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DataModel.py
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# -*- coding:utf-8 -*-
# ----------------------------------------------------------------------
# gHRV: a graphical application for Heart Rate Variability analysis
# Copyright (C) 2016 Milegroup - Dpt. Informatics
# University of Vigo - Spain
# www.milegroup.net
#
# Authors:
# - Leandro Rodríguez-Liñares
# - Arturo Méndez
# - María José Lado
# - Xosé Antón Vila
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# ----------------------------------------------------------------------
import os, random
import numpy as np
from sys import platform
from configvalues import *
import matplotlib
import Utils
from matplotlib.widgets import Button
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
listofsettings=['interpfreq','windowsize','windowshift','ulfmin','ulfmax','vlfmin','vlfmax','lfmin','lfmax','hfmin','hfmax','name']
class DM:
data={}
labelColors=['Orange','cyan','red','blue','green','yellow','grey','pink','purple','maroon','lightgreen']
def __init__(self,Verbose):
"""Initialization of the data model"""
self.ClearAll()
self.data["Verbose"]=Verbose
if (self.data["Verbose"]==True):
print("** Creating data model")
def SetVerbose(self,verboseValue):
self.data["Verbose"] = verboseValue
def ClearAll(self):
self.data={}
self.data["Verbose"]=Verbose
self.data["name"]=""
#self.data["version"]=Version
self.ClearColors()
self.ClearBands()
self.ClearPP()
if (self.data["Verbose"]==True):
print("** Clearing all data")
def ClearColors(self):
"""Resets colors for episodes"""
self.data["ColorIndex"]=0
self.data["DictColors"]={}
def ClearBands(self):
self.data["Bands"]=["LF/HF","ULF","VLF","LF","HF","Power","Mean HR","HR STD","pNN50","rMSSD","ApEn","FracDim","Heart rate"]
self.data["VisibleBands"]=["LF/HF","ULF","VLF","LF","HF","Heart rate"]
self.data["FixedBands"]=["Heart rate"]
def ClearPP(self):
self.data["PPActiveTagLeft"]="Global"
self.data["PPActiveTagRight"]="None"
def AssignEpisodeColor(self,Tag):
"""Assigns color to episodes tags"""
if self.data["ColorIndex"] == len(self.labelColors)-1:
self.data["DictColors"][Tag]=(random.random(),random.random(),random.random())
else:
self.data["DictColors"][Tag]=self.labelColors[self.data["ColorIndex"]]
self.data["ColorIndex"] += 1
def GetEpisodeColor(self,Tag):
"""Returns color assigned to an episode Tag"""
return self.data["DictColors"][Tag]
def LoadFileAscii(self,asciiFile,settings):
"""Loads from ascii file
One data (beats instants in seconds, rr in msec. or rr in sec.) per line"""
if (self.data["Verbose"]==True):
print("** Loading ascii file "+asciiFile)
asciiData = np.loadtxt(asciiFile)
asciiDataDiffs=np.diff(asciiData)
asciiDataNeg = [ x for x in asciiDataDiffs if x<0]
if len(asciiDataNeg)>0: # The file contains an RR series
asciiDataBig = [x for x in asciiData if x>100]
if len(asciiDataBig)>0:
if (self.data["Verbose"]==True):
print(" File contains RR data in milliseconds")
self.LoadRRMillisec(asciiData,settings)
else:
if (self.data["Verbose"]==True):
print(" File contains RR data in seconds")
self.LoadRRMillisec(asciiData*1000.0,settings)
else:
if (self.data["Verbose"]==True):
print(" File contains beats instants in seconds")
self.LoadBeatSec(asciiData,settings)
self.data["name"]=os.path.splitext(os.path.basename(asciiFile))[0]
if (self.data["Verbose"]):
print(" Project created: "+self.data["name"])
self.data["version"]=Version
def LoadBeatSec(self,dataSec,settings):
"""Loads a vector containing beats positions in seconds"""
self.data["BeatTime"]=dataSec
self.data["niHR"] = 60.0/(self.data["BeatTime"][1:]-self.data["BeatTime"][0:-1])
self.data["niHR"] = np.insert(self.data["niHR"],[0],self.data["niHR"][0])
self.data["RR"] = 1000.0*(self.data["BeatTime"][1:]-self.data["BeatTime"][0:-1])
self.data["RR"] = np.insert(self.data["RR"],[0],self.data["RR"][0])
if (self.data["Verbose"]):
print(" BeatTime: "+str(len(self.data["BeatTime"]))+" points (max: "+str(self.data["BeatTime"][-1])+")")
print(" niHR: "+str(len(self.data["niHR"]))+" points")
print(" RR: "+str(len(self.data["RR"]))+" points")
for k in settings.keys():
self.data[k]=float(settings[k])
if (self.data["Verbose"]):
print(" Parameters set to default values")
def LoadRRMillisec(self,dataMSec,settings):
"""Loads a vector containing milliseconds"""
self.data["RR"]=np.array(dataMSec)
self.data["BeatTime"]=np.cumsum(self.data["RR"])/1000.0
self.data["niHR"]=60.0/(self.data["RR"]/1000.0)
if (self.data["Verbose"]==True):
print(" BeatTime: "+str(len(self.data["BeatTime"]))+" points (max: "+str(self.data["BeatTime"][-1])+")")
print(" RR: "+str(len(self.data["RR"]))+" points")
print(" niHR: "+str(len(self.data["niHR"]))+" points")
for k in settings.keys():
self.data[k]=float(settings[k])
if (self.data["Verbose"]):
print(" Parameters set to default values")
def LoadFilePolar(self,polarFile,settings):
"""Loads polar file
Polar files contain rr series, expresed in milliseconds"""
if (self.data["Verbose"]==True):
print("** Loading polar file "+polarFile)
dataMillisec=[]
dataFound=False
File = open(polarFile,'r')
for line in File:
if dataFound:
data=line.strip()
if data:
dataMillisec.append(float(data))
if line.strip() == "[HRData]":
dataFound=True
File.close()
self.LoadRRMillisec(dataMillisec,settings)
self.data["name"]=os.path.splitext(os.path.basename(polarFile))[0]
if (self.data["Verbose"]):
print(" Project created: "+self.data["name"])
self.data["version"]=Version
def LoadFileSuunto(self,suuntoFile,settings):
"""Loads suunto file
suunto files contain rr series, expresed in milliseconds"""
if (self.data["Verbose"]==True):
print("** Loading suunto file "+suuntoFile)
dataMillisec=[]
dataFound=False
File = open(suuntoFile,'r')
for line in File:
if dataFound:
data=line.strip()
if data:
dataMillisec.append(float(data))
if line.strip() == "[CUSTOM1]":
dataFound=True
File.close()
self.LoadRRMillisec(dataMillisec,settings)
self.data["name"]=os.path.splitext(os.path.basename(suuntoFile))[0]
if (self.data["Verbose"]):
print(" Project created: "+self.data["name"])
self.data["version"]=Version
def LoadBeatWFDB(self,wfdbheaderfile,settings):
"""Loads wfdb file"""
import glob
if (self.data["Verbose"]==True):
print("** Loading WFDB file "+wfdbheaderfile)
heaFile = open(wfdbheaderfile,'r')
line=heaFile.readline()
heaFile.close()
lineFields = line.split(" ")
if len(lineFields)>2:
try:
samplingFrequency = float(lineFields[2])
except:
samplingFrequency = 250.0
else:
samplingFrequency = 250.0
if (self.data["Verbose"]==True):
print(" Sampling frequency: "+str(samplingFrequency))
filesfound = glob.glob(wfdbheaderfile[:-4]+".*")
extensionsfound=[]
for filefound in filesfound:
extension = os.path.splitext(filefound)[1][1:]
extensionsfound.append(extension)
extensionsfound.remove('hea')
if len(extensionsfound)==0:
Utils.ErrorWindow(messageStr="No data file found with: "+wfdbheaderfile,captionStr="Error loading beats ")
return
if 'dat' in extensionsfound:
extensionsfound.remove('dat')
if 'atr' in extensionsfound:
extensionsfound.remove('atr')
extensionsfound.insert(0,'atr')
if 'qrs' in extensionsfound:
extensionsfound.remove('qrs')
extensionsfound.insert(0,'qrs')
if len(extensionsfound)>1:
AnnotatorSelection=Utils.SelectAnnotator(extensionsfound)
extensionSelected = AnnotatorSelection.GetValue()
if extensionSelected == '':
return
else:
extensionSelected=extensionsfound[0]
# 'qrs' in first place, then 'atr'
wfdbdatafile=wfdbheaderfile[:-4]+"."+extensionSelected
if (self.data["Verbose"]==True):
print(" Trying data file: "+wfdbdatafile)
try:
datafile = open(wfdbdatafile,'rb')
accumulator=0.0
beats=[]
while True:
value = ord(datafile.read(1))+ord(datafile.read(1))*256
code = value >> 10
time = value % 1024
# print ("Value: "+str(int(value)))
# print ("Code: "+str(code))
# print ("Time: "+str(time))
if code==0 and time==0:
break
# Original code:
# if code==1: # Only normal beats
# Modified code:
if code<50:
accumulator = accumulator+time
# print "Sec: ",accumulator/samplingFrequency
beats.append(accumulator/samplingFrequency)
else:
if code==63:
# Modified code:
jump = int(time) + int(time)%2
x = datafile.read(jump)
value = ord(datafile.read(1))+ord(datafile.read(1))*256
# Original code:
# jump = int(time)/2 + int(time)%2
# for i in range(jump):
# value = ord(datafile.read(1))+ord(datafile.read(1))*256
else:
if code==59 and time==0:
for i in range(2):
value = ord(datafile.read(1))+ord(datafile.read(1))*256
else:
if code!=60 and code!=61 and code!=62 and code!=22 and code!=0:
accumulator = accumulator+time
except:
if (self.data["Verbose"]==True):
print(" File "+wfdbdatafile+" didn't work")
Utils.ErrorWindow(messageStr="Error loading file: "+wfdbdatafile,captionStr="Error loading beats ")
return
else:
if (self.data["Verbose"]==True):
print(" File "+wfdbdatafile+" has been loaded")
self.LoadBeatSec(np.array(beats),settings)
self.data["name"]=os.path.splitext(os.path.basename(wfdbheaderfile))[0]
if (self.data["Verbose"]):
print(" Project created: "+self.data["name"])
self.data["version"]=Version
def LoadEpisodesAscii(self,episodesFile):
"""Reads espisodes from ascii file
episodesFile -> file containing episodes. Must be in the following format:
Init_Time Resp_Events Durat SaO2
00:33:00 GEN_HYPO 120.0 82.9
01:30:00 OBS_APNEA 60.0 81.0
...
First line of file is discarded
Duration in seconds"""
if (self.data["Verbose"]):
print("** Opening episodes file: "+episodesFile)
epFile = open(episodesFile,'r')
index=0
for line in epFile:
if index!=0:
linedata=line.strip().split()
if not self.data.has_key("EpisodesType"):
self.__CreatesEpisodesInfo()
self.data["EpisodesType"].append(linedata[1])
self.data["EpisodesDuration"].append(float(linedata[2]))
HMS=linedata[0].split(":")
self.data["EpisodesInitTime"].append(float(HMS[0])*3600.0+float(HMS[1])*60.0+float(HMS[2]))
index += 1
epFile.close()
self.data["EpisodesVisible"]=list(set(self.data["EpisodesType"]))
if (self.data["Verbose"]):
print(" Read "+str(len(self.data["EpisodesType"]))+" episodes from file")
print(" Read "+str(len(self.data["EpisodesVisible"]))+" types of episodes")
def LoadEpisodesWFDB(self,wfdbheaderfile):
"""Loads episodes from physionet files"""
import glob
if (self.data["Verbose"]==True):
print("** Loading episodes from WFDB file "+wfdbheaderfile)
heaFile = open(wfdbheaderfile,'r')
line=heaFile.readline()
heaFile.close()
lineFields = line.split(" ")
if len(lineFields)>2:
try:
samplingFrequency = float(lineFields[2])
except:
samplingFrequency = 250.0
else:
samplingFrequency = 250.0
if (self.data["Verbose"]==True):
print(" Sampling frequency: "+str(samplingFrequency))
filesfound = glob.glob(wfdbheaderfile[:-4]+".*")
extensionsfound=[]
for filefound in filesfound:
extension = os.path.splitext(filefound)[1][1:]
extensionsfound.append(extension)
extensionsfound.remove('hea')
if len(extensionsfound)==0:
Utils.ErrorWindow(messageStr="No data file found with: "+wfdbheaderfile,captionStr="Error loading episodes ")
return
if 'dat' in extensionsfound:
extensionsfound.remove('dat')
if 'atr' in extensionsfound:
extensionsfound.remove('atr')
extensionsfound.append('atr')
if 'qrs' in extensionsfound:
extensionsfound.remove('qrs')
extensionsfound.append('qrs')
if len(extensionsfound)>1:
AnnotatorSelection=Utils.SelectAnnotator(extensionsfound)
extensionSelected = AnnotatorSelection.GetValue()
if extensionSelected == '':
return
else:
extensionSelected=extensionsfound[0]
wfdbdatafile=wfdbheaderfile[:-4]+"."+extensionSelected
if (self.data["Verbose"]==True):
print(" Trying data file: "+wfdbdatafile)
try:
ApneaTag="Apnea"
datafile = open(wfdbdatafile,'rb')
accumulator=0.0
ActiveTags=[]
ActiveTagsOnsets=[]
EpisodesTypes=[]
EpisodesInits=[]
EpisodesEnds=[]
if extensionSelected=="apn":
while True:
value = ord(datafile.read(1))+ord(datafile.read(1))*256
code = value >> 10
time = value % 1024
if code==0 and time==0:
break
if code==8 and ApneaTag not in ActiveTags:
ActiveTags.append(ApneaTag)
ActiveTagsOnsets.append(accumulator)
if code==1 and ApneaTag in ActiveTags:
EpisodesTypes.append(ApneaTag)
EpisodesInits.append(ActiveTagsOnsets[0])
EpisodesEnds.append(accumulator)
del ActiveTags[0]
del ActiveTagsOnsets[0]
if code == 59:
interval = (ord(datafile.read(1))+ord(datafile.read(1))*256)*65536+(ord(datafile.read(1))+ord(datafile.read(1))*256)
accumulator=accumulator+interval/samplingFrequency
next
else:
while True:
value = ord(datafile.read(1))+ord(datafile.read(1))*256
code = value >> 10
time = value % 1024
if code==0 and time==0:
break
if code <= 49:
next
if code == 59:
interval = (ord(datafile.read(1))+ord(datafile.read(1))*256)*65536+(ord(datafile.read(1))+ord(datafile.read(1))*256)
accumulator=accumulator+interval/samplingFrequency
next
if code==22:
ll = ord(datafile.read(1))
datafile.read(1) # value 252
comment = datafile.read(ll)
# print " String: ",comment
Tags=comment.split()
if (ll%2):
datafile.read(1)
for ActiveTag in ActiveTags:
if ActiveTag not in Tags:
ii=ActiveTags.index(ActiveTag)
EpisodesTypes.append(ActiveTag)
EpisodesInits.append(ActiveTagsOnsets[ii])
EpisodesEnds.append(accumulator)
del ActiveTags[ii]
del ActiveTagsOnsets[ii]
for Tag in Tags:
if Tag not in ActiveTags:
ActiveTags.append(Tag)
ActiveTagsOnsets.append(accumulator)
for ActiveTag in ActiveTags:
ii=ActiveTags.index(ActiveTag)
EpisodesTypes.append(ActiveTag)
EpisodesInits.append(ActiveTagsOnsets[ii])
EpisodesEnds.append(self.GetHRDataPlot()[0][-1]) # Last beat
except:
if (self.data["Verbose"]==True):
print(" File "+wfdbdatafile+" didn't work")
Utils.ErrorWindow(messageStr="Error loading file: "+wfdbdatafile,captionStr="Error loading episodes ")
return
else:
if (self.data["Verbose"]==True):
print(" File "+wfdbdatafile+" has been loaded")
# print EpisodesTypes
# print EpisodesInits
# print EpisodesEnds
if len(EpisodesTypes)==0:
Utils.ErrorWindow(messageStr="No valid episodes found in: "+wfdbdatafile,captionStr="Error loading episodes ")
return
if extensionSelected=="apn":
TagsSelected=[ApneaTag]
else:
TagsDetected=sorted(list(set(EpisodesTypes)))
TagsSelection=Utils.SelectEpisodesTags(TagsDetected)
IndexTagsSelected = TagsSelection.GetValues()
if len(IndexTagsSelected) == 0:
return
TagsSelected=[]
for indexTag in IndexTagsSelected:
TagsSelected.append(TagsDetected[indexTag])
numAddedEpisodes=0
for indexEpisode in range(len(EpisodesTypes)):
if EpisodesTypes[indexEpisode] in TagsSelected:
self.AddEpisode(EpisodesInits[indexEpisode],EpisodesEnds[indexEpisode],EpisodesTypes[indexEpisode])
numAddedEpisodes += 1
Utils.InformEpisodesFile(wfdbdatafile,numAddedEpisodes)
def LoadProject(self,datamodelFile):
"""Loads the data model from a zip file"""
import zipfile, tempfile, shutil
tempDir = tempfile.mkdtemp(prefix="gHRV")
if self.data["Verbose"]:
print("** Loading project: "+datamodelFile)
print(" Temporal directory: "+tempDir)
zf = zipfile.ZipFile(datamodelFile, mode='r')
for zfitem in zf.namelist():
zf.extract(zfitem,tempDir)
fileName=tempDir+os.sep+zfitem
dataName=zfitem[1:]
# print("--- Reading file: "+fileName)
if zfitem[0]=="#":
self.data[dataName]=np.loadtxt(fileName)
# print(" Length: "+str(len(self.data[dataName])))
else:
tempF = open(fileName,'r')
if dataName=="name" or dataName=='PPActiveTagLeft' or dataName=='PPActiveTagRight':
self.data[dataName]=tempF.read()
else:
self.data[dataName]=eval(tempF.read())
tempF.close()
# print(" Data: "+str(self.data[dataName]))
zf.close()
if "version" in self.data.keys():
self.data["version"] = str(self.data["version"])
# version needs to be a string for comparison purposes
# print ("Keys: "+str(self.data.keys()))
#print self.data["name"]
if "interpfreq" not in self.data.keys(): # Project generated with gHRV 0.17
if self.data['Verbose']:
print(" Importing project from gHRV 0.17")
if 'FreqHR' in self.data.keys():
del self.data['FreqHR']
for k in factorySettings.keys():
self.data[k]=float(factorySettings[k])
self.data['name']='mygHRVproject'
if "version" not in self.data.keys(): # Project generated with gHRV 0.18 or older
if self.data['Verbose']:
print(" Importing project from gHRV 0.18 or older")
self.ClearBands()
if self.HasFrameBasedParams():
self.ClearFrameBasedParams()
self.CalculateFrameBasedParams(showProgress=True)
self.data["version"]=Version
if self.data["version"]<Version:
if self.data['Verbose']:
print(" gHRV version: *"+Version+"*")
print(" Project build with gHRV version: *"+self.data["version"]+"*")
print(" Importing project from an old version of gHRV")
self.ClearBands()
if self.HasFrameBasedParams():
self.ClearFrameBasedParams()
self.CalculateFrameBasedParams(showProgress=True)
self.data["version"]=Version
shutil.rmtree(tempDir)
def GetSettings(self):
"""Returns parameters of the project"""
settings={}
for k in listofsettings:
settings[k]=str(self.data[k])
return settings
def SetSettings(self,settings):
"""Sets parameters of the project"""
for k in listofsettings:
if k != 'name':
self.data[k]=float(settings[k])
else:
self.data[k]=settings[k]
def SaveProject(self,datamodelFile):
"""Saves the data model into a zip file"""
import zipfile,shutil,tempfile
tempDir = tempfile.mkdtemp(prefix="gHRV")
if self.data["Verbose"]:
print("** Saving project: "+datamodelFile)
#print(" Temporal directory: "+tempDir)
for kData in self.data.keys():
if type(self.data[kData])==np.ndarray:
tempFName=tempDir+os.sep+"#"+str(kData)
np.savetxt(tempFName,self.data[kData])
else:
# print kData, ": ", type(self.data[kData])
tempFName=tempDir+os.sep+"%"+str(kData)
tempF = open(tempFName,'w')
tempF.write(str(self.data[kData]))
tempF.close()
zf = zipfile.ZipFile(datamodelFile, mode='w',compression=zipfile.ZIP_DEFLATED)
list = os.listdir(tempDir)
for file in list:
#print("File: "+str(file))
zf.write(tempDir+os.sep+file,str(file))
zf.close()
shutil.rmtree(tempDir)
def SaveFrameBasedData(self,dataFile,listOfBands,SepChar,RHeader,CHeader):
if self.data["Verbose"]:
print("** Saving frame-based data: "+dataFile)
print(" List of bands: "+str(listOfBands))
print(" Separator: '"+SepChar+"'")
print(" Row header: "+str(RHeader))
print(" Column header: "+str(CHeader))
NumFrames=len(self.data["ULF"])
File = open(dataFile,'w')
if RHeader:
FirstColumn = True
if CHeader:
File.write("Frame")
FirstColumn=False
for Band in listOfBands:
if FirstColumn:
FirstColumn=False
else:
File.write(SepChar)
File.write(Band.replace(" ","_"))
File.write("\n")
for x in range(NumFrames):
FirstColumn = True
if CHeader:
File.write(str(x))
FirstColumn=False
for Band in listOfBands:
if FirstColumn:
FirstColumn = False
else:
File.write(SepChar)
if Band == "LF/HF":
File.write(str(self.data["LFHF"][x]))
else:
File.write(str(self.data[Band][x]))
File.write("\n")
File.close()
if self.data["Verbose"]:
print(" No. of lines: "+str(NumFrames))
def ClearEpisodes(self):
"""Purges episodes from data model"""
del self.data["EpisodesType"]
del self.data["EpisodesInitTime"]
del self.data["EpisodesDuration"]
del self.data["EpisodesVisible"]
if (self.data["Verbose"]):
print("** Episodes removed from data model")
def ClearHR(self):
"""Purges interpolated HR from data model"""
del self.data["HR"]
del self.data["PlotHRXMin"]
del self.data["PlotHRXMax"]
if (self.data["Verbose"]):
print("** Interpolated HR removed from data model")
def ClearFrameBasedParams(self):
"""Purges power bands information from data model"""
del self.data["ULF"]
del self.data["VLF"]
del self.data["LF"]
del self.data["HF"]
del self.data["LFHF"]
if (self.data["Verbose"]):
print("** Power bands removed from data model")
def __CreatesEpisodesInfo(self):
"""Creates blank episodes structure"""
self.data["EpisodesType"]=[]
self.data["EpisodesInitTime"]=[]
self.data["EpisodesDuration"]=[]
self.data["EpisodesVisible"]=[]
def AddEpisode(self,init,end,tag):
"""Adds information of one episode"""
if (self.data["Verbose"]):
print("** Adding an episode ({0:.2f},{1:.2f}) with label {2:s}".format(init,end,tag))
if not self.data.has_key("EpisodesType"):
self.__CreatesEpisodesInfo()
self.data["EpisodesType"].append(tag)
self.data["EpisodesInitTime"].append(init)
self.data["EpisodesDuration"].append(float(end)-float(init))
if tag not in self.data["EpisodesVisible"]:
self.data["EpisodesVisible"].append(tag)
def SetEpisodes(self,Episodes):
if (self.data["Verbose"]):
print ("** Changing episodes from manual edition")
if len(Episodes)==0:
self.ClearEpisodes()
self.ClearColors()
if (self.data["Verbose"]):
print (" Episodes information removed")
return
EpVis = list(self.data["EpisodesVisible"])
self.__CreatesEpisodesInfo()
for Ep in Episodes:
self.data["EpisodesType"].append(Ep[0])
self.data["EpisodesInitTime"].append(Ep[1])
self.data["EpisodesDuration"].append(Ep[3])
# Removes tags label if all episodes of this label were removed
self.data["EpisodesVisible"]=[Tag for Tag in EpVis if Tag in self.data["EpisodesType"]]
if (self.data["Verbose"]):
print(" Number of episodes: "+str(len(Episodes)))
def ReplaceHRVectors(self,xvector,yvector,rrvector):
"""After EditNIHR the beats (Time, niHR and RR) are replaced"""
self.data["BeatTime"]=xvector
self.data["niHR"]=yvector
self.data["RR"]=rrvector
if (self.data["Verbose"]):
print("** HR vectors replaced")
print(" BeatTime: "+str(len(self.data["BeatTime"]))+" points (max: "+str(self.data["BeatTime"][-1])+")")
print(" niHR: "+str(len(self.data["niHR"]))+" points")
print(" RR: "+str(len(self.data["RR"]))+" points")
def FilterNIHR(self,winlength=50,last=13,minbpm=24,maxbpm=198):
"""Removes outliers from non interpolated heart rate"""
if (self.data["Verbose"]):
print ("** Filtering non-interpolated heart rate")
print (" Number of original beats: "+str(len(self.data["niHR"])))
# threshold initialization
ulast=last
umean=1.5*ulast
index=1
while index<len(self.data["niHR"])-1:
v=self.data["niHR"][max(index-winlength,0):index]
M=np.mean(v)
if ( ( (100*abs((self.data["niHR"][index]-self.data["niHR"][index-1])/self.data["niHR"][index-1]) < ulast) |
(100*abs((self.data["niHR"][index]-self.data["niHR"][index+1])/self.data["niHR"][index+1]) < ulast) |
(100*abs((self.data["niHR"][index]-M)/M) < umean) )
& (self.data["niHR"][index] > minbpm) & (self.data["niHR"][index] < maxbpm)):
index += 1
else:
self.data["BeatTime"]=np.delete(self.data["BeatTime"],index)
self.data["niHR"]=np.delete(self.data["niHR"],index)
self.data["RR"]=np.delete(self.data["RR"],index)
if (self.data["Verbose"]):
print (" Number of filtered beats: "+str(len(self.data["BeatTime"])))
def InterpolateNIHR(self):
"Interpolates instantaneous heart rate (linear method)"
from scipy import interpolate
if self.data["Verbose"]:
print ("** Interpolating instantaneous heart rate (method: linear interpolation)")
print (" Frequency: "+str(self.data["interpfreq"])+" Hz")
xmin=self.data["BeatTime"][0]
xmax=self.data["BeatTime"][-1]
step=1.0/self.data["interpfreq"]
tck = interpolate.interp1d(self.data["BeatTime"],self.data["niHR"])
xnew = np.arange(xmin,xmax,step)
if self.data["Verbose"]:
print (" Original signal from: "+str(self.data["BeatTime"][0])+" to "+str(self.data["BeatTime"][-1]))
print (" Interpolating from "+str(xmin)+" to "+str(xmax)+" seconds")
self.data["HR"] = tck(xnew)
if self.data["Verbose"]:
print (" Obtained "+str(len(self.data["HR"]))+" points")
def GetNumFrames(self,interfreq,windowsize,windowshift):
shiftsamp=windowshift*interfreq
sizesamp=windowsize*interfreq
numframes=int(((len(self.data["HR"])-sizesamp)/shiftsamp)+1.0)
return numframes
def CalculateFrameBasedParams(self, showProgress=False):
"""Calculates power per band
size -> size of window (seconds)
shift -> displacement of window (seconds)"""
hammingfactor=1.586
def power(spec,freq,fmin,fmax):
band = [spec[i] for i in range(len(spec)) if freq[i] >= fmin and freq[i]<fmax]
powerinband = hammingfactor*np.sum(band)/(2*len(spec)**2)
return powerinband
if self.data["Verbose"]:
print("** Calculating power per band")
signal=1000/(self.data["HR"]/60.0) # msec.
shiftsamp=self.data['windowshift']*self.data["interpfreq"]
sizesamp=self.data['windowsize']*self.data["interpfreq"]
numframes=int(((len(signal)-sizesamp)/shiftsamp)+1.0)
lenZeroPadding=2**np.ceil(np.log2(sizesamp))-int(sizesamp)
if (numframes < minNumFrames):
raise Utils.FewFramesException(numframes)
sizesamp2=sizesamp
if (sizesamp2%2 != 0):
sizesamp2=sizesamp2+1
hw=np.hamming(sizesamp2)
if numframes<=10:
showProgress = False
if showProgress:
import wx
dlg = wx.ProgressDialog("Calculating parameters","Preparing data...",maximum = (numframes-1)//10,
style=wx.PD_CAN_ABORT | wx.PD_AUTO_HIDE | wx.PD_REMAINING_TIME | wx.PD_ESTIMATED_TIME)
if self.data["Verbose"]:
print(" Signal length: "+str(len(signal))+" samples")
print(" Frame length: "+str(sizesamp)+" samples")
print(" Frame shift: "+str(shiftsamp)+" samples")
print(" Number of frames: "+str(numframes))
self.data["ULF"]=[]
self.data["VLF"]=[]
self.data["LF"]=[]
self.data["HF"]=[]
self.data["LFHF"]=[]
self.data["Power"]=[]
self.data["Mean HR"]=[]
self.data["HR STD"]=[]
self.data["pNN50"]=[]
self.data["rMSSD"]=[]
self.data["ApEn"]=[]
self.data["FracDim"]=[]
KeepGoing = True
indexframe = 0
while indexframe<numframes and KeepGoing:
if showProgress:
if indexframe%10 == 0:
KeepGoing = dlg.Update(indexframe//10, "Frame number: %s/%s" % (indexframe,numframes))[0]
# print "Keep: "+str(KeepGoing)
begframe=int(indexframe*shiftsamp)
endframe=int(begframe+sizesamp) # samples
frame=signal[begframe:endframe]
if (len(frame)%2 != 0):
frame=np.append(frame,[0])
begtime=indexframe*self.data['windowshift']
endtime=begtime+self.data['windowsize'] # seconds
frame=frame-np.mean(frame)
frame=frame*hw
frame = np.append(frame,np.zeros(lenZeroPadding))
# print("-----------------------")
# print("Frame "+str(indexframe))
# print("Frame power (time): "+str(hammingfactor*np.mean(frame*frame))+" ms^2")
spec_tmp=np.absolute(np.fft.fft(frame))**2
spec=spec_tmp[0:(len(spec_tmp)/2)] # Only positive half of spectrum
freqs = np.linspace(start=0,stop=self.data["interpfreq"]/2,num=len(spec),endpoint=True)
# print("Frame power (frequency): "+str(power(spec,freqs,0,self.data["interpfreq"]/2)))
ulfpower=power(spec,freqs,self.data["ulfmin"],self.data["ulfmax"])
self.data["ULF"].append(ulfpower)
#print("ULF power: "+str(ulfpower))
vlfpower=power(spec,freqs,self.data["vlfmin"],self.data["vlfmax"])
self.data["VLF"].append(vlfpower)
#print("VLF power: "+str(vlfpower))
lfpower=power(spec,freqs,self.data["lfmin"],self.data["lfmax"])
self.data["LF"].append(lfpower)
#print("LF power: "+str(lfpower))
hfpower=power(spec,freqs,self.data["hfmin"],self.data["hfmax"])
self.data["HF"].append(hfpower)
#print("HF: "+str(hfpower))
totalpower=power(spec,freqs,0,self.data["interpfreq"]/2.0)