R/readCounts.R

In acc: Exploring Accelerometer Data

#' @export
#' @importFrom DBI dbConnect
#' @importFrom RSQLite SQLite
#' @importFrom stats complete.cases
#' @importFrom Rcpp evalCpp
#' @useDynLib acc




readCounts <- function (filename) {
  
  myfiletype <- substring(filename, nchar(filename) - 3, nchar(filename))
  if (myfiletype == ".dat" | myfiletype == ".csv") {
    Tfile <- file(filename, "r")
    if (isOpen(Tfile, "r")) {
      seek(Tfile, 0, rw = "r")
      lines = readLines(Tfile)
      close(Tfile)
    }
    skipPos = grep("-----", lines)[2]
    startTPos = grep("Start Time", lines)
    startEPos = grep("Epoch Period", lines)
    startDPos = grep("------------ Data File Created By ActiGraph ", lines)
    if(length(startDPos)==0){
      startDPos = grep("------------ Data Table File Created By ActiGraph ", lines)
    }  
    deviceName = gsub("------------ Data File Created By ActiGraph ","", lines[startDPos])
    deviceName = head(strsplit(deviceName, split = " ")[[1]],1)
    if(substring(deviceName,1,1)!='G'){
      deviceName = gsub("------------ Data Table File Created By ActiGraph ", "", lines[startDPos])
      deviceName = head(strsplit(deviceName, split = " ")[[1]],1)
    }
    startSPos = grep("Serial Number: ", lines)
    startTime = gsub("Start Time ", "", lines[startTPos])
    startTime = gsub("\\,", "", startTime)
    startTime = gsub("[[:blank:]]", "", startTime)
    startDatePos = grep("Start Date ", lines)
    startDateChr = gsub("Start Date ", "", lines[startDatePos])
    startDateChr = gsub("\\,", "", startDateChr)
    startDateChr = gsub("[[:blank:]]", "", startDateChr)
    
    
    if (grepl("/",startDateChr) == TRUE) {
      startDate = strsplit(startDateChr, "/")[[1]]
      if (nchar(startDate[1]) == 1) {
        startDate[1] = paste("0", startDate[1], sep = "")
      }
      if (nchar(startDate[2]) == 1) {
        startDate[2] = paste("0", startDate[2], sep = "")
      }
      startDate = paste(startDate[3], startDate[1], startDate[2], 
                        sep = "-")
    }
    
    if (grepl("-",startDateChr) == TRUE) {
      startDate = strsplit(startDateChr, "-")[[1]]
      if (nchar(startDate[1]) == 1) {
        startDate[1] = paste("0", startDate[1], sep = "")
      }
      if (nchar(startDate[2]) == 1) {
        startDate[2] = paste("0", startDate[2], sep = "")
      }
      startDate = paste(startDate[3], startDate[2], startDate[1], 
                        sep = "-")
    }
    
    
    rawTimeStamp1 = paste(startDate, startTime, sep = " ")
    epochTime = gsub("Epoch Period (hh:mm:ss) ", "", lines[startEPos])
    epochTime = gsub("\\,", "", epochTime)
    epochTime = substr(epochTime, nchar(epochTime) - 7, nchar(epochTime))
    ep = as.numeric(as.difftime(c(epochTime), units = "secs"))
    
    serialNumber = gsub("Serial Number: ", "", lines[startSPos])
    serialNumber = gsub("\\,", "", serialNumber)
  }
  if (myfiletype == ".agd") {
    con = DBI::dbConnect(SQLite(), dbname = filename)
    settings <- DBI::dbReadTable(con, "settings")
    deviceName <- settings$settingValue[settings$settingName == 
                                          "devicename"]
    serialNumber <- settings$settingValue[settings$settingName == 
                                            "deviceserial"]
    ep <- as.numeric(as.character(settings$settingValue[settings$settingName == 
                                                          "epochlength"]))
    startdatetime <- settings$settingValue[settings$settingName == 
                                             "startdatetime"]
    startdatetime2 <- as.POSIXlt((as.numeric(startdatetime)/1e+07), 
                                 origin = "0001-01-01 00:00:00", tz = "GMT")
    startDate <- substring(startdatetime2, 1, 10)
  }
  type <- NA
  if (deviceName == "GT1M") {
    type <- "uni-axial"
  }
  if (deviceName == "GT3X") {
    type <- "tri-axial"
  }
  if (deviceName == "GT3XPlus") {
    type <- "tri-axial"
  }
  cat(noquote(paste("Raw data read for ", deviceName, " device. This is a ", 
                    type, " device.", sep = "")))
  cat("\n")
  cat(noquote(paste("Serial number: ", serialNumber, ".", sep = "")))
  cat("\n")
  cat(noquote(paste("Start date is ", startDate, " and epoch is ", 
                    ep, " seconds.", sep = "")))
  cat("\n")
  
  if (myfiletype == ".dat" | myfiletype == ".csv") {
    startline = skipPos + 1
    endline = length(lines)
    col0 = gsub("[[:blank:]]+", " ", lines[startline])
    col = strsplit(col0, c("\\, |\\,| "))[[1]]
    col = length(col[col != ""])
    timeline = c()
    
    if(substring(gsub("[[:blank:]]+", " ", lines[startline])[1],1,4)!="Date"){
      mymatrix <- matrix(NA, (endline - startline + 1), col)
      for (i in startline:endline) {
        temp0 = gsub("[[:blank:]]+", " ", lines[i])
        temp = strsplit(temp0, c("\\, |\\,| "))[[1]]
        temp = temp[temp != ""]
        if (length(temp) > 0) {
          mymatrix[(i - startline + 1), 1:length(temp)] <- temp
        } 
      } 
      counts = as.numeric(as.vector(t(mymatrix))) # View(counts)
      counts <- counts[!is.na(counts)]
      if (type == "uni-axial") {
        timeline = (0:as.integer((length(counts)) - 1) * 
                      ep)
        rawTimeStamp = rep(rawTimeStamp1, (length(counts)))
        rst = gsub(" GMT", "", as.POSIXlt(rawTimeStamp, tz = "GMT") + 
                     timeline)
        data = data.frame(TimeStamp = as.vector(rst), counts = counts)
      }
      if (type == "tri-axial") {
        n <- length(counts)
        x = counts[seq(1, n, 3)]
        y = counts[seq(2, n, 3)]
        z = counts[seq(3, n, 3)]
        maxlength <- max(length(x), length(y), length(z))
        if (length(x) < maxlength) {
          x <- c(x, NA)
        }
        if (length(y) < maxlength) {
          y <- c(y, NA)
        }
        if (length(z) < maxlength) {
          z <- c(z, NA)
        }
        timeline = (0:(maxlength - 1) * ep)
        rawTimeStamp = rep(rawTimeStamp1, maxlength)
        rst = gsub(" GMT", "", as.POSIXlt(rawTimeStamp, tz = "GMT") + 
                     timeline)
        data = data.frame(TimeStamp = as.vector(rst), x = x, 
                          y = y, z = z)
      }
    }
    
    if(substring(gsub("[[:blank:]]+", " ", lines[startline])[1],1,4)=="Date"){
      mymatrix <- matrix(NA, (endline - startline), col)
      for (i in startline:endline) { # i <- startline
        temp0 = gsub("[[:blank:]]+", " ", lines[i])
        temp = strsplit(temp0, c("\\, |\\,| "))[[1]]
        temp = temp[temp != ""]
        if (length(temp) > 0 & temp[1]!="Date") {
          mymatrix[(i - startline), 1:length(temp)] <- temp
        } 
      }
      if (type == "uni-axial") {
        data = data.frame(TimeStamp = paste(mymatrix[,1],mymatrix[,2]), counts = mymatrix[, 3])
      }
      if (type == "tri-axial") {
        data = data.frame(TimeStamp = paste(mymatrix[,1],mymatrix[,2]), x = mymatrix[, 3], y = mymatrix[, 4], z = mymatrix[, 5])
      }
    }
  }
  
  if (myfiletype == ".agd") {
    counts <- DBI::dbReadTable(con, "data")
    counts <- counts[complete.cases(counts), ]
    timeline = (0:as.integer((dim(counts)[1]) - 1) * ep)
    rawTimeStamp = rep(startdatetime2, dim(counts)[1])
    rst = gsub(" GMT", "", as.POSIXlt(rawTimeStamp, tz = "GMT") + 
                 timeline)
    if (type == "uni-axial") {
      data = data.frame(TimeStamp = as.vector(rst), counts = counts[, 2])
    }
    if (type == "tri-axial") {
      data = data.frame(TimeStamp = as.vector(rst), x = counts[, 2], y = counts[, 3], z = counts[, 4])
    }
  }
  data
}