Quality control of dark spectra

Function used to check the number of pixels that deviate from the median.

Usage

QC_dark(
  x,
  range = NULL,
  tol.margin = 1,
  max.hot = 60,
  max.cold = 20,
  spct.label = "Spectrum",
  verbose = getOption("photobiology.verbose", default = TRUE),
  QC.enabled = getOption("ooacquire.qc.enabled", default = TRUE)
)

Arguments

x

cps_spct or raw_spct A spectrum measured in darkness.

range

numeric A wavelength range [nm].

tol.margin

numeric A multiplier applied to MAD, the default 1 corresponds to 1 pixel per 1000 pixels as the expected random Normal noise.

max.hot, max.cold

integer Maximum number of hot and cold pixels exceeding the tolerance per 1000 array pixels.

spct.label

character A character string to use in message.

verbose

logical If true a message is emitted in addition to returning the outcome.

QC.enabled

logical If FALSE return NA skipping QC.

Value

A logical value.

Details

The expectation is that in a spectrum measured in the dark, to be used as a reference, the variation among pixel counts is small. This also applies in some cases to ranges of pixels protected from radiation by a long pass or short pass filter. By default the whole spectrum is included in the QC check, but if needed an argument can be passed to range to select a smaller region.

Note

Disabling the quality control is necessary when the "dark" reference is a measurement of ambient light instead of true darkness; i.e., when the irradiance of one light source is measured as the difference between background illumination and background illuminations plus the target light source.