R/parse_avantes_converted.R

In lightr: Read Spectrometric Data and Metadata

#' Parse Avantes converted file
#'
#' Parse Avantes converted file.
#' <https://www.avantes.com/products/spectrometers/>
#'
#' @inheritParams lr_parse_generic
#'
#' @inherit lr_parse_generic return details
#'
#' @examples
#' res_ttt <- lr_parse_ttt(
#'   system.file("testdata", "avantes_export.ttt", package = "lightr")
#' )
#' head(res_ttt$data)
#' res_ttt$metadata
#'
#' res_trt <- lr_parse_trt(
#'   system.file("testdata", "avantes_export2.trt", package = "lightr")
#' )
#' head(res_trt$data)
#' res_trt$metadata
#'
#' @export
#'
lr_parse_ttt <- function(filename) {

  # FIXME: grep to find appropriate lines instead of relying on fixed indices

  content <- readLines(filename, skipNul = TRUE)

  author <- NA_character_

  # FIXME: from what I understand, this "timestamp" is arbitrary since it
  # represents the 10*microsecond units since last reset and we don't know
  # when last reset occurred
  #
  # savetime <- grep("^Timestamp", content, value = TRUE)
  # savetime <- gsub("^Timestamp \\[.+\\]([[:digit:]]+)$", "\\1", savetime)
  # if (length(savetime)==0) {
  #   savetime <- NA_character_
  # }
  savetime <- NA_character_

  specmodel <- NA_character_
  inttime <- gsub("^Integration time: ([[:graph:]]+) ms$", "\\1", content[2])
  average <- gsub("^Average: ([[:digit:]]+) scans$", "\\1", content[3])
  boxcar <- gsub("^Nr of pixels used for smoothing: ", "", content[4])

  # The ID is also sometimes included in the first line (comment line) but not
  # always so it's better not to rely on this.
  specID <- gsub("^.*: ([[:alnum:]]{9}).*$", "\\1", content[5])

  # Avantes does not allow different values between measurements
  dark_inttime <- white_inttime <- scope_inttime <- inttime
  dark_average <- white_average <- scope_average <- average
  dark_boxcar <- white_boxcar <- scope_boxcar <- boxcar


  metadata <- c(author, savetime, specmodel, specID,
                dark_inttime, white_inttime, scope_inttime,
                dark_average, white_average, scope_average,
                dark_boxcar, white_boxcar, scope_boxcar)

  data_ind <- grep("^([[:digit:];.,-])+$", content)
  data <- strsplit(content[data_ind], ";")
  data <- do.call(rbind, data)

  # Fix decimal for non-English files
  data <- gsub(",", ".", data)

  colnames(data) <- strsplit(content[data_ind[1]-2], ";")[[1]]

  # Remove trailing whitespaces in names
  colnames(data) <- gsub("[[:space:]]*$", "", colnames(data))

  storage.mode(data) <- "numeric"

  cornames <- c("wl" = "Wave",
                "dark" = "Dark",
                "white" = "Ref",
                "scope" = "Sample",
                "processed" = "Transmittance")

  data_final <- setNames(
    as.data.frame(matrix(NA_real_, nrow = nrow(data), ncol = 5)),
    names(cornames)
  )

  data_final[match(colnames(data), cornames)] <- data

  return(list("data" = data_final, "metadata" = metadata))
}

#' @rdname lr_parse_ttt
#'
#' @export
#'
lr_parse_trt <- lr_parse_ttt