable=False)
# Flatten the second and third dimensions
train_inputs = np.reshape(train_inputs, [num_strides, -1])
# Return results
return train_inputs
from python_speech_features import mfcc
def audiofile_to_input_vector(audio_filename, numcep, numcontext):
@ -60,4 +14,14 @@ def audiofile_to_input_vector(audio_filename, numcep, numcontext):
# Load wav files
fs, audio = wav.read(audio_filename)
return audioToInputVector(audio, fs, numcep, numcontext)
# Get mfcc coefficients
features = mfcc(audio, samplerate=fs, numcep=numcep)
# We only keep every second feature (BiRNN stride = 2)
features = features[::2]
# Add empty initial and final contexts
empty_context = np.zeros((numcontext, numcep), dtype=features.dtype)
features = np.concatenate((empty_context, features, empty_context))
return features

70
util/feeding.py
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@ -1,12 +1,12 @@
import pandas
import numpy as np
import tensorflow as tf
from threading import Thread
from math import ceil
from six.moves import range
from util.audio import audiofile_to_input_vector
from threading import Thread
from util.gpu import get_available_gpus
from util.text import ctc_label_dense_to_sparse, text_to_char_array
from util.text import ctc_label_dense_to_sparse
class ModelFeeder(object):
'''
@ -24,7 +24,7 @@ class ModelFeeder(object):
numcontext,
alphabet,
tower_feeder_count=-1,
threads_per_queue=2):
threads_per_queue=4):
self.train = train_set
self.dev = dev_set
@ -35,7 +35,7 @@ class ModelFeeder(object):
self.tower_feeder_count = max(len(get_available_gpus()), 1) if tower_feeder_count < 0 else tower_feeder_count
self.threads_per_queue = threads_per_queue
self.ph_x = tf.placeholder(tf.float32, [None, numcep + (2 * numcep * numcontext)])
self.ph_x = tf.placeholder(tf.float32, [None, 2*numcontext+1, numcep])
self.ph_x_length = tf.placeholder(tf.int32, [])
self.ph_y = tf.placeholder(tf.int32, [None,])
self.ph_y_length = tf.placeholder(tf.int32, [])
@ -77,27 +77,19 @@ class ModelFeeder(object):
'''
return self._tower_feeders[tower_feeder_index].next_batch()
class DataSet(object):
'''
Represents a collection of audio samples and their respective transcriptions.
Takes a set of CSV files produced by importers in /bin.
'''
def __init__(self, csvs, batch_size, skip=0, limit=0, ascending=True, next_index=lambda i: i + 1):
def __init__(self, data, batch_size, skip=0, limit=0, ascending=True, next_index=lambda i: i + 1):
self.data = data
self.data.sort_values(by="features_len", ascending=ascending, inplace=True)
self.batch_size = batch_size
self.next_index = next_index
self.files = None
for csv in csvs:
file = pandas.read_csv(csv, encoding='utf-8', na_filter=False)
if self.files is None:
self.files = file
else:
self.files = self.files.append(file)
self.files = self.files.sort_values(by="wav_filesize", ascending=ascending) \
.ix[:, ["wav_filename", "transcript"]] \
.values[skip:]
if limit > 0:
self.files = self.files[:limit]
self.total_batches = int(ceil(len(self.files) / batch_size))
self.total_batches = int(ceil(len(self.data) / batch_size))
class _DataSetLoader(object):
'''
@ -109,9 +101,9 @@ class _DataSetLoader(object):
def __init__(self, model_feeder, data_set, alphabet):
self._model_feeder = model_feeder
self._data_set = data_set
self.queue = tf.PaddingFIFOQueue(shapes=[[None, model_feeder.numcep + (2 * model_feeder.numcep * model_feeder.numcontext)], [], [None,], []],
self.queue = tf.PaddingFIFOQueue(shapes=[[None, 2 * model_feeder.numcontext + 1, model_feeder.numcep], [], [None,], []],
dtypes=[tf.float32, tf.int32, tf.int32, tf.int32],
capacity=data_set.batch_size * 2)
capacity=data_set.batch_size * 8)
self._enqueue_op = self.queue.enqueue([model_feeder.ph_x, model_feeder.ph_x_length, model_feeder.ph_y, model_feeder.ph_y_length])
self._close_op = self.queue.close(cancel_pending_enqueues=True)
self._alphabet = alphabet
@ -138,25 +130,35 @@ class _DataSetLoader(object):
'''
Queue thread routine.
'''
file_count = len(self._data_set.files)
file_count = len(self._data_set.data)
index = -1
while not coord.should_stop():
index = self._data_set.next_index(index) % file_count
wav_file, transcript = self._data_set.files[index]
source = audiofile_to_input_vector(wav_file, self._model_feeder.numcep, self._model_feeder.numcontext)
source_len = len(source)
target = text_to_char_array(transcript, self._alphabet)
target_len = len(target)
if source_len < target_len:
raise ValueError('Error: Audio file {} is too short for transcription.'.format(wav_file))
features, _, transcript, transcript_len = self._data_set.data.iloc[index]
# One stride per time step in the input
num_strides = len(features) - (self._model_feeder.numcontext * 2)
# Create a view into the array with overlapping strides of size
# numcontext (past) + 1 (present) + numcontext (future)
window_size = 2*self._model_feeder.numcontext+1
features = np.lib.stride_tricks.as_strided(
features,
(num_strides, window_size, self._model_feeder.numcep),
(features.strides[0], features.strides[0], features.strides[1]),
writeable=False)
try:
session.run(self._enqueue_op, feed_dict={ self._model_feeder.ph_x: source,
self._model_feeder.ph_x_length: source_len,
self._model_feeder.ph_y: target,
self._model_feeder.ph_y_length: target_len })
session.run(self._enqueue_op, feed_dict={
self._model_feeder.ph_x: features,
self._model_feeder.ph_x_length: num_strides,
self._model_feeder.ph_y: transcript,
self._model_feeder.ph_y_length: transcript_len
})
except tf.errors.CancelledError:
return
class _TowerFeeder(object):
'''
Internal class that represents a switchable input queue for one tower.

98
util/preprocess.py Normal file
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@ -0,0 +1,98 @@
import numpy as np
import os
import pandas
import tables
from functools import partial
from multiprocessing.dummy import Pool
from util.audio import audiofile_to_input_vector
from util.text import text_to_char_array
def pmap(fun, iterable, threads=8):
pool = Pool(threads)
results = pool.map(fun, iterable)
pool.close()
return results
def process_single_file(row, numcep, numcontext, alphabet):
# row = index, Series
_, file = row
features = audiofile_to_input_vector(file.wav_filename, numcep, numcontext)
transcript = text_to_char_array(file.transcript, alphabet)
if (2*numcontext + len(features)) < len(transcript):
raise ValueError('Error: Audio file {} is too short for transcription.'.format(file.wav_filename))
return features, len(features), transcript, len(transcript)
# load samples from CSV, compute features, optionally cache results on disk
def preprocess(csv_files, batch_size, numcep, numcontext, alphabet, hdf5_cache_path=None):
COLUMNS = ('features', 'features_len', 'transcript', 'transcript_len')
print('Preprocessing', csv_files)
if hdf5_cache_path and os.path.exists(hdf5_cache_path):
with tables.open_file(hdf5_cache_path, 'r') as file:
features = file.root.features[:]
features_len = file.root.features_len[:]
transcript = file.root.transcript[:]
transcript_len = file.root.transcript_len[:]
# features are stored flattened, so reshape into
# [n_steps, (n_input + 2*n_context*n_input)]
for i in range(len(features)):
features[i] = np.reshape(features[i], [features_len[i], -1])
in_data = list(zip(features, features_len,
transcript, transcript_len))
print('Loaded from cache at', hdf5_cache_path)
return pandas.DataFrame(data=in_data, columns=COLUMNS)
source_data = None
for csv in csv_files:
file = pandas.read_csv(csv, encoding='utf-8', na_filter=False)
if source_data is None:
source_data = file
else:
source_data = source_data.append(file)
step_fn = partial(process_single_file,
numcep=numcep,
numcontext=numcontext,
alphabet=alphabet)
out_data = pmap(step_fn, source_data.iterrows())
if hdf5_cache_path:
print('Saving to', hdf5_cache_path)
# list of tuples -> tuple of lists
features, features_len, transcript, transcript_len = zip(*out_data)
with tables.open_file(hdf5_cache_path, 'w') as file:
features_dset = file.create_vlarray(file.root,
'features',
tables.Float32Atom(),
filters=tables.Filters(complevel=1))
# VLArray atoms need to be 1D, so flatten feature array
for f in features:
features_dset.append(np.reshape(f, -1))
features_len_dset = file.create_array(file.root,
'features_len',
features_len)
transcript_dset = file.create_vlarray(file.root,
'transcript',
tables.Int32Atom(),
filters=tables.Filters(complevel=1))
for t in transcript:
transcript_dset.append(t)
transcript_len_dset = file.create_array(file.root,
'transcript_len',
transcript_len)
print('Preprocessing done')
return pandas.DataFrame(data=out_data, columns=COLUMNS)