R/readData.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"readData" <-
  function(filenm, typ = "", sep = "") {
    inten <- matrix()
    if (typ == "plain") {
      psisim <- as.matrix(read.table(filenm))
      x <- as.numeric(rownames(psisim))
      nt <- length(x)
      x2 <- as.numeric(scan(filenm, nlines = 1))
      nl <- length(x2)
    } else {
      typ <- scan(filenm, sep = sep, skip = 2, what = "", nmax = 1)

      # taking out the NetCDF support since we have to work out
      # the dependency issue
      # filespl <- strsplit(filenm, split=".",fixed=TRUE)[[1]]
      # endn <- filespl[length(filespl)]
      # if(endn =="cdf" || endn == "CDF") {
      #  newdat <- readNetCDF_TIMP(filenm)
      #  return(newdat)
      # }
      if (typ[1] == "FLIM") {
        file.str <- scan(filenm, sep = sep, skip = 3, what = "")
        origheight <- as.integer(file.str[1])
        origwidth <- as.integer(file.str[2])
        nt <- as.integer(file.str[3])
        x <- vector(mode = "numeric", length = nt)
        nl <- as.integer(file.str[4])
        x2 <- vector(mode = "numeric", length = nl)
        psisim <- matrix(nrow = nt, ncol = nl)
        for (i in 1:nt) {
          x[i] <- as.numeric(file.str[i + 4])
        }
        cnt <- nt + 5
        for (i in 1:nl) {
          for (j in 1:(nt + 1)) {
            if (j == 1) {
              x2[i] <- as.numeric(file.str[cnt])
              cnt <- cnt + 1
            } else {
              psisim[(j - 1), i] <- as.numeric(file.str[cnt])
              cnt <- cnt + 1
            }
          }
        }
        cnt <- cnt + 2
        inten <- matrix(nrow = origheight, ncol = origwidth)
        for (i in 1:origwidth) {
          for (j in 1:origheight) {
            inten[j, i] <- as.numeric(file.str[cnt])
            cnt <- cnt + 1
          }
        }
      }
      if ((typ[1] == "time") || (typ[1] == "Time")) {
        file.str <- scan(filenm, sep = sep, skip = 3, what = "")
        nt <- as.integer(file.str[2])
        x <- as.numeric(file.str[3:(2 + nt)])
        ioff <- nt + 2
        nl <- as.integer((length(file.str) - ioff) / (nt + 1))
        x2 <- vector(mode = "numeric", length = nl)
        psisim <- matrix(nrow = nt, ncol = nl)
        for (i in 1:nl) {
          x2[i] <- as.numeric(file.str[ioff + 1])
          psisim[, i] <- as.numeric(file.str[(ioff + 2):(ioff +
            nt + 1)])
          ioff <- ioff + nt + 1
        }
        if (x2[1] > x2[nl]) {
          psi2 <- psisim
          for (j in 1:nrow(psi2)) {
            psi2[j, ] <- rev(psi2[j, ])
          }
          psisim <- psi2
          x2 <- rev(x2)
        }
      }
      if ((typ[1] == "wavelength") || (typ[1] == "Wavelength")) {
        file.str <- scan(filenm, sep = sep, skip = 3, what = "")
        nl <- as.integer(file.str[2])
        x2 <- as.numeric(file.str[3:(2 + nl)])
        ioff <- nl + 2
        nt <- as.integer((length(file.str) - ioff) / (nl + 1))
        x <- vector(mode = "numeric", length = nt)
        psisim <- matrix(nrow = nt, ncol = nl)
        for (i in 1:nt) {
          x[i] <- as.numeric(file.str[ioff + 1])
          psisim[i, ] <- as.numeric(file.str[(ioff + 2):(ioff +
            nl + 1)])
          ioff <- ioff + nl + 1
        }
        if (x2[1] > x2[nl]) {
          psi2 <- psisim
          for (j in 1:nrow(psi2)) {
            psi2[j, ] <- rev(psi2[j, ])
          }
          psisim <- psi2
          x2 <- rev(x2)
        }
      }
      if (typ[1] == "MG") {
        bd <- read.table(filenm, skip = 4, header = FALSE, sep = ";")
        x <- na.omit(as.numeric(read.table(filenm, skip = 3, header = FALSE, sep = ";")[1, 2:ncol(bd)]))
        attributes(x) <- NULL
        x2 <- na.omit(bd[2:nrow(bd), 1])
        attributes(x2) <- NULL
        nl <- as.integer(length(x2))
        nt <- as.integer(length(x))
        psisim <- t(as.matrix(bd[2:(nl + 1), 2:(nt + 1)]))
      }
    }
    dat(
      psi.df = psisim, x = x, nt = nt, x2 = x2, nl = nl, simdata = FALSE,
      datCall = list(match.call()), inten = inten, datafile = filenm
    )
  }