Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object

The function provides several methods for cosmic-ray removal and spectrum smoothing RLum.Data.Spectrum objects and such objects embedded in list or RLum.Analysis objects.

Usage

apply_CosmicRayRemoval(
  object,
  method = "smooth",
  method.Pych.smoothing = 2,
  method.Pych.threshold_factor = 3,
  MARGIN = 2,
  verbose = FALSE,
  plot = FALSE,
  ...
)

Arguments

object

RLum.Data.Spectrum or RLum.Analysis (required): input object to be treated. This can be also provided as list. If an RLum.Analysis object is provided, only the RLum.Data.Spectrum objects are treated. Please note: this mixing of objects does not work for a list of RLum.Data objects.

method

character (with default): Defines method that is applied for cosmic ray removal. Allowed methods are smooth, the default, (smooth), smooth.spline (smooth.spline) and Pych. See details for further information.

method.Pych.smoothing

integer (with default): Smoothing parameter for cosmic ray removal according to Pych (2003). The value defines how many neighbouring values in each frame are used for smoothing (e.g., 2 means that the two previous and two following values are used).

method.Pych.threshold_factor

numeric (with default): Threshold for zero-bins in the histogram. Small values mean that more peaks are removed, but signal might be also affected by this removal.

MARGIN

integer (with default): on which part the function cosmic ray removal should be applied on:

1 = along the time axis (line by line),
2 = along the wavelength axis (column by column).

Note: This argument currently only affects the methods smooth and smooth.spline

verbose

logical (with default): Option to suppress terminal output.,

plot

logical (with default): If TRUE the histograms used for the cosmic-ray removal are returned as plot including the used threshold. Note: A separate plot is returned for each frame! Currently only for method = "Pych" a graphical output is provided.

...

further arguments and graphical parameters that will be passed to the smooth function.

Value

Returns same object as input.

Details

method = "Pych"

This method applies the cosmic-ray removal algorithm described by Pych (2003). Some aspects that are different to the publication:

For interpolation between neighbouring values the median and not the mean is used.
The number of breaks to construct the histogram is set to: length(number.of.input.values)/2

For further details see references below.

method = "smooth"

Method uses the function smooth to remove cosmic rays.

Arguments that can be passed are: kind, twiceit

method = "smooth.spline"

Method uses the function smooth.spline to remove cosmic rays.

Arguments that can be passed are: spar

How to combine methods?

Different methods can be combined by applying the method repeatedly to the dataset (see example).

Function version

0.3.0

How to cite

Kreutzer, S., 2024. apply_CosmicRayRemoval(): Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object. Function version 0.3.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.26. https://r-lum.github.io/Luminescence/

References

Pych, W., 2004. A Fast Algorithm for Cosmic-Ray Removal from Single Images. The Astronomical Society of the Pacific 116 (816), 148-153. doi:10.1086/381786

Author

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

Examples


##(1) - use with your own data and combine (uncomment for usage)
## run two times the default method and smooth with another method
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "Pych")
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "Pych")
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "smooth")