R/LoadEpisodesAscii.R

In RHRV: Heart Rate Variability Analysis of ECG Data

LoadEpisodesAscii <-
  function(HRVData, FileName, RecordPath=".", Tag="", InitTime="0:0:0", verbose=NULL, header = TRUE) {	
    #-------------------------------
    # Loads episodes from ascii file
    #-------------------------------
    #	FileName -> file containing episodes
    # RecordPath -> path to the file containing episodes
    #   Tag -> specifies type of episodes
    #	InitTime -> time (HH:MM:SS) absolute time of beginning of the record (subtracted from time of episodes)
    
    #  	Example of file containing episodes:
    
    #  	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 if the header argument is set to TRUE
    #  	Duration in seconds
    
    dir = getwd()
    on.exit(setwd(dir))
    setwd(RecordPath)
    
    HRVData = HandleVerboseArgument(HRVData, verbose)
    
    
    VerboseMessage(HRVData$Verbose, paste("Loading episodes file:", FileName))
    VerboseMessage(HRVData$Verbose, paste("Path:", RecordPath))
    
    if (header) {
      # skip first line
      x = read.table(FileName, skip = 1)
    } else{
      # Do not skip the first line,
      x = read.table(FileName, skip = 0)
    }
    
    
    VerboseMessage(HRVData$Verbose, 
                   ifelse(Tag == "",  "No tag specified",  paste("Tag:", Tag))
    )
    
    # obtaining time
    options(digits.secs=3)
    timeaux = strptime(InitTime,"%H:%M:%OS")
    if (is.na(timeaux)) {
      stop("Time format is HH:MM:SS")
    }	
    
    VerboseMessage(HRVData$Verbose,
                   paste0("Initial time: ",sprintf("%02d",timeaux$hour),":",
                          sprintf("%02d",timeaux$min),":",
                          sprintf("%02.3f",timeaux$sec))
    )
    
    
    # calculating time in seconds, considering the initial time for the register
    
    EpisodeTimeAbs=strptime(x$V1,"%H:%M:%OS")
    EpisodeTimeRel=difftime(EpisodeTimeAbs,timeaux, units="secs")
    x$V1=as.numeric(EpisodeTimeRel)
    
    if (Tag=="") {
      y=x
    } else {
      y=subset(x,x$V2==Tag)
    }
    
    added=length(y$V1)
    
    VerboseMessage(HRVData$Verbose,
                   ifelse(is.null(y$V4),
                          "Data does not include values associated to episodes",
                          "Data includes values associated to episodes")
    )
    
    if (added==0) {
      VerboseMessage(HRVData$Verbose, "No episode was loaded")
    } else {
      if (is.null(y$V4)) {
        HRVData$Episodes=rbind(HRVData$Episodes,data.frame(InitTime=y$V1,Type=y$V2,Duration=y$V3))
      } else {
        HRVData$Episodes=rbind(HRVData$Episodes,data.frame(InitTime=y$V1,Type=y$V2,Duration=y$V3,Value=y$V4))
      }
      
      HRVData$Episodes=HRVData$Episodes[order(HRVData$Episodes$InitTime),]  # Sorts episodes by InitTime
      HRVData$Episodes=HRVData$Episodes[!duplicated(HRVData$Episodes),]  # Removes duplicated episodes
      
      VerboseMessage(HRVData$Verbose, 
                     paste("Loaded", added, "episodes from file"))
      
    }
    
    VerboseMessage(HRVData$Verbose,
                   paste("Number of episodes:",length(HRVData$Episodes$InitTime))
    )
    
    return(HRVData)
  }