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

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

#' Read 1D NMR Data (1 col)
#'
#' 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 (with or without imaginary)
#' @return A data frame containing the NMR data (ppm,intensity)
#' @examples
#' read.nmr.text.1d.1col("/path/to/file.txt")
#' @keywords internal
read.nmr.text.1d.1col <- function(nmrfile) {
  jms.classes::log.info("Reading 1D 1 column file: %s", nmrfile)
  ppmscale <- read.nmr.text.1d.1col.ppm(nmrfile)

  # Read all data ignoring comment lines (Thus also ignoring row separators)
  fullTable <- read.table(nmrfile)

  # Make data frame
  nmrdata <- nmr.data.object(ppmscale, fullTable$V1)
  # Rename columns
  names(nmrdata) <- c("ppm", "intensity")
  return(nmrdata)
}

#' Read 1D NMR Data (2 / 4 col)
#'
#' This function is used to import NMR data.
#' @param nmrfile Path to txt file
#' @return A data frame containing the NMR data (ppm,intensity,...)
#' @examples
#' read.nmr.text.1d.2col("/path/to/file.txt")
#' @keywords internal
read.nmr.text.1d.2col <- function(file, skip, sep="") {
  jms.classes::log.info("Reading 1D 2 column file: %s", file)
  tab <- read.table.nmr(file, skip=skip, sep=sep)
  n <- ncol(tab)
  if (n == 2) {
    names(tab) <- c("ppm", "intensity")
  } else {
    # ascii-spec
    names(tab) <- c("point", "intensity", "hz", "ppm")
  }
  tab
}

#' Read 1D NMR Data
#'
#' 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 (with or without imaginary)
#' @return A data frame containing the NMR data (ppm,intensity)
#' @examples
#' read.nmr.text.1d("/path/to/file.txt")
#' @keywords internal
read.nmr.text.1d <- function(file) {
  type_skip <- determine_1d_file_type(file)
  if (type_skip[[1]] == 1) {
    data <- read.nmr.text.1d.1col(file)
  } else if (type_skip[[1]] == 2) {
    data <- read.nmr.text.1d.2col(file, type_skip[[2]], type_skip[[3]])
  } else {
    stop("File type not supported")
  }
  jms.classes::xcol(data) <- "ppm"
  jms.classes::ycol(data) <- "intensity"
  data
}

#' Read ppm scale for 1D data
#'
#' This function attempts to determine the ppm scale from a bruker text file by examining the preamble.
#' @param file Path to txt file saved using topspin's File->Save->Save visible region as text file (with or without imaginary)
#' @return A vector containing the ppm scale
#' @examples
#' read.nmr.text.1d.1col.ppm("/path/to/file.txt")
#' @keywords internal
read.nmr.text.1d.1col.ppm <- function(file) {
  # Extract info from preamble
  # Open file for reading
  con <- file(file, open="r")
  # Read first 8 lines
  lines <- readLines(con, n=8)
  # Close file
  close(con)
  # Extract lines
  lr <- lines[[4]]
  nr <- lines[[6]]

  # Get data from lines
  l <- as.numeric(gsub("# LEFT = ([[:digit:]\\.-]*) .*", "\\1", lr))
  r <- as.numeric(gsub("# LEFT = [[:digit:]\\.-]* ppm\\. RIGHT = ([[:digit:]\\.-]*) .*", "\\1", lr))
  nrows <- as.numeric(gsub("# SIZE = ([[:digit:]]*).*", "\\1", nr))

  # Calculate ppm scale
  ppmscale <- seq(l, r, (r - l) / (nrows - 1))
  return(ppmscale)
}