def test_perform(self):
x = lscalar()
f = function([x], self.op(x))
M = np.random.randint(3, 51, size=())
assert np.allclose(f(M), np.bartlett(M))
assert np.allclose(f(0), np.bartlett(0))
assert np.allclose(f(-1), np.bartlett(-1))
b = np.array([17], dtype="uint8")
assert np.allclose(f(b[0]), np.bartlett(b[0]))
def test_perform(self):
x = tensor.lscalar()
f = function([x], self.op(x))
M = numpy.random.random_integers(3, 50, size=())
assert numpy.allclose(f(M), numpy.bartlett(M))
assert numpy.allclose(f(0), numpy.bartlett(0))
assert numpy.allclose(f(-1), numpy.bartlett(-1))
b = numpy.array([17], dtype='uint8')
assert numpy.allclose(f(b[0]), numpy.bartlett(b[0]))
def test_perform(self):
x = tensor.lscalar()
f = function([x], self.op(x))
M = numpy.random.random_integers(3, 50, size=())
assert numpy.allclose(f(M), numpy.bartlett(M))
assert numpy.allclose(f(0), numpy.bartlett(0))
assert numpy.allclose(f(-1), numpy.bartlett(-1))
b = numpy.array([17], dtype='uint8')
assert numpy.allclose(f(b[0]), numpy.bartlett(b[0]))
def test_bartlett_1(self):
b = np.bartlett(5)
print(b)
b = np.bartlett(10)
print(b)
b = np.bartlett(12)
print(b)
return
def acf(f, lag=2000, window=2, conv=True):
"""My own interface to scipy"""
from scipy import signal
import numpy as np
f2 = np.concatenate(
(f, np.zeros((f.shape[0], f.shape[1]))
)) ##This is needed due how scipy computes the ACF (it rolls)
if not conv:
acf = signal.correlate(
f2, f, mode="valid",
method='direct')[:-1] #Usually we need only the sum
else:
acf = signal.correlate(
f2, f, mode="valid")[:-1] #Usually we need only the sum
#Normalize
acf = np.divide(acf.flatten(), np.flip(np.arange(1, acf.size + 1), axis=0))
#Select window
if window == 1:
win = np.blackman(2 * lag)
elif window == 2:
win = np.hanning(2 * lag)
elif window == 3:
win = np.hamming(2 * lag)
elif window == 4:
win = np.bartlett(2 * lag)
else:
win = np.ones(2 * lag)
#Apply window
acf = np.multiply(acf[:lag], win[lag:])
return acf
def main_true():
# load true ecg data
num = 1
for i in range(1, 15):
val = "{}-1".format(i)
try:
data = np.load("{}resampled-{}.npy".format(dirs, val))
except IOError:
print("{} doesn't exist.".format(val))
continue
else:
print("Start processing {}".format(val))
for k in range(len(data)):
y = data[k]
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
# spectrogram param keeps the same to Matlab. (include the window if using hamming)
plt.axis("off")
plt.specgram(y, NFFT=nfft, Fs=fs, noverlap=int(fs*(475/512)), window=np.bartlett(fs))
extent = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
# save fig without the white border.
plt.savefig("./dataset/Specgrams/1/{}.png".format(num), bbox_inches=extent)
plt.close()
num += 1
print("{} finished. pic num is {}".format(val, num-1))
def smooth(x, windowLen, windowType="boxcar"):
"""Smooth a numpy array, returning the smoothed values
Adapted from http://www.scipy.org/Cookbook/SignalSmooth"""
if x.ndim != 1:
raise ValueError("smooth only accepts 1 dimension arrays.")
if x.size < windowLen:
raise ValueError("Input vector needs to be bigger than window size.")
if windowLen < 3:
return x
if windowType == "boxcar":
w = np.ones(windowLen,'d')
elif windowType == "hamming":
w = np.hamming(windowLen)
elif windowType == "hanning":
w = np.hanning(windowLen)
elif windowType == "bartlett":
w = np.bartlett(windowLen)
elif windowType == "blackman":
w = np.blackman(windowLen)
else:
raise ValueError("windowType %s is not one of 'boxcar', 'hanning', 'hamming', 'bartlett', 'blackman'"
% windowType)
s = np.r_[x[windowLen-1:0:-1],x,x[-1:-windowLen:-1]]
y = np.convolve(w/w.sum(), s, mode='valid')
return y[windowLen//2:-windowLen//2 + 1]
def apply_filter(self, array):
if len(array.shape)!=1:
return False # need 2D data
nx = array.shape[0]
# Apodization function
if self.type == 1:
ft = np.bartlett(nx)
elif self.type == 2:
ft = np.blackman(nx)
elif self.type == 3:
ft = np.hamming(nx)
elif self.type == 4:
ft = np.hanning(nx)
elif self.type == 5:
# Blackman-Harris window
a0 = 0.35875
a1 = 0.48829
a2 = 0.14128
a3 = 0.01168
x = np.linspace(0,1,nx)
ft = a0 - a1*np.cos(2*np.pi*x) + a2*np.cos(4*np.pi*x) + a3*np.cos(6*np.pi*x)
elif self.type == 6:
# Lanczos window
x = np.linspace(-1,1,nx)
ft = np.sinc(x)
elif self.type == 7:
x = np.linspace(-1,1,nx)
exec('x='+self.custom)
ft = x
else:
ft = np.ones(nx)
array.data = array.data*ft
return True
def smooth(x, window_len=11, window='hanning'):
"""
"""
if x.ndim != 1:
raise ValueError("smooth only accepts 1 dimension arrays.")
if x.size < window_len:
raise ValueError("Input vector needs to be bigger than window size.")
if window_len < 3:
return x
s = np.r_[2 * x[0] - x[window_len - 1::-1], x,
2 * x[-1] - x[-1:-window_len:-1]]
if window == 'flat': # moving average
w = np.ones(window_len)
elif window == 'hanning':
w = np.hanning(window_len)
elif window == 'hamming':
w = np.hamming(window_len)
elif window == 'bartlett':
w = np.bartlett(window_len)
elif window == 'blackman':
w = np.blackman(window_len)
else:
raise ValueError(
"Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'"
)
y = np.convolve(w / w.sum(), s, mode='same')
return y[window_len:-window_len + 1]
def power_spectrum(trace, time_window=1000, overlap_window=None, enforce_pow2=True, freq_range=None):
# -----------------------------------------------------------------------------
'''
Returns the power spectrum of trace. Parameters set to fit with what Paolo
does within his project.
'''
from matplotlib.mlab import psd
from matplotlib.pylab import detrend_linear, detrend_mean, detrend_none
from neurovivo.common import nextpow2
dt = (trace._time[1]-trace._time[0]).rescale(pq.ms).item()
Fs = 1000./dt
NFFT=int(time_window/dt)
if enforce_pow2:
NFFT=nextpow2(NFFT)
time_window = 1.*time_window*NFFT/int(time_window/dt)
if overlap_window == None:
overlap_window = 0.75 * time_window
noverlap=int(overlap_window/dt)
window = np.bartlett(NFFT)
#print dt, Fs, NFFT, noverlap
pows, freqs = psd(detrend_mean(trace._data), NFFT=NFFT, Fs=Fs, noverlap=noverlap, window=window, detrend=detrend_none)
if freq_range == None:
return pows, freqs
else:
freqs, pows = cmn.splice_two_vectors(freqs, pows, freq_range)
return pows, freqs
def plotPSD(data, fftWindow, Fs):
assert fftWindow in [
'rectangular', 'bartlett', 'blackman', 'hamming', 'hanning'
]
N = len(data)
# Generate the selected window
if fftWindow == "rectangular":
window = np.ones(N)
elif fftWindow == "bartlett":
window = np.bartlett(N)
elif args.fftWindow == "blackman":
window = np.blackman(N)
elif fftWindow == "hamming":
window = np.hamming(N)
elif fftWindow == "hanning":
window = np.hanning(N)
dft = np.fft.fft(data * window)
if Fs == None:
# If the sample rate is known then plot PSD as
# Power/Freq in (dB/Hz)
plt.psd(data * window, NFFT=N)
print("first")
else:
# If sample rate is not known then plot PSD as
# Power/Freq as (dB/rad/sample)
plt.psd(data * window, NFFT=N, Fs=Fs)
print("second")
plt.show()
def bartlett_window(self, show=0): apod = N.bartlett(self.data_points) for i in range(2): self.the_result.y[i] = self.the_result.y[i]*apod if show == 1: return self.the_result return self
def gen_mel_filts(num_filts, framelength, samp_freq):
mel_filts = numpy.zeros((framelength, num_filts))
step_size = int(framelength/float((num_filts + 1))) #Sketch it out to understand
filt_width = math.floor(step_size*2)
filt = numpy.bartlett(filt_width)
step = 0
for i in xrange(num_filts):
mel_filts[step:step+filt_width, i] = filt
step = step + step_size
# Let's find the linear filters that correspond to the mel filters
# The freq axis goes from 0 to samp_freq/2, so...
samp_freq = samp_freq/2
filts = numpy.zeros((framelength, num_filts))
for i in xrange(num_filts):
for j in xrange(framelength):
freq = (j/float(framelength)) * samp_freq
# See which freq pt corresponds on the mel axis
mel_freq = 1127 * numpy.log( 1 + freq/700 )
mel_samp_freq = 1127 * numpy.log( 1 + samp_freq/700 )
# where does that index in the discrete frequency axis
mel_freq_index = int((mel_freq/mel_samp_freq) * framelength)
if mel_freq_index >= framelength-1:
mel_freq_index = framelength-1
filts[j,i] = mel_filts[mel_freq_index,i]
# Let's normalize each filter based on its width
for i in xrange(num_filts):
nonzero_els = numpy.nonzero(filts[:,i])
width = len(nonzero_els[0])
filts[:,i] = filts[:,i]*(10.0/width)
return filts
def construct_window(width, family, scale):
if family == "bartlett":
return numpy.bartlett(width) * scale
if family == "blackman":
return numpy.blackman(width) * scale
if family == "hamming":
return numpy.hamming(width) * scale
if family == "hann":
import scipy.signal
return scipy.signal.hann(width) * scale
if family == "hanning":
return numpy.hanning(width) * scale
if family == "kaiser":
beta = 14
return numpy.kaiser(width, beta) * scale
if family == "tukey":
import scipy.signal
return scipy.signal.tukey(width) * scale
print("window family %s not supported" % family)
def single_taper_spectrum(data, delta, taper_name=None):
"""
Returns the spectrum and the corresponding frequencies for data with the
given taper.
"""
length = len(data)
good_length = length // 2 + 1
# Create the frequencies.
# XXX: This might be some kind of hack
freq = abs(np.fft.fftfreq(length, delta)[:good_length])
# Create the tapers.
if taper_name == 'bartlett':
taper = np.bartlett(length)
elif taper_name == 'blackman':
taper = np.blackman(length)
elif taper_name == 'boxcar':
taper = np.ones(length)
elif taper_name == 'hamming':
taper = np.hamming(length)
elif taper_name == 'hanning':
taper = np.hanning(length)
elif 'kaiser' in taper_name:
taper = np.kaiser(length, beta=14)
# Should never happen.
else:
msg = 'Something went wrong.'
raise Exception(msg)
# Detrend the data.
data = detrend(data)
# Apply the taper.
data *= taper
spec = abs(np.fft.rfft(data)) ** 2
return spec, freq
def smooth(input_data, nth_octave = 6, window_type='hamming'):
""" Smooth input data over 1/n octave """
f_min = 30
f_max = 20e3
number_of_octaves = math.log(f_max / f_min, 2)
# ideally, this should be computed from the display resolution
number_of_points = 4048
points_per_octave = number_of_points / number_of_octaves
log_data = _distribute_over_log(input_data, f_min, f_max,
number_of_points)
window_length = points_per_octave / nth_octave
if window_type == 'hamming':
window = np.hamming(window_length)
elif window_type == 'bartlett':
window = np.bartlett(window_length)
elif window_type == 'blackman':
window = np.blackman(window_length)
elif window_type == 'hanning':
window = np.hanning(window_length)
output = np.convolve(window / window.sum(), log_data, mode='same')
return output
def create_window(size, window_id="blackman", param=None):
"""
Create a new window numpy array
param is only used for some windows.
window_id can also be a function/functor which
is used to create the window.
>>> create_window("blackman", 500)
... # NumPy array of size 500
>>> create_window(myfunc, 500, param=3.5)
... # result of calling myfunc(500, 3.5)
"""
if window_id == "blackman":
return np.blackman(size)
elif window_id == "bartlett":
return np.bartlett(size)
elif window_id == "hamming":
return np.hamming(size)
elif window_id == "hanning":
return np.hanning(size)
elif window_id == "kaiser":
return np.kaiser(size, 2.0 if param is None else param)
elif window_id in ["ones", "none"]:
return np.ones(size)
elif callable(window_id):
return window_id(size, param)
else:
raise ValueError(f"Unknown window {window_id}")
def windowing(input, window_type, axis=0):
"""Window the input based on given window type.
Args:
input: input numpy array to be windowed.
window_type: enum chosen between Bartlett, Blackman, Hamming, Hanning and Kaiser.
axis: the axis along which the windowing will be applied.
Returns:
"""
window_length = input.shape[axis]
if window_type == Window.BARTLETT:
window = np.bartlett(window_length)
elif window_type == Window.BLACKMAN:
window = np.blackman(window_length)
elif window_type == Window.HAMMING:
window = np.hamming(window_length)
elif window_type == Window.HANNING:
window = np.hanning(window_length)
else:
raise ValueError("The specified window is not supported!!!")
output = input * window
return output
def get_window(window, wlen):
if type(window) == str:
# types:
# boxcar, triang, blackman, hamming, hann, bartlett, flattop, parzen,
# bohman, blackmanharris, nuttall, barthann
if window == 'hamming':
fft_window = np.hamming(wlen)
elif window == 'bartlett':
fft_window = np.bartlett(wlen)
elif window == 'hann' or window == 'hanning':
fft_window = np.hanning(wlen)
else:
#try:
# scipy.signal.get_window gives non-symmetric results for hamming with even length :(
#fft_window = scipy.signal.get_window(window, wlen)
#except:
#raise Exception('cannot obtain window type {}'.format(window))
raise Exception('cannot obtain window type {}'.format(window))
# fft_window = scipy.signal.hamming(win_length, sym=False)
elif six.callable(window):
# User supplied a windowing function
fft_window = window(wlen)
else:
# User supplied a window vector.
# Make it into an array
fft_window = np.asarray(window)
assert (len(fft_window) == wlen)
fft_window.flatten()
return fft_window
def window(self, window):
window_size = self._window_packetsize
buffer = allocate(shape=(window_size, ), dtype=np.int32)
self._window_address = buffer.device_address
if window == 'rectangular':
buffer[:] = np.int32(np.ones(window_size)[:] * 2**14)
elif window == 'bartlett':
buffer[:] = np.int32(np.bartlett(window_size)[:] * 2**14)
elif window == 'blackman':
buffer[:] = np.int32(np.blackman(window_size)[:] * 2**14)
elif window == 'hamming':
buffer[:] = np.int32(np.hamming(window_size)[:] * 2**14)
elif window == 'hanning':
buffer[:] = np.int32(np.hanning(window_size)[:] * 2**14)
else:
buffer[:] = np.int32(np.ones(window_size)[:] * 2**14)
window = 'rectangular'
self._window_transfer = 1
while not self.window_ready:
pass
self._window_transfer = 0
self._window_type = window
self._window_squaresum = np.sum(
(np.array(buffer, dtype=np.single) * 2**-14)**2)
self._window_sum = np.sum((np.array(buffer, dtype=np.single)))
buffer.freebuffer()
self._spectrum_typescale = \
int(struct.unpack('!i',struct.pack('!f',float((self._sample_frequency/self._decimation_factor)/(self._number_samples))))[0])
self._spectrum_powerscale = \
int(struct.unpack('!i',struct.pack('!f',float(1/((self._sample_frequency/self._decimation_factor)*self._window_squaresum))))[0])
def generate_window(fs, wave_int, duration, apply_start, apply_end, window_function):
"""
:param fs: number of samples per second (standard)
:param wave_int: base sound where the window will be applied
:param duration: duration of the window (it will be the same on the start and end)
:param apply_start: True if the window should be created at the start, False otherwise.
:param apply_end: True if the window should be created at the end, False otherwise.
:param window_function: window function to be generated. Possible values accepted:
'Hanning', 'Hamming', 'Blackman', 'Bartlett'. It will revert to 'Hanning' if an unknown option is given.
:return: Returns the modified sound with the window applied to it.
"""
len_fade = int(duration * fs)
if window_function == 'Hanning':
fade_io = np.hanning(len_fade * 2)
elif window_function == 'Hamming':
fade_io = np.hamming(len_fade * 2)
elif window_function == 'Blackman':
fade_io = np.blackman(len_fade * 2)
elif window_function == 'Bartlett':
fade_io = np.bartlett(len_fade * 2)
else: # default
fade_io = np.hanning(len_fade * 2)
fadein = fade_io[:len_fade]
fadeout = fade_io[len_fade:]
win = np.ones(len(wave_int))
if apply_start:
win[:len_fade] = fadein
if apply_end:
win[-len_fade:] = fadeout
wave_int = wave_int * win
return wave_int
def plotWindowFunc(): plt.clf() plt.plot(np.arange(20), np.kaiser(20,3.5)) plt.plot(np.arange(20), np.bartlett(20)) plt.plot(np.arange(20), np.blackman(20)) plt.plot(np.arange(20), np.hamming(20)) plt.plot(np.arange(20), np.hanning(20))
def mdist_curves(mdist_real):
"""
fit curve comparing median location error to the actual location error
"""
CHUNKS = 10
dists_ = np.array(list(mdist_real))
dists = dists_[dists_[:,0].argsort()]
dist_count = dists.shape[0]
# cut off the start to make even chunks
chunks = np.split(dists[(dist_count%CHUNKS):,:],CHUNKS)
bins = utils.dist_bins(30)
for index,chunk in enumerate(chunks):
row = chunk[:,1]
hist,b = np.histogram(row,bins)
bin_mids = (b[:-1]+b[1:])/2
bin_areas = np.pi*(b[1:]**2 - b[:-1]**2)
scaled_hist = hist/(bin_areas*len(row))
window = np.bartlett(5)
smooth_hist=np.convolve(scaled_hist,window,mode='same')/sum(window)
coeffs = np.polyfit(
np.log(bin_mids[1:121]),
np.log(smooth_hist[1:121]),
3)
yield dict(
coeffs = list(coeffs),
cutoff = 0 if index==0 else chunk[0,0],
local = scaled_hist[0],
)
def shortTermEny(signal, framelen, stride, fs, window='hamming'):
"""
:param signal: raw signal of waveform, unit: μV
:param framelen: length of per frame, type: int
:param stride: length of translation per frame
:param fs: sampling rate per microsecond
:param window: window's function
:return: time_stE, stE
"""
if signal.shape[0] <= framelen:
nf = 1
else:
nf = int(np.ceil((1.0 * signal.shape[0] - framelen + stride) / stride))
pad_length = int((nf - 1) * stride + framelen)
zeros = np.zeros((pad_length - signal.shape[0],))
pad_signal = np.concatenate((signal, zeros))
indices = np.tile(np.arange(0, framelen), (nf, 1)) + np.tile(np.arange(0, nf * stride, stride),
(framelen, 1)).T.astype(np.int32)
frames = pad_signal[indices]
allWindows = {'hamming': np.hamming(framelen), 'hanning': np.hanning(framelen), 'blackman': np.blackman(framelen),
'bartlett': np.bartlett(framelen)}
t = np.arange(0, nf) * (stride * 1.0 / fs)
eny, amp = np.zeros(nf), np.zeros(nf)
try:
windows = allWindows[window]
except:
print("Please select window's function from: hamming, hanning, blackman and bartlett.")
return t, eny, amp
for i in range(0, nf):
b = np.square(frames[i:i + 1][0]) * windows * 1.0 / fs
eny[i] = np.sum(b)
amp[i] = max(abs(frames[i:i + 1][0] * windows))
return t, eny, amp
def echo_decode(marked_audio: Audio, key: dict = None) -> bytes:
np.fft.fft = pyfftw.interfaces.numpy_fft.fft
np.fft.ifft = pyfftw.interfaces.numpy_fft.ifft
pyfftw.interfaces.cache.enable()
pyfftw.interfaces.cache.set_keepalive_time(1.0)
m = key['m']
fragment_len = key['fragment_len']
bits_len = key['bits_len']
encoded_len = fragment_len * bits_len
samples_width = marked_audio.sample_width
marked_samples_reg = marked_audio.get_reshaped_samples()
channel0_samples_reg = np.reshape(marked_samples_reg[0, :encoded_len],
(fragment_len, bits_len), 'F')
bits = []
for i in range(bits_len):
# 这个 rcep 是求倒谱
rcep = np.real(
np.fft.ifft(
np.log(
np.abs(
np.fft.fft(
np.multiply(channel0_samples_reg[:, i],
np.bartlett(fragment_len)))))))
# 比较峰值的大小来确定原来的信息
if rcep[m[0]] >= rcep[m[1]]:
bits.append(0)
else:
bits.append(1)
try:
decoded_bytes = get_all_bytes(bits)
except IndexError:
raise WrongKeyError("Invalid key.")
return decoded_bytes
def construct_window(width, family, scale):
if family == 'bartlett':
return numpy.bartlett(width) * scale
if family == 'blackman':
return numpy.blackman(width) * scale
if family == 'hamming':
return numpy.hamming(width) * scale
if family == 'hann':
import scipy.signal
return scipy.signal.hann(width) * scale
if family == 'hanning':
return numpy.hanning(width) * scale
if family == 'kaiser':
beta = 14
return numpy.kaiser(width, beta) * scale
if family == 'tukey':
import scipy.signal
return scipy.signal.tukey(width) * scale
print('window family %s not supported' % family)
def estimate_unbnd_conc_in_region(
motif, score_cov, atacseq_cov, chipseq_rd_cov,
frag_len, max_chemical_affinity_change):
# trim the read coverage to account for the motif length
trimmed_atacseq_cov = atacseq_cov[len(motif)+1:]
chipseq_rd_cov = chipseq_rd_cov[len(motif)+1:]
# normalzie the atacseq read coverage
atacseq_weights = trimmed_atacseq_cov/trimmed_atacseq_cov.max()
# build the smoothing window
sm_window = np.ones(frag_len, dtype=float)/frag_len
sm_window = np.bartlett(2*frag_len)
sm_window = sm_window/sm_window.sum()
def build_occ(log_tf_conc):
raw_occ = logistic(log_tf_conc + score_cov/(R*T))
occ = raw_occ*atacseq_weights
smoothed_occ = np.convolve(sm_window, occ/occ.sum(), mode='same')
return raw_occ, occ, smoothed_occ
def calc_lhd(log_tf_conc):
raw_occ, occ, smoothed_occ = build_occ(-log_tf_conc)
#diff = (100*smoothed_occ - 100*rd_cov/rd_cov.sum())**2
lhd = -(np.log(smoothed_occ + 1e-12)*chipseq_rd_cov).sum()
#print log_tf_conc, diff.sum()
return lhd
res = brute(calc_lhd, ranges=(
slice(0, max_chemical_affinity_change, 1.0),))[0]
log_tf_conc = max(0, min(max_chemical_affinity_change, res))
return -log_tf_conc
def get_boardsize_by_fft(zoomed_img):
CLIP = 5000
width = zoomed_img.shape[1]
# 1D fft per row, magnitude per row, average them all into a 1D array, clip
magspec_clip = np.clip(
np.average(np.abs(np.fft.fftshift(np.fft.fft(zoomed_img))), axis=0), 0,
CLIP)
# Smooth it
smooth_magspec = np.convolve(magspec_clip, np.bartlett(7), 'same')
if not len(smooth_magspec) % 2:
smooth_magspec = np.append(smooth_magspec, 0.0)
# The first frequency peak above 9 should be close to the board size.
half = len(smooth_magspec) // 2
plt.subplot(111)
plt.plot(range(-half, half + 1), smooth_magspec)
plt.show()
MINSZ = 9
highf = smooth_magspec[width // 2 + MINSZ:]
maxes = scipy.signal.argrelextrema(highf, np.greater)[0] + MINSZ
res = maxes[0] if len(maxes) else 0
print(res)
if res > 19:
res = 19
#elif res > 13: res = 13
else:
res = 9
return res
def blakmanTukey(signal, M=0, win="Bartlett", n1=0, n2=0, ax=0):
if n1 == 0 and n2 == 0: # por defecto usa la selal completa
n1 = 0
n2 = len(signal)
N = n2 - n1
if M == 0:
M = int(N / 5)
M = 2 * M - 1
if M > N:
raise ValueError('Window cannot be longer than data')
if win == "Bartlett":
w = np.bartlett(M)
elif win == "Hanning":
w = np.hanning(M)
elif win == "Hamming":
w = np.hamming(M)
elif win == "Blackman":
w = np.blackman(M)
elif win == "Flattop":
w = sg.flattop(M)
else:
w = sg.boxcar(M)
r, lags = acorrBiased(signal)
r = r[np.logical_and(lags >= 0, lags < M)]
rw = r * w
Px = 2 * fft(rw).real - rw[0]
return Px
def __init__(self):
self._glue_app = gj.jglue()
self._history = []
self._3d_data = {}
self._2d_data = {}
self._1d_data = {}
self._3d_processing = {}
self.add_3d_processing("Median Collapse over Wavelenths", np.nanmedian,
'a', (('axis', 0), ))
self.add_3d_processing("Mean Collapse over Wavelenths", np.nanmean,
'a', (('axis', 0), ))
self.add_3d_processing("Median Collapse over Space", np.nanmedian, 'a',
(('axis', (1, 2)), ))
self.add_3d_processing("Mean Collapse over Space", np.nanmean, 'a',
(('axis', (1, 2)), ))
self._2d_processing = {}
self._1d_processing = {}
self.add_1d_processing("Median Smoothing", scipy.signal.medfilt,
'volume', (('kernel_size', 3), ))
self.add_1d_processing("Hanning Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.hanning(3))))
self.add_1d_processing("Hamming Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.hamming(3))))
self.add_1d_processing("Bartlett Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.bartlett(3))))
self.add_1d_processing("Blackman Smoothing", np.convolve, 'a',
(('mode', 'valid'), ('w', np.blackman(3))))
def addWindow(points):
# use a window function on the data to make the data fit
# TODO choose a better window function
windowFunction = np.bartlett(len(points))
for i, windowFactor in enumerate(windowFunction):
points[i] = points[i] * windowFactor
return points
def apply_window(sinogram):
window = np.bartlett(len(sinogram))
for i in range(len(sinogram[0])):
fft = np.fft.fft(sinogram[:, i])
fft = fft * window
ifft = np.real(np.fft.ifft(fft))
sinogram[:, i] = ifft
return sinogram
def nonlinear(x):
"""
Nonlinear energy operator for spike detection
"""
xo = np.int32(x)
y = [xo[n]**2 + xo[n - 1] * xo[n + 1] for n in range(1, len(x) - 1)]
window = np.bartlett(12)
return np.convolve(y, window)
def nonlinear(x):
"""
Nonlinear energy operator for spike detection
"""
xo = np.int32(x)
y = [xo[n] ** 2 + xo[n - 1] * xo[n + 1] for n in range(1, len(x) - 1)]
window = np.bartlett(12)
return np.convolve(y, window)
def get_windows():
bartlett = np.bartlett(M)
rectangular = np.ones(shape=M)
blackman = np.blackman(M)
hamming = np.hamming(M)
hanning = np.hanning(M)
return (bartlett, rectangular, blackman, hamming, hanning)
def SelectWindowsFun(self, index):
#global window
x = {0: np.ones(self.CHUNK),
1: np.hamming(self.CHUNK),
2: np.hanning(self.CHUNK),
3: np.bartlett(self.CHUNK),
4: np.blackman(self.CHUNK)}
self.window = x[index]
def Conditioned_spec(self):
datafile = (str(self.lineEdit.text()))
t, Q, I = np.loadtxt(datafile)
#I = I/np.max(I)
#Q = Q/np.max(Q)
fs = np.round(1/(t[1]-t[0]), -3)
#fs = np.round(10e6, -3)
phase = np.unwrap(np.arctan2(Q,I))
#Original Signal using I and Q Data
signal = I + 1j*Q
n = len(I)
#signal = signal - np.mean(signal)
#Filter: high and low
order = (float(self.lineEdit_2.text()))
cutoff = (float(self.lineEdit_3.text()))
if(str(self.comboBox.currentText())=='Signal - LowPass Filtered Signal'):
b,a = butter(order,2*cutoff/fs,'low')
signal_low = filtfilt(b,a,signal)
filt_signal = signal - signal_low
if(str(self.comboBox.currentText())=='HighPass Filtered Signal'):
b,a = butter(order,2*cutoff/fs,'high')
filt_signal = filtfilt(b,a,signal)
order = (float(self.lineEdit_4.text()))
fcutlow = (float(self.lineEdit_5.text()))
fcuthigh = (float(self.lineEdit_6.text()))
b,a = butter(order,[2*fcutlow,2*fcuthigh]/fs,'bandpass')
cond_signal = filtfilt(b,a,filt_signal)
#Spectrogram
self.Status_Bar('Do not press another button before closing the graph')
fft_pts = (int(self.lineEdit_11.text()))
overlap_pts = (int(self.lineEdit_12.text()))
pad = (int(self.lineEdit_13.text()))
if(str(self.comboBox_2.currentText())=='Hanning'):
windfn=np.hanning(fft_pts)
if(str(self.comboBox_2.currentText())=='Blackman'):
windfn=np.blackman(fft_pts)
if(str(self.comboBox_2.currentText())=='Hamming'):
windfn=np.hamming(fft_pts)
if(str(self.comboBox_2.currentText())=='Bartlett'):
windfn=np.bartlett(fft_pts)
xmin = self.isnum((str(self.lineEdit_14.text())))
xmax = self.isnum((str(self.lineEdit_15.text())))
ymin = self.isnum((str(self.lineEdit_16.text())))
ymax = self.isnum((str(self.lineEdit_17.text())))
plt.figure()
plt.specgram(cond_signal,NFFT=fft_pts,Fs=fs,window=windfn,noverlap=overlap_pts,pad_to=pad,scale ='linear')
if((xmin!=-1) and (xmax!=-1)):
plt.xlim(float(xmin),float(xmax))
if((ymin!=-1) and (ymax!=-1)):
plt.ylim(float(ymin),float(ymax))
plt.colorbar()
plt.grid()
plt.show()
self.Status_Bar('Another button can be pressed now')
def PowerSpectrum2(im, win=2, n1=1, n2=0):
"""2D spectrum estimation using the modified periodogram.
This one includes a window function to decrease variance in \
the estimate.
:param x: input sequence
:type x: numpy.array
:param n1: starting index, x(n1)
:type n1: int
:param n2: ending index, x(n2)
:type n2: int
:param win: The window type \n
1 = Rectangular \n
2 = Hamming \n
3 = Hanning \n
4 = Bartlett \n
5 = Blackman \n
:type win: int
:returns: spectrum estimate.
:rtype: numpy.array
.. note::
If n1 and n2 are not specified the periodogram of the entire
sequence is computed.
"""
if n2 == 0:
n2 = len(im[:,1])
N = n2 - n1 + 1
w = np.ones((N))
if (win == 2):
w = np.hamming(N)
elif (win == 3):
w = np.hanning(N)
elif (win == 4):
w = np.bartlett(N)
elif (win == 5):
w = np.blackman(N);
xs, ys = im.shape
if xs/ys != 1:
raise ValueError('Dimensions must be equal')
m = w[:] * w[:][np.newaxis,:]
U = np.linalg.norm(w)**2.0 / N**2.0
fftim = np.abs(np.fft.fftshift(np.fft.fft2(((im) * m)))) / ( (N**2.0) * U)
return fftim
def SelectWindowsFun(self, index):
#global window
x = {
0: np.ones(self.CHUNK),
1: np.hamming(self.CHUNK),
2: np.hanning(self.CHUNK),
3: np.bartlett(self.CHUNK),
4: np.blackman(self.CHUNK)
}
self.window = x[index]
def fid_to_spec(self, window_f = ' ', beta = 2, t_start = 0., t_end = 100.0):
'''
FFT with zero-padding of the FID.
Saves the result in self.spec
Parameters
----------
window_f: is the applied window function. The following window functions are
applicable: hanning, hamming, blackman, bartlett, kaiser (beta (float) is only used
by the kaiser window)
t_start (float): specifies the beginning of the FID. The corresponding data points
will be cut away.
t_end (float): specifies the end of the FID. The corresponding data points
will be cut away.
Returns
-------
none
Notes
-----
none
'''
if len(self.fid) != 0:
fid = slice_fid(self.fid, t_start, t_end)
window_f = window_f.lower() # Choose the window function (default: rect / none)
if window_f == 'hanning':
fid[:,1] = fid[:,1] * np.hanning(len(fid))
elif window_f == 'hamming':
fid[:,1] = fid[:,1] * np.hamming(len(fid))
elif window_f == 'blackman':
fid[:,1] = fid[:,1] * np.blackman(len(fid))
elif window_f == 'bartlett':
fid[:,1] = fid[:,1] * np.bartlett(len(fid))
elif window_f == 'kaiser':
fid[:,1] = fid[:,1] * np.kaiser(len(fid), beta)
h = (int(np.sqrt(len(fid))) + 1) ** 2 # Zero padding to n**2 length to enhance computing speed
spec = np.absolute(np.fft.rfft(fid[:,1], h)) ** 2 / h
spec = spec[0:int(h/2)]
freq = np.fft.fftfreq(h, np.abs(fid[2,0] - fid[1,0])) / 1.E6
freq = freq[0:int(h/2)] # Combine FFT and frequencies
self.spec = np.column_stack([freq, spec])
self.spec_params['npoints'] = len(spec)
self.spec_params['max_f'] = np.max(freq)
self.spec_params['min_f'] = np.min(freq)
self.spec_params['delta_f'] = np.abs(freq[1]-freq[0])
def FT_old(f, step=1.0, lag=2000, window=2, nzeros=10000):
"""My own interface to scipy FFT
f: function
step: time step in fs
window: boolean wich decides if a window is applied"""
import numpy as np
from scipy.fftpack import fft, dct
from tools import units
print('')
print('@FT: PLEASE CLEAN ME')
print('')
n = lag
if window == 1:
win = np.blackman(2 * n)
elif window == 2:
win = np.hanning(2 * n)
elif window == 3:
win = np.hamming(2 * n)
elif window == 4:
win = np.bartlett(2 * n)
else:
win = np.ones(2 * n)
#Apply window
fw = np.multiply(f[:n], win[n:])
#Add zeros
print('test1', fw.shape)
fw = np.concatenate((fw, np.zeros(nzeros)))
print('test2', fw.shape)
#Apply an average
#m = n // av
#fww = np.mean(fw.reshape(m,av),axis=1)
#Compute FT considering an even function of time
ft = np.fft.hfft(fw)
ft = dct(fw, type=1) #It is the same as hfft
#Compute FT NOT considering an even function of time and takin abs
#ff = np.abs(fft(f))
#Add units
FT = np.zeros((2, n + nzeros))
print('Unit convertion {}'.format(1. / units.convert.cm2Phz))
FT[0] = np.linspace(0, 1. /
(2. * float(step)), n + nzeros) / units.convert.cm2Phz
FT[1] = ft.copy()
###FT=np.zeros((2,m))
###FT[0]=np.linspace(0,1./(2*float(step*av)),m)/ units.convert.cm2Phz
###FT[1]=ft[:m]
return FT.T
def smooth_1d_boundaries(input_signal: np.ndarray,
window_len: int = 51,
window_type: str = 'flat',
mode: str = 'mirror',
mean_for_short_signals: bool = False) -> np.ndarray:
"""
apply's a smoothing function to a rolling window for 1d signals using convolution. This
function is generally faster than the apply_rolling_fun_1d_boundaries.
:param input_signal: the 1d input signal.
:param window_len: window length in number of samples.
:param window_type: the window type, valid selectors:
'flat': a convolution operator with ones for a standard average smoothing function
'hanning': a hanning window operator
'hamming': a hamming window operator
'bartlett' a bartlett window operator
'blackman' a blackman winowd operator
:param mode: valid selectors:
'valid': no padding is applied, the output signal is starts window_len/2 after the signal
start and ends window_len/2 before the signal end
'same' the output signal has the same length as the input signal. the input signal is
padded with zeros at the start and end to achieve this.
'mirror': the output signal has the same length as the input signal. this is achieved by
mirroring the input signal at it's begin and end.
:param mean_for_short_signals: return the arithmetic mean if the input signal is shorter than
the window length.
:return: the resulting 1d output signal.
"""
if window_len % 2 == 0:
raise ValueError("window length needs to be odd")
if input_signal.shape[0] < window_len:
if mean_for_short_signals:
return np.mean(input_signal)
raise ValueError("the signal needs to be longer than the window")
# moving average
if window_type == 'flat':
c_filter = np.ones(window_len, dtype='float32')
elif window_type == 'hanning':
c_filter = np.hanning(window_len)
elif window_type == 'hamming':
c_filter = np.hamming(window_len)
elif window_type == 'bartlett':
c_filter = np.bartlett(window_len)
elif window_type == 'blackman':
c_filter = np.blackman(window_len)
else:
raise ValueError("unknown window type")
c_filter = c_filter / c_filter.sum()
filtered_signal = convolve_1d_boundaries(input_signal, c_filter, mode=mode)
return filtered_signal
def SelectWindowsFun(self, index):
global window
if index == 0:
window = np.ones(CHUNK)
elif index == 1:
window = np.hamming(CHUNK)
elif index == 2:
window = np.hanning(CHUNK)
elif index == 3:
window = np.bartlett(CHUNK)
elif index == 4:
window = np.blackman(CHUNK)
def changeWF(self, s):
if s == 'boxcar':
self.window = np.ones(self.nSamples)
elif s == 'hamming':
self.window = np.hamming(self.nSamples)
elif s == 'blackman':
self.window = np.blackman(self.nSamples)
elif s == 'bartlett':
self.window = np.bartlett(self.nSamples)
elif s == 'hanning':
self.window = np.hanning(self.nSamples)
self.restartAvg()
def applyWindow(self, samples, window='hanning'):
if window == 'bartlett':
return samples*np.bartlett(len(samples))
elif window == 'blackman':
return samples*np.hanning(len(samples))
elif window == 'hamming':
return samples*np.hamming(len(samples))
elif window == 'kaiser':
return samples*np.kaiser(len(samples))
else:
return samples*np.hanning(len(samples))
def removeGating(self, view=False):
self.info("Removing gating gain (gating freq.: %.2f Hz)..." % self.gatefreq)
N = int(1.0 / (self.gatefreq * self.deltaT)) # samples for one gating gain cycle
maxN = int(self.Nfft / 2) # max number of samples
gategain = np.ones((maxN, 1)) # vector with length=Nfft/2
n = int(np.floor(maxN / N)) # how many gating cycles are included in time window
rest = maxN - (n * N) # how many samples are left after n full cycles?
for i in range(n):
gategain[i * N:(i + 1) * N, 0] = np.bartlett(N) # creates one triangle for full cycle
gategain[n * N:, 0] = np.bartlett(N)[:rest] # creates part of triangle for incomplete cycle
self.gategain = 1.0 / gategain[self.samplendx]
if view == True:
from pylab import show, plot, xlabel, ylabel
plot(self.t[:len(self.samplendx)], 10 * np.log10(1.0 / gategain[self.samplendx]))
xlabel("Time [ns]")
ylabel("Gating Gain [dB]")
show()
self.data = self.data * self.gategain
self.done()
def get_window(self, n=None):
if not n:
n = self.lframes
assert self.window in ['rectangular',
'bartlett', 'blackman', 'hamming', 'hanning']
if self.window == 'rectangular':
return np.ones(n)
elif self.window == 'bartlett':
return np.bartlett(n)
elif self.window == 'blackman':
return np.blackman(n)
elif self.window == 'hamming':
return np.hamming(n)
else:
return np.hanning(n)
def bartlett1d(data, M, **kwargs):
"""Bartlett 1D filter
:Params:
- **data**: A :mod:`MV2` variable.
- **M**: Size of the Bartlett window.
- Keywords are passed to :func:`generic1d`.
:Return:
- A :mod:`MV2` variable
"""
weights = N.bartlett(M).astype(data.dtype.char)
return generic1d(data, weights, **kwargs)
def pickWinType(winType, N): """ Allow the user to pick a window type""" # Select window type if winType is "bartlett": window = np.bartlett(N) elif winType is "blackman": window = np.blackman(N) elif winType is "hamming": window = np.hamming(N) elif winType is "hanning": window = np.hanning(N) else: window = None return window
def smooth_1D(arr, n=10, smooth_type="flat") -> np.ndarray:
"""Smooth 1D data using a window function.
Edge effects will be present.
Parameters
----------
arr : array_like
Input array, 1D.
n : int (optional)
Window length.
smooth_type : {'flat', 'hanning', 'hamming', 'bartlett', 'blackman'} (optional)
Type of window function to convolve data with.
'flat' window will produce a moving average smoothing.
Returns
-------
array_like
Smoothed 1D array.
"""
# check array input
if arr.ndim != 1:
raise wt_exceptions.DimensionalityError(1, arr.ndim)
if arr.size < n:
message = "Input array size must be larger than window size."
raise wt_exceptions.ValueError(message)
if n < 3:
return arr
# construct window array
if smooth_type == "flat":
w = np.ones(n, dtype=arr.dtype)
elif smooth_type == "hanning":
w = np.hanning(n)
elif smooth_type == "hamming":
w = np.hamming(n)
elif smooth_type == "bartlett":
w = np.bartlett(n)
elif smooth_type == "blackman":
w = np.blackman(n)
else:
message = "Given smooth_type, {0}, not available.".format(str(smooth_type))
raise wt_exceptions.ValueError(message)
# convolve reflected array with window function
out = np.convolve(w / w.sum(), arr, mode="same")
return out
def graph_vect_fit(vect_fit, in_paths, env):
""" graph four example pContact curves and all the curves of best fit """
if in_paths[0][-1] != '0':
return
ratios = (ratio
for vers,cutoff,ratio in env.load('vect_ratios.0')
if vers=='leaf')
fits = (fit for vers,cutoff,fit in vect_fit if vers=='leaf')
bins = dist_bins(120)
miles = np.sqrt([bins[x-1]*bins[x] for x in xrange(2,482)])
with axes('vect_fit',legend_loc=1) as ax:
ax.set_xlim(1,10000)
ax.set_ylim(1e-8,1e-3)
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel('distance in miles')
ax.set_ylabel('probability of being a contact')
colors = iter([FL_PURP,FL_BLUE,FL_GREEN,'k'])
labels = iter([
'edges predicted in nearest 10%',
'edges in 60th to 70th percentile',
'edges in 30th to 40th percentile',
'edges predicted in most distant 10%',
])
for index,(ratio,fit) in enumerate(zip(ratios, fits)):
if index%3==0:
color = next(colors)
label = next(labels)
fitstyle='dashed'
else:
color = ".6"
label = None
fitstyle='dotted'
window = np.bartlett(5)
smooth_ratio = np.convolve(ratio,window,mode='same')/sum(window)
if label:
ax.plot(miles, smooth_ratio, '-', color=color, label=label,
linewidth=2)
ax.plot(miles, peek.contact_curve(miles,*fit), '-',
linewidth=2,
linestyle=fitstyle,
color=color,
)
def pitch_shifter(mono, pitch, time):
sigout = np.array(mono,dtype='f4')
size = time # delay time in samples
delay = np.zeros((size,),dtype='f4') # delay line
env = np.bartlett(size) # fade envelope table
tap1,tap2,wp = 0 ,size/2,0 #taps
for i in range(len(mono)):
delay = sigout[i] # fill the delay line
frac = tap1 - int(tap1) # first tap, linear interp readout
if tap1 < size - 1 : delaynext = delay[tap1+1] # not at boundry
else: delaynext = delay[0] # wrap back to the begining
sig1 = delay[int(tap1)] + frac*(delaynext - delay[int(tap1)]) # invert and mix
frac = tap2 - int(tap2) # second tap, linear interp readout
if tap2 < size - 1 : delaynext = delay[tap2+1]
else: delaynext = delay[0]
sig2 = delay[int(tap2)] + frac*(delaynext - delay[int(tap2)])
# fade envelope positions
ep1 = tap1 - wp
if ep1 < 0: ep1 += size
ep2 = tap2 - wp
if ep2 < 0: ep2 += size
# combine tap signals
sigout[i] = env[ep1]*sig1 + env[ep2]*sig2
# increment tap pos according to pitch transposition
tap1 += pitch
tap2 = tap1 + size/2
# keep tap pos within the delay memory bounds
while tap1 >= size: tap1 -= size
while tap1 < 0: tap1 += size
while tap2 >= size: tap2 -= size
while tap2 < 0: tap2 += size
# increment write pos
wp += 1
if wp == size: wp = 0
return np.array(sigout,dtype='int16')
(sr,signalin) = wavfile.read(sys.argv[2])
pitch = 2.**(float(sys.argv[1])/12.)
signalout = zeros(len(signalin))
fund = 131.
dsize = int(sr/(fund*0.5))
print dsize
signalout = pitchshifter(signalin,signalout,pitch,dsize)
wavfile.write(sys.argv[3],sr,array((signalout+signalin)/2., dtype='int16'))
def record(self,forever=True):
"""record secToRecord seconds of audio."""
while True:
if self.threadsDieNow: break
try:
for i in range(self.chunksToRecord):
self.audio[i*self.BUFFERSIZE:(i+1)*self.BUFFERSIZE]=self.getAudio()
#self.audio *= numpy.hanning(len(self.audio))
except IOError:
print "dropped frames"
self.newAudio = False
self.dropFrames += 1
if(self.dropFrames >= 5):
break
else:
self.dropFrames = 0
self.newAudio=True
self.audio *= numpy.bartlett(len(self.audio))
if forever==False: break
def synthesize(raw_samples, beats, factor):
array_shape = (2, raw_samples.shape[1]*2)
output = np.zeros(array_shape)
offset = 0
val = (factor - 1) / (5*factor + 2)
factor1 = 1-2*val
factor2 = 1+5*val
winsize = 512
window = np.bartlett(winsize*2-1)
winsize1 = int(math.floor(winsize * factor1))
winsize2 = int(math.floor(winsize * factor2))
for start, end in beats:
frame = raw_samples[:, start:end]
# timestretch the eigth notes
mid = int(math.floor((frame.shape[1])/2))
left = frame[:, :mid + winsize1]
right = frame[:, max(0, mid - winsize2):]
left = timestretch(left, factor1)
right = timestretch(right, factor2)
# taper the ends to 0 to avoid discontinuities
left[:, :winsize] = left[:, :winsize] * window[:winsize]
left[:, -winsize:] = left[:, -winsize:] * window[-winsize:]
right[:, :winsize] = right[:, :winsize] * window[:winsize]
right[:, -winsize:] = right[:, -winsize:] * window[-winsize:]
# zero pad and add for the overlap
overlap = sum_signals([left[:, -winsize:], right[:, :winsize]])
frame = np.hstack([left[:, :-winsize], overlap, right[:, winsize:]])
if offset > 0:
overlap = sum_signals([output[:, offset-winsize:offset], frame[:, :winsize]])
output[:, max(0, offset - winsize):offset] = overlap
output[:, offset:(offset+frame.shape[1]-winsize)] = frame[:, winsize:]
offset += frame.shape[1] - winsize
output = output[:, 0:offset]
return output
def __call__(self, inputs):
if self.get_input('window')=='hanning':
from numpy import hanning
return hanning(self.get_input('n'))
elif self.get_input('window')=='hamming':
from numpy import hamming
return hamming(self.get_input('n'))
elif self.get_input('window')=='bartlett':
from numpy import bartlett
return bartlett(self.get_input('n'))
elif self.get_input('window')=='blackman':
from numpy import blackman
return blackman(self.get_input('n'))
elif self.get_input('window')=='kaiser':
from numpy import kaiser
return kaiser(self.get_input('n'), self.get_input('beta (kaiser only)'))
elif self.get_input('window')=='None':
from numpy import kaiser
return kaiser(self.get_input('n'), 0.)
else:
raise ValueError("should never enter here since window values is an enum selector")
def isoluminant(rng, num_cycles=1, num_colors=256, reverse=False, **traits):
"""
Generator function for a Chaco color scale that cycles through the hues
@num_cycles times, while maintaining monotonic luminance (i.e., if it is
printed in black and white, then it will be perceptually equal to a linear
grayscale.
Ported from the Matlab(R) code from: McNames, J. (2006). An effective color
scale for simultaneous color and gray-scale publications. IEEE Signal
Processing Magazine 23(1), 82--87.
"""
# Triangular window function
window = N.sqrt(3.0) / 8.0 * N.bartlett(num_colors)
# Independent variable
t = N.linspace(N.sqrt(3.0), 0.0, num_colors)
# Initial values
operand = (t - N.sqrt(3.0) / 2.0) * num_cycles * 2.0 * N.pi / N.sqrt(3.0)
r0 = t
g0 = window * N.cos(operand)
b0 = window * N.sin(operand)
# Convert RG to polar, rotate, and convert back
r1, g1 = _rotate(r0, g0, N.arcsin(1.0 / N.sqrt(3.0)))
b1 = b0
# Convert RB to polar, rotate, and convert back
r2, b2 = _rotate(r1, b1, N.pi / 4.0)
g2 = g1
# Ensure finite precision effects don't exceed unit cube boundaries
r = r2.clip(0.0, 1.0)
g = g2.clip(0.0, 1.0)
b = b2.clip(0.0, 1.0)
the_map = N.vstack((r, g, b)).T
return ColorMapper.from_palette_array(the_map[::-1 if reverse else 1],
range=rng, **traits)
def window_bartlett(N):
r"""Bartlett window (wrapping of numpy.bartlett) also known as Fejer
:param int N: window length
The Bartlett window is defined as
.. math:: w(n) = \frac{2}{N-1} \left(
\frac{N-1}{2} - \left|n - \frac{N-1}{2}\right|
\right)
.. plot::
:width: 80%
:include-source:
from spectrum import window_visu
window_visu(64, 'bartlett')
.. seealso:: numpy.bartlett, :func:`create_window`, :class:`Window`.
"""
from numpy import bartlett
return bartlett(N)
def update(self):
if self.structure:
N_lame = self.N_lame - self.struct_N
else:
N_lame = self.N_lame
damp = lambda t: 1.0 - np.exp(
-np.abs(np.mod(t + self.period / 2, self.period) - self.period / 2) / self.damp_tau
)
N_periods = 1
i = np.mod(np.int(self.t / self.period * self.vague.shape[2] / N_periods), self.vague.shape[2])
surface = np.zeros_like(self.lames[2, :N_lame])
# for k, amp in zip([-2, -1, 0, 1, 2], [.125, .25, .5, .25, .125]):
# surface += amp * self.vague[self.x_offset:(self.x_offset+N_lame), self.y_offset, self.t_offset+i+k]
surface = self.vague[self.x_offset : (self.x_offset + N_lame), self.y_offset, self.t_offset + i]
surface = np.convolve(surface, np.arange(5), mode="same")
dsurface = np.gradient(surface)
dsurface *= np.bartlett(N_lame)
# print(dsurface.mean(), dsurface.max(), damp(self.t))
dsurface /= np.abs(dsurface).max()
dsurface *= np.tan(np.pi / 32) # maximum angle achieved
self.lames[2, :N_lame] = np.arctan(dsurface) * damp(self.t)
def gen_mel_filts(num_filts, framelength, samp_freq):
mel_filts = numpy.zeros((framelength, num_filts))
step_size = int(framelength/float((num_filts + 1))) #Sketch it out to understand
filt_width = math.floor(step_size*2)
filt = numpy.bartlett(filt_width)
step = 0
for i in xrange(num_filts):
mel_filts[step:step+filt_width, i] = filt
step = step + step_size
# Let's find the linear filters that correspond to the mel filters
# The freq axis goes from 0 to samp_freq/2, so...
samp_freq = samp_freq/2
filts = numpy.zeros((framelength, num_filts))
for i in xrange(num_filts):
for j in xrange(framelength):
freq = (j/float(framelength)) * samp_freq
# See which freq pt corresponds on the mel axis
mel_freq = 1127 * numpy.log( 1 + freq/700 )
mel_samp_freq = 1127 * numpy.log( 1 + samp_freq/700 )
# where does that index in the discrete frequency axis
mel_freq_index = int((mel_freq/mel_samp_freq) * framelength)
if mel_freq_index >= framelength-1:
mel_freq_index = framelength-1
filts[j,i] = mel_filts[mel_freq_index,i]
# Let's normalize each filter based on its width
for i in xrange(num_filts):
nonzero_els = numpy.nonzero(filts[:,i])
width = len(nonzero_els[0])
filts[:,i] = filts[:,i]*(10.0/width)
return filts
