def process(fname):
Fs, x = wavfile.read(fname)
a = string.split(fname,".wav")
b = string.split(a[0],"cw")
sys.stdout.write(b[1])
sys.stdout.write(",")
# find frequency peaks of high volume CW signals
if fft_scan:
f,s = periodogram(x,Fs,'blackman',4096,'linear',False,scaling='spectrum')
# download peakdetect from # https://gist.github.com/endolith/250860
from peakdetect import peakdet
threshold = max(s)*0.4 # only 0.4 ... 1.0 of max value freq peaks included
maxtab, mintab = peakdet(abs(s[0:len(s)/2-1]), threshold,f[0:len(f)/2-1] )
if plotter:
plt.plot(f[0:len(f)/2-1],abs(s[0:len(s)/2-1]),'g-')
print maxtab
from matplotlib.pyplot import plot, scatter, show
scatter(maxtab[:,0], maxtab[:,1], color='blue')
plt.show()
# process all CW stations with higher than threshold volume
if fft_scan:
for freq in maxtab[:,0]:
print "\nfreq:%5.2f" % freq
demodulate(x,Fs,freq)
else:
demodulate(x,Fs,MORSE_FREQUENCY)
def findPeaksAndTroughs(self, ydataset, delta, xdataset=None): '''returns a list of peaks and troughs in tuple of (peak_position, peak_value). If x data set is not provided, it returns as tuple of (peak_index, peak_value)''' if xdataset != None: peaks,troughs=peakdet(ydataset[:], delta, xdataset[:]) else: peaks,troughs=peakdet(ydataset[:], delta) return peaks, troughs
def findPeaksAndTroughs(self, ydataset, delta, xdataset=None):
'''returns a list of peaks and troughs in tuple of (peak_position, peak_value).
If x data set is not provided, it returns as tuple of (peak_index, peak_value)'''
if xdataset != None:
peaks, troughs = peakdet(ydataset[:], delta, xdataset[:])
else:
peaks, troughs = peakdet(ydataset[:], delta)
return peaks, troughs
def get_actpeaks(nn, thresh=30):
ch = 0
act_peaks = []
for gr in range(nn.n_ass):
r = nn.mon_rate_Mg[ch][gr].smooth_rate(width=2.0 * ms)
act_peaks.append(peakdet(r, thresh)[0])
return act_peaks
def findPeaksAndTroughs(self, ydataset, delta, xdataset=None):
'''returns a list of peaks and troughs in tuple of (peak_position, peak_value).
If x data set is not provided, it returns as tuple of (peak_index, peak_value)'''
if xdataset is not None:
xdataset = dnp.asarray(xdataset)
return peakdet(dnp.asarray(ydataset), delta, xdataset)
def findPeaksAndTroughs(self, ydataset, delta, xdataset=None):
'''returns a list of peaks and troughs in tuple of (peak_position, peak_value).
If x data set is not provided, it returns as tuple of (peak_index, peak_value)'''
if xdataset is not None:
xdataset = dnp.asarray(xdataset)
return peakdet(dnp.asarray(ydataset), delta, xdataset)
def find_peak(Fs, signal):
""" Find the signal frequency and maximum value
"""
f,s = periodogram(signal, Fs, 'blackman', 1024*32, 'linear', False, scaling='spectrum')
threshold = max(s)*0.9 # only 0.4 ... 1.0 of max value freq peaks included
maxtab, mintab = peakdet(abs(s[0:int(len(s)/2-1)]), threshold, f[0:int(len(f)/2-1)])
return maxtab, f, s
def get_peaks(data, delta=0.085, damping=True, RATE=8000, CHUNK=1024):
'''
:param data: spectrum data
:param delta: see peakdetect.py
:param damping: neglect a point if amplitude is lower than threshold
:return: peaks as array of points(freq;amplitude)
'''
maxs, mins = peakdetect.peakdet(data, delta) # 0.035
# Convert taps number in frequencies
if (len(maxs) > 0):
for i in range(len(maxs)):
maxs[i][0] *= RATE / CHUNK * 0.8
# maxs[0:len(maxs)][0] *= RATE/CHUNK
maxs = maxs[:len(maxs) // 2] # Get first part of vector
# Delete peaks lower then threshold
while (damping):
damping = False
for i in range(len(maxs)):
if (maxs[i][1] < 0.7): # 0.5
maxs = np.delete(maxs, i, 0)
damping = True
break
# Print peaks
# if (len(maxs)>0):
# print(list(maxs))
return maxs
def computeRidgeFrequency(image, allowed_range=None):
length = np.min(image.shape)
# Compute the FFT of the image using a gaussian window
kernel = hannWin2D(image.shape)
img = image * kernel
img = (img - img.mean()) / img.std()
img = np.fft.fftshift(np.absolute(np.fft.fft2(img)))
# Convert the image to polar representation
img = cart2pol(img, 32)
# Sum (L2-norm) along the angle axis, to get the energy for each circle
circle_energy = np.sqrt(np.sum(img**2, axis=1))
# Suppress low order terms
if allowed_range != None:
radii = np.arange(0, len(circle_energy))
radii_upper = radii < length / allowed_range[0]
radii_lower = radii > length / allowed_range[1]
radii_nallowed = np.logical_not(
np.logical_and(radii_upper, radii_lower))
radii = radii[radii_nallowed]
circle_energy[radii] = circle_energy.min()
# Find the most energetic circle
circle_logen = np.log(circle_energy)
circle_logen = scipy.ndimage.filters.gaussian_filter(circle_logen,
sigma=2,
mode="nearest")
peakind, _ = peakdet(circle_logen, circle_logen.std() / 2)
if len(peakind) == 0:
return 10
else:
max_peak = np.argmax(peakind[:, 1])
if peakind[max_peak, 0] == 0:
return 10
else:
return length / peakind[max_peak, 0]
def threshold_data(data, threshold, noise, other_data):
intensity_high_enough = data > thresh
intensity_greater_than_other = data > other_data[idx - 1]
firing_points = np.where(intensity_high_enough
& intensity_greater_than_other)[0]
boundary_points = np.diff(firing_points)
boundary_idxs = list(np.concatenate(np.argwhere(boundary_points)))
firing_bounds = list(zip(boundary_idxs[::2], boundary_idxs[1::2]))
for start, end in firing_bounds:
# sp = start_points[idx]
# ep = end_points[idx] + 1
# end += 1
x_values = np.arange(start, end)
intensities = intensity[start:end]
curve_pen = pg.mkPen(colors[idx], width=2)
curve = pg.PlotDataItem(x=x_values, y=intensities, pen=curve_pen)
firing_plot_list.append(curve)
# Plotting the curves highlighting each base
image_plot.getRoiPlot().addItem(curve)
try:
peaks, mins = peakdet(v=intensities, delta=noise, x=x_values)
if len(peaks) == 0 or len(mins) == 0:
peaks = np.NAN
substack = np.mean(stack[start:end], 0)
call = get_call(substack, czpro, idx)
seqdf = seqdf.append(pd.DataFrame({
'base': [call],
'times': [start]
}),
ignore_index=True)
else:
# point = pg.PlotDataItem(maxes, pen = None, symbol = 'o', symbolBrush = 'g')
# self.p1.getRoiPlot().addItem(point)
# self.firingplotlist.append(point)
# point = pg.PlotDataItem(mins, pen = None, symbol = 'o', symbolBrush = 'r')
# self.p1.getRoiPlot().addItem(point)
# self.firingplotlist.append(point)
for idx, x in enumerate(peaks):
if idx == 0:
ssp = start
sep = int(mins[idx][0])
elif idx == len(peaks) - 1:
ssp = int(mins[idx - 1][0])
sep = end
else:
ssp = int(mins[idx - 1][0])
sep = int(mins[idx][0])
substack = np.mean(stack[ssp:sep + 1], 0)
call = get_call(substack, czpro, idx)
seqdf = seqdf.append(pd.DataFrame({
'base': [call],
'times': [ssp]
}),
ignore_index=True)
peak_series = peak_series.append(pd.Series([peaks]))
min_series = min_series.append(pd.Series([mins]))
except Exception as e:
raise ValueError
def removeClutter(self, clutRatio = 0.5, dist = 10):
surfclut = self.firstReturn(self.clutim)
bclutim = np.zeros_like(self.img)
for col in xrange(self.clutim.shape[1]):
iprofile = self.clutim[:,col]
bgnoise = np.max(iprofile)
peakmx, peakmn = pd.peakdet(iprofile,1e-26)
if peakmx.shape[0] <= 0:
continue
peakind = peakmx[:,0].astype(int)
ind = np.where(peakmx[:,1] > bgnoise * clutRatio)[0]
peakind = peakind[ind]
#peakind = np.where(iprofile > bgnoise * 0.5)[0].astype(int)
bclutim[peakind,col] = 1
plt.figure()
xy = np.where(bclutim == 1)
x = xy[0]
y = xy[1]
plt.scatter(y,x - 1300, color='r',marker = '.',zorder = 1)
plt.xlim(0,self.clutim.shape[1])
plt.imshow(self.clutim[1300:3600,:], zorder = 0)
filename = self.outpath + '/s_' + self.trackID + '_rmclut.png'
plt.savefig(filename)
plt.close()
for col in xrange(self.peakim.shape[1]):
deltaH = int(self.surfecho[col] - surfclut[col])
peakind = np.where(self.peakim[:,col] != 0)[0].astype(int)
tmp = peakind
peakind = np.delete(tmp, np.where(tmp - deltaH >= self.peakim.shape[0])[0])
if len(peakind) <= 0 or abs(deltaH) > 15:
continue
if abs(deltaH) > 0:
self.peakim[peakind - deltaH, col] = self.peakim[peakind,col]
self.peakim[peakind,col] = 0
for col in xrange(self.peakim.shape[1]):
self.peakim[1:self.surfecho[col] + 1,col] = 0
clind = np.where(bclutim[:,col] > 0)[0]
pkind = np.where(self.peakim[:,col] > 0)[0]
if len(pkind) <= 0:
self.peakim[self.surfind[col], col] = 1
continue
#self.peakim[pkind[0], col] = 0
for k in clind:
anyind = np.where(abs(pkind - k) < dist)[0]
if len(anyind) <= 0:
continue
else:
self.peakim[pkind[anyind],col] = 0
self.peakim[self.surfind[col], col] = 1
def get_peaks(rates, cmpf, thresh):
'''returns peaks above some thresh given the rates of multiple groups'''
peaks = []
for gr in range(len(rates)):
r = numpy.interp(numpy.arange(len(rates[gr])*cmpf)/cmpf,\
numpy.arange(len(rates[gr])),rates[gr])
peaks.append(peakdet(r, thresh)[0])
return peaks
def peak_windows(data, width=80):
highs, lows = peakdet(data, 0.75)
peak_centers = np.array(np.r_[highs[:, 0], lows[:, 0]], dtype=np.uint32)
windows = np.zeros((peak_centers.shape[0], width))
for ind, center in enumerate(peak_centers):
windows[ind, :] = data[center - width / 2:center + width / 2]
return windows
def peak_windows(data, width=80):
highs, lows = peakdet(data, 0.75)
peak_centers = np.array(np.r_[highs[:,0], lows[:,0]], dtype=np.uint32)
windows = np.zeros((peak_centers.shape[0], width))
for ind, center in enumerate(peak_centers):
windows[ind, :] = data[center-width/2:center+width/2]
return windows
def peak():
global voltage0, voltage1, timeval
maxtab0, mintab0 = peakdetect.peakdet(voltage0, 0.1, timeval) # change 2nd argument to fine tune peak detection
maxtab1, mintab1 = peakdetect.peakdet(voltage1, 0.1, timeval) # change 2nd argument to fine tune peak detection
filelog(maxtab0,'Maximum',1,'w')
filelog(mintab0, 'Minimum', 1, 'a')
filelog(maxtab1, 'Maximum', 2, 'a')
filelog(mintab1, 'Minimum', 2, 'a')
plt.subplot(2,1,1)
plt.plot(timeval,voltage0)
plt.scatter(array(maxtab0)[:, 0], array(maxtab0)[:, 1], color='blue')
plt.scatter(array(mintab0)[:, 0], array(mintab0)[:, 1], color='red')
plt.subplot(2,1,2)
plt.plot(timeval, voltage1)
plt.scatter(array(maxtab1)[:, 0], array(maxtab1)[:, 1], color='blue')
plt.scatter(array(mintab1)[:, 0], array(mintab1)[:, 1], color='red')
os.startfile('timelog.csv')
plt.show()
def find_peaks(x,y, delta = .004):
""" this applies the peak detection algorithm.
look at the source code to find out....
"""
print('x', len(x))
print('y',len(y))
print('delta',delta)
mx,mn= peakdet(y,delta,x=x)
return mx.T,mn.T
def detect_optimal_knn(arr, rad_lst=[0.1, 0.2, 0.3], sample_size=10000):
"""
Detects optimal values for knn in order to facilitate material separation.
Parameters
----------
arr: array
Set of 3D points.
rad_lst: list
Set of radius values to generate samples of neighborhoods. This is
used to select points to calculate a number of neighboring points
distribution from the point cloud.
sample_size: int
Number of points in arr to process in order to genrate a distribution.
Returns
-------
knn_lst: list
Set of k-nearest neighbors values.
"""
# Generating sample indices.
sids = np.random.choice(np.arange(arr.shape[0]),
sample_size,
replace=False)
# Obtaining nearest neighbors' indices and distance for sampled points.
# This process is done just once, with the largest value of radius in
# rad_lst. Later on, it is possible to subsample indices by limiting
# their distances for a smaller radius.
dist, ids = set_nbrs_rad(arr, arr[sids], np.max(rad_lst), True)
# Initializing empty list to store knn values.
knn_lst = []
# Looping over each radius value.
for r in rad_lst:
# Counting number of points inside radius r.
n_pts = [len(i[d <= r]) for i, d in zip(ids, dist)]
# Binning n_pts into a histogram.
y, x = np.histogram(n_pts)
# Detecting peaks of accumulated points from n_pts.
maxtab, mintab = peakdet(y, 100)
maxtab = np.array(maxtab)
# Appending knn values relative to peaks detected in n_pts.
knn_lst.append(x[maxtab[:, 0]])
# Flattening nested lists into a final list of knn values.
knn_lst = [i for j in knn_lst for i in j]
return knn_lst
def PeakDetect(data):
'''
This function uses the accompanying program peakdetect.py to find peaks in
the transformed data, and saves them out as an array of arrays, where each
element array corresponds to each transformed signal.
'''
peakData = []
for i in range(1, len(data[0,:])):
Peaks, Lows = pd.peakdet(data[:,i],(max(data[:,i])/15),data[:,0])
peakData.append(Peaks)
return peakData
def perfind2():
P = 200.
tbase = 1000.
nf = 5000
s2n = logspace( log10(3),log10(15),5 )
print "S/N sig-noise noise-noise"
for s in s2n:
# Generate a lightcurve.
f,t = keptoy.lightcurve(P=P,tbase=tbase,s2n=s)
o = blsw.blswrap(t,f,nf=nf,fmax=1/50.)
# Subtract off the trend
o['p'] -= median_filter(o['p'],size=200)
# Find the highest peak.
mxid = argmax(o['p'])
mxpk = o['p'][mxid]
# Find all the peaks
mxt,mnt = peakdet(o['p'],delta=1e-3*mxpk,x=o['parr'])
mxt = array(mxt)
# Restrict attention to the highest 100 but leaving off top 10
t1id = where( (mxt[::,1] > sort( mxt[::,1] )[-100]) &
(mxt[::,1] < sort( mxt[::,1] )[-10]) )
fig = plt.gcf()
fig.clf()
ax = fig.add_subplot(111)
ax.plot(o['parr'],o['p'],label='Signal')
ax.scatter( mxt[t1id,0],mxt[t1id,1],label='Tier 1' )
# tpyical values of the highest 100 peaks.
hair = median(mxt[t1id,1])
left = min(o['parr'])
right = max(o['parr'])
ax.hlines(hair,left,right)
if mxpk > 3*hair:
print "Peroid is %.2f" % (o['parr'][mxid])
else:
print "No signal"
ax.legend()
plt.show()
def find_peak(fname):
"""Find the signal frequency and maximum value"""
#print("find_peak",fname)
Fs, x = wavfile.read(fname)
f,s = periodogram(x, Fs,'blackman',8192,'linear', False, scaling='spectrum')
threshold = max(s)*0.8 # only 0.4 ... 1.0 of max value freq peaks included
maxtab, mintab = peakdet(abs(s[0:int(len(s)/2-1)]), threshold,f[0:int(len(f)/2-1)] )
try:
val = maxtab[0,0]
except:
print("Error: {}".format(maxtab))
val = 600.
return val
def peakimCWT(self, scales, bgSkip = 20):
# CWT-based peak detection
if self.surfecho is None:
return
if self.filtim is not None:
im = self.filtim
elif self.img is not None:
im = self.img
else:
return
self.peakim = np.zeros_like(im)
num = np.zeros((len(scales),im.shape[1]))
for col in xrange(im.shape[1]):
# direct peak detection after strong logGabor filtering is not working
#peakmx, peakmn = pd.peakdet(im[:,col],0.000001)
#peakind = peakmx[:,0].astype(int)
#self.peakim[peakind,col] = 1
cwtMatr = signal.cwt(im[:,col], signal.ricker, scales)
idxStart = int(self.surfecho[col])
for r in xrange(cwtMatr.shape[0]):
cwtRow = cwtMatr[r,:]
bgmax = 0
# take the first pixels till surfecho to be the background
bgSig = cwtRow[1:idxStart - bgSkip]
bgmax = max(bgSig)
if bgmax is None:
bgmax = 0
peakmx, peakmn = pd.peakdet(cwtRow,0.000001)
if peakmx.shape[0] <= 0:
continue
peakind = peakmx[:,0].astype(int)
ind = np.where(peakmx[:,1] > bgmax)[0]
peakind = peakind[ind]
#if col == 0 and r == 0:
# plt.plot(im[:,col])
# plt.plot(peakind, im[peakind,col],'ro')
# plt.show()
self.peakim[peakind,col] = self.peakim[peakind,col] + cwtRow[peakind]
#num[peakind,col] = num[peakind,col] + 1
num[r,col] = len(peakind)
return num
def Calculate_cycles(self):
Dankle = list()
PersonFrames = self.Person.Fdata
for x in xrange(len(PersonFrames)):
each = PersonFrames[x].CompleteFrame
distance = self.Horizontal_distance(each, 16, 17)
Dankle.append(distance)
x = xrange(0, Dankle.__len__(), 1)
#print max(Dankle)
Norm = self.Moving_Average(Dankle)
maximum, minimum = peakdet(Norm, 0.2)
if len(maximum) < 3:
print "Not Enough Frames"
else:
cycle_frames = maximum[:, 0]
self.Calculate_Half_Cycle(cycle_frames)
def audioRead(self):
buffer_bytes = self.audio_buffer.readAll()
if buffer_bytes:
buffer_bytes = buffer_bytes[:self.audio_nsamples *
self.audio_bytes] # truncate
data = np.frombuffer(buffer_bytes, dtype=np.single)
if max(data) > 0:
#print(max(data))
data /= max(data)
self.sc_time.new_data(data)
nb_samples = len(buffer_bytes) // self.audio_bytes
self.peak_signal[self.
peak_signal_index:self.peak_signal_index +
nb_samples] = data
self.peak_signal_index += nb_samples
if self.peak_signal_index > self.nfft_peak:
f, s = periodogram(self.peak_signal,
self.audio_rate,
'blackman',
self.nfft_peak,
'linear',
False,
scaling='spectrum')
threshold = max(s) * 0.9
if threshold > self.thr:
maxtab, mintab = peakdet(abs(s[0:int(len(s) / 2 - 1)]),
threshold,
f[0:int(len(f) / 2 - 1)])
tone = maxtab[0, 0]
#print(f'tone: {tone} thr: {(10.0 * np.log10(threshold)):.2f} dB')
self.sc_peak.new_data(f, s, maxtab, tone)
nside_bins = 1
f, t, img = specimg(self.audio_rate,
self.peak_signal[:self.nfft_peak],
tone, self.nfft, self.noverlap,
nside_bins)
print(t.shape, f)
if len(f) != 0:
img_line = np.sum(img, axis=0)
img_line /= max(img_line)
self.test_line(img_line, 0.75)
self.sc_tenv.new_data(img_line, 50)
self.sc_zenv.new_data(img_line[:50])
self.peak_signal = np.roll(self.peak_signal,
self.nfft_peak,
axis=0)
self.peak_signal_index -= self.nfft_peak
def findSubPeaks(red, blue, redstart, redend, bluestart, blueend, redsubthresh,
bluesubthresh):
pulsecount = 0
df = pd.DataFrame({
"ident": [],
'stimes': [],
'etimes': [],
'peaks': [],
'mins': []
})
df['peaks'] = df['peaks'].astype(object)
df['mins'] = df['mins'].astype(object)
for i, x in enumerate([[redstart, redend], [bluestart, blueend]]):
df = df.append(pd.DataFrame({
"ident": [i] * len(x[0]),
'stimes': x[0],
'etimes': x[1]
}),
ignore_index=True)
df = df.sort_values(by='stimes').reset_index()
for i, x in enumerate(df.ident):
sp = int(df.stimes[i])
ep = int(df.etimes[i])
if x == 0:
intensity = red
noise = redsubthresh
else:
intensity = blue
noise = bluesubthresh
peaks, mins = peakdet(v=intensity[sp:ep],
delta=noise,
x=np.arange(sp, ep))
if len(peaks) == 0 or len(mins) == 0:
pulsecount += 1
else:
df.set_value(i, 'peaks', peaks.astype(object))
df.set_value(i, 'mins', mins.astype(object))
pulsecount += 1 + len(peaks)
print(pulsecount)
return df
def process(fname):
Fs, x = wavfile.read(fname)
a = string.split(fname,".wav")
b = string.split(a[0],"cw")
sys.stdout.write(b[1])
sys.stdout.write(",")
# find frequency peaks of high volume CW signals
if fft_scan:
f,s = periodogram(x,Fs,'blackman',4096,'linear',False,scaling='spectrum')
# download peakdetect from # https://gist.github.com/endolith/250860
from peakdetect import peakdet
threshold = max(s)*0.4 # only 0.4 ... 1.0 of max value freq peaks included
maxtab, mintab = peakdet(abs(s[0:len(s)/2-1]), threshold,f[0:len(f)/2-1] )
if plotter:
plt.plot(f[0:len(f)/2-1],abs(s[0:len(s)/2-1]),'g-')
print maxtab
def track_freqs(self):
if self.bouts != None:
# initiate bout maxima & minima coord lists
self.peak_maxes_y = []
self.peak_maxes_x = []
self.peak_mins_y = []
self.peak_mins_x = []
# initiate instantaneous frequency array
self.tail_frequencies = np.zeros(self.tail_angle_arrays[self.current_tracking_num].shape[0])
for i in range(self.bouts.shape[0]):
# get local maxima & minima
peak_max, peak_min = peakdetect.peakdet(self.tail_end_angle_arrays[self.current_tracking_num][self.current_crop][self.bouts[i, 0]:self.bouts[i, 1]], 0.02)
# change local coordinates (relative to the start of the bout) to global coordinates
peak_max[:, 0] += self.bouts[i, 0]
peak_min[:, 0] += self.bouts[i, 0]
# add to the bout maxima & minima coord lists
self.peak_maxes_y += list(peak_max[:, 1])
self.peak_maxes_x += list(peak_max[:, 0])
self.peak_mins_y += list(peak_min[:, 1])
self.peak_mins_x += list(peak_min[:, 0])
# calculate instantaneous frequencies
for i in range(len(self.peak_maxes_x)-1):
self.freqs[self.peak_maxes_x[i]:self.peak_maxes_x[i+1]] = 1.0/(self.peak_maxes_x[i+1] - self.peak_maxes_x[i])
extra_tracking = { 'bouts': self.bouts,
'peak_points': self.peak_points,
'valley_points': self.valley_points,
'frequencies': self.tail_frequencies }
# update plot
# self.smoothed_deriv_checkbox.setChecked(False)
# self.tail_canvas.plot_tail_angle_array(self.tail_end_angle_array[self.current_crop], self.bouts, self.peak_maxes_y, self.peak_maxes_x, self.peak_mins_y, self.peak_mins_x, self.freqs, keep_limits=True)
# update plot
self.analysis_window.update_plot(self.plot_array, self.current_plot_type, extra_tracking=extra_tracking, keep_limits=True)
def _power_dispersion_scalar(self, inten_spec, uwb_scan, uwb_pcd):
'''
This scalar is only applicable to the R1 region. The lowest value of this scalar is 0.5
Input:
-uwb_pcd, dtype: pointcloud. Pointcloud representing uwb mask in global frame with appropiate channel for encoding
The region channel shall be set with appropiate values
-inten_spec dtype: dictionary. Index by the range_bin index, containing [mean_return, std_return]
-uwb_scan dtype: struct/UWBScan.msg. Contains a list with intensity values for each bin starting from zero
Output: pointcloud, with original channels and a channel representing the _power_dispersion_scalar scalar value,
if _power_dispersion_scalar scalar is unknown then -1
'''
# YH used a guassian kernal as a scalar
kern = np.array( signal.get_window(('gaussian', 4), 9))
# for the inten_spectrum determine the peaks
intensity = list(uwb_scan.intensity)
[max_pks, values] = peakdet(intensity,2)
pk_bins = [pair[0] for pair in max_pks]
points = uwb_pcd.points
region = uwb_pcd.channels[5].values
pow_dip = uwb_pcd.channels[7].values
ranges = uwb_pcd.channels[0].values
for i, point in enumerate(points):
if i > 0:
if region[i] == 1:
range_bin = int(m.floor(ranges[i]/self.range_res))
dist2peak = self._distance_to_peak(pk_bins, range_bin)
# the kernal specifies weightings based on the distance to peak
# index 0 applies to a pkdist of 4, index 1 appliest to a pkdist of 3 ...
kern_index = 4 - dist2peak
pow_dip[i] = kern[kern_index]
else:
pow_dip[i] = -1
else:
pow_dip[i] = -1
def findPeaksMultiple(signal, scale, figTitle):
fs = int(app.getEntry("Sampling Frequency")) or 8000
highestFreq = fs / 2
#The smallest number that we deem a valid point before which is likely Noise
lowestQuefrency = 1.0 / highestFreq
cutOff = app.getEntry('Source Cut Off Frequency') or 170.0
timePeriod = 1.0 / cutOff
cutOffIndex = len(scale) - 1
startIndex = None
for index, value in enumerate(scale):
if value >= timePeriod:
cutOffIndex = index
break
if startIndex is None and value >= lowestQuefrency:
startIndex = index
new_scale = [1.0 / x for x in scale[startIndex:]]
peak_tuples = peakdet(signal[startIndex:], 0.0001, new_scale)[0]
peak_frequencies = [x[0] for x in peak_tuples]
m = findMultiples(peak_frequencies, True)
z = sorted(peak_frequencies)
print(figTitle + '---------')
print(z[0])
print(z[-1])
maximum_index = 0
max_val = -1
for val in m:
if val > 40.0 and val < 110.0:
print(val, m[val])
if len(m[val]) > max_val:
max_val = len(m[val])
maximum_index = val
print(maximum_index)
print(len(m[maximum_index]))
print(m[maximum_index][-1])
print(figTitle + '---------\\')
def window(fseq, window_size=1000, moving_size=100):
WinNum = int((len(fseq) - window_size) / moving_size + 1)
Feature = np.zeros((WinNum, 6))
for i in range(int((len(fseq) - window_size) / moving_size + 1)):
# yield fseq[i*moving_size:i*moving_size+window_size]
Feature[i, 0] = np.mean(fseq[i * moving_size:i * moving_size +
window_size])
Feature[i, 1] = np.std(fseq[i * moving_size:i * moving_size +
window_size])
p = peakdetect.peakdet(
fseq[i * moving_size:i * moving_size + window_size], 60)
Feature[i, 2] = len(p[0])
Feature[i, 3] = len(p[1])
Feature[i,
4] = max(fseq[i * moving_size:i * moving_size + window_size])
a = 0
for j in range(i * moving_size, i * moving_size + window_size):
a += fseq[j]**2
Feature[i, 5] = (np.sum(p[0]**2) + np.sum(p[1]**2)) / a * 100
return Feature
def num_beats(self):
"""Determines the number of beats in the data set
:return num_beats: number of beats in the data set
"""
norm_voltage = list(self.voltage - numpy.mean(self.voltage))
norm_voltage_ref = list(self.voltage_ref -
numpy.mean(self.voltage_ref))
corr_voltage = numpy.convolve(norm_voltage,
norm_voltage_ref[144:504],
mode='same')
voltage_delta = numpy.sqrt(numpy.mean(corr_voltage**2)) * 2.5
[self.max_corr, min_corr] = peakdet(corr_voltage, voltage_delta,
self.time)
max_corr_voltage = []
for i in self.max_corr:
max_corr_voltage.append(i[0])
num_beats = len(max_corr_voltage)
logging.info("Number of beats successfully counted.")
return num_beats
sns.set_style('whitegrid')
# Choose between DetectorBank response to tone, white noise, or both noise
# and tone at SNR of -4dB or -15dB
modes = ['tone', 'noise', 'snr-4', 'snr-15']
mode = modes[0]
file = os.path.join('../Data', 'freqz_400_48000_5e-04_{}.csv'.format(mode))
arr = np.loadtxt(file, delimiter='\t', skiprows=1)
freq = arr[:, 0]
mx = arr[:, 1]
max_db = 20 * np.log10(mx)
maxtab, _ = pk.peakdet(max_db, 15, freq)
peaks = maxtab[:, 0]
for n in range(1, len(peaks)):
diff = peaks[n] - peaks[n - 1]
data = (peaks[n - 1], peaks[n], diff)
print('Difference between {:9.3f} and {:9.3f}: {:8.3f} Hz'.format(*data))
plt.semilogx(freq, max_db, color='dodgerblue')
xtx = 2 * np.logspace(0, 4, num=5)
xlab = ['{:g}'.format(x) for x in xtx]
plt.xticks(xtx, xlab)
plt.xlabel('Frequency (Hz)')
plt.ylabel('Peak amplitude (dB)')
plt.grid(True, which='both')
def segmentvad(feat, amplitude, dist_1, numfrwin, nsh, pflin, fs):
#Performing Segmentation
win_ind_1 = 0
win_ind_2 = win_ind_1 + numfrwin
dim = len(feat[:, 1]) #to find the dimensions of the FEATURE
dist = 0
count = 0
w1 = np.zeros((dim, numfrwin))
w2 = np.zeros((dim, numfrwin))
d = []
frame_no = []
num_frame = len(feat[1, :])
Nw = math.floor(fs * 0.03)
Nsh = math.floor(fs * nsh) #0.010 by default
frame_index_w1 = 0
frame_index_w2 = 0 + numfrwin * Nsh
while (win_ind_2 + numfrwin < num_frame):
#finding the KL-DIVERGENCE between W1/W2
w1[:, 0:numfrwin] = feat[:, win_ind_1:win_ind_1 + numfrwin]
w2[:, 0:numfrwin] = feat[:, win_ind_2:win_ind_2 + numfrwin]
cov1 = []
cov2 = []
mean1 = []
mean2 = []
mean1 = np.mean(w1, 1)
mean2 = np.mean(w2, 1)
cov1 = np.var(w1, 1)
cov1 = np.diag(cov1)
cov2 = np.var(w2, 1)
cov2 = np.diag(cov2)
mean1.shape = (1, dim)
mean2.shape = (1, dim)
dist1 = (np.trace(np.dot(inv(cov2), cov1)))
dist2 = np.dot((mean2 - mean1), inv(cov2))
mean1.shape = (dim, 1)
mean2.shape = (dim, 1)
dist2 = np.dot(dist2, (mean2 - mean1))
k = dim
dist3 = (np.linalg.det(cov2) / np.linalg.det(cov1))
dist3 = np.log(dist3)
dist = 0.5 * (dist1 + dist2 - k + dist3)
d.append(dist)
frame_no.append(frame_index_w2)
win_ind_1 = win_ind_1 + 1
win_ind_2 = win_ind_2 + 1
frame_index_w2 = win_ind_2 * Nsh
frame_index_w3 = win_ind_1 * Nsh
d = np.array(d)
d.shape = (len(d), )
d = d.tolist()
frame_no = np.array(frame_no)
time_stamps = frame_no / fs
frame_no.shape = (len(frame_no), )
time_stamps.shape = (len(frame_no), )
frame_no = frame_no.tolist()
time_stamps = time_stamps.tolist()
d1 = np.zeros((numfrwin, ))
d1 = d1.tolist()
d1.extend(d)
#Finding the Peaks to Identify the Change points
b = []
max1, min2 = peakdet(
d1, dist_1) #max1 gives maxima peaks;min2 gives minima peaks
temp = []
temp.append(feat)
siz = max1.size
if (siz == 0
): #If no change point found, return the entire feat file as it is
return b, b, b, b, temp, temp
time_stamp = []
for i in range(0, len(max1[:, 0])):
if (max1[i, 1] < amplitude):
max1[i, 1] = 0
else:
time_stamp.append(max1[i, 0] * (Nsh) / fs)
frame_stamp = max1[:, 0]
frame_stamp = frame_stamp.tolist()
clus = []
i = 0
lasfram = len(feat[1, :])
#segmenting the features depending on change points
Nen = int(frame_stamp[0])
Nst = 0
clus.append(feat[:, Nst:Nen])
while (i < len(time_stamp) - 1):
Nst = int(frame_stamp[i])
Nen = int(frame_stamp[i + 1])
clus.append(feat[:, Nst:Nen])
i = i + 1
Nst = int(frame_stamp[len(frame_stamp) - 1])
Nen = lasfram
clus.append(feat[:, Nst:Nen])
counlin = 1
cluslin = []
cov_lin = []
mfcc_lin = []
clus2 = clus
ts_lin = []
fs_lin = []
#performing linear clustering
while (counlin < len(clus2)):
if (counlin <= 1):
bicdist = bicdist_single(clus2[counlin], clus2[counlin - 1], pflin)
if (bicdist < 0):
clus3 = np.concatenate((clus2[counlin], clus2[counlin - 1]),
axis=1)
cluslin.append(clus3)
else:
cluslin.append(clus2[counlin - 1])
cluslin.append(clus2[counlin])
ts_lin.append(time_stamp[counlin - 1])
fs_lin.append(frame_stamp[counlin - 1])
else:
bicdist = bicdist_single(clus2[counlin], cluslin[len(cluslin) - 1],
pflin)
if (bicdist < 0):
clus3 = np.concatenate(
(cluslin[len(cluslin) - 1], clus2[counlin]), axis=1)
cluslin[len(cluslin) - 1] = clus3
else:
cluslin.append(clus2[counlin])
ts_lin.append(time_stamp[counlin - 1])
fs_lin.append(frame_stamp[counlin - 1])
counlin = counlin + 1
return time_stamp, frame_stamp, ts_lin, fs_lin, clus, cluslin
def analyze_peaks(self, delta, x=None):
self.peaks, vals_ = peakdetect.peakdet(self.v, delta, x)
def audioRead(self):
buffer_bytes = self.audio_buffer.readAll()
if buffer_bytes:
buffer_bytes = buffer_bytes[:self.audio_nsamples *
self.audio_bytes] # truncate
data = np.frombuffer(buffer_bytes, dtype=np.single)
if max(data) > 0:
#print(type(data), data.shape)
data /= max(max(data), -min(data))
# data /= (max(data)/2.0)
# data[data > 1] = 1
# data[data < -1] = -1
self.sc_time.new_data(data)
nb_samples = len(buffer_bytes) // self.audio_bytes
self.peak_signal[self.
peak_signal_index:self.peak_signal_index +
nb_samples] = data
self.peak_signal_index += nb_samples
if self.peak_signal_index > self.nfft_peak:
f, s = periodogram(self.peak_signal,
self.audio_rate,
'blackman',
self.nfft_peak,
'linear',
False,
scaling='spectrum')
threshold = max(s) * 0.9
if threshold > self.thr:
self.thr_count = 2
else:
if self.thr_count > 0:
self.thr_count -= 1
if self.thr_count > 0:
maxtab, mintab = peakdet(abs(s[0:int(len(s) / 2 - 1)]),
threshold,
f[0:int(len(f) / 2 - 1)])
tone = maxtab[0, 0]
#print(f'tone: {tone} thr: {(10.0 * np.log10(threshold)):.2f} dB')
self.sc_peak.new_data(f, s, maxtab, tone)
nside_bins = 1
f, t, img = specimg(self.audio_rate,
self.peak_signal[:self.nfft_peak],
tone, self.nfft, self.noverlap,
nside_bins)
#print(t.shape, f)
if len(f) != 0:
img_line = np.sum(img, axis=0)
if threshold > self.thr: # update scaling factor if signal present
self.img_norm = max(img_line) / 1.5
img_line /= self.img_norm
img_line[img_line > 1] = 1
if len(img_line) != self.pred_len:
self.pred_len = len(img_line)
self.sc_pred.set_mp(self.pred_len * 3)
self.dataq.put(img_line)
#self.test_line(img_line, 0.75)
self.sc_tenv.new_data(img_line, 50)
self.sc_zenv.new_data(img_line[:50])
self.peak_signal = np.roll(self.peak_signal,
self.nfft_peak,
axis=0)
self.peak_signal_index -= self.nfft_peak
def online_FE(inputfile, featurefile):
# read input from 3 files
inputraw = pd.read_csv(inputfile)
tempselected = [line.strip('\n') for line in open(featurefile)]
selectedfeature = [line.split(':', 1) for line in tempselected]
featuresetlist = ['mean','var','skewness','kurtosis','maximum','minimum',
'RMS','std','range','iqr','maxpeak','minpeak','all']
# take the selected attribute out for calculating features
calculist = list()
for (attr, feature) in selectedfeature:
for a in inputraw.columns:
if a.find(attr)>0 and feature in featuresetlist:
calculist.append((a, feature))
break
elif a == inputraw.columns[-1]:
print(attr+'_'+feature+" is not a valid feture!Either attrname"\
" or feature is not a valid one.")
if not calculist:
print("No feature calculated!")
return
result = list()
# calculate features
for (attr, f) in calculist:
if f == 'all':
try:
result.append(inputraw[attr].mean())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].var())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].skew())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].kurt())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].max())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].min())
except:
result.append(float('nan'))
try:
result.append(numpy.sqrt(numpy.mean(numpy.square(
inputraw[attr]))))
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].std())
except:
result.append(float('nan'))
try:
result.append(inputraw[attr].max()-inputraw[attr].min())
except:
result.append(float('nan'))
try:
result.append((inputraw[attr].quantile(0.75) -
inputraw[attr].quantile(0.25))/2)
except:
result.append(float('nan'))
try:
maxtab, mintab = peakdetect.peakdet(inputraw[attr],.3)
result.append(maxtab[:,1].max())
except:
result.append(float('nan'))
try:
maxtab, mintab = peakdetect.peakdet(inputraw[attr],.3)
result.append(mintab[:,1].min())
except:
result.append(float('nan'))
elif f == 'maxpeak':
try:
maxtab, mintab = peakdetect.peakdet(inputraw[attr],.3)
result.append(maxtab[:,1].max())
except:
result.append(float('nan'))
elif f == 'minpeak':
try:
maxtab, mintab = peakdetect.peakdet(inputraw[attr],.3)
result.append(mintab[:,1].min())
except:
result.append(float('nan'))
elif f == 'mean':
try:
result.append(inputraw[attr].mean())
except:
result.append(float('nan'))
elif f == 'var':
try:
result.append(inputraw[attr].var())
except:
result.append(float('nan'))
elif f == 'skewness':
try:
result.append(inputraw[attr].skew())
except:
result.append(float('nan'))
elif f == 'kurtosis':
try:
result.append(inputraw[attr].kurt())
except:
result.append(float('nan'))
elif f == 'maximum':
try:
result.append(inputraw[attr].max())
except:
result.append(float('nan'))
elif f == 'minimum':
try:
result.append(inputraw[attr].min())
except:
result.append(float('nan'))
elif f == 'RMS':
try:
result.append(numpy.sqrt(numpy.mean(numpy.square(
inputraw[attr]))))
except:
result.append(float('nan'))
elif f == 'std':
try:
result.append(inputraw[attr].std())
except:
result.append(float('nan'))
elif f == 'range':
try:
result.append(inputraw[attr].max()-inputraw[attr].min())
except:
result.append(float('nan'))
elif f == 'iqr':
try:
result.append((inputraw[attr].quantile(0.75) -
inputraw[attr].quantile(0.25))/2)
except:
result.append(float('nan'))
else:
print("Please Enter valid Feature:mean,variance,skewness,kurtosis"\
",max,min,RMS,std,range,iqr")
# output
if not result:
print("No feature calculated!")
return
os.chdir(".\\")
if sys.version_info >= (3, 0, 0):
f = open("Result.csv", 'w', newline='')
else:
f = open("Result.csv", 'wb')
w = csv.writer(f)
namelist = []
# create the column labels
for a, f in calculist:
if f == 'all':
for fl in featuresetlist[:-1]:
namelist.append(a+"_"+fl)
else:
namelist.append(a+"_"+f)
out = dict()
for i in range(0,numpy.size(namelist)):
out[namelist[i]] = result[i]
# write labels
w.writerow(namelist)
# write values
w.writerow(result)
return out
"""
n = 2**12
n_window = int(len(zs) / 2)
window = signal.blackmanharris(n_window)
z_fft = np.fft.rfft(zs[0:n_window] * window, n=n) * 4 / n_window
z_fft_mag = np.absolute(z_fft)
f = np.fft.rfftfreq(n, d=dt)
# peak detection
# this stuff isn't working
# peaks = peakdetect_parabola(z_fft_mag, f)
# print(peaks)
# indices = peakutils.indexes(z_fft_mag, thres=0.1, min_dist=1)
# this one works
maxtab, _ = peakdetect.peakdet(z_fft_mag, 0.01 * np.max(z_fft_mag),
range(int(n / 2) + 1))
plt.figure()
plt.plot(f, z_fft_mag)
plt.scatter(f[np.array(maxtab)[:, 0].astype(int)],
np.array(maxtab)[:, 1],
color='blue')
plt.show()
print(f[np.array(maxtab)[0, 0].astype(int)])
fft_motion = SinusoidalMotion(acc_mag=np.array(maxtab)[1, 1],
f=f[np.array(maxtab)[1, 0].astype(int)],
dt=dt,
noise_std=q,
meas_noise_std=R)
# initial conditions
#In [21]: len(d)
#Out[21]: 32
#
#In [22]: len(d[0])
#Out[22]: 131071
for fname in h5files:
f = H.File(source_dir+runtag+"/"+fname, 'r')
d = N.array(f['/data/data'])
nasic = len(d)
nhist = len(d[0])
adu = N.arange(nhist)-65535
f.close()
for asics in N.arange(nasic):
[max, min] = PD.peakdet(d[asics][65535-100:65535+2000], 20)
xmax = [max[i][0]-100 for i in N.arange(len(max))]
ymax = [max[i][1] for i in N.arange(len(max))]
xmin = [min[i][0]-100 for i in N.arange(len(min))]
ymin = [min[i][1] for i in N.arange(len(min))]
#print xmax, ymax, xmin, ymin
fig = P.figure()
P.plot(adu, d[asics])
P.scatter(xmax, ymax, c='g', marker='o')
P.scatter(xmin, ymin, c='r', marker='o')
canvas = fig.add_subplot(111)
canvas.set_title(fname + "_asic%s"%(asics+1))
P.xlim(options.min_value, options.max_value)
P.xlabel("Intensity (ADUs)")
P.ylabel("Number of Pixels")
#P.draw()
indir="D:/measuring/data/20160419"
data = pd.read_csv(os.path.join(indir,"FSR_80nm_Q600_it10000.csv"), usecols=[2,4,5])
max_WL = data['Wavelength'].max()
min_WL = data['Wavelength'].min()
max_I = data['Intensity'].max()
min_I = data['Intensity'].min()
data_mean=data.groupby('Column').agg([np.mean])
# Peak detection method for higher order modes
if peak_detect_H_order_modes == True:
I_array = np.asarray(data_mean['Intensity']) # write intensity dataframe as array
peak_1=peakdet(I_array, order_peak_detect_higher_modes) # use peakdet definition to detect all peaks from intensity
peak_WL_1=np.transpose(np.asarray(data_mean.loc[peak_1[0][:,0],'Wavelength']))[0] #get corresponding wavelengths
peak_I_1=peak_1[0][:,1]
peak_freq_1 = 3.e8/(peak_WL_1*1.e-9)
else:
print 'There are no higher order modes in this plot.'
# Peak detection method for TEM00 modes
if peak_detect_TEM00 == True:
I_avg_array = np.asarray(data_mean['Intensity']) # argrelextrema only takes an array
indices = argrelextrema(I_avg_array, np.greater, order=order_peak_detection) # the number 100 is somewhat arbitrary, but seems to work.
peak_WL= [] #connect indices with the values for the wavelength, creating arrays
peak_I=[]
def peakdetection(self):
cscore = ascore = gscore = tscore = spseries = pd.Series()
markers = ['C', 'A', 'G', 'T']
time, intensity = self.p1.roiCurve1.getData()
noise = np.std(intensity[intensity < np.mean(intensity)])
thresh = np.median(intensity) + 2 * noise
firing = np.where(intensity > thresh)[0]
startandend = np.diff(firing)
startpoints = np.insert(startandend, 0, 2)
endpoints = np.insert(startandend, -1, 2)
startpoints = np.where(startpoints > 1)[0]
endpoints = np.where(endpoints > 1)[0]
startpoints = firing[startpoints]
endpoints = firing[endpoints]
peakseries = pd.Series()
minseries = pd.Series()
for i, x in enumerate(startpoints):
sp = startpoints[i]
ep = endpoints[i] + 1
# self.p1.getRoiPlot().plot(x = np.arange(sp, ep), y = intensity[sp:ep], pen = 'b')
try:
peaks, mins = peakdet(v=intensity[sp:ep],
delta=noise,
x=np.arange(sp, ep))
if len(peaks) == 0:
peaks = np.NAN
if len(mins) == 0:
peaks = np.NAN
# else:
# self.p1.getRoiPlot().plot(peaks, pen = None, symbol = 'o', symbolBrush = 'g')
# self.p1.getRoiPlot().plot(mins, pen = None, symbol = 'o', symbolBrush = 'r')
peakseries = peakseries.append(pd.Series([peaks]))
minseries = minseries.append(pd.Series([peaks]))
# p1.plot(df[i], pen = None, symbol = 'o', symbolBrush = 'b')
except:
ValueError
if np.size(peaks) < 4:
substack = np.mean(self.stack[sp:ep], 0)
cscore = cscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[0].ravel())),
ignore_index=True)
ascore = ascore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[1].ravel())),
ignore_index=True)
gscore = gscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[2].ravel())),
ignore_index=True)
tscore = tscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[3].ravel())),
ignore_index=True)
spseries = spseries.append(pd.Series(sp), ignore_index=True)
else:
for j, y in enumerate(peaks):
if j == 0:
ssp = sp
sep = int(mins[j][0])
elif j == len(peaks) - 1:
ssp = int(mins[j - 1][0])
sep = ep
else:
ssp = int(mins[j - 1][0])
sep = int(mins[j][0])
substack = np.mean(self.stack[ssp:sep + 1], 0)
cscore = cscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[0].ravel())),
ignore_index=True)
ascore = ascore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[1].ravel())),
ignore_index=True)
gscore = gscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[2].ravel())),
ignore_index=True)
tscore = tscore.append(pd.Series(
np.dot(substack.ravel(), self.czpro[3].ravel())),
ignore_index=True)
spseries = spseries.append(pd.Series(ssp),
ignore_index=True)
scoredf = pd.DataFrame({
'C': cscore,
'A': ascore,
'G': gscore,
'T': tscore,
'sp': spseries
})
sequence = scoredf[['A', 'C', 'G', 'T']].idxmax(axis=1)
print(sequence.str.cat())
for i, x in enumerate(sequence):
if x == 'C':
color = 'r'
if x == 'A':
color = 'y'
if x == 'G':
color = 'g'
if x == 'T':
color = 'b'
text = pg.TextItem(x, color=color)
seqplot = self.p1.getRoiPlot().addItem(text)
if i == 0:
self.seqplotlist = [text]
else:
self.seqplotlist.append(text)
text.setPos(spseries[i], intensity[spseries[i]])
return sequence
def peakdetection(self,blueThresh,redThresh,bluePeakThresh,redPeakThresh):
markers = ['C','A','G','T']
colors = ['r','b']
score = ascore = gscore = tscore = spseries = pd.Series()
df = pd.DataFrame({"ident":[],'stimes':[],'etimes':[],
'peaks':[],'mins':[]})
seqdf = pd.DataFrame({'base':[],'times':[]})
time1, intensity1 = self.p1.roiCurve1.getData()
time2, intensity2 = self.p1.roiCurve2.getData()
intensities = [intensity1,intensity2]
self.firingplotlist = []
peakseries = pd.Series()
minseries = pd.Series()
for ind,intensity in enumerate(intensities):
if ind == 0:
thresh = redThresh
noise = redPeakThresh
if ind ==1:
thresh = blueThresh
noise = bluePeakThresh
firing = np.where(((intensity > thresh) & (intensity > intensities[ind-1])))[0]
startandend = np.diff(firing)
startpoints = np.insert(startandend, 0, 2)
endpoints = np.insert(startandend, -1, 2)
startpoints = np.where(startpoints>1)[0]
endpoints = np.where(endpoints>1)[0]
startpoints = firing[startpoints]
endpoints = firing[endpoints]
df = df.append(pd.DataFrame({"ident":[ind]*len(startpoints),
'stimes':startpoints,'etimes':endpoints}),ignore_index=True)
for i,x in enumerate(startpoints):
sp = startpoints[i]
ep = endpoints[i]+1
curve = pg.PlotDataItem(x = np.linspace(sp, ep,ep-sp),
y = intensity[sp:ep],
pen = pg.mkPen(colors[ind], width = 2))
self.firingplotlist.append(curve)
self.p1.getRoiPlot().addItem(curve)
try:
peaks, mins = peakdet(v = intensity[sp:ep],delta = noise, x = np.arange(sp,ep))
if len(peaks) == 0 or len(mins) == 0:
peaks = np.NAN
substack = np.mean(self.stack[sp:ep],0)
if ind == 0:
cscore = np.dot(substack.ravel(),self.czpro[0].ravel())
ascore = np.dot(substack.ravel(),self.czpro[1].ravel())
if cscore > ascore:
call = 'C'
else:
call = 'A'
if ind == 1:
gscore = np.dot(substack.ravel(),self.czpro[2].ravel())
tscore = np.dot(substack.ravel(),self.czpro[3].ravel())
if gscore > tscore:
call = 'G'
else:
call = 'T'
seqdf = seqdf.append(pd.DataFrame({'base':[call],'times':[sp]}),
ignore_index = True)
else:
# point = pg.PlotDataItem(peaks, pen = None, symbol = 'o', symbolBrush = 'g')
# self.p1.getRoiPlot().addItem(point)
# self.firingplotlist.append(point)
# point = pg.PlotDataItem(mins, pen = None, symbol = 'o', symbolBrush = 'r')
# self.p1.getRoiPlot().addItem(point)
# self.firingplotlist.append(point)
for i,x in enumerate(peaks):
if i == 0:
ssp = sp
sep = int(mins[i][0])
elif i == len(peaks)-1:
ssp = int(mins[i-1][0])
sep = ep
else:
ssp = int(mins[i-1][0])
sep = int(mins[i][0])
substack = np.mean(self.stack[ssp:sep+1],0)
if ind == 0:
cscore = np.dot(substack.ravel(),self.czpro[0].ravel())
ascore = np.dot(substack.ravel(),self.czpro[1].ravel())
if cscore > ascore:
call = 'C'
else:
call = 'A'
if ind == 1:
gscore = np.dot(substack.ravel(),self.czpro[2].ravel())
tscore = np.dot(substack.ravel(),self.czpro[3].ravel())
if gscore > tscore:
call = 'G'
else:
call = 'T'
seqdf = seqdf.append(pd.DataFrame({'base':[call],'times':[ssp]}),
ignore_index = True)
peakseries = peakseries.append(pd.Series([peaks]))
minseries = minseries.append(pd.Series([mins]))
except:
ValueError
seqdf = seqdf.sort(['times','base'])
for i,x in enumerate(seqdf.index):
base = seqdf.base[i]
if base == 'C':
color = 'r'
intensity = intensities[0][int(seqdf.times[i])]
if base == 'A':
color = 'y'
intensity = intensities[0][int(seqdf.times[i])]
if base == 'G':
color = 'g'
intensity = intensities[1][int(seqdf.times[i])]
if base == 'T':
color = 'b'
intensity = intensities[1][int(seqdf.times[i])]
text = pg.TextItem(base,color = color)
seqplot = self.p1.getRoiPlot().addItem(text)
if i == 0:
self.seqplotlist = [text]
else:
self.seqplotlist.append(text)
text.setPos(seqdf.times[i],intensity)
print(seqdf.base.str.cat())
return seqdf
def FE(begin,\
end,\
userfilename = "E:\\LED_Data\\LifeCycleList.csv",\
filedir = "E:\\LED_Data\\18.non_nominal_0912\\current\\",\
featurefile = "E:\\pythonanalysis\\feature.txt"):
# read input from 3 files
userfileList = pd.read_csv(userfilename)
featureList = [line.strip('\n') for line in open(featurefile)]
#read current file and filtered by time period
os.chdir(filedir)
currentfilenameList = glob.glob("*.csv")
currentfilelist = list()
cfilteredfilenameList = list()
for filename in currentfilenameList:
for filenum in range(begin,end+1):
if (int(filename[3:7]) >= userfileList.ix[filenum,1]) & (int(filename[3:7]) <= userfileList.ix[filenum,2]):
temp = pd.read_csv(filename)
if numpy.size(temp, 0) >= 900:
currentfilelist.append(temp)
cfilteredfilenameList.append(filename)
totalresult = list()
result = list()
#calculate features
index = 0
for file in currentfilelist:
index = index + 1
result.append(index)
for i,col in file.iteritems():
if i!="DataTime":
for fea in featureList:
if fea == 'maxpeak':
try:
maxtab, mintab = peakdetect.peakdet(col,.3)
result.append(maxtab[:,1].max())
except:
result.append(float('nan'))
elif fea == 'minpeak':
try:
maxtab, mintab = peakdetect.peakdet(col,.3)
result.append(mintab[:,1].min())
except:
result.append(float('nan'))
elif fea == 'mean':
try:
result.append(col.mean())
except:
result.append(float('nan'))
elif fea == 'variance':
try:
result.append(col.var())
except:
result.append(float('nan'))
elif fea == 'skewness':
try:
result.append(col.skew())
except:
result.append(float('nan'))
elif fea == 'kurtosis':
try:
result.append(col.kurt())
except:
result.append(float('nan'))
elif fea == 'max':
try:
result.append(col.max())
except:
result.append(float('nan'))
elif fea == 'min':
try:
result.append(col.min())
except:
result.append(float('nan'))
elif fea == 'RMS':
try:
result.append(numpy.sqrt(numpy.mean(numpy.square(
col))))
except:
result.append(float('nan'))
elif fea == 'std':
try:
result.append(col.std())
except:
result.append(float('nan'))
elif fea == 'range':
try:
result.append(col.max()-col.min())
except:
result.append(float('nan'))
elif fea == 'iqr':
try:
result.append((col.quantile(0.75) -
col.quantile(0.25)))
except:
result.append(float('nan'))
else:
print("Please Enter valid Feature:mean,variance,skewness,kurtosis\
,max,min,RMS,std,range,iqr")
if result:
totalresult.append(result[:])
result.clear()
# output
if not totalresult:
print("No feature calculated!")
return
f = open("totalResult.csv", 'w', newline='')
w = csv.writer(f)
namelist = []
# create the column labels
namelist.append("Filenum")
for name in currentfilelist[1].columns.values.tolist():
if name != "DataTime":
for fea in featureList:
namelist.append(name+"_"+fea)
# write labels
w.writerow(namelist)
# write values
for r in totalresult:
w.writerow(r)
f.close()
