R/guesswavelength.R

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

#' guess wavelengths from character vector
#' 
#' character vectors used for names (e.g. colnames for matrices or data.frames) 
#' are often treated by \code{\link[base]{make.names}} or similar functions that
#' produce suitable names (e.g. by prepending "X" to numbers.). Such names 
#' cannot be directly converted to numeric.
#' 
#' \code{guess.wavlength} tries to extract numbers from X which may be
#' surrounded by such "protecting" characters.
#' 
#' @param X character with numbers hidden inside
#'   
#' @return numeric
#' @export
#' 
#' @examples
#' tmp <- data.frame(flu [[,, 400 ~ 410]])
#' (wl <- colnames (tmp))
#' guess.wavelength (wl)
guess.wavelength <- function (X) {
  wl <- regmatches (X, regexpr(.PATTERN.number, X))
  wl <- as.numeric (wl)
  
  if (is.null (wl) || length (wl) == 0L || any (is.na (wl))){
    if (hy.getOption("debuglevel") >= 1L)
      message("could not guess wavelengths")
    wl <- NULL
  }

  wl  
}

##' @include regexps.R
##' @include options.R
.test (guess.wavelength) <- function (){
  context ("guess.wavelength")
      
  test_that("simple test", { 
      expect_equal (guess.wavelength(1:5), 1:5)
  }) 
  
  test_that("wavelengths containing characters", { 
      wl <- seq(600,602,length.out = 11)
      expect_equal (guess.wavelength(make.names(wl)), wl)
  }) 
  
  test_that("return NULL if could not guess wavelenths", { 
      expect_equal (guess.wavelength(colnames(matrix(1:12,3))), NULL)
      expect_equal (guess.wavelength(letters[1:4]), NULL)
  }) 
}