def switch_signal(self, label):
# Update Lines
self.signal_line.set_data(range(len(self.signal)), self.signal_amp_slider.val * self.signal)
self.cutoff_freq = self.cutoff_amp_slider.val
self.smoothed_signal = hb.lowpass_filter(signal = self.signal,
cutoff_freq = self.cutoff_freq)
self.smooth_signal_line.set_data(range(len(self.signal)), self.signal_amp_slider.val * self.smoothed_signal)
self.first_line.set_data(range(len(self.signal)), (self.first_amp_slider.val * 5* self.first) + self.first_height_slider.val + 1)
# T Peak
self.T_point.set_offsets((self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]]))
self.T_text.set_position((self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# ST Start Peak
self.ST_start_point.set_offsets((self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]]))
self.ST_start_text.set_position((self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# T'max Peak
self.dT_point.set_offsets((self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]]))
self.dT_text.set_position((self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# # T''max Peak
# self.ddT_point.set_offsets((self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]]))
# self.ddT_text.set_position((self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
self.y = self.signal_amp_slider.val * self.smoothed_signal
self.fig.canvas.draw()
def clip_signals(self):
max_time = max(self.time)
min_time = min(self.time)
if (max_time - min_time) < self.area_around_echo_size:
interval = range(np.searchsorted(self.time, min_time), np.searchsorted(self.time, max_time))
elif self.echo_time - self.area_around_echo_size/2 < min_time:
interval = range(np.searchsorted(self.time, min_time), int(np.searchsorted(self.time, min_time + self.area_around_echo_size)))
elif self.echo_time + self.area_around_echo_size/2 > max_time:
interval = range(int(np.searchsorted(self.time, (max_time - self.area_around_echo_size))), np.searchsorted(self.time, max_time))
else:
interval = range(int(np.searchsorted(self.time, self.echo_time - (self.area_around_echo_size/2))), int(np.searchsorted(self.time, self.echo_time + (self.area_around_echo_size/2))))
self.interval_near_echo = interval
self.time = self.time[interval]
self.signal = self.signal[interval]
self.seis = self.seis[interval]
self.phono = self.phono[interval]
self.signal = hb.bandpass_filter(time = self.time,
signal = self.signal,
freqmin = 59,
freqmax = 61)
self.seis = hb.bandpass_filter(time = self.time,
signal = self.seis,
freqmin = 59,
freqmax = 61)
self.phono = hb.bandpass_filter(time = self.time,
signal = self.phono,
freqmin = 59,
freqmax = 61)
self.signal = hb.lowpass_filter(time = self.time,
signal = self.signal,
cutoff_freq = 10)
self.seis = hb.lowpass_filter(time = self.time,
signal = self.seis,
cutoff_freq = 50)
def update_plot(self):
# Update index
self.i_text.set_text("Heartbeat: " + str(self.index + 1) + "/" + str(len(self.peaks.R.data) - 1))
self.signal = hb.normalize(self.peaks.signal[range(self.peaks.P.data[self.index], self.peaks.R.data[self.index + 1])])
# Pass through a Low pass
self.smoothed_signal = hb.lowpass_filter(signal = self.signal,
cutoff_freq = self.cutoff_freq)
# Calculate first derivative
self.first, _ = hb.get_derivatives(self.smoothed_signal)
# Update cross hairs
self.switch_signal(None)
# Plot ECG, Phono and Seismo
self.signal_line.set_data(range(len(self.signal)), self.signal_amp_slider.val * self.signal)
self.smooth_signal_line.set_data(range(len(self.signal)), self.signal_amp_slider.val * self.smoothed_signal)
self.first_line.set_data(range(len(self.signal)), (self.first_amp_slider.val * 5*self.first) + self.first_height_slider.val + 1)
self.ax.set_xlim(0, len(self.signal))
# T Peak
self.T_point.set_offsets((self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]]))
self.T_text.set_position((self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# ST Start Peak
self.ST_start_point.set_offsets((self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]]))
self.ST_start_text.set_position((self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# T''max Peak
self.dT_point.set_offsets((self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]]))
self.dT_text.set_position((self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
# # T''max Peak
# self.ddT_point.set_offsets((self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]]))
# self.ddT_text.set_position((self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.signal_amp_slider.val * self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]] + 0.2))
self.fig.canvas.draw()
# Load Data
time, signal, seis1, seis2, phono1, phono2 = hb.load_file_data( files, folder_name,
dosage, file_number,
interval_number, preloaded_signal,
save_signal)
# Calculate Composite
lowpass_signal = hb.bandpass_filter(time = time,
signal = signal,
freqmin = 59,
freqmax = 61)
# Low-Pass filter under 10Hz
lowpass_signal = hb.lowpass_filter(time = time,
signal = lowpass_signal,
cutoff_freq = 50)
peaks = hb.get_peaks_for_composites(time = time,
signal = lowpass_signal,
dosage = dosage,
seis1 = seis1,
phono1 = phono1)
peaks.get_inital_statistics()
print("Time Length: ", max(time) - min(time))
print("R Peaks: ", len(peaks.R.data))
if (len(peaks.R.data) > 10):
composite_peaks = CompositePeaks(peaks)
hb.plot_signal(time,
signal,
intervals=files[folder_name][dosage][1]["intervals"]
if use_intervals else None)
# View Frequency Domain
if show_freq_domain == True:
hb.get_fft(time=time, signal=signal, plot=True)
# hb.get_spectrum(time = time,
# signal = signal)
# Bandblock
if show_bandpass == True:
bandpass_signal = hb.lowpass_filter(time=time,
signal=signal,
cutoff_freq=10)
hb.get_fft(time=time, signal=bandpass_signal, plot=True)
# View Derivatives
if show_derivatives == True:
bandpass_signal = hb.bandpass_filter(time=time,
signal=signal,
freqmin=59,
freqmax=61)
hb.get_derivatives(signal=bandpass_signal, plot=True)
# Find Peaks
if show_peaks:
def plot_signals(self):
# Create figure
self.fig, self.ax = plt.subplots()
self.signal = hb.normalize(self.peaks.signal[range(self.peaks.P.data[self.index], self.peaks.T.data[self.index + 1])])
# Determine what cutoff freq to use
self.cutoff_freq = 15 if np.mean(np.diff(self.peaks.R.data)) > 2500 else 10
# Pass through a Low pass
self.smoothed_signal = hb.lowpass_filter(signal = self.signal,
cutoff_freq = self.cutoff_freq)
# Calculate first derivative
self.first, _ = hb.get_derivatives(self.smoothed_signal)
# Plot ECG, Phono and Seismo
self.signal_line, = self.ax.plot(range(len(self.signal)), self.signal, linewidth = 0.75, c = "r", label = "ECG")
self.smooth_signal_line, = self.ax.plot(range(len(self.signal)), self.smoothed_signal, linewidth = 1, c = "b", label = "Low Pass ECG")
self.first_line, = self.ax.plot(range(len(self.signal)), 1 + 5*self.first,
'--', linewidth = 0.5, c = 'k', label = "ECG 1st Derv.")
self.ax.set_xlim(0, len(self.signal))
sig_min = min(self.signal)
sig_max = max(self.signal)
self.ax.set_ylim(sig_min - 0.2*(sig_max - sig_min), sig_max + 0.2*(sig_max - sig_min))
plt.legend(loc='upper right')
# T Peak
self.T_point = self.ax.scatter(self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]], c = '#9467bd')
self.T_text = self.ax.text(self.peaks.T.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.T.data[self.index] - self.peaks.P.data[self.index]] + 0.2, "T", fontsize=9, horizontalalignment = 'center')
# ST Start Peak
self.ST_start_point = self.ax.scatter(self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]], c = 'y')
self.ST_start_text = self.ax.text(self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.ST_start.data[self.index] - self.peaks.P.data[self.index]] + 0.2, "ST Start", fontsize=9, horizontalalignment = 'center')
# T'max Peak
self.dT_point = self.ax.scatter(self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]], c = '#2ca02c')
self.dT_text = self.ax.text(self.peaks.dT.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.dT.data[self.index] - self.peaks.P.data[self.index]] + 0.2, "T'max", fontsize=9, horizontalalignment = 'center')
# # T''max Peak
# self.ddT_point = self.ax.scatter(self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]], c = '#2ca02c')
# self.ddT_text = self.ax.text(self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index], self.smoothed_signal[self.peaks.ddT.data[self.index] - self.peaks.P.data[self.index]] + 0.2, "T''max", fontsize=9, horizontalalignment = 'center')
# Initalize axes and data points
self.x = range(len(self.signal))
self.y = self.smoothed_signal
# Cross hairs
self.lx = self.ax.axhline(color='k', linewidth=0.2) # the horiz line
self.ly = self.ax.axvline(color='k', linewidth=0.2) # the vert line
# Add data
left_shift = 0.45
start = 0.96
space = 0.04
self.ax.text(0.01, start, transform = self.ax.transAxes,
s = "Folder: " + self.folder_name, fontsize=12, horizontalalignment = 'left')
self.ax.text(0.01, start - space, transform = self.ax.transAxes,
s = "Dosage: " + str(self.dosage), fontsize=12, horizontalalignment = 'left')
self.i_text = self.ax.text(0.60 - left_shift, 1.1 - space, transform = self.ax.transAxes,
s = "Heartbeat: " + str(self.index + 1) + "/" + str(len(self.peaks.R.data) - 1), fontsize=12, horizontalalignment = 'left')
# Add index buttons
ax_prev = plt.axes([0.575 - left_shift, 0.9, 0.1, 0.075])
self.bprev = Button(ax_prev, 'Previous')
self.bprev.on_clicked(self.prev)
ax_next = plt.axes([0.8 - left_shift, 0.9, 0.1, 0.075])
self.b_next = Button(ax_next, 'Next')
self.b_next.on_clicked(self.next)
self.fig.canvas.mpl_connect('motion_notify_event', self.mouse_move)
self.fig.canvas.mpl_connect('button_press_event', self.on_click)
self.fig.canvas.mpl_connect('button_release_event', self.off_click)
# Add Sliders
start = 0.91
slider_width = 0.0075
slider_height = 0.47
self.cutoff_amp_slider = Slider(plt.axes([0.05, 0.15, 2*slider_width, slider_height]),
label = "Cutoff (Hz)",
valmin = 1,
valmax = 50,
valinit = self.cutoff_freq,
orientation = 'vertical',
valfmt='%0.0f')
self.cutoff_amp_slider.label.set_size(8)
self.cutoff_amp_slider.on_changed(self.switch_signal)
self.signal_amp_slider = Slider(plt.axes([start, 0.15, slider_width, slider_height]),
label = "ECG\n\nA",
valmin = 0.01,
valmax = 10,
valinit = 1,
orientation = 'vertical')
self.signal_amp_slider.label.set_size(8)
self.signal_amp_slider.on_changed(self.switch_signal)
self.signal_amp_slider.valtext.set_visible(False)
self.first_height_slider = Slider(plt.axes([start + 2*slider_width, 0.15, slider_width, slider_height]),
label = " 1st\n Derv.\nH",
valmin = 1.5 * min(self.signal),
valmax = 1.5 * max(self.signal),
valinit = 0,
orientation = 'vertical')
self.first_height_slider.label.set_size(8)
self.first_height_slider.on_changed(self.switch_signal)
self.first_height_slider.valtext.set_visible(False)
self.first_amp_slider = Slider(plt.axes([start + 3*slider_width, 0.15, slider_width, slider_height]),
label = "\nA",
valmin = 0.01,
valmax = 10,
valinit = 1,
orientation = 'vertical')
self.first_amp_slider.label.set_size(8)
self.first_amp_slider.on_changed(self.switch_signal)
self.first_amp_slider.valtext.set_visible(False)
# Maximize frame
mng = plt.get_current_fig_manager()
mng.full_screen_toggle()
plt.show()