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Commit 92f95258 authored by Anthony Larcher's avatar Anthony Larcher
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mostly doc

parent 88f4d2b9
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__init__.py
View file @ 92f95258
......@@ -4,7 +4,7 @@
#
# SIDEKIT is a python package for speaker verification.
# Home page: http://www-lium.univ-lemans.fr/sidekit/
#
#PARALLEL_MODULE
# SIDEKIT is a python package for speaker verification.
# Home page: http://www-lium.univ-lemans.fr/sidekit/
#
......@@ -50,8 +50,8 @@ if 'SIDEKIT' in os.environ:
if val == "true":
SIDEKIT_CONFIG["mpi"] = True
if k == "cuda":
if val == "true":
SIDEKIT_CONFIG["cuda"] = True
if val == "false":
SIDEKIT_CONFIG["cuda"] = False
PARALLEL_MODULE = 'multiprocessing' # can be , threading, multiprocessing MPI is planned in the future
......@@ -187,5 +187,5 @@ __maintainer__ = "Anthony Larcher"
__email__ = "anthony.larcher@univ-lemans.fr"
__status__ = "Production"
__docformat__ = 'reStructuredText'
__version__="1.4"
__version__="1.9"
bosaris/idmap.py
View file @ 92f95258
......@@ -259,6 +259,14 @@ class IdMap:
return ok
def set(self, left, right, start=None, stop=None):
"""
Fill the IdMap object with numpy array of leftids, rightids, and optionally starts and stops
:param left: a numpy array for leftids
:param right: a numpy array for rightids
:param start: a numpy array for start time (optional)
:param stop: a numpy array for stop time (optional)
"""
self.leftids = copy.deepcopy(left)
self.rightids = copy.deepcopy(right)
......
bosaris/key.py
View file @ 92f95258
......@@ -108,6 +108,14 @@ class Key:
@classmethod
def create(cls, modelset, segset, tar, non):
"""
Class method that creates a Key object
:param modelset: a numpy array with model IDs
:param segset: a numpy array with segment IDs
:param tar: a matrix of boolean, True if the trial is target, dimensions must be: number of models X number of segments
:param non: a matrix of boolean, True if the trial is impostor, dimensions must be: number of models X number of segments
:return: a new key object
"""
key = Key()
key.modelset = modelset
key.segset = segset
......
features_server.py
View file @ 92f95258
......@@ -48,7 +48,7 @@ __maintainer__ = "Anthony Larcher"
__email__ = "anthony.larcher@univ-lemans.fr"
__status__ = "Production"
__docformat__ = 'reStructuredText'
#comment
class FeaturesServer(object):
"""
......@@ -494,12 +494,12 @@ class FeaturesServer(object):
def get_features_per_speaker(self, show, idmap, channel=0, input_feature_filename=None, label=None):
"""
Load a single file and return a dictionary with spk_ids as keys and (feature, label) as data
:param show:
:param channel:
:param input_feature_filename:
:param label:
:param idmap:
:return:
:param show: name of the show
:param channel: number of the audio channel
:param input_feature_filename: name of the input file to read from
:param label: voice activity detection labels (optional)
:param idmap: idmap to select the features
:return: a numpy array of acoustic features
"""
if input_feature_filename is not None:
self.feature_filename_structure = input_feature_filename
......@@ -641,7 +641,6 @@ class FeaturesServer(object):
return numpy.vstack(features_list)
def _stack_features_worker(self,
input_queue,
output_queue):
......@@ -660,8 +659,6 @@ class FeaturesServer(object):
output_queue.put(self.load(*next_task)[0])
input_queue.task_done()
#@profile
def stack_features_parallel(self, # fileList, numThread=1):
show_list,
channel_list=None,
......
frontend/io.py
View file @ 92f95258
......@@ -99,6 +99,12 @@ def write_pcm(data, output_file_name):
@check_path_existance
def write_wav(data, output_file_name, fs):
"""Write signal to single channel WAV 16 bits
:param data: audio signal to write
:param output_file_name: name of the file to write
:param fs: sample rate in Hz
"""
if data.dtype != numpy.int16:
if data.dtype == numpy.float32:
data /= numpy.abs(data).max()
......@@ -980,6 +986,7 @@ def read_htk_segment(input_file_name,
m = numpy.r_[numpy.repeat(m[[0]], s-start, axis=0), m, numpy.repeat(m[[-1]], stop-e, axis=0)]
return m.astype(numpy.float32)
def _add_dataset_header(fh,
dataset_id,
_min_val,
......@@ -988,6 +995,12 @@ def _add_dataset_header(fh,
"""
Create a dataset in the HDF5 file and write the data
after compressing float to int
:param fh: file handler in HDF5 format
:param dataset_id: name of the new dataset to create
:param _min_val: minimum value in the dataset (used for compression)
:param _range: range of the values in the dataset (used for compression)
:param _header: header of the dataset
"""
_c_header = (_header - _min_val) / _range
numpy.clip(_c_header, 0., 1.)
......@@ -1004,6 +1017,7 @@ def _add_dataset_header(fh,
compression="gzip",
fletcher32=True)
def _add_percentile_dataset(fh,
dataset_id,
data):
......@@ -1011,6 +1025,10 @@ def _add_percentile_dataset(fh,
Create the dataset in the HDF5 file, write the data
compressed in int8 format and the header compressed in
int format
:param fh: file handler in HDF5 format
:param dataset_id: name of the new dataset to create
:param data: data to fill the dataset
"""
_min_val = data.min()
_range = data.ptp()
......@@ -1044,28 +1062,71 @@ def _add_percentile_dataset(fh,
fletcher32=True)
def _read_dataset(h5f, dataset_id):
"""
Read a dataset from HDF5 file
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read
:return: the data stored in the dataset
"""
data = h5f[dataset_id][()]
if data.ndim == 1:
data = data[:, numpy.newaxis]
return data
def _read_segment(h5f, dataset_id, s, e):
"""
Read a sequence of features stored in an HDF5 dataset.
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read from
:param s: start index of the sequence to read
:param e: end index of the sequence to read
:return: the sequence of features in a numpy array format
"""
data = h5f[dataset_id][s:e]
return data
def _read_dataset_htk(h5f, dataset_id):
"""
Read a dataset from HDF5 file
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read
:return: the sequence of features in a numpy array format
"""
(A, B) = h5f[dataset_id + "comp"][()]
data = (h5f[dataset_id][()] + B) / A
if data.ndim == 1:
data = data[:, numpy.newaxis]
return data
def _read_segment_htk(h5f, dataset_id, e, s):
"""
Read a sequence of features stored in an HDF5 dataset written in HTK format
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read from
:param s: start index of the sequence to read
:param e: end index of the sequence to read
:return: the sequence of features in a numpy array format
"""
(A, B) = h5f[dataset_id + "comp"][()]
data = (h5f[dataset_id][s:e, :] + B) / A
return data
def read_dataset_percentile(h5f, dataset_id):
"""
Read a compressed dataset from HDF5 file
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read
:return: the sequence of features in a numpy array format
"""
# read the header
(_min_val, _range) = h5f[dataset_id + "_min_range"][()]
c_header = h5f[dataset_id + "_header"][()]
......@@ -1079,7 +1140,17 @@ def read_dataset_percentile(h5f, dataset_id):
mat3 = (_header[:,[2]] + (_header[:,[3]] - _header[:,[2]]) * (c_data.T - 192) * (1/63)) * (c_data.T > 192)
return (mat1+mat2+mat3).T
def _read_segment_percentile(h5f, dataset_id, s, e):
"""
Read a sequence of features stored in a compressed HDF5 dataset
:param h5f: file handler in HDF5 format
:param dataset_id: name of the dataset to read from
:param s: start index of the sequence to read
:param e: end index of the sequence to read
:return: the sequence of features in a numpy array format
"""
# read the header
(_min_val, _range) = h5f[dataset_id + "_min_range"][()]
c_header = h5f[dataset_id + "_header"][()]
......@@ -1100,6 +1171,25 @@ def _write_show(show,
fb, fb_mean, fb_std,
bnf, bnf_mean, bnf_std,
label):
"""
Write features for a given show in HDF5 format
:param show: name of the show to write
:param fh: file handler in HDF5 format
:param cep: cepstral coefficients
:param cep_mean: mean vector of the cepstral coefficients
:param cep_std: standard deviation vector of the cepstral coefficients
:param energy: energy value per frame
:param energy_mean: mean of the energy
:param energy_std: standard deviation of the energy
:param fb: filterbank coefficients
:param fb_mean: mean vector of the filterbank coefficients
:param fb_std: standard deviation vector of filterbank coefficients
:param bnf: bottleneck features
:param bnf_mean: mean vector of the bottleneck features
:param bnf_std: standard deviation vector of bottleneck features
:param label: voice activity detection labels per frame
"""
if cep is not None:
fh.create_dataset(show + '/cep', data=cep.astype('float32'),
maxshape=(None, None),
......@@ -1161,6 +1251,7 @@ def _write_show(show,
compression="gzip",
fletcher32=True)
def _write_show_htk(show,
fh,
cep, cep_mean, cep_std,
......@@ -1168,6 +1259,24 @@ def _write_show_htk(show,
fb, fb_mean, fb_std,
bnf, bnf_mean, bnf_std,
label):
"""
Write features for a given show in HDF5 and HTK format
:param fh: file handler in HDF5 format
:param cep: cepstral coefficients
:param cep_mean: mean vector of the cepstral coefficients
:param cep_std: standard deviation vector of the cepstral coefficients
:param energy: energy value per frame
:param energy_mean: mean of the energy
:param energy_std: standard deviation of the energy
:param fb: filterbank coefficients
:param fb_mean: mean vector of the filterbank coefficients
:param fb_std: standard deviation vector of filterbank coefficients
:param bnf: bottleneck features
:param bnf_mean: mean vector of the bottleneck features
:param bnf_std: standard deviation vector of bottleneck features
:param label: voice activity detection labels per frame
"""
if cep is not None:
A_cep = 2 * 32767. / (cep.max() - cep.min())
B_cep = (cep.max() + cep.min()) * 32767. / (cep.max() - cep.min())
......@@ -1253,6 +1362,7 @@ def _write_show_htk(show,
compression="gzip",
fletcher32=True)
def _write_show_percentile(show,
fh,
cep, cep_mean, cep_std,
......@@ -1260,6 +1370,25 @@ def _write_show_percentile(show,
fb, fb_mean, fb_std,
bnf, bnf_mean, bnf_std,
label):
"""
Write features for a given show in HDF5 and HTK format
:param show: name of the sow to write
:param fh: file handler in HDF5 format
:param cep: cepstral coefficients
:param cep_mean: mean vector of the cepstral coefficients
:param cep_std: standard deviation vector of the cepstral coefficients
:param energy: energy value per frame
:param energy_mean: mean of the energy
:param energy_std: standard deviation of the energy
:param fb: filterbank coefficients
:param fb_mean: mean vector of the filterbank coefficients
:param fb_std: standard deviation vector of filterbank coefficients
:param bnf: bottleneck features
:param bnf_mean: mean vector of the bottleneck features
:param bnf_std: standard deviation vector of bottleneck features
:param label: voice activity detection labels per frame
"""
if cep is not None:
_add_percentile_dataset(fh, show + '/cep', cep)
......@@ -1318,7 +1447,6 @@ def _write_show_percentile(show,
fletcher32=True)
def write_hdf5(show,
fh,
cep, cep_mean, cep_std,
......@@ -1343,7 +1471,7 @@ def write_hdf5(show,
:param bnf_mean: pre-computed mean of the bottleneck features
:param bnf_std: pre-computed standard deviation of the bottleneck features
:param label: vad labels to store
:param compressed: boolean, default is False
:param compression: boolean, default is False
:return:
"""
#write the the type of compression: could be:
......@@ -1382,13 +1510,14 @@ def write_hdf5(show,
bnf, bnf_mean, bnf_std,
label)
def read_hdf5(h5f, show, dataset_list=("cep", "fb", "energy", "vad", "bnf")):
"""
:param h5f: HDF5 file handler to read from
:param show: identifier of the show to read
:param dataset_list: list of datasets to read and concatenate
:return:
:return: a numpy array with acoustic features and one with VAD labels
"""
compression_type = {0:'none', 1:'htk', 2:'percentile'}
if "compression" not in h5f:
......@@ -1464,17 +1593,18 @@ def read_hdf5(h5f, show, dataset_list=("cep", "fb", "energy", "vad", "bnf")):
return feat.astype(numpy.float32), label
def _rms_energy(x):
return 10*numpy.log10((1e-12 + x.dot(x))/len(x))
def _add_noise(signal, noise_file_name, snr, sample_rate):
"""
Add noise to a speech signal
:param signal:
:param noise_file_name:
:param snr:
:return:
:param signal: the original signal to augmente
:param noise_file_name: the name fo the noise file to use
:param snr: signal to noise ratio
:return: the signal augmented with noise
"""
# Open noise file
if isinstance(noise_file_name, numpy.ndarray):
......@@ -1502,6 +1632,7 @@ def _add_noise(signal, noise_file_name, snr, sample_rate):
return (noisy - noisy.mean()) / noisy.std()
def bin_interp(upcount, lwcount, upthr, lwthr, margin, tol=0.1):
n_iter = 1
if abs(upcount - upthr - margin) < tol:
......@@ -1525,6 +1656,7 @@ def bin_interp(upcount, lwcount, upthr, lwthr, margin, tol=0.1):
diff = midcount - midthr - margin
return midcount
def asl_meter(x, fs, nbits=16):
'''Measure the Active Speech Level (ASR) of x following ITU-T P.56.
If x is integer, it will be scaled to (-1, 1) according to nbits.
......@@ -1587,6 +1719,7 @@ def asl_meter(x, fs, nbits=16):
return asl
def _add_reverb(signal, reverb_file_name, sample_rate, reverb_level=-26.0, ):
'''Adds reverb (convolutive noise) to a speech signal.
The output speech level is normalized to asl_level.
......@@ -1600,107 +1733,3 @@ def _add_reverb(signal, reverb_file_name, sample_rate, reverb_level=-26.0, ):
return (y - y.mean()) / y.std()
def degrade_audio(input_path,
input_extension,
output_path,
output_extension,
input_filename,
output_filename,
sampling_frequency=16000,
noise_file_name=None,
snr=-10,
reverb_file_name=None,
reverb_level=-26.):
"""
:param input_filename:
:param output_filename:
:return:
"""
# Open audio file, get the signal and possibly the sampling frequency
signal, sample_rate = read_audio(input_filename, sampling_frequency)
if signal.ndim == 1:
signal = signal[:, numpy.newaxis]
for channel in range(signal.shape[1]):
if noise_file_name is not None:
signal[:, channel] = _add_noise(signal[:, channel], noise_file_name, snr, sampling_frequency)
if reverb_file_name is not None:
signal[:, channel] = _add_reverb(signal[:, channel], reverb_file_name, sampling_frequency, reverb_level)
write_wav(signal, output_filename, sample_rate)
@process_parallel_lists
def augment_list(input_path,
input_extension,
output_path,
output_extension,
sampling_frequency,
show_list,
channel_list,
audio_file_list=None,
feature_file_list=None,
noise_file_list=None,
snr_list=None,
reverb_file_list=None,
reverb_levels=None,
num_thread=1):
"""
Compute the acoustic parameters (filter banks, cepstral coefficients, log-energy and bottleneck features
for a list of audio files and save them to disk in a HDF5 format
The process is parallelized if num_thread is higher than 1
:param show_list: list of IDs of the show to process
:param channel_list: list of channel indices corresponding to each show
:param audio_file_list: list of input audio files if the name is independent from the ID of the show
:param feature_file_list: list of output audio files if the name is independent from the ID of the show
:param num_thread: number of parallel process to run
:return:
"""
# get the length of the longest list
max_length = max([len(l) for l in [show_list, channel_list, audio_file_list, feature_file_list]
if l is not None])
if show_list is None:
show_list = numpy.empty(int(max_length), dtype='|O')
if audio_file_list is None:
audio_file_list = numpy.empty(int(max_length), dtype='|O')
if feature_file_list is None:
feature_file_list = numpy.empty(int(max_length), dtype='|O')
if noise_file_list is None:
noise_file_list = numpy.empty(int(max_length), dtype='|O')
snr_list = numpy.empty(int(max_length), dtype='|O')
elif snr_list is None:
snr_list = numpy.full(int(max_length), 5.)
if reverb_file_list is None:
reverb_file_list = numpy.empty(int(max_length), dtype='|O')
reverb_levels = numpy.empty(int(max_length), dtype='|O')
elif reverb_levels is None:
reverb_levels = numpy.full(int(max_length), -26.)
for show, channel, input_file, output_file, noise_file, snr, reverb_file, reverb_level in zip(show_list,
channel_list,
audio_file_list,
feature_file_list,
noise_file_list,
snr_list,
reverb_file_list,
reverb_levels):
degrade_audio(input_path, input_extension, output_path, output_extension,
show,
input_file,
output_file,
sampling_frequency,
noise_file,
snr,
reverb_file,
reverb_level)
nnet/xsets.py
View file @ 92f95258
......@@ -26,15 +26,12 @@ Copyright 2014-2021 Anthony Larcher
"""
import math
import numpy
import pandas
import random
import torch
import torchaudio
import tqdm
import soundfile
import yaml
from .augmentation import data_augmentation
from ..bosaris.idmap import IdMap
......@@ -64,15 +61,17 @@ class SideSampler(torch.utils.data.Sampler):
rank=0,
num_process=1,
num_replicas=1):
"""[summary]
Args:
data_source ([type]): [description]
spk_count ([type]): [description]
examples_per_speaker ([type]): [description]
samples_per_speaker ([type]): [description]
batch_size ([type]): [description]
num_replicas: number of GPUs for parallel computing
"""
:param data_source:
:param spk_count:
:param examples_per_speaker:
:param samples_per_speaker:
:param batch_size:
:param seed:
:param rank:
:param num_process:
:param num_replicas: number of GPUs for parallel computing
"""
self.train_sessions = data_source
self.labels_to_indices = dict()
......@@ -89,7 +88,6 @@ class SideSampler(torch.utils.data.Sampler):
assert (self.samples_per_speaker * self.spk_count * self.examples_per_speaker) % self.num_process == 0
self.batch_size = batch_size // (self.examples_per_speaker * self.num_replicas)
#self.batch_size = batch_size // self.examples_per_speaker
# reference all segment indexes per speaker
for idx in range(self.spk_count):
......@@ -105,8 +103,11 @@ class SideSampler(torch.utils.data.Sampler):
self.segment_cursors = numpy.zeros((len(self.labels_to_indices),), dtype=numpy.int)
def __iter__(self):
"""
:return:
"""
g = torch.Generator()
g.manual_seed(self.seed + self.epoch)
numpy.random.seed(self.seed + self.epoch)
......@@ -159,14 +160,14 @@ class SideSampler(torch.utils.data.Sampler):
#return (self.samples_per_speaker * self.spk_count * self.examples_per_speaker) // self.num_process
return (self.samples_per_speaker * self.spk_count * self.examples_per_speaker * self.num_replicas) // self.num_process
def set_epoch(self, epoch: int) -> None:
self.epoch = epoch
class SideSet(Dataset):
"""
Dataset that loads the data for network training
"""
def __init__(self,
dataset,
set_type="train",
......@@ -179,10 +180,15 @@ class SideSet(Dataset):
):
"""
:param dataset_yaml: name of the YAML file describing the dataset
:param dataset: name of the YAML file describing the dataset
:param set_type: string, can be "train" or "validation"
:param chunk_per_segment: number of chunks to select for each segment
default is 1 and -1 means select all possible chunks
:param transform_number:
:param overlap:
:param dataset_df:
:param min_duration:
:param output_format:
"""
self.data_path = dataset["data_path"]
self.sample_rate = int(dataset["sample_rate"])
......@@ -283,7 +289,6 @@ class SideSet(Dataset):
# load the RIR database
self.rir_df = tmp_rir_df.set_index(tmp_rir_df.type)
def __getitem__(self, index):
"""
......@@ -337,13 +342,21 @@ class SideSet(Dataset):
def __len__(self):
"""
Return the length of the dataset
:param self:
:return:
"""
return self.len
def get_sample(path, resample=None):
"""
:param path:
:param resample: