R/PROCESS-rebin.R

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

#' Rebins the data to ensure a minimum offset between scans
#'
#' @param data 2D NMR data
#' @param min_offset Minimum offset between adjacent scans. Scans too close together will be dealt
#'                   with according to the \code{method} option.
#' @param method One of the following:
#' \describe{
#'  \item{discard}{Scans that are not sufficiently offset from the previous scan are discarded.}
#'  \item{average_before}{Scans that are not sufficiently offset from the previous scan are averaged with the previous scan.}
#'  \item{average_after}{Scans that are not sufficiently offset from the previous scan are averaged with the next scan.}
#' }
#' @export
#' @examples
#' rebin(data, 10)
#' rebin(data, 10, "average_before")
rebin <- function(data, min_offset, method=c("discard", "average_before", "average_after")) {
  method <- method[[1]]
  jms.classes::log.info("Rebinning data (method=%s)", method)

  offsets <- as.numeric(colnames(data)[-1])

  scans_to_remove <- c()
  scans_to_average <- c()

  poff <- -Inf
  last_good <- NA
  for (i in 1:length(offsets)) {
    off <- offsets[[i]]
    if (abs(off - poff) < min_offset) {
      scans_to_remove <- append(scans_to_remove, i)

      if (method == "average_before") {
        data[, last_good + 1] <- rowMeans(data[, c(last_good, i) + 1])
      } else if (method == "average_after") {
        scans_to_average <- append(scans_to_average, i)
      }
    } else {
      poff <- off
      last_good <- i

      if (length(scans_to_average) > 0) {
        scans_to_average <- append(scans_to_average, i)
        data[, i + 1] <- rowMeans(data[, scans_to_average + 1])
      }
      scans_to_average <- c()
    }
  }
  if (length(scans_to_remove) > 0) {
    jms.classes::log.debug("Rebinning removed %s scans", length(scans_to_remove))
    return(data[, -(scans_to_remove + 1)])
  }
  jms.classes::log.debug("Rebinning did not remove any scans")
  data
}