ggircal: Raw Accelerometer Data Analysis

Documented in g.inspectfile

g.inspectfile = function(datafile) {
  # note that if the file is an RData file then this function will not be called
  # the output of this function for the original datafile is stored inside the RData file in the form of object I
  getbrand = function(filename=c(),datafile=c()) {
    sf = c(); isitageneactive = c();  isitagenea = c();  mon = c();dformat = c() #generating empty variables
    tmp1 = unlist(strsplit(filename,"[.]cs"))
    tmp2 = unlist(strsplit(filename,"[.]b"))
    tmp3 = unlist(strsplit(filename,"[.]w"))
    tmp4 = unlist(strsplit(filename,"[.]r"))
    tmp5 = unlist(strsplit(filename,"[.]cw"))
    if (tmp1[length(tmp1)] == "v") { #this is a csv file
      dformat = 2 #2 = csv
      testcsv = read.csv(paste(datafile,sep=""),nrow=10,skip=10)
      if (ncol(testcsv) == 2) { #it is a geneactivefile
        mon = 2
      } else if (ncol(testcsv) >= 3) {	#it is an actigraph file
        mon = 3
      }
    } else if (tmp2[length(tmp2)] == "in") { #this is a bin file
      dformat = 1 #1 = binary
    } else if (tmp3[length(tmp3)] == "av") { #this is a wav file
      dformat = 3 #3 = wav
      mon = 4 # Axivity
    } else if (tmp5[length(tmp5)] == "a") { #this is a cwa file
      dformat = 4 #4 = cwa
      mon = 4 # Axivity
    }
    if (dformat == 1) { # .bin
      # try read the file as if it is a geneactiv and store output in variable 'isitageneactive'
      suppressWarnings(try(expr={isitageneactive = GENEAread::header.info(binfile=datafile)},silent=TRUE))
      # try read the file as if it is a genea and store output in variable 'isitagenea'
      try(expr={isitagenea = g.binread(datafile,0,1)},silent=TRUE)
      #size and content of variables 'isitagenea' and 'isitageneactive' will now tell us what it is
      if (length(isitagenea) > 1) {
        mon = 1 #mon = 1 is code for saying that it is a genea
        H = isitagenea$header
        tmp = strsplit(H[which(H[,1] == "Sample_Rate"),2],"Hz")
        tmp2 = unlist(strsplit(as.character(tmp[1]),","))
        if (length(tmp2) > 1) { #decimals seperated by comma
          sf = as.numeric(tmp2[1])
          sf = sf + (as.numeric(tmp2[2]))/10	
        } else { #decimals seperated by dot
          sf = as.numeric(tmp[1])			
        }
        if (sf == 0 | is.na(sf) == T) {
          skip = 1 #reconsider decision to analyse this file as it is possibly corrupt
          print("Possibibly corrupt genea File")
        }
      } else if (length(as.matrix(isitageneactive)) >= 1 & length(isitagenea) == 0) {
        ppp = unlist(isitageneactive)
        if (ppp[2] != "NA:NA") {
          mon = 2 #mon = 1 is code for saying that it is a geneactive
          H = isitageneactive
          tmp = unlist(strsplit(unlist(H[2,1])," "))
          tmp2 = unlist(strsplit(as.character(tmp[1]),","))
          if (length(tmp2) > 1) { #decimals seperated by comma
            sf = as.numeric(tmp2[1])
            sf = sf + (as.numeric(tmp2[2]))/10	
          } else { #decimals seperated by dot
            sf = as.numeric(tmp[1])			
          }
          #also try to read sf from first page header
          sf_r = sf
          csvr = c()
          suppressWarnings(expr={
            try(expr={csvr = as.matrix(read.csv(datafile,nrow=10,skip=200,sep=""))},silent=TRUE)
          })
          if (length(csvr) > 1) {
            for (ii in 1:nrow(csvr)) {
              tmp3 = unlist(strsplit(as.character(csvr[ii,1]),"quency:")) #part of 'frequency'
              if (length(tmp3) > 1) {
                #			print(csvr[ii,1])
                sf_r = tmp3[2]#a s.numeric(tmp3[2]) + as.numeric(csvr[ii,]/10) #sample frequency from the page header
              }
            }
            #check whether it is comma separated
            tmp4 = unlist(strsplit(as.character(sf_r),","))
            if (length(tmp4) >1) { #comma
              sf_r = as.numeric(tmp4[1]) + as.numeric(tmp4[2]) / 10
            } else { #dot
              sf_r = as.numeric(sf_r)
            }
            if (length(sf_r) > 0) {
              if (is.na(sf_r) == FALSE) {
                if (sf_r != sf & abs(sf_r-sf) > 5) { #use pageheader sample frequency if it is not the same as header sample frequency
                  sf = sf_r
                  print(paste("sample frequency used from page header: ",sf," Hz",sep=""))
                }
              }
            }
          }
        } else {
          print("Possibibly corrupt geneactive File")
        }
      }
    } else if (dformat == 2) { #no checks for corrupt file yet...maybe not needed for csv-format?
      if (mon == 2) {
        tmp = read.csv(datafile,nrow=50,skip=0)
        sf = as.character(tmp[which(as.character(tmp[,1]) == "Measurement Frequency"),2])
        tmp = as.numeric(unlist(strsplit(sf," "))[1])
        tmp2 = unlist(strsplit(as.character(tmp[1]),","))
        if (length(tmp2) > 1) { #decimals seperated by comma
          sf = as.numeric(tmp2[1])
          sf = sf + (as.numeric(tmp2[2]))/10	
        } else { #decimals seperated by dot
          sf = as.numeric(tmp[1])			
        }
      } else if (mon == 3) {
        tmp0 = read.csv(datafile,nrow=9,skip=0)
        tmp = colnames(tmp0)
        tmp2 = as.character(unlist(strsplit(tmp,".Hz"))[1])
        tmp3 = as.character(unlist(strsplit(tmp2,"yy.at."))[2])
        tmp5 = unlist(strsplit(tmp3,","))
        if (length(tmp5) > 1) { #decimals seperated by comma
          sf = as.numeric(tmp5[1])
          sf = sf + (as.numeric(tmp5[2]))/10	
        } else { #decimals seperated by dot
          sf = as.numeric(tmp3[1])			
        }
      }
    } else if (dformat == 3) { # wav
      H = tuneR::readWave(datafile,from = 1, to = 10,units = c("seconds"), header = TRUE)
      sf = H$sample.rate
    } else if (dformat == 4) { # cwa
      PP = g.cwaread(datafile,start = 1, end = 10)
      H = PP$header
      sf = H$frequency
    }
    invisible(list(dformat=dformat,mon=mon,sf=sf))
  }
  #======================================================================
  # main script
  filename = unlist(strsplit(as.character(datafile),"/"))
  filename = filename[length(filename)]
  monnames = c("genea","geneactive","actigraph","axivity") #monitor names
  fornames = c("bin","csv","wav","cwa") #monitor names
  if (length(filename) == 0) {
    print("no files to analyse")
  }
  INFI = getbrand(filename,datafile)
  mon = INFI$mon
  dformat = INFI$dformat
  sf = INFI$sf
  if (dformat == 1) { #binary data
    if (mon == 1) { #genea
      genea = g.binread(datafile,0,1)
      H = genea$header
    } else if (mon == 2) { #geneactive
      H = GENEAread::header.info(binfile=datafile)
    }
  } else if (dformat == 2) { #csv data
    if (mon == 2) { #genea
      H = read.csv(datafile,nrow=20,skip=0) #note that not the entire header is copied
    } else if (mon == 3) { #geneactive
      H = read.csv(datafile,nrow=9,skip=0)
    }
   
  } else if (dformat == 3) { #wav data
    header = c()
    try(expr={header = rownames(read.csv(datafile,nrow=15,header=TRUE))},silent=TRUE)
    if (length(header) == 0) {
      header = rownames(read.csv(datafile,skipNul=TRUE,nrow=15,header=TRUE,fileEncoding="WINDOWS-1252"))
    }
    if (length(header) == 0) {
      header = rownames(read.csv(datafile,skipNul=TRUE,nrow=15,header=TRUE,fileEncoding="UTF-8"))
    }
    if (length(header) == 0) {
      header = rownames(read.csv(datafile,skipNul=TRUE,nrow=15,header=TRUE,fileEncoding="latin1"))
    }
    if (length(which(header %in% paste0(1:15,sep="") == TRUE)) == 15) { #
      header = read.csv(datafile,skipNul=TRUE,nrow=15,skip=1,header=FALSE)
      if (ncol(header) == 2) {
        ii = which(is.na(header[,2]) == FALSE)
        if (length(ii) > 0) header = header[-ii,]
        header = header[,-2]
      }
    }
    if (length(header) <= 5) {
      header = rownames(read.csv(datafile,skipNul=TRUE,nrow=15,header=TRUE))
    }
    H = sapply(header,function(x) {
      tmp = as.character(unlist(strsplit(as.character(x),": ")))
      if (length(tmp) == 1) {
        tmp = c(tmp, NA)
      }
      tmp
    })
    if (is.list(H) == TRUE) {
      conv = c()
      for (jj in 1:length(H)) {
        conv = rbind(conv,H[[jj]])
      }
      H = as.data.frame(conv)
    } else {
      H = as.data.frame(t(H))
    }
    names(H) = c("hnames","hvalues")
  } else if (dformat == 4) { #cwa data
    PP = g.cwaread(datafile,start = 1, end = 10)
    H = PP$header
  }
  
  H = as.matrix(H)
  if (ncol(H) == 1 & dformat == 2) {
    if (mon == 3) {
      vnames = c("Number:","t Time","t Date",":ss)","d Time","d Date","Address:","Voltage:","Mode =")
      Hvalues = Hnames = rep(" ",length(H))
      firstline = colnames(H)
      for (run in 1:length(H)) {
        for (runb in 1:length(vnames)) {
          tmp = unlist(strsplit(H[run],vnames[runb]))
          if (length(tmp) > 1) {
            Hnames[run] = paste(tmp[1],vnames[runb],sep="")
            Hvalues[run] = paste(tmp[2],sep="")
          }
        }
      }
      H = cbind(Hnames,Hvalues)
      H = rbind(c("First line",firstline),H)
    } else {
      H = cbind(c(1:length(H)),H)
    }
  }
  if (dformat == 4) {
    header = data.frame(value=H,row.names=rownames(H))
  } else {
    if (mon == 2 & dformat == 1) {
      varname = rownames(as.matrix(H))
      H = data.frame(varname = varname,varvalue = as.character(H))
    } else {    
      H = data.frame(varname = H[,1],varvalue = H[,2])
    }
  }
  closeAllConnections()
  if (dformat != 4) header = data.frame(value=H[,2],row.names=H[,1])
  monc = mon
  monn = monnames[mon]
  dformc = dformat
  dformn = fornames[dformat]
  invisible(list(header=header,monc=monc,monn=monn,
                 dformc=dformc,dformn=dformn,sf=sf,filename=filename))
}