I have to analyse a PPG signal. I found something to find the peaks but I can’t use the values of the heights. They are stored in like a dictionary array or something and I don’t know how to extract the values out of it. I tried using dict.values()
but that didn’t work.
import matplotlib.pyplot as plt import numpy as np from scipy.signal import savgol_filter data = pd.read_excel('test_heartpy.xlsx') arr = np.array(data) time = arr[1:,0] # time in s ECG = arr[1:,1] # ECG PPG = arr[1:,2] # PPG filtered = savgol_filter(PPG, 251, 3) plt.plot(time, filtered) plt.xlabel('Time (in s)') plt.ylabel('PPG') plt.grid('on')
The PPG signal looks like this. To search for the peaks I used:
# searching peaks from scipy.signal import find_peaks peaks, heights_peak_0 = find_peaks(PPG, height=0.2) heights_peak = heights_peak_0.values() plt.plot(PPG) plt.plot(peaks, np.asarray(PPG)[peaks], "x") plt.plot(np.zeros_like(PPG), "--", color="gray") plt.title("PPG peaks") plt.show() print(heights_peak_0) print(heights_peak) print(peaks)
Printing:
{'peak_heights': array([0.4822998 , 0.4710083 , 0.43884277, 0.46728516, 0.47094727, 0.44702148, 0.43029785, 0.44146729, 0.43933105, 0.41400146, 0.45318604, 0.44335938])} dict_values([array([0.4822998 , 0.4710083 , 0.43884277, 0.46728516, 0.47094727, 0.44702148, 0.43029785, 0.44146729, 0.43933105, 0.41400146, 0.45318604, 0.44335938])]) [787 2513 4181 5773 7402 9057 10601 12194 13948 15768 17518 19335]
Signal with highlighted peaks looks like this.
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Answer
heights_peak_0
is the properties dict returned by scipy.signal.find_peaks
You can find more information about what is returned here
You can extract the array containing all the heights of the peaks with heights_peak_0["peak_heights"]