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HRV-GUI.py
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# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'lol.ui'
#
# Created by: PyQt5 UI code generator 5.11.3
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtGui import QImage, QPixmap, QPalette, QDoubleValidator
from PyQt5.QtWidgets import QApplication, QWidget, QPlainTextEdit
import pyqtgraph as pg
import scipy.io
from scipy.signal import butter, lfilter
import numpy as np
from pyhrv.hrv import hrv
from biosppy.signals.ecg import ecg
import pyhrv.tools as tools
import matplotlib.pyplot as plt
from scipy import signal
from openpyxl import Workbook
import os
global name, data, pre, flag_obelezi, results, rpeaks, nni, sample_rate, folder
data = None
flag_obelezi=0
def notch_filter(data, f0, fs):
Q=50.0
b, a = signal.iirnotch(f0, Q, fs)
y = lfilter(b, a, data)
return y
def butter_bandpass(lowcut, highcut, fs, order=5):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
b, a = butter(order, [low, high], btype='band')
return b, a
def butter_bandpass_filter(data, lowcut, highcut, fs, order=5):
b, a = butter_bandpass(lowcut, highcut, fs, order=order)
y = lfilter(b, a, data)
return y
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow")
MainWindow.resize(1130, 1004)
MainWindow.setWindowFlags(QtCore.Qt.WindowCloseButtonHint | QtCore.Qt.WindowMinimizeButtonHint)
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
#self.graphicsView = pg.PlotWidget(self.centralwidget)
#self.graphicsView.setGeometry(QtCore.QRect(90, 10, 1021, 321))
#self.graphicsView.setObjectName("graphicsView")
self.view_tab = QtWidgets.QTabWidget(self.centralwidget)
self.view_tab.setGeometry(QtCore.QRect(90, 10, 1021, 321))
self.view_tab.setObjectName("view_tab")
self.signal_tab = QtWidgets.QWidget()
self.signal_tab.setObjectName("signal_tab")
self.view_signal = pg.PlotWidget(self.signal_tab)
self.view_signal.setGeometry(QtCore.QRect(0, 0, 1011, 291))
self.view_signal.setObjectName("view_signal")
self.view_tab.addTab(self.signal_tab, "")
self.tachogram_tab = QtWidgets.QWidget()
self.tachogram_tab.setObjectName("tachogram_tab")
self.tachogram_view = pg.PlotWidget(self.tachogram_tab)
self.tachogram_view.setGeometry(QtCore.QRect(0, 0, 1011, 291))
self.tachogram_view.setObjectName("tachogram_view")
self.view_tab.addTab(self.tachogram_tab, "")
self.load = QtWidgets.QPushButton(self.centralwidget)
self.load.setGeometry(QtCore.QRect(10, 10, 71, 321))
self.load.setObjectName("load")
self.filter_box = QtWidgets.QGroupBox(self.centralwidget)
self.filter_box.setGeometry(QtCore.QRect(10, 340, 221, 161))
self.filter_box.setObjectName("filter_box")
self.filter = QtWidgets.QPushButton(self.filter_box)
self.filter.setGeometry(QtCore.QRect(60, 120, 111, 31))
self.filter.setObjectName("filter")
self.label_2 = QtWidgets.QLabel(self.filter_box)
self.label_2.setGeometry(QtCore.QRect(20, 20, 71, 21))
self.label_2.setObjectName("label_2")
self.label_3 = QtWidgets.QLabel(self.filter_box)
self.label_3.setGeometry(QtCore.QRect(20, 50, 71, 21))
self.label_3.setObjectName("label_3")
self.label_4 = QtWidgets.QLabel(self.filter_box)
self.label_4.setGeometry(QtCore.QRect(20, 80, 71, 21))
self.label_4.setObjectName("label_4")
self.sample_rate = QtWidgets.QLineEdit(self.filter_box)
self.sample_rate.setGeometry(QtCore.QRect(100, 20, 113, 22))
self.sample_rate.setValidator(QDoubleValidator())
self.sample_rate.setObjectName("sample_rate")
self.lowcut = QtWidgets.QLineEdit(self.filter_box)
self.lowcut.setGeometry(QtCore.QRect(100, 50, 113, 22))
self.lowcut.setValidator(QDoubleValidator())
self.lowcut.setObjectName("lowcut")
self.highcut = QtWidgets.QLineEdit(self.filter_box)
self.highcut.setGeometry(QtCore.QRect(100, 80, 113, 22))
self.highcut.setValidator(QDoubleValidator())
self.highcut.setObjectName("highcut")
self.cutter_box = QtWidgets.QGroupBox(self.centralwidget)
self.cutter_box.setGeometry(QtCore.QRect(10, 580, 221, 161))
self.cutter_box.setObjectName("cutter_box")
self.select = QtWidgets.QPushButton(self.cutter_box)
self.select.setGeometry(QtCore.QRect(10, 40, 101, 41))
self.select.setObjectName("select")
self.select.setEnabled(False)
self.cut = QtWidgets.QPushButton(self.cutter_box)
self.cut.setGeometry(QtCore.QRect(110, 40, 101, 41))
self.cut.setObjectName("cut")
self.cut.setEnabled(False)
self.undo = QtWidgets.QPushButton(self.cutter_box)
self.undo.setGeometry(QtCore.QRect(10, 100, 101, 41))
self.undo.setObjectName("undo")
self.undo.setEnabled(False)
self.redo = QtWidgets.QPushButton(self.cutter_box)
self.redo.setGeometry(QtCore.QRect(110, 100, 101, 41))
self.redo.setObjectName("redo")
self.redo.setEnabled(False)
self.results_box = QtWidgets.QGroupBox(self.centralwidget)
self.results_box.setGeometry(QtCore.QRect(240, 480, 871, 471))
self.results_box.setObjectName("results_box")
self.results_tab = QtWidgets.QTabWidget(self.results_box)
self.results_tab.setGeometry(QtCore.QRect(0, 20, 871, 471))
self.results_tab.setObjectName("results_tab")
self.time = QtWidgets.QWidget()
self.time.setObjectName("time")
self.time_results = QtWidgets.QTabWidget(self.time)
self.time_results.setGeometry(QtCore.QRect(0, 0, 871, 421))
self.time_results.setObjectName("time_results")
self.nni_hist = QtWidgets.QWidget()
self.nni_hist.setObjectName("nni_hist")
self.nni_hist_label = QtWidgets.QLabel(self.nni_hist)
self.nni_hist_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.nni_hist_label.setObjectName("nni_hist_label")
self.time_results.addTab(self.nni_hist, "")
self.time_param = QtWidgets.QWidget()
self.time_param.setObjectName("time_param")
self.time_results.addTab(self.time_param, "")
self.results_tab.addTab(self.time, "")
self.frequency = QtWidgets.QWidget()
self.frequency.setObjectName("frequency")
self.freq_results = QtWidgets.QTabWidget(self.frequency)
self.freq_results.setGeometry(QtCore.QRect(0, 0, 871, 421))
self.freq_results.setObjectName("freq_results")
self.welch = QtWidgets.QWidget()
self.welch.setObjectName("welch")
self.welch_label = QtWidgets.QLabel(self.welch)
self.welch_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.welch_label.setObjectName("welch_label")
self.freq_results.addTab(self.welch, "")
self.psd_ls = QtWidgets.QWidget()
self.psd_ls.setObjectName("psd_ls")
self.psd_ls_label = QtWidgets.QLabel(self.psd_ls)
self.psd_ls_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.psd_ls_label.setObjectName("psd_ls_label")
self.freq_results.addTab(self.psd_ls, "")
self.psd_autoregressive = QtWidgets.QWidget()
self.psd_autoregressive.setObjectName("psd_autoregressive")
self.psd_autoregressive_label = QtWidgets.QLabel(self.psd_autoregressive)
self.psd_autoregressive_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.psd_autoregressive_label.setObjectName("psd_autoregressive_label")
self.freq_results.addTab(self.psd_autoregressive, "")
self.freq_param = QtWidgets.QWidget()
self.freq_param.setObjectName("freq_param")
self.freq_results.addTab(self.freq_param, "")
self.results_tab.addTab(self.frequency, "")
self.nonlinear = QtWidgets.QWidget()
self.nonlinear.setObjectName("nonlinear")
self.nonlinear_results = QtWidgets.QTabWidget(self.nonlinear)
self.nonlinear_results.setGeometry(QtCore.QRect(0, 0, 871, 421))
self.nonlinear_results.setObjectName("nonlinear_results")
self.poincare = QtWidgets.QWidget()
self.poincare.setObjectName("poincare")
self.poincare_label = QtWidgets.QLabel(self.poincare)
self.poincare_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.poincare_label.setObjectName("poincare_label")
self.nonlinear_results.addTab(self.poincare, "")
self.dfa = QtWidgets.QWidget()
self.dfa.setObjectName("dfa")
self.dfa_label = QtWidgets.QLabel(self.dfa)
self.dfa_label.setGeometry(QtCore.QRect(0, 0, 861, 391))
self.dfa_label.setObjectName("dfa_label")
self.nonlinear_results.addTab(self.dfa, "")
self.nonlin_param = QtWidgets.QWidget()
self.nonlin_param.setObjectName("nonlin_param")
self.nonlinear_results.addTab(self.nonlin_param, "")
self.results_tab.addTab(self.nonlinear, "")
self.export_2 = QtWidgets.QPushButton(self.centralwidget)
self.export_2.setGeometry(QtCore.QRect(10, 890, 221, 41))
self.export_2.setObjectName("export_2")
self.builtin_box = QtWidgets.QGroupBox(self.centralwidget)
self.builtin_box.setGeometry(QtCore.QRect(10, 500, 221, 80))
self.builtin_box.setObjectName("builtin_box")
self.filter_builtin = QtWidgets.QPushButton(self.builtin_box)
self.filter_builtin.setGeometry(QtCore.QRect(60, 30, 111, 31))
self.filter_builtin.setObjectName("radio_notch")
self.rpeaks_view = pg.PlotWidget(self.centralwidget)
self.rpeaks_view.setGeometry(QtCore.QRect(240, 350, 871, 121))
self.rpeaks_view.setObjectName("label_5")
self.calculateresults_box = QtWidgets.QGroupBox(self.centralwidget)
self.calculateresults_box.setGeometry(QtCore.QRect(10, 740, 221, 141))
self.calculateresults_box.setObjectName("calculateresults_box")
self.calculate = QtWidgets.QPushButton(self.calculateresults_box)
self.calculate.setGeometry(QtCore.QRect(50, 100, 111, 31))
self.calculate.setObjectName("calculate")
self.radio_group = QtWidgets.QGroupBox(self.calculateresults_box)
self.radio_group.setGeometry(QtCore.QRect(10, 20, 201, 71))
self.radio_group.setTitle("")
self.radio_group.setObjectName("radio_group")
self.results_whole = QtWidgets.QRadioButton(self.radio_group)
self.results_whole.setGeometry(QtCore.QRect(20, 10, 161, 20))
self.results_whole.setObjectName("results_whole")
self.results_whole.setChecked(True)
self.results_part = QtWidgets.QRadioButton(self.radio_group)
self.results_part.setGeometry(QtCore.QRect(20, 40, 161, 20))
self.results_part.setObjectName("results_part")
self.time_txt = QPlainTextEdit(self.time_param)
self.time_txt.setGeometry(QtCore.QRect(10, 10, 841, 371))
self.time_txt.setObjectName("textBrowser")
self.time_txt.setReadOnly(True)
self.freq_txt = QPlainTextEdit(self.freq_param)
self.freq_txt.setGeometry(QtCore.QRect(10, 10, 841, 371))
self.freq_txt.setObjectName("textBrowser")
self.time_txt.setReadOnly(False)
self.nonlin_txt = QPlainTextEdit(self.nonlin_param)
self.nonlin_txt.setGeometry(QtCore.QRect(10, 10, 841, 371))
self.nonlin_txt.setObjectName("textBrowser")
self.time_txt.setReadOnly(False)
MainWindow.setCentralWidget(self.centralwidget)
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 1130, 26))
self.menubar.setObjectName("menubar")
MainWindow.setMenuBar(self.menubar)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
MainWindow.setStatusBar(self.statusbar)
MainWindow.setCentralWidget(self.centralwidget)
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 1124, 26))
self.menubar.setObjectName("menubar")
MainWindow.setMenuBar(self.menubar)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
self.statusbar.setSizeGripEnabled(False)
MainWindow.setStatusBar(self.statusbar)
self.lr = pg.LinearRegionItem([50000, 80000])
self.retranslateUi(MainWindow)
self.results_tab.setCurrentIndex(0)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
self.filter_builtin.clicked.connect(self.builtinFilter)
self.load.clicked.connect(self.file_open)
self.select.clicked.connect(self.selectf)
self.cut.clicked.connect(self.cutf)
self.undo.clicked.connect(self.undof)
self.redo.clicked.connect(self.redof)
self.filter.clicked.connect(self.filter_signal)
self.sample_rate.editingFinished.connect(self.getSampleRate)
self.calculate.clicked.connect(self.getResults)
self.results_part.toggled.connect(lambda:self.selectPartResults())
self.results_whole.toggled.connect(lambda:self.selectPartResults())
self.export_2.clicked.connect(self.exportResults)
def exportResults(self):
global results, name
s=folder + '/' + name + '_export.xlsx'
wb=Workbook()
sheet1=wb.active
sheet1.append(['ID', 'Mean HR', 'Min HR', 'Max HR', 'Std. Dev. HR', 'Mean NN', 'Min NN', 'Max NN', 'Mean NN diff.', 'Min NN diff.', 'Max NN diff.', 'SDNN', 'SDNN Index', 'SDANN', 'RMMSD', 'SDSD', 'NN50', 'pNN50', 'NN20', 'pNN20', 'Triangular Index', 'TINN', 'Geometrical param. N', 'Geometrical param. M', 'Weltch\'s peaks (VLF, LF, HLF) [Hz]', 'Weltch\'s Absolute powers (VLF, LF, HLF) [ms^2]', 'Weltch\'s Relative powers (VLF, LF, HLF) [%]', 'Weltch\'s Logaritmic powers (VLF, LF, HLF) [-]', 'Weltch\'s Total power [ms^2]', 'Weltch\'s LF/HF ratio [-]', 'PSD - LS peaks (VLF, LF, HLF) [Hz]', 'PSD - LS Absolute powers (VLF, LF, HLF) [ms^2]', 'PSD - LS Relative powers (VLF, LF, HLF) [%]', 'PSD - LS Logaritmic powers (VLF, LF, HLF) [-]', 'PSD - LS Total power [ms^2]', 'PSD - LS LF/HF ratio [-]', 'PSD - AR peaks (VLF, LF, HLF) [Hz]', 'PSD - AR Absolute powers (VLF, LF, HLF) [ms^2]', 'PSD - AR Relative powers (VLF, LF, HLF) [%]', 'PSD - AR Logaritmic powers (VLF, LF, HLF) [-]', 'PSD - AR Total power [ms^2]', 'PSD - AR LF/HF ratio [-]', 'Poincaré SD1 [ms]', 'Poincaré SD2 [ms]', 'Poincaré SD2/SD1 [-]', 'Area S [ms]', 'Sample Entropy', 'DFA alpha1 [ms]', 'DFA alpha2[ms]'])
sheet1.append([str(name), results['hr_mean'], results['hr_min'], results['hr_max'], results['hr_std'], results['nni_mean'], results['nni_min'], results['nni_max'], results['nni_diff_mean'], results['nni_diff_min'], results['nni_diff_max'], results['sdnn'], results['sdnn_index'], results['sdann'], results['rmssd'], results['sdsd'], results['nn50'], results['pnn50'], results['nn20'], results['pnn20'], results['tri_index'], results['tinn'], results['tinn_n'], results['tinn_m'], str(results['fft_peak']), str(results['fft_abs']), str(results['fft_rel']), str(results['fft_log']), results['fft_total'], results['fft_ratio'], str(results['lomb_peak']), str(results['lomb_abs']), str(results['lomb_rel']), str(results['lomb_log']), results['lomb_total'], results['lomb_ratio'], str(results['ar_peak']), str(results['ar_abs']), str(results['ar_rel']), str(results['ar_log']), results['ar_total'], results['ar_ratio'], results['sd1'], results['sd2'], results['sd_ratio'], results['ellipse_area'], results['sampen'], results['dfa_alpha1'], results['dfa_alpha2']])
wb.save(s)
def nonlin_domain_txt(self):
global results, folder
s=str(folder + '/nonlinear_domain.txt')
file = open(s,"w")
file.write("============================================ \n")
file.write(" NONLINEAR ANALYSIS\n")
file.write("============================================ \n")
file.write("Poincaré Plot\n")
file.write("SD1: %f [ms]\n" % results['sd1'])
file.write("SD2: %f [ms]\n" % results['sd2'])
file.write("SD2/SD1: %f [-]\n" % results['sd_ratio'])
file.write("Area S: %f [ms]\n" % results['ellipse_area'])
file.write("Sample Entropy: %f\n" % results['sampen'])
file.write("DFA alpha1: %f [ms]\n" % results['dfa_alpha1'])
file.write("DFA alpha2: %f [ms]\n" % results['dfa_alpha2'])
file.close()
def freq_domain_txt(self):
global results, folder
s=str(folder + '/frequency_domain.txt')
file = open(s,"w")
file.write("============================================ \n")
file.write(" FREQUENCY DOMAIN PARAMETERS\n")
file.write("============================================ \n")
file.write("\nWELCH'S METHOD \n \n")
file.write("Peak Frequencies:\n")
file.write("VLF: %f [Hz]\n" % results['fft_peak'][0])
file.write("LF : %f [Hz]\n" % results['fft_peak'][1])
file.write("HLF: %f [Hz]\n" % results['fft_peak'][2])
file.write("Absolute Powers:\n")
file.write("VLF: %f [ms^2]\n" % results['fft_abs'][0])
file.write("LF : %f [ms^2]\n" % results['fft_abs'][1])
file.write("HLF: %f [ms^2]\n" % results['fft_abs'][2])
file.write("Relative Powers:\n")
file.write("VLF: %f [%%]\n" % results['fft_rel'][0])
file.write("LF : %f [%%]\n" % results['fft_rel'][1])
file.write("HLF: %f [%%]\n" % results['fft_rel'][2])
file.write("Logarithmic Powers:\n")
file.write("VLF: %f [-]\n" % results['fft_log'][0])
file.write("LF : %f [-]\n" % results['fft_log'][1])
file.write("HLF: %f [-]\n" % results['fft_log'][2])
file.write("Total Power: %f [ms^2]\n" % results['fft_total'])
file.write("LF/HF ratio: %f [-]\n" % results['fft_ratio'])
file.write("\nPSD - LOMB-SCARGLE \n \n")
file.write("Peak Frequencies:\n")
file.write("VLF: %f [Hz]\n" % results['lomb_peak'][0])
file.write("LF : %f [Hz]\n" % results['lomb_peak'][1])
file.write("HLF: %f [Hz]\n" % results['lomb_peak'][2])
file.write("Absolute Powers:\n")
file.write("VLF: %f [ms^2]\n" % results['lomb_abs'][0])
file.write("LF : %f [ms^2]\n" % results['lomb_abs'][1])
file.write("HLF: %f [ms^2]\n" % results['lomb_abs'][2])
file.write("Relative Powers:\n")
file.write("VLF: %f [%%]\n" % results['lomb_rel'][0])
file.write("LF : %f [%%]\n" % results['lomb_rel'][1])
file.write("HLF: %f [%%]\n" % results['lomb_rel'][2])
file.write("Logarithmic Powers:\n")
file.write("VLF: %f [-]\n" % results['lomb_log'][0])
file.write("LF : %f [-]\n" % results['lomb_log'][1])
file.write("HLF: %f [-]\n" % results['lomb_log'][2])
file.write("Total Power: %f [ms^2]\n" % results['lomb_total'])
file.write("LF/HF ratio: %f [-]\n" % results['lomb_ratio'])
file.write("\nPSD - AUTOREGRESSIVE \n \n")
file.write("Peak Frequencies:\n")
file.write("VLF: %f [Hz]\n" % results['ar_peak'][0])
file.write("LF : %f [Hz]\n" % results['ar_peak'][1])
file.write("HLF: %f [Hz]\n" % results['ar_peak'][2])
file.write("Absolute Powers:\n")
file.write("VLF: %f [ms^2]\n" % results['ar_abs'][0])
file.write("LF : %f [ms^2]\n" % results['ar_abs'][1])
file.write("HLF: %f [ms^2]\n" % results['ar_abs'][2])
file.write("Relative Powers:\n")
file.write("VLF: %f [%%]\n" % results['ar_rel'][0])
file.write("LF : %f [%%]\n" % results['ar_rel'][1])
file.write("HLF: %f [%%]\n" % results['ar_rel'][2])
file.write("Logarithmic Powers:\n")
file.write("VLF: %f [-]\n" % results['ar_log'][0])
file.write("LF : %f [-]\n" % results['ar_log'][1])
file.write("HLF: %f [-]\n" % results['ar_log'][2])
file.write("Total Power: %f [ms^2]\n" % results['ar_total'])
file.write("LF/HF ratio: %f [-]\n" % results['ar_ratio'])
file.close()
def time_domain_txt(self):
global results, folder
s=str(folder + '/time_domain.txt')
file = open(s,"w")
file.write("============================================ \n")
file.write(" TIME DOMAIN Results \n")
file.write("============================================\n")
file.write('HR Results\n')
file.write('Mean HR: %f [bpm]\n' % results['hr_mean'])
file.write('Min HR: %f [bpm]\n' % results['hr_min'])
file.write('Max HR: %f [bpm]\n' % results['hr_max'])
file.write('Std. Dev. HR: %f [bpm]\n' % results['hr_std'])
file.write('NN Results\n')
file.write('Mean NN: %f [ms]\n' % results['nni_mean'])
file.write('Min NN: %f [ms]\n' % results['nni_min'])
file.write('Max NN: %f [ms]\n' % results['nni_max'])
file.write('NN diff. Results\n')
file.write('Mean NN diff: %f [ms]\n' % results['nni_diff_mean'])
file.write('Min NN diff: %f [ms]\n' % results['nni_diff_min'])
file.write('Max NN diff: %f [ms]\n' % results['nni_diff_max'])
file.write('SDNN: %f [ms]\n' % results['sdnn'])
file.write('SDNN Index: %f [ms]\n' % results['sdnn_index'])
file.write('SDANN: %f [ms]\n' % results['sdann'])
file.write('RMMSD: %f [ms]\n' % results['rmssd'])
file.write('SDSD: %f [ms]\n' % results['sdsd'])
file.write('NN50: %i [-]\n' % results['nn50'])
file.write('pNN50: %f [%%]\n' % results['pnn50'])
file.write('NN20: %i [-]\n' % results['nn20'])
file.write('pNN20: %f [%%]\n' % results['pnn20'])
file.write('=== Geometrical Parameters\n')
file.write('Triangular Index: %f [-]\n' % results['tri_index'])
file.write('TINN: %f [ms]\n' % results['tinn'])
file.write('N: %f [ms]\n' % results['tinn_n'])
file.write('M: %f [ms]\n' % results['tinn_m'])
file.close()
def getSampleRate(self):
global sample_rate
sample_rate=float(self.sample_rate.text())
def builtinFilter(self):
global data, sample_rate, rpeaks, pre
if data is None:
self.showMsg('No data to filter')
else:
filt, rpeaks=ecg(signal=data, sampling_rate=float(sample_rate), show=False)[1:3]
pre=data
data=filt
self.undo.setEnabled(True)
self.redo.setEnabled(False)
self.update()
def plotPeaks(self, signal, peaks):
global sample_rate
self.rpeaks_view.clear()
t=tools.time_vector(signal=signal, sampling_rate=sample_rate)
self.rpeaks_view.plot(t, signal, pen=pg.mkPen('r'))
p=np.array([])
for x in peaks:
p=np.append(p, signal[x])
r=t[peaks]
scatter=pg.ScatterPlotItem(pen=pg.mkPen(width=5, color='g'), symbol='d', size=1)
scatter.setData(r, p)
self.rpeaks_view.addItem(scatter)
self.rpeaks_view.setLimits(xMin=0, xMax=t[-1])
self.rpeaks_view.setXRange(5, 10)
self.rpeaks_view.setMouseEnabled(x=True, y=False)
self.rpeaks_view.setLabel('bottom', text='Time [s]')
def showPlots(self):
global folder
#Time Domain plots
s=str(folder + '/nni_histogram.jpg')
results['nni_histogram'].savefig(s)
nni_histogram = QImage(s)
self.nni_hist_label.setPixmap(QPixmap.fromImage(nni_histogram).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.nni_hist_label.setAlignment(QtCore.Qt.AlignCenter)
#Frequency Domain plots
s=str(folder + '/fft_plot.jpg')
results['fft_plot'].savefig(s)
fft_plot = QImage(s)
self.welch_label.setPixmap(QPixmap.fromImage(fft_plot).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.welch_label.setAlignment(QtCore.Qt.AlignCenter)
s=str(folder + '/lomb_plot.jpg')
results['lomb_plot'].savefig(s)
lomb_plot = QImage(s)
self.psd_ls_label.setPixmap(QPixmap.fromImage(lomb_plot).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.psd_ls_label.setAlignment(QtCore.Qt.AlignCenter)
s=str(folder + '/ar_plot.jpg')
results['ar_plot'].savefig(s)
ar_plot = QImage(s)
self.psd_autoregressive_label.setPixmap(QPixmap.fromImage(ar_plot).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.psd_autoregressive_label.setAlignment(QtCore.Qt.AlignCenter)
#Nonlinear plots
s=str(folder + '/poincare_plot.jpg')
results['poincare_plot'].savefig(s)
poincare_plot = QImage(s)
self.poincare_label.setPixmap(QPixmap.fromImage(poincare_plot).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.poincare_label.setAlignment(QtCore.Qt.AlignCenter)
s=str(folder + '/dfa_plot.jpg')
results['dfa_plot'].savefig(s)
dfa_plot = QImage(s)
self.dfa_label.setPixmap(QPixmap.fromImage(dfa_plot).scaled(861, 391, aspectRatioMode=QtCore.Qt.KeepAspectRatio, transformMode=QtCore.Qt.SmoothTransformation))
self.dfa_label.setAlignment(QtCore.Qt.AlignCenter)
for key in results.keys():
print(key, results[key])
def selectPartResults(self):
if self.view_tab.currentIndex()==0:
plot=self.view_signal
else:
plot=self.tachogram_view
if self.results_part.isChecked():
geom=plot.getPlotItem().getViewBox().viewRange()
a=geom[0][0]+(geom[0][1]-geom[0][0])*0.2
b=geom[0][1]-(geom[0][1]-geom[0][0])*0.2
self.lr.setRegion([int(a), int(b)])
plot.addItem(self.lr)
elif self.results_whole.isChecked():
plot.removeItem(self.lr)
def getResults(self):
global data, results, rpeaks, sample_rate
if self.results_whole.isChecked():
filt, rpeaks=ecg(signal=data, sampling_rate=sample_rate, show=False)[1:3]
self.plotPeaks(data, rpeaks)
rpeaks=rpeaks/sample_rate
nni=tools.nn_intervals(rpeaks=rpeaks)
results=hrv(nni=nni, rpeaks=rpeaks, sampling_rate=sample_rate, interval=[0, int(len(data)/sample_rate)], show=False)
self.showPlots()
self.time_domain_txt()
s=str(folder + '/time_domain.txt')
text=open(s).read()
self.time_txt.setPlainText(text)
self.freq_domain_txt()
s=str(folder + '/frequency_domain.txt')
text=open(s).read()
self.freq_txt.setPlainText(text)
self.nonlin_domain_txt()
s=str(folder + '/nonlinear_domain.txt')
text=open(s).read()
self.nonlin_txt.setPlainText(text)
elif self.results_part.isChecked():
limits = self.lr.getRegion()
x=int(limits[0]*sample_rate)
y=int(limits[1]*sample_rate)
if x<0:
signal_t=data[0:y]
elif y>len(data):
signal_t=data[x:]
else:
signal_t=data[x:y]
filt, rpeaks=ecg(signal=signal_t, sampling_rate=sample_rate, show=False)[1:3]
self.plotPeaks(signal_t, rpeaks)
rpeaks=rpeaks/sample_rate
nni=tools.nn_intervals(rpeaks=rpeaks)
results=hrv(nni=nni, rpeaks=rpeaks, sampling_rate=sample_rate, interval=[0, int(len(signal_t)/sample_rate)], show=False)
self.showPlots()
else:
self.showMsg('Please select if you want HRV parameters for whole signal or for selected part')
def showMsg(self, message):
msgBox=QtWidgets.QMessageBox()
msgBox.setIcon(QtWidgets.QMessageBox.Warning)
msgBox.setWindowTitle('Warning')
msgBox.setText(message)
msgBox.setStandardButtons(QtWidgets.QMessageBox.Ok)
msgBox.exec_()
def filter_signal(self):
global data, rpeaks
sample_rate=self.sample_rate.text()
lowcut=self.lowcut.text()
highcut=self.highcut.text()
if data is None:
self.showMsg('No data to filter')
elif sample_rate=='' or lowcut=='' or highcut=='':
self.showMsg('Enter all parameters for filter')
else:
a=butter_bandpass_filter(data, float(lowcut), float(highcut), float(sample_rate))
data=a
#filt, rpeaks=ecg(signal=data, sampling_rate=float(sample_rate), show=False)[1:3]
#data=filt
self.update()
self.undo.setEnabled(True)
self.redo.setEnabled(False)
def undof(self):
global pre, data
temp=data
data=pre
pre=temp
self.redo.setEnabled(True)
self.undo.setEnabled(False)
self.update()
def redof(self):
global pre, data
temp=data
data=pre
pre=temp
self.redo.setEnabled(False)
self.undo.setEnabled(True)
self.update()
def selectf(self):
global flag_obelezi
if self.view_tab.currentIndex()==0:
plot=self.view_signal
else:
plot=self.tachogram_view
geom=plot.getPlotItem().getViewBox().viewRange()
a=geom[0][0]+(geom[0][1]-geom[0][0])*0.2
b=geom[0][1]-(geom[0][1]-geom[0][0])*0.2
self.lr.setRegion([int(a), int(b)])
if flag_obelezi==0:
plot.addItem(self.lr)
self.cut.setDisabled(False)
flag_obelezi=1
else:
flag_obelezi=0
plot.removeItem(self.lr)
self.cut.setDisabled(True)
def cutf(self):
global flag_obelezi, rpeaks, sample_rate, pre, data
if self.view_tab.currentIndex()==0:
plot=self.view_signal
else:
plot=self.tachogram_view
self.redo.setEnabled(False)
self.undo.setEnabled(True)
limits = self.lr.getRegion()
pre=data
x=int(limits[0]*sample_rate)
y=int(limits[1]*sample_rate)
if x<0:
data=pre[y:]
elif y>len(data):
data=pre[0:x]
else:
a=pre[0:x]
b=pre[y:]
data=np.concatenate((a,b))
plot.removeItem(self.lr)
flag_obelezi=0
filt, rpeaks=ecg(signal=data, sampling_rate=sample_rate, show=False)[1:3]
self.update()
self.cut.setEnabled(False)
self.select.setDisabled(False)
def file_open(self):
global name, data, pre, folder
if self.sample_rate.text()=='':
self.showMsg('Please enter sampling rate first')
else:
name, _ =QtWidgets.QFileDialog.getOpenFileName(None, "Open File", "", "Mat Files (*.mat)")
if name!='':
di=name
mat= scipy.io.loadmat(name)
a=mat['ALLEEG']
b=a['data']
c=b[0,0]
data=c[19]
pre=data
sample_rate=float(self.sample_rate.text())
name=name.split(".")[0]
name=name.split("/")[-1]
s=di.split("/")
del s[-1]
folder=("/").join(s) + '/' + name + '_results'
if os.path.exists(folder)==False:
os.mkdir(folder)
self.update()
self.undo.setEnabled(False)
self.redo.setEnabled(False)
self.rpeaks_view.clear()
self.nni_hist_label.clear()
self.welch_label.clear()
self.psd_ls_label.clear()
self.psd_autoregressive_label.clear()
self.poincare_label.clear()
self.dfa_label.clear()
self.time_txt.clear()
self.freq_txt.clear()
self.nonlin_txt.clear()
self.select.setDisabled(False)
def update(self):
global data, rpeaks, nni, sample_rate
t=tools.time_vector(signal=data, sampling_rate=sample_rate)
self.view_signal.clear()
self.view_signal.plot(t, data, pen=pg.mkPen('r'))
self.view_signal.setLimits(xMin=0, xMax=t[-1])
self.view_signal.setMouseEnabled(x=True, y=False)
self.view_signal.setLabel('bottom', text='Time [s]')
filt, rpeaks=ecg(signal=data, sampling_rate=sample_rate, show=False)[1:3]
rpeaks=rpeaks/sample_rate
nni=tools.nn_intervals(rpeaks=rpeaks)
t = np.cumsum(nni) / 1000.
self.tachogram_view.clear()
self.tachogram_view.plot(t, nni, pen=pg.mkPen('r'))
self.tachogram_view.setLimits(xMin=0, xMax=t[-1])
self.tachogram_view.setMouseEnabled(x=True, y=False)
self.tachogram_view.setLabel('bottom', text='Time [s]')
def retranslateUi(self, MainWindow):
_translate = QtCore.QCoreApplication.translate
MainWindow.setWindowTitle(_translate("MainWindow", "HRV"))
self.load.setText(_translate("MainWindow", "Load"))
self.filter_box.setTitle(_translate("MainWindow", "Bandpass Filter"))
self.filter.setText(_translate("MainWindow", "Filter"))
self.label_2.setText(_translate("MainWindow", "Sample rate"))
self.label_3.setText(_translate("MainWindow", "Low Cut"))
self.label_4.setText(_translate("MainWindow", "High Cut"))
self.cutter_box.setTitle(_translate("MainWindow", "Cut signal"))
self.select.setText(_translate("MainWindow", "Select"))
self.cut.setText(_translate("MainWindow", "Cut"))
self.undo.setText(_translate("MainWindow", "Undo"))
self.redo.setText(_translate("MainWindow", "Redo"))
self.results_box.setTitle(_translate("MainWindow", "Results"))
self.time_results.setTabText(self.time_results.indexOf(self.nni_hist), _translate("MainWindow", "NNI Histogram"))
self.time_results.setTabText(self.time_results.indexOf(self.time_param), _translate("MainWindow", "Parameters"))
self.results_tab.setTabText(self.results_tab.indexOf(self.time), _translate("MainWindow", "Time Domain"))
self.freq_results.setTabText(self.freq_results.indexOf(self.welch), _translate("MainWindow", "Welch\'s Method"))
self.freq_results.setTabText(self.freq_results.indexOf(self.psd_ls), _translate("MainWindow", "PSD - Lomb-Scargle"))
self.freq_results.setTabText(self.freq_results.indexOf(self.psd_autoregressive), _translate("MainWindow", "PSD - Autoregressive"))
self.freq_results.setTabText(self.freq_results.indexOf(self.freq_param), _translate("MainWindow", "Parameters"))
self.results_tab.setTabText(self.results_tab.indexOf(self.frequency), _translate("MainWindow", "Frequency Domain"))
self.nonlinear_results.setTabText(self.nonlinear_results.indexOf(self.poincare), _translate("MainWindow", "Poincare"))
self.nonlinear_results.setTabText(self.nonlinear_results.indexOf(self.dfa), _translate("MainWindow", "Detrended Fluctuation Analysis"))
self.nonlinear_results.setTabText(self.nonlinear_results.indexOf(self.nonlin_param), _translate("MainWindow", "Parameters"))
self.results_tab.setTabText(self.results_tab.indexOf(self.nonlinear), _translate("MainWindow", "Nonlinear"))
self.calculate.setText(_translate("MainWindow", "Calculate results"))
self.export_2.setText(_translate("MainWindow", "Export"))
self.builtin_box.setTitle(_translate("MainWindow", "Built-in filter"))
self.filter_builtin.setText(_translate("MainWindow", "Filter"))
self.calculateresults_box.setTitle(_translate("MainWindow", "Calculate results"))
self.calculate.setText(_translate("MainWindow", "Calculate results"))
self.results_whole.setText(_translate("MainWindow", "for whole signal"))
self.results_part.setText(_translate("MainWindow", "for selected part"))
self.view_tab.setTabText(self.view_tab.indexOf(self.signal_tab), _translate("MainWindow", "Signal"))
self.view_tab.setTabText(self.view_tab.indexOf(self.tachogram_tab), _translate("MainWindow", "Tachogram"))
if __name__ == "__main__":
import sys
app = QtWidgets.QApplication(sys.argv)
MainWindow = QtWidgets.QMainWindow()
ui = Ui_MainWindow()
ui.setupUi(MainWindow)
MainWindow.show()
sys.exit(app.exec_())