R/splice.R

In inspectr: Storing, manipulating and analysis spectroscopy and associated data in R.

## Code for splice-correction
##
#
# x a vector
# y the wavelengths 
# wl the wavelengths at which the splice correction should take place
#
# ASD version is using cubic splines
#
# The SWIR part of the spectrum (1000-1800 nm) is taken as a reference 
# for corrections as it is stable to the instrument sensitivity drift
# (Beal & Eamon, 2010)
#
# http://support.asdi.com/Document/Documents.aspx
#

# x and y giving the coordinates of the points to be interpolated
# x: wavelengths
# y: NIR value at these wavelengths
splice.numeric <- function(x, y, wl = c(725:1020, 1801:1950), method = "spline") {
  # Getting index of WLs to be interpolated
  idx <- which(x %in% wl)
  y_cutted <- y[-1*idx]
  x_cutted <- x[-1*idx]
  # Interpolation
  r <- interp1(x = x_cutted, y = y_cutted, xi = x, method = method)
  r
}

splice.Spectra <- function(x, wl = c(725:1020, 1801:1950), method = "spline") {
  nir <- apply_spectra(x, function(spec) {
    splice.numeric(x = wl(x), y = as.vector(spec), wl = wl, method = method)
  })
}

# if (!isGeneric("splice"))
setGeneric("splice", function(x, wl, method="spline")
  standardGeneric("splice"))

setMethod("splice", 
          signature(x="Spectra"),
          function(x, wl = c(725:1020, 1801:1950), method = "spline") {
            splice.Spectra(x, wl, method)
          }
)