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Correct cps readings for stray light, using either measured stray light, or using a non-excited region of the detector array.

Usage

filter_correction(
  x,
  flt,
  stray.light.method = "original",
  stray.light.wl = c(218.5, 228.5),
  flt.dark.wl = c(193, 209.5),
  flt.ref.wl = c(360, 379.5),
  flt.Tfr = 1,
  trim = 0.05,
  filter.nir.adjust = FALSE,
  hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1),
  verbose = getOption("photobiology.verbose", default = FALSE)
)

no_filter_correction(
  x,
  stray.light.wl = c(218.5, 228.5),
  flt.dark.wl = c(193, 209.5),
  flt.ref.wl = NULL,
  flt.Tfr = 1,
  trim = 0,
  hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1),
  verbose = getOption("photobiology.verbose", default = FALSE)
)

Arguments

x, flt

cps_spct objects, containing spectral data from which to subtract stray light, and measured stray light, respectively.

stray.light.method

Method variant used, "original" (Ylianttila), "simple", "full", "sun", "raw", "none".

stray.light.wl

numeric vector of length 2 giving the range of wavelengths to use for the final stray light correction.

flt.dark.wl, flt.ref.wl

numeric vectors of length 2 giving the ranges of wavelengths to use for the "dark" and "illuminated" regions of the array in the filter correction.

flt.Tfr

numeric fractional transmittance of the filter to the source of stray light, used only for method "simple".

trim

a numeric value to be used as argument for mean

filter.nir.adjust

logical Flag indicating if the cps in the "filter" reference spectrum need to be adjust based on NIR region cps in the "light" spectrum. EXPERIMENTAL!!

hdr.tolerance

numeric Tolerance for mean deviation among cps columns as a fraction of one. Used in check of HDR consistency.

verbose

Logical indicating the level of warnings wanted.