R/MakeAvgSliceTiff.r

In jrminter/rXEDS: Process X-ray EDS spectra from NIST DTSA-II and data cubes from NIST Lispix.

#' Make a TIF image from a matrix
#'
#' Useful for analysis in NIST Lispix
#'
#' @param mat The matrix with the average slice to convert 
#' 
#' @param name The base name for the TIF file
#'
#' @param tifDir A directory for the pdf histogram. Defaults to ../tif.
#'
#' @return none
#'
#' @keywords keywords
#'
#' @export
#' @include flipMatrix.r
make.avg.slice.tif <- function(mat, name, tifDir='../tif'){
  # create the directory if it does not exist
  dir.create(tifDir, showWarnings = FALSE, recursive = TRUE)
  tifFile <- paste0(tifDir, '/', name, '.tif' )
  if(file.exists(tifFile)) file.remove(tifFile)
  writeTiff(flip.matrix(rotate90.matrix(mat)), tifFile)
}