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paulvangentcom / heartrate_analysis_python

Python Heart Rate Analysis Package, for both PPG and ECG signals
MIT License
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Threshold algorythm #6

Closed yurasmol closed 5 years ago

yurasmol commented 5 years ago

If the first stage of signal have the distortions, the second (good) stage fully marked as rejected bad_samp.pdf good_samp.pdf

paulvangentcom commented 5 years ago

Hi Yurasmol,

Interesting. Can you provide the raw data files for me? I'll have a look.

Cheers, Paul

yurasmol commented 5 years ago

Hi Paul!

This is my RAW signal (sample rate is 100 Hz) and the test module where I four times cut 1/3 starting portion (noisy) of the signal. I think that your threshold algorythm get information from the start portion of a signal (noisy in my case) and therefore rest of signal marked rejected.

Yuri

----- Original Message ----- From: Paul van Gent To: paulvangentcom/heartrate_analysis_python Cc: yurasmol ; Author Sent: Sunday, January 20, 2019 5:11 PM Subject: Re: [paulvangentcom/heartrate_analysis_python] Threshold algorythm (#6)

Hi Yurasmol,

Interesting. Can you provide the raw data files for me? I'll have a look.

Cheers, Paul

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

from matplotlib.backends.backend_pdf import PdfPages import heartpy as hp import matplotlib.pyplot as plt import numpy as np import warnings, sys, os from scipy.signal import savgol_filter

pdf = PdfPages("test.pdf") # Create the PDF document

data = hp.get_data('RAW.txt')

f = plt.figure(0, figsize=(12, 6)) plt.plot(data, linewidth=0.2) pdf.savefig(f, bbox_inches="tight")

f = plt.figure(1, figsize=(12, 6))

working_data, measures = hp.process(data, 100, windowsize=1, freq_method='welch', calc_freq=True)

p = hp.plotter(working_data, measures, show=False)

pdf.savefig(f, bbox_inches="tight")

data = data - savgol_filter(data, 501, 4)

f = plt.figure(2, figsize=(12, 6)) plt.plot(data, linewidth=0.2) pdf.savefig(f, bbox_inches="tight")

f = plt.figure(3, figsize=(12, 6)) working_data, measures = hp.process(data, 100, windowsize=1, freq_method='welch', calc_freq=True) p = hp.plotter(working_data, measures, show=False) pdf.savefig(f, bbox_inches="tight")

f = plt.figure(4, figsize=(12, 6)) data = data[int(len(data)/3):] working_data, measures = hp.process(data, 100, windowsize=1, freq_method='welch', calc_freq=True) p = hp.plotter(working_data, measures, show=False) pdf.savefig(f, bbox_inches="tight")

f = plt.figure(5, figsize=(12, 6)) data = data[int(len(data)/3):] working_data, measures = hp.process(data, 100, windowsize=1, freq_method='welch', calc_freq=True) p = hp.plotter(working_data, measures, show=False) pdf.savefig(f, bbox_inches="tight")

f = plt.figure(6, figsize=(12, 6)) data = data[int(len(data)/3):] working_data, measures = hp.process(data, 100, windowsize=1, freq_method='welch', calc_freq=True) p = hp.plotter(working_data, measures, show=False) pdf.savefig(f, bbox_inches="tight")

d = pdf.infodict() d['Author'] = 'Yuri Smolyakov' pdf.close()

os.startfile("test.pdf")

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paulvangentcom commented 5 years ago

Can you send the RAW.txt file to info@paulvangent.com? I cannot open it from here.

Cheers, Paul

paulvangentcom commented 5 years ago

Yes I see what's happening. It tries to minimize certain parameters globally. Usually a process that gives good results by default, except when a large enough portion of the signal is noisy like here. I will flag this since the current method needs to be refined and I need to allot some time for this soon.

For now a solution is to use the built-in peak enhancer enhance_peaks and butter_lowpass_filter filtering methods:

import heartpy as hp

data = hp.get_data('RAW.txt')
filtered = hp.butter_lowpass_filter(data, 5, 100.0, 3) #third order butterworth with cutoff @ 5Hz
filtered_and_scaled = hp.scale_data(filtered)

wd, measures = hp.process(filtered_and_scaled, 100.0, reject_segmentwise=True, calc_freq=True)

hp.plotter(wd, measures)

Yielding: yurasmol_filtered

As mentioned it is a suboptimal solution that throws away a portion of the signal. I will close this issue and make it a point on the to-do to refine the methods.