R/IMPORT-nmr.text.2d.1col.R

In jmstrat/NMR.Utils: Importing and processing Bruker NMR data

#' Read 2D NMR Data (real only)
#'
#' This function is used to import NMR data.
#' @param nmrfile Path to txt file saved using topspin's File->Save->Save visible region as text file (topspin doesn't support immaginary)
#' @param imaginary_file Path to txt file as above, but set to 90 degrees out of phase in topspin
#' @return A data frame containing the NMR data (ppm,intensity1, intensity2, ...)
#' @examples
#' read.nmr.text.2d.1col("/path/to/file.txt")
#' @keywords internal
read.nmr.text.2d.1col <- function(nmrfile, imaginary_file=NA) {
  jms.classes::log.info("Reading 2D 1 column file: %s", nmrfile)
  # Open file for reading
  con <- file(nmrfile, open="r")
  # Read first 8 lines
  lines <- readLines(con, n=8)
  # Close file
  close(con)
  # Extract lines
  f2 <- lines[[5]]
  nr <- lines[[7]]
  nc <- lines[[8]]

  # Get data from lines
  f2l <- as.numeric(gsub("# F2LEFT = ([[:digit:]\\.-]*) .*", "\\1", f2))
  f2r <- as.numeric(gsub("# F2LEFT = [[:digit:]\\.-]* ppm\\. F2RIGHT = ([[:digit:]\\.-]*) .*", "\\1", f2))
  nrows <- as.numeric(gsub("# NROWS = ([[:digit:]]*).*", "\\1", nr))
  ncols <- as.numeric(gsub("# NCOLS = ([[:digit:]]*).*", "\\1", nc))

  # Calculate ppm scale
  ppmscale <- seq(f2l, f2r, (f2r - f2l) / (ncols - 1))

  # Read all data ignoring comment lines (Thus also ignoring row separators)
  fullTable <- read.table(nmrfile)
  if (!is.na(imaginary_file)) {
    jms.classes::log.info("Reading 2D 1 column file: %s", imaginary_file)
    imaginaryTable <- read.table(imaginary_file)
  }

  # Split table into multiple columns of length ncols
  cols <- c()
  for (i in 1:nrows) {
    if (!is.na(imaginary_file)) {
      cols[[i]] <- complex(real=fullTable[((i - 1) * ncols + 1):(i * ncols), ], imaginary=imaginaryTable[((i - 1) * ncols + 1):(i * ncols), ])
    } else {
      cols[[i]] <- fullTable[((i - 1) * ncols + 1):(i * ncols), ]
    }
  }

  # Make data frame
  nmrdata <- nmr.data.object(ppmscale, cols)
  # Rename columns
  names(nmrdata) <- c("ppm", 0:(nrows - 1))
  # return data
  return(as.nmr2d.data.object(nmrdata))
}