def prepostfilter(reader):
scaled_csi = reader.csi_trace
no_frames = len(scaled_csi)
no_subcarriers = scaled_csi[0]["csi"].shape[0]
finalEntry = getCSI(scaled_csi)[15]
stdev = running_stdev(finalEntry, 2)
hampelData = hampel(finalEntry, 15)
smoothedData = running_mean(hampelData.copy(), 15)
y = finalEntry
y2 = hampelData
y3 = smoothedData
x = list([x["timestamp"] for x in scaled_csi])
plt.plot(x, y, label="Raw")
plt.plot(x, y2, label="Hampel")
# plt.plot(x, stdev, label="Standard Deviation")
plt.plot(x, y3, "r", label="Hampel + Running Mean")
plt.xlabel("Time (s)")
plt.ylabel("Amplitude (dBm)")
plt.legend(loc="upper right")
plt.show()
def updateContents(self, data):
self.all_data.append(data)
if not self.updateTimestamps():
self.all_data = self.all_data[:-1]
return None
scaled_csi = self.all_data
no_frames = len(scaled_csi)
no_subcarriers = 30
finalEntry = [
db(abs(scaled_csi[x]["csi"][14][1][0])) for x in range(no_frames)
]
x = list([x["timestamp"] for x in scaled_csi])
#self.plotStand.set_xdata(x)
#self.plotStand.set_ydata(finalEntry)
hampelData = hampel(finalEntry, 20)
#smoothedData = running_mean(hampelData.copy(), 15)
self.plotHampel.set_xdata(x)
self.plotHampel.set_ydata(hampelData)
#self.plotAll.set_xdata(x)
#self.plotAll.set_ydata(smoothedData)
self.ax.relim()
self.ax.autoscale_view()
self.fig.canvas.draw()
self.fig.canvas.flush_events()
def heatmap(scaled_csi):
xax = getTimestamps(scaled_csi)
csi, no_frames, no_subcarriers = getCSI(scaled_csi)
Fs = 1 / np.mean(np.diff(xax))
print("Sampling Rate: " + str(Fs))
limits = [0, xax[-1], 1, no_subcarriers]
#x = subcarrier index
#y = time (s)
#z = amplitude (dBm)
for x in range(no_subcarriers):
hampelData = hampel(csi[x].flatten(), 5)
smoothedData = running_mean(hampelData, 5)
# b, a = signal.butter(9, [1/int(Fs/2), 2/int(Fs/2)], "bandpass")
# csi[x] = signal.lfilter(b, a, csi[x].flatten())
csi[x] = smoothedData
fig, ax = plt.subplots()
im = ax.imshow(csi, cmap="jet", extent=limits, aspect="auto")
cbar = ax.figure.colorbar(im, ax=ax)
cbar.ax.set_ylabel("Amplitude (dBm)")
plt.xlabel("Time (s)")
plt.ylabel("Subcarrier Index")
plt.show()
def beatsfilter(scaled_csi):
xax = getTimestamps(scaled_csi)
csi, no_frames, no_subcarriers = getCSI(scaled_csi)
Fs = 1 / np.mean(np.diff(xax))
stabilities = []
for x in range(no_subcarriers):
finalEntry = csi[x].flatten()
variation = stats.variation(finalEntry)
if not np.isnan(variation) and variation < 0.5:
hampelData = hampel(finalEntry, 5)
smoothedData = running_mean(hampelData, 5)
filtData = bandpass(5, 1, 1.3, Fs, smoothedData)
wLength = 1 * Fs
N = np.mod(len(filtData), wLength)
windows = np.array_split(filtData, N)
psds = []
for window in windows:
f, Pxx_den = signal.welch(window, Fs)
fMax = f[np.argmax(Pxx_den)]
psds.append(fMax)
specStab = 1 / np.var(psds)
print("Sub: {} has spectral stability: {}".format(x, specStab))
# plt.plot(xax, filtData, alpha=0.5)
stabilities.append({
"sub": x,
"stability": specStab,
"data": filtData
})
stabilities.sort(key=lambda x: x["stability"], reverse=True)
bestStab = stabilities[0]["stability"]
news = []
for stab in stabilities:
if stab["stability"] >= (bestStab / 100) * 20:
news.append(stab)
print("Using {} subcarriers.".format(len(news)))
pxxs = []
for sub in news:
filtData = sub["data"]
f, Pxx_den = signal.welch(filtData, Fs)
pxxs.append(Pxx_den)
meanPsd = np.mean(pxxs, axis=0)
plt.plot(f * 60, meanPsd, alpha=0.5)
plt.xlabel("Estimated Heart Rate [bpm]")
plt.ylabel("PSD [V**2/Hz]")
plt.legend(loc="upper right")
plt.show()
def heatmap(scaled_csi):
timestamps = getTimestamps(scaled_csi)
csi, no_frames, no_subcarriers = getCSI(scaled_csi)
Fs = 1 / np.mean(np.diff(timestamps))
print("Sampling Rate: " + str(Fs))
limits = [0, timestamps[-1], 1, no_subcarriers]
for x in range(no_subcarriers):
hampelData = hampel(csi[x].flatten(), 5)
smoothedData = running_mean(hampelData, 5)
butteredData = bandpass(7, 0.2, 0.3, Fs, smoothedData)
csi[x] = butteredData
fig, ax = plt.subplots()
im = ax.imshow(csi, cmap="jet", extent=limits, aspect="auto")
cbar = ax.figure.colorbar(im, ax=ax)
cbar.ax.set_ylabel("Amplitude (dBm)")
plt.xlabel("Time (s)")
plt.ylabel("Subcarrier Index")
plt.show()
def fft(reader):
scaled_csi = reader.csi_trace
no_frames = len(scaled_csi)
no_subcarriers = scaled_csi[0]["csi"].shape[0]
finalEntry = getCSI(scaled_csi)[15].flatten()
hampelData = hampel(finalEntry, 20)
smoothedData = running_mean(hampelData, 30)
y = smoothedData.flatten()
y -= np.mean(y)
b, a = signal.butter(5, [1 / 10, 2 / 10], "bandpass")
y = signal.lfilter(b, a, y)
x = [i / 20 for i in range(no_frames)]
tdelta = (x[-1] - x[0]) / len(x)
Fs = 1 / tdelta
n = no_frames
#rfft is a real Fast Fourier Transform, as we aren't interested in the imaginary parts.
#as half of the points lie in the imaginary/negative domain, we get an n/2 point FFT.
#rfftfreq produces a list of frequency bins, which requires calculation to produce
#interpretable frequencies for BPM tracking. by plotting calculated bpm values,
#the graph can be more easily read.
#despite rfft producing an n/2 point fft, the calculation still uses n,
#because the point spacing is still based on n points.
# ((binNumber*samplingRate)/n)*60 produces a per minute rate.
ffty = np.fft.rfft(y, len(y))
freq = np.fft.rfftfreq(len(y), tdelta)
freqX = [((i * Fs) / n) * 60 for i in range(len(freq))]
plt.subplot(211)
plt.xlabel("Time (s)")
plt.ylabel("Amplitude (Hz)")
plt.plot(x, y)
plt.subplot(212)
plt.xlabel("Breaths Per Minute (BPM)")
plt.ylabel("Amplitude (dB/Hz)")
axes = plt.gca()
axes.set_xlim([0, 30])
plt.plot(freqX, np.abs(ffty))
plt.show()
def updateButterworth(self, data):
self.all_data.append(data)
self.updateTimestamps()
if not self.updateTimestamps():
self.all_data = self.all_data[:-1]
return None
scaled_csi = self.all_data
no_frames = len(scaled_csi)
no_subcarriers = scaled_csi[0]["csi"].shape[0]
if no_frames < 50:
return None
#Replace complex CSI with amplitude.
finalEntry = [
db(abs(scaled_csi[x]["csi"][15][0][0])) for x in range(no_frames)
]
hampelData = hampel(finalEntry, 10)
smoothedData = running_mean(hampelData, 30)
y = smoothedData
x = list([x["timestamp"] for x in scaled_csi])
tdelta = (x[-1] - x[0]) / len(x)
Fs = 1 / tdelta
n = no_frames
y = bandpass(5, 1.0, 1.3, Fs, y)
ffty = np.fft.rfft(y, len(y))
freq = np.fft.rfftfreq(len(y), tdelta)
freqX = [((i * Fs) / n) * 60 for i in range(len(freq))]
self.plotButt.set_xdata(freqX)
self.plotButt.set_ydata(np.abs(ffty))
self.ax.relim()
self.ax.autoscale_view()
self.fig.canvas.draw()
self.fig.canvas.flush_events()
def varianceGraph(reader):
scaled_csi = reader.csi_trace
no_frames = len(scaled_csi)
no_subcarriers = scaled_csi[1]["csi"].shape[0]
y = []
finalEntry = getCSI(scaled_csi)
for x in range(no_subcarriers):
hampelData = hampel(finalEntry[x], 10)
smoothedData = running_mean(hampelData, 25)
y.append(variance(smoothedData))
plt.xlabel("Subcarrier Index")
plt.ylabel("Variance")
plt.plot(y)
plt.show()
def breathingfilter(scaled_csi):
xax = getTimestamps(scaled_csi)
csi, no_frames, no_subcarriers = getCSI(scaled_csi)
# Zeroing out invalid subcarriers.
# for i in []:
# for x in range(no_frames):
# csi[i][x] = 0
# for x in range(no_subcarriers):
for x in range(80, 100):
finalEntry = csi[x].flatten()
hampelData = hampel(finalEntry, 10)
smoothedData = running_mean(hampelData, 10)
# csi[x] = hampelData
csi[x] = smoothedData
plt.plot(xax, csi[x], alpha=0.5, label=x)
plt.xlabel("Time (s)")
plt.ylabel("Amplitude")
plt.legend(loc="upper right")
plt.show()
def specstabfilter(reader, Fs):
scaled_csi = reader.csi_trace
no_frames, no_subcarriers, finalEntries = getCSI(scaled_csi)
#Using CSI phase difference data.
stabilities = []
for x in range(no_subcarriers):
finalEntry = finalEntries[x]
#CardioFi paper uses 100Hz uniformly sampled data, which may mean we need to use different
#filter parameters. For now, we will copy them verbatim.
#Currently the initial hampel filter is run using T1=0.5s t1=0.4
# dynamic_detrending is run with c=5 l=3 alpha=1.2 Fs=Fs
# the second hampel filter is run using T1=0.5s t1=0.1
# the bandpass filter is run at 5th order with a range of 1-2Hz.
hampelData = hampel(finalEntry, 20)
detrended = dynamic_detrend(hampelData, 5, 3, 1.2, Fs)
rehampeledData = hampel(detrended, 20)
filtData = bandpass(7, 1, 1.5, Fs, rehampeledData)
#Spectral Stability section.
#The spectral stability metric aims to score subcarriers based on the
#variance of their heart rate estimations.
#To do this, both the length of the data being used for estimations,
#and a sliding window length must be selected.
#While the dataLength should ideally be around 40s to mirror that used
#in the CardioFi paper, this is difficult to replicate using the data
#which was produced over the last few months.
#Shorter data and window lengths are being experimented with but do not
#appear to be working well. This is evidenced by the number of subcarriers
#being selected using the metric, which is typically lower than that seen
#in the CardioFi paper.
#Notably, it is also difficult to take consistent ground truth heart rate
#measurements over a 40 second period.
wLength = 5 * Fs
dataLength = 10 * Fs
windows = []
position = 0
#This sliding window system splits filtData into wLength-sized windows,
#except for the final window which contains the remainder of the data.
#Each sliding window has an overlap of 1 second (or Fs).
while position < dataLength:
if (position + wLength) > dataLength:
window = filtData[position:]
else:
window = filtData[position:position + wLength]
windows.append(window)
position += wLength - Fs
#PSD measurements are then taken for each window, and the variance of
#these measurements are then collected to produce a final score for
#this subcarrier.
psds = []
for window in windows:
f, Pxx_den = signal.welch(window, Fs)
fMax = f[np.argmax(Pxx_den)]
psds.append(fMax)
specStab = 1 / np.var(psds)
if specStab == np.inf:
specStab = 0
stabilities.append([x, specStab, filtData])
# print("Sub: {} has spectral stability: {}".format(x, specStab))
# print("Sub: {} mean pred: {}".format(x, np.mean(psds)*60))
stabilities.sort(key=lambda x: x[1], reverse=True)
bestStab = stabilities[0][1]
news = [x for x in stabilities if x[1] > bestStab * 0.2]
print("Using {} subcarriers.".format(len(news)))
pxxs = []
for sub in news:
data = sub[2]
f, Pxx_den = signal.welch(data, Fs)
pxxs.append(Pxx_den)
#The mean PSD of the top subcarriers is then selected, with the
#peak taken as the final heart rate estimation.
meanPsd = np.mean(pxxs, axis=0)
return f[np.argmax(meanPsd)] * 60
def shorttime(reader, subcarrier):
scaled_csi = reader.csi_trace
no_frames = len(scaled_csi)
no_subcarriers = scaled_csi[0]["csi"].shape[0]
finalEntry = np.zeros((no_frames, 1))
hampelData = np.zeros((no_frames, 1))
smoothedData = np.zeros((no_frames, 1))
#Replace complex CSI with amplitude.
finalEntry = [
db(
abs(scaled_csi[x]["csi"][subcarrier][reader.x_antenna][
reader.y_antenna])) for x in range(no_frames)
]
hampelData = hampel(finalEntry, 30)
smoothedData = running_mean(hampelData, 20)
y = smoothedData
tdelta = 0.01
x = list([x * tdelta for x in range(0, no_frames)])
Fs = 1 / tdelta
n = no_frames
fmin = 0.7
fmax = 2.3
b, a = signal.butter(3, [fmin / (Fs / 2), fmax / (Fs / 2)], "bandpass")
y = signal.lfilter(b, a, y)
f, t, Zxx = signal.stft(y, Fs, nperseg=2000, noverlap=1750)
#bin indices for the observed amplitude peak in each segment.
Zxx = np.abs(Zxx)
maxAx = np.argmax(Zxx, axis=0)
freqs = []
for i in maxAx:
arc = f[i]
if arc >= fmin and arc <= fmax:
arc *= 60
freqs.append(arc)
else:
freqs.append(None)
bpms = []
for freq in freqs:
if freq != None:
bpms.append(freq)
print(bpms)
print("Average HR: " + str(np.average(bpms)))
#We're only interested in frequencies between 0.5 and 2.
freq_slice = np.where((f >= fmin) & (f <= fmax))
f = f[freq_slice]
Zxx = Zxx[freq_slice, :][0]
plt.pcolormesh(t, f * 60, np.abs(Zxx))
plt.plot(t, freqs, color="red", marker="x")
plt.title('STFT Magnitude')
# plt.ylabel('Frequency [Hz]')
plt.ylabel('Heart Rate [BPM]')
plt.xlabel('Time [sec]')
plt.show()