R/PROCESS-reduce_scans.R

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

#' Reduces the number of scans in the data frame
#'
#' @param spectra A dataframe of NMR data
#' @param scan_range A vector of scans to include c(first, last)
#' @return An idential data frame whose scans are limited to those in scan_range
#' @export
#' @examples
#' reduceScans(spectra, c(1, 50))
reduceScans <- function(spectra, scan_range) {
  if (missing(scan_range)) scan_range <- c(1, find_last_scan(spectra))
  jms.classes::log.info("Removing scans outside of range %s - %s", scan_range[[1]], scan_range[[2]])
  scan_range <- scan_range + 1
  if (scan_range[[1]] < 2) {
    scan_range[[1]] <- 2
  }
  n <- ncol(spectra)
  if (scan_range[[2]] > n) {
    scan_range[[2]] <- n
  }
  spectra[, c(1, scan_range[[1]]:scan_range[[2]])]
}

#' Finds the number of the last (non-empty) scan
#'
#' @param spectra A dataframe of NMR data
#' @param tol If all the intensities are equal to within this tolerance the scan is considered empty
#' @return The number of the last scan
#' @export
#' @examples
#' find_last_scan(spectra)
find_last_scan <- function(spectra, tol=0.01) {
  if (any_complex(spectra)) spectra <- makeReal(spectra)
  not_missing_scans <- which(!sapply(spectra, function(y) abs(max(y) - min(y)) < tol))
  if (length(not_missing_scans)) {
    return(not_missing_scans[[length(not_missing_scans)]] - 1)
  }
  0
}