R/read.mat.Cytospec.R

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

##' Import for Cytospec mat files
##' 
##' These functions allow to import .mat (Matlab V5) files written by Cytospec.
##' 
##' \code{read.cytomat} has been renamed to \code{read.mat.Cytospec} and is now 
##' deprecated. Use \code{read.mat.Cytospec} instead.
##' 
##' @param file The complete file name (or a connection to) the .mat file.
##' @param keys2data specifies which elements of the \code{Info} should be
##'   transferred into the extra data
##' @param blocks which blocks should be read? \code{TRUE} reads all blocks.
##' @param ... \code{read.cytomat} for now hands all arguments to
##'   \code{read.mat.Cytospec} for backwards compatibility.
##' @note This function is an ad-hoc implementation and subject to changes.
##' @return hyperSpec object if the file contains a single spectra block,
##'   otherwise a list with one hyperSpec object for each block.
##' @author C. Beleites
##' @rdname read.mat.Cytospec
##' @seealso \code{R.matlab::readMat}
##' @export
##' @keywords IO file
read.mat.Cytospec <- function (file, keys2data = FALSE, blocks = TRUE) {
  if (! requireNamespace ("R.matlab"))
      stop ("package 'R.matlab' needed.")
  
  tmp <- R.matlab::readMat(file)
  
  ## read spectra matrix
  spc <- tmp$C
  d <- dim (spc)
  
  ## get wavelength information
  fileinfo<-(tmp$Info[[1]])
  lwn <- as.numeric (fileinfo [grep ("LWN", fileinfo) - 1])
  hwn <- as.numeric (fileinfo [grep ("VWN", fileinfo) - 1])
  wn <- seq (lwn, hwn, length.out = dim (spc)[3])

  ## x + y coordinates
  x <- rep (1 : d [1], d [2])
  y <- rep (1 : d [2], each = d [1])
  
  extra.data <- data.frame (x = x, y = y)
  
  nblocks <- d [4]
  if (is.na (nblocks)) { # only one block => 3d array
    nblocks <- 1
    dim (spc) <- c (dim (spc), 1L)
  }
  
  blocks <- seq (nblocks) [blocks]

  if (any (is.na (blocks))) {
    warning ("Dropping requests to unavailable blocks.")
    blocks <- blocks [! is.na (blocks)]
  }

  if (length (blocks) == 1L) {
    result <- .block2hyperSpec (spc, extra.data, wn, blocks, file)
  } else {
    result <- list ()
    for (b in blocks) 
        result [[b]] <- .block2hyperSpec (spc, extra.data, wn, b, file)
  }
  
  ## consistent file import behaviour across import functions
  ## .fileio.optional is called inside .block2hyperSpec
  
  result  
}

.block2hyperSpec <- function (spc, df, wn, block, file) {
  spc <- spc [,,, block]
  
  d <- dim (spc)
  dim (spc) <- c (d [1] * d[2], d [3])

  df$block <- block
  
  ## consistent file import behaviour across import functions
  .fileio.optional (new ("hyperSpec", spc = spc, wavelength = wn, data = df),
                    filename = file)
}

##' @export 
##' @rdname read.mat.Cytospec
read.cytomat <- function (...){
  warning("read.cytomat has been renamed and is now deprecated.\nPlease use read.mat.Cytospec instead.")
  read.mat.Cytospec (...)
}