def encode_audio(signal):
"""
Convert a 2D numpy array into a byte sequence for PyAudio
Signal should be a numpy array with shape (chunk_size, NUM_CHANNELS)
"""
interleaved = signal.flatten()
out_data = interleaved.astype(np.float32).tostring()
return out_data
def parser(signal, signal_ID, measurement_ID, label):
parsed_data = {
'signal': signal.flatten(order='C'), #Makes it 50000 float32 1D vector
'signal_ID': signal_ID,
'measurement_ID': measurement_ID,
'label': label
}
return parsed_data
def encode(signal):
"""
Convert a 2D numpy array into a byte stream for PyAudio
Signal should be a numpy array with shape (chunk_size, channels)
"""
interleaved = signal.flatten()
# TODO: handle data type as parameter, convert between pyaudio/numpy types
out_data = interleaved.astype(np.int16).tostring()
return out_data
def encode(signal):
"""
Convert a 2D numpy array into a byte stream for PyAudio
Signal should be a numpy array with shape (chunk_size, channels)
"""
interleaved = signal.flatten()
# TODO: handle data type as parameter, convert between pyaudio/numpy types
out_data = interleaved.astype(np.int16).tostring()
return out_data
def meda(signal, sizeFilter=30):
"""
reference : Multipoint Optimal Minimum Entropy Deconvolutionand Convolution Fix:
Application to vibration fault detectionGeoff L. McDonalda Qing Zhao
MEDA algorithm used to get a signal closer from the original one
(1 * n float) signal : waveForm data
(int) sizeFilter : size of the filter used to get the original signal back
returns :
(1 * n float) filtered signal
(1 * m float) coefficient of the filter
"""
sig = signal.flatten()
# Step 1 : initialize filter
filt = np.zeros((sizeFilter))
filt[sizeFilter // 2] = 1
filt[sizeFilter // 2 + 1] = -1
filtNew = np.ones(sizeFilter)
# Step 2 : Calculate X0 and inv(X0 * X0.T) from input signal x
nbPts = len(sig)
X0 = np.zeros((sizeFilter, nbPts - sizeFilter + 1))
# filling the X0 array with the appropriate values (making it a upper diagonal)
for k in range(sizeFilter):
X0[k, k:] = sig[np.arange(sizeFilter - 1, nbPts - k)]
X0[k, :k] = sig[np.arange(sizeFilter - k - 1, sizeFilter - 1)]
while np.sum(np.abs(filtNew - filt)) > 0.001:
filt = filtNew
k += 1
# Step 3: Calculate y as X0.T * f
y = np.dot(X0.T, filt)
# Step 4 : finding the new coefficients of the filter
coefficient = np.sum(y[:nbPts - sizeFilter + 1]**2) / np.sum(
y[:nbPts - sizeFilter + 1]**4)
matrix = np.linalg.solve(np.dot(X0, X0.T), X0)
filtNew = coefficient * matrix
filtNew = np.dot(filtNew, (y[:nbPts - sizeFilter + 1].T)**3)
# normalizing the filter result
filtNew = filtNew / (np.sum(filtNew**2))**0.5
originalSig = np.dot(X0.T, filtNew)
return (originalSig, filtNew)
def compute_fourier_coefficients(signal, window, overlap, frequencies,
sampling_rate):
"""Compuses the complex fourier coefficients for the given frequencies in the given signal with the given sampling rate (windowed using "window" and "overlap").
:param signal: Time domain signal.
:type signal: np.ndarray
:param window: Vector containing window function.
:type window: np.ndarray
:param overlap: Overlap given in samples.
:type overlap: int
:param frequencies: Vector of frequencies to compute of fourier coefficients for (Hz)
:type frequencies: np.ndarray
:param sampling_rate: Sampling rate of the given signal (Hz)
:type sampling_rate: int or float
:return: x: complex fourier coefficients, t: time in sec of window positions
:rtype: tuple[np.ndarray, np.ndarray]
"""
signal = signal.flatten()
frequencies = (frequencies / 60).flatten()
win_len = window.size
hopsize = win_len - overlap
two_pi_t = 2 * np.pi * (np.arange(0, win_len) / sampling_rate)
win_num = int(np.fix((signal.size - overlap) / hopsize))
coefficients = np.zeros((win_num, frequencies.size), dtype=complex)
t = np.arange(win_len / 2, signal.size - win_len / 2 + 1,
hopsize) / sampling_rate
for f0 in range(0, frequencies.size):
two_pi_ft = frequencies[f0] * two_pi_t
cosine = np.cos(two_pi_ft)
sine = np.sin(two_pi_ft)
for w in range(0, win_num):
start = w * hopsize
stop = start + win_len
sig = signal[start:stop] * window
co = float(np.sum(sig * cosine))
si = float(np.sum(sig * sine))
coefficients[w, f0] = complex(real=co, imag=si)
coefficients = coefficients.T
return coefficients, t
def plot_signals(signals, names=None, start=0, end=None):
"""
Plot the signals specified in list <signals> with their names specified in
list <names>. Each signal is plotted in its full length unless differently
specified.
"""
# Identify the signals by index if their name is not specified
if (names is None):
legend = []
count = 0
else:
legend = names
# Loop over the signals
t_max = 0
for signal in signals:
signal = signal.flatten()
t_max = np.amax([t_max, len(signal)])
plt.plot(signal)
# If no name is given use the list index to identify the signals
if (names is None):
legend.append('Signal [' + str(count) + ']')
count += 1
# Plot and format
plt.xlabel('Index')
plt.ylabel('Value')
plt.grid(b=True)
plt.legend(legend)
if (end is None):
plt.xlim(start, t_max)
else:
plt.xlim(start, end)
plt.show()
def test_subbands(rfn, erb_filter_mode='all', verbose=0):
print('Testing subband equality for %s' % rfn)
# load matlab-generated reference file
mlab = sio.loadmat(rfn)
# print(list(mlab.keys()))
# extract parameters used to generate these filterbanks
signal = mlab['wavData'] # everything is in an 2D array
# remove 2x zero padding, if necessary
if mlab['zp'][0, 0] == 1:
signal = signal[:signal.shape[0]/2]
print(np.shape(signal))
signal_length = len(signal)
sr = mlab['Fs'][0, 0]
N = mlab['N_human'][0, 0]
low_lim = mlab['low_lim_human'][0, 0]
hi_lim = mlab['high_lim_human'][0, 0]
sample_factor_list = [1, 2, 4]
matlab_api_fx_list = [erb.make_erb_cos_filters_1x, erb.make_erb_cos_filters_2x, erb.make_erb_cos_filters_4x]
# use 1x, 2x, and 4x oversampling to test make_erb_cos_filters_nx
try:
for i in range(len(sample_factor_list)):
sample_factor = sample_factor_list[i]
# get keynames for looking up matlab reference values
freqs_key = 'freqs_%s' % sample_factor
hz_cutoffs_key = 'Hz_cutoffs_%s' % sample_factor
filts_key = 'fft_filts_%s' % sample_factor
fft_sample_key = 'fft_sample_%s' % sample_factor
subbands_key = 'subbands_%s' % sample_factor
if verbose > 1:
print('<Input Params: signal_length: %s, sr: %s, N: %s, low_lim: %s, hi_lim: %s, sample_factor: %s>' %
(signal_length, sr, N, low_lim, hi_lim, sample_factor))
if mode == 'all' or mode == 'nx':
if verbose > 1:
print('making erb filters')
# test make_erb_cos_filters_nx
filts, hz_cutoffs, freqs = erb.make_erb_cos_filters_nx(signal_length, sr, N,
low_lim, hi_lim, sample_factor,
pad_factor=1, full_filter=True, strict=False)
if verbose > 1:
print('performing subband decomposition')
start_time = time.time()
subbands_dict = sb.generate_subbands(signal.flatten(), filts, 1, debug_ret_all=True)
tot_time = time.time() - start_time
print('TIME --> %s' % tot_time)
# print(subbands.shape, mlab[subbands_key].shape)
# subbands = sb.generate_subbands(signal.flatten(), filts, 1, debug_ret_all=False)
# print(list(subbands_dict.keys()))
if verbose > 1:
print('running assertions')
# check *full* filterbanks and associated data
assert np.allclose(filts, mlab[filts_key].T), 'filts mismatch: make_erb_cos_filters_nx(...)' # transpose because of python
assert np.allclose(freqs, mlab[freqs_key]), 'Freqs mismatch: make_erb_cos_filters_nx(...)'
assert np.allclose(hz_cutoffs, mlab[hz_cutoffs_key]), 'Hz_cutoff mismatch: make_erb_cos_filters_nx(...)'
if verbose > 0:
print('PASSED ERB Filters: make_erb_cos_filters_nx(%s)' % sample_factor)
# check variables associated with subband decomposition
assert np.allclose(subbands_dict['fft_sample'], mlab['fft_sample_1'].flatten()), 'fft sample mismatch: make_erb_cos_filters_nx(...)'
assert np.allclose(subbands_dict['subbands'], mlab[subbands_key].T), 'subband mismatch: make_erb_cos_filters_nx(...)'
if verbose > 0:
print('PASSED Subbands: make_erb_cos_filters_nx(%s)' % sample_factor)
# pdb.set_trace()
if erb_filter_mode == 'matlab':
raise NotImplementedError()
if erb_filter_mode == 'literal':
raise NotImplementedError()
except AssertionError as e:
print('FAILED')
print('<Input Params: signal_length: %s, sr: %s, N: %s, low_lim: %s, hi_lim: %s, sample_factor: %s>' %
(signal_length, sr, N, low_lim, hi_lim, sample_factor))
pdb.set_trace()
raise(e)
def test_cochleagram(rfn, erb_filter_mode='all', coch_mode='fast',verbose=0):
print('<Testing cochleagrams with coch_mode: %s>' % coch_mode)
# load matlab-generated reference file
mlab = sio.loadmat(rfn)
# print(list(mlab.keys()))
# get the function to generate the cochleagrams with
coch_fx = _get_coch_function(coch_mode)
# extract parameters used to generate these filterbanks
signal = mlab['wavData'] # everything is in an 2D array
# remove 2x zero padding, if necessary
if mlab['zp'][0, 0] == 1:
signal = signal[:signal.shape[0]/2]
print(np.shape(signal))
signal_length = len(signal)
sr = mlab['Fs'][0, 0]
N = mlab['N_human'][0, 0]
low_lim = mlab['low_lim_human'][0, 0]
hi_lim = mlab['high_lim_human'][0, 0]
sample_factor_list = [1, 2, 4]
# use 1x, 2x, and 4x oversampling to test make_erb_cos_filters_nx
try:
for i in range(len(sample_factor_list)):
sample_factor = sample_factor_list[i]
# get keynames for looking up matlab reference values
freqs_key = 'freqs_%s' % sample_factor
hz_cutoffs_key = 'Hz_cutoffs_%s' % sample_factor
filts_key = 'fft_filts_%s' % sample_factor
fft_sample_key = 'fft_sample_%s' % sample_factor
if verbose > 1:
print('<Input Params: signal_length: %s, sr: %s, N: %s, low_lim: %s, hi_lim: %s, sample_factor: %s>' %
(signal_length, sr, N, low_lim, hi_lim, sample_factor))
if erb_filter_mode == 'all' or erb_filter_mode == 'nx':
if coch_mode == 'coch':
sub_envs_key = 'sub_envs_%s' % sample_factor
coch = cgram.human_cochleagram(signal, sr, N, low_lim, hi_lim, sample_factor, pad_factor=1, strict=False)
assert np.allclose(coch, mlab[sub_envs_key].T), 'subband_env mismatch: make_erb_cos_filters_nx(...)' # transpose for matlab-to-python
if verbose > 0:
print('\tPASSED Quick Cochleagram: make_erb_cos_filters_nx(%s)' % sample_factor)
else:
# test make_erb_cos_filters_nx
filts, hz_cutoffs, freqs = erb.make_erb_cos_filters_nx(signal_length, sr, N,
low_lim, hi_lim, sample_factor,
pad_factor=1, full_filter=True, strict=False)
# pdb.set_trace()
# check *full* filterbanks and associated data
assert np.allclose(filts, mlab[filts_key].T), 'filts mismatch: make_erb_cos_filters_nx(...)' # transpose because of python
assert np.allclose(freqs, mlab[freqs_key]), 'Freqs mismatch: make_erb_cos_filters_nx(...)'
assert np.allclose(hz_cutoffs, mlab[hz_cutoffs_key]), 'Hz_cutoff mismatch: make_erb_cos_filters_nx(...)'
if verbose > 0:
print('\tPASSED ERB Filters: make_erb_cos_filters_nx(%s)' % sample_factor)
# pdb.set_trace()
if coch_mode == 'subband':
subbands_key = 'subbands_%s' % sample_factor
# perform subband decomposition
start_time = time.time()
subbands_dict = sb.generate_subbands(signal.flatten(), filts, 1, debug_ret_all=True)
tot_time = time.time() - start_time
print('TIME --> %s' % tot_time)
# check variables associated with subband decomposition
# assert np.allclose(subbands_dict['fft_sample'], mlab[fft_sample_key].flatten()), 'fft sample mismatch: make_erb_cos_filters_nx(...)'
assert np.allclose(subbands_dict['subbands'], mlab[subbands_key].T), 'subband mismatch: make_erb_cos_filters_nx(...)'
if verbose > 0:
print('\tPASSED Subbands: make_erb_cos_filters_nx(%s)' % sample_factor)
elif coch_mode != 'coch':
sub_envs_key = 'sub_envs_%s' % sample_factor
# generate cochleagrams
start_time = time.time()
subband_envs = coch_fx(signal,filts, 1)
tot_time = time.time() - start_time
print('TIME --> %s' % tot_time)
# check variables associated with subband envelopes (cochleagrams)
assert np.allclose(subband_envs, mlab[sub_envs_key].T), 'subband_env mismatch: make_erb_cos_filters_nx(...)' # transpose for matlab-to-python
if verbose > 0:
print('\tPASSED Cochleagram: make_erb_cos_filters_nx(%s)' % sample_factor)
if erb_filter_mode == 'matlab':
raise NotImplementedError('Tests are only implemented for make_erb_cos_filters_nx')
if erb_filter_mode == 'literal':
raise NotImplementedError('Tests are only implemented for make_erb_cos_filters_nx')
except AssertionError as e:
print('\tFAILED')
print('<Input Params: signal_length: %s, sr: %s, N: %s, low_lim: %s, hi_lim: %s, sample_factor: %s>' %
(signal_length, sr, N, low_lim, hi_lim, sample_factor))
pdb.set_trace()
raise(e)
def median_filter(signal, size=5):
med_signal = medfilt(signal.flatten(), size)
return med_signal