R/LoadBeatEDFPlus.R

In RHRV: Heart Rate Variability Analysis of ECG Data

LoadBeatEDFPlus <- function(HRVData, RecordName, RecordPath = ".", annotationType ="QRS", verbose = NULL) {
#-------------------------------
# Loads beats from an EDF+ file
#-------------------------------
#	RecordName -> record containing values
#	RecordPath -> path
#	typeAnnotation -> type of the annotation to read
#-------------------------------

	dir = getwd()
	setwd(RecordPath)

	# VerboseDebug = FALSE

	HRVData = HandleVerboseArgument(HRVData, verbose)
	

	VerboseMessage(HRVData$Verbose, paste("Loading beats positions for record:", RecordName))
	VerboseMessage(HRVData$Verbose, paste("Path:", RecordPath))
	

	con = file(RecordName,"rb")

	#version
	version=c()
	for(i in 1:8)
	{
		value = readBin(con,"integer",n=1,size=1,signed=FALSE)
		version=c(version,value)
	}

	# if (VerboseDebug) {
	# 	message("------------- version:",rawToChar(as.raw(version)),"\n")
	# }

	#patient identification
	patient=c()
	for(i in 1:80)
	{
		value = readBin(con,"integer",n=1,size=1,signed=FALSE)
		patient=c(patient,value)
	}

	# if (VerboseDebug) {
	# 	message("------------- patient:",rawToChar(as.raw(patient)),"\n")
	# }

	#recording identification
	recording=c()
	for(i in 1:80)
	{
		value = readBin(con,"integer",n=1,size=1,signed=FALSE)
		recording=c(recording,value)
	}

	# if (VerboseDebug) {
	# 	message("------------- recording:",rawToChar(as.raw(recording)),"\n")
	# }

	#date
	startdate=c()
	for(i in 1:8)
	{
		value = readBin(con,"integer",n=1,size=1,signed=FALSE)
		startdate=c(startdate,value)
	}

	# if (VerboseDebug) {
	# 	message("------------- startdate:",rawToChar(as.raw(startdate)),"\n")
	# }

	#time
	starttime=c()
	for(i in 1:8)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  starttime=c(starttime,value)
	}
	
	# if (VerboseDebug) {
	# 	message("------------- starttime:",rawToChar(as.raw(starttime)),"\n")
	# }
	
	dateAux = intToCharacter(startdate)
	dateAux = gsub("\\.","-",dateAux)
	
	time = intToCharacter(starttime)
	time = gsub("\\.",":",time)
	
	VerboseMessage(HRVData$Verbose, paste("Date: ",dateAux))
	VerboseMessage(HRVData$Verbose, paste("Time: ",time))
	datetimeinfo = paste(dateAux,time,sep = " ")
	HRVData$datetime = datetimeinfo
	
	#number of bytes in header
	numberBytes=c()
	for(i in 1:8)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  numberBytes=c(numberBytes,value)
	}
	
	# if (VerboseDebug) {
	# 	message("------------- numberBytes:",rawToChar(as.raw(numberBytes)),"\n")
	# }
	
	#reserved
	reserved=c()
	for(i in 1:44)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  reserved=c(reserved,value)
	}
	
	#number of data records
	numberDataRecords=c()
	for(i in 1:8)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  numberDataRecords=c(numberDataRecords,value)
	}
	numberDataRecords = as.integer(intToCharacter(numberDataRecords))
	
	# if (VerboseDebug) {
	# 	message("------------- numberDataRecords:",numberDataRecords,"\n")
	# }
	
	#duration of a data record in seconds
	durationDataRecord=c()
	for(i in 1:8)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  durationDataRecord=c(durationDataRecord,value)
	}
	
	# if (VerboseDebug) {
	# 	message("------------- durationDataRecord:",rawToChar(as.raw(durationDataRecord)),"\n")
	# }
	
	#number of signals in data record
	signalsDataRecord=c()
	for(i in 1:4)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  signalsDataRecord=c(signalsDataRecord,value)
	}
	numberSignals = as.integer(intToCharacter(signalsDataRecord))
	
	# if (VerboseDebug) {
	# 	message("------------- numberSignals:",numberSignals,"\n")
	# }
	
	#Signals
	#label
	labels=c()
	limit = numberSignals * 16
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  labels=c(labels,value)
	}
	signalLabelList = stringToStringList(intToCharacter(labels))
	
	# if (VerboseDebug) {
	# 	message("------------- labels:",labels,"\n")
	# 	message("------------- signalLabelList:",signalLabelList,"\n")
	# }
	
	VerboseMessage(HRVData$Verbose, 
	               paste("Labels:", paste(signalLabelList, collapse = ", ")))
	
	for(i in 1:length(signalLabelList))
	{
	  if(signalLabelList[i]=="EDF")
	  {
	    if(i<length(signalLabelList) && signalLabelList[i+1]=="Annotations")
	    {
	      signalLabelList[i+1]=paste(signalLabelList[i],signalLabelList[i+1],sep=" ")
	      signalLabelList = signalLabelList[-i]
	    }
	    break
	  }
	}
	
	#transducer types
	types=c()
	limit = numberSignals * 80
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  types=c(types,value)
	}
	
	#physical dimension
	dimension=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  dimension=c(dimension,value)
	}
	
	#physical minimum
	minimum=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  minimum=c(minimum,value)
	}
	
	#physical maximum
	maximum=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  maximum=c(maximum,value)
	}
	
	#digital minimum
	dminimum=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  dminimum=c(dminimum,value)
	}
	
	#digital maximum
	dmaximum=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  dmaximum=c(dmaximum,value)
	}
	
	#prefiltering
	prefiltering=c()
	limit = numberSignals * 80
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  prefiltering=c(prefiltering,value)
	}
	
	#number of samples in each data record
	samples=c()
	limit = numberSignals * 8
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  samples=c(samples,value)
	}
	numberSamplesList = stringToIntList(intToCharacter(samples))
	
	#reserved
	reserved2=c()
	limit = numberSignals * 32
	for(i in 1:limit)
	{
	  value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	  reserved2=c(reserved2,value)
	}
	
	VerboseMessage(HRVData$Verbose,
	               "Reading data: this operation may take a few seconds ...")
	
	
	#Read annotations
	beats=c()
	
	for(i in 1:numberDataRecords)
	{
	  for(j in 1:numberSignals)
	  {
	    if( signalLabelList[j] != "EDF Annotations")
	    {
	      limit = numberSamplesList[j]
	      for(k in 1:limit)
	      {
	        value = readBin(con,"integer",n=1,size=2,signed=FALSE)
	      }
	    }
	    else
	    {
	      limit = numberSamplesList[j] *2
	      value=1
	      while(value!=0)
	      {
	        value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	        limit=limit-1
	      }
	      
	      seconds=c()
	      annotation=c()
	      
	      value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	      limit=limit-1
	      while(value!=0)
	      {
	        if(value==21)
	        {
	          while(value!=20)
	          {
	            value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	            limit=limit-1
	          }
	        }
	        if(value!=20)
	        {
	          seconds=c(seconds,value)
	        }
	        else
	        {
	          value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	          limit=limit-1
	          while(value!=0)
	          {
	            if(value==20)
	            {
	              if(intToCharacter(annotation)==annotationType)
	              {
	                seconds=intToCharacter(seconds)
	                beats=c(beats,as.numeric(substr(seconds,2,nchar(seconds))))
	              }
	              annotation=c()
	            }
	            else
	            {
	              annotation=c(annotation,value)
	            }
	            value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	            limit=limit-1
	          }
	          
	          seconds=c()
	          annotation=c()
	        }
	        value = readBin(con,"integer",n=1,size=1,signed=FALSE)		
	        limit=limit-1
	      }
	      for(k in 1:limit)
	      {
	        value = readBin(con,"integer",n=1,size=1,signed=FALSE)
	      }
	    }
	  }
	}
	
	close(con)
	setwd(dir)
	
	if (length(beats) == 0) {
	  stop("Beats not found in file ",RecordName,"!")
	}
	
	HRVData$Beat = data.frame(Time = beats)
	
	VerboseMessage(HRVData$Verbose, 
	               paste("Number of beats:", length(beats)))
	
	return(HRVData)
}