Detect Saturated Channels in Spectra

Finds the channels at the saturation limit of the detector, for each spectrum and for each wavelength. Saturated lines are clipped, so their intensity and width are wrong and they respond nonlinearly to concentration.

Usage

saturation_summary(x, limit = 65535, tolerance = 0)

Arguments

x

A numeric matrix or data frame of spectra, one per row, with the wavelengths as column names.

limit

The saturation limit of the detector, in counts. Default is 65535 (16-bit detectors).

tolerance

Channels within tolerance counts of limit are counted as saturated. Default is 0.

Value

A list with two tibbles:

• spectra: for each spectrum (row), the number n_saturated and fraction of saturated channels;

• channels: for each channel saturated in at least one spectrum, its wavelength (from the column names; NA if they are not numeric), column index, and the number and fraction of saturated spectra.

Examples

data(forageLIBS)
sat <- saturation_summary(forageLIBS[-(1:14)], limit = 65535)
sat$channels
#> # A tibble: 6 × 4
#>   wavelength index n_spectra fraction
#>        <dbl> <int>     <dbl>    <dbl>
#> 1       388.  2229        30   0.0815
#> 2       393.  2297        48   0.130 
#> 3       393.  2298       133   0.361 
#> 4       397.  2339        82   0.223 
#> 5       399.  2368       124   0.337 
#> 6       399.  2369        46   0.125