Calibrates the energy scale of a gamma spectrum.

## Usage

energy_calibrate(object, lines, ...)

has_energy(object)

has_calibration(object)

# S4 method for GammaSpectrum,list
energy_calibrate(object, lines, ...)

# S4 method for GammaSpectrum,PeakPosition
energy_calibrate(object, lines, ...)

# S4 method for GammaSpectrum
has_energy(object)

# S4 method for GammaSpectra
has_energy(object)

# S4 method for GammaSpectrum
has_calibration(object)

# S4 method for GammaSpectra
has_calibration(object)

## Arguments

object

A GammaSpectrum or GammaSpectra object.

lines

A PeakPosition object or a list of length two. If a list is provided, each element must be a named numeric vector giving the observed peak position ("channel") and the corresponding expected "energy" value (in keV).

...

Currently not used.

## Value

• energy_calibrate() returns a GammaSpectrum object.

• has_energy() and has_calibration() return a logical vector.

## Details

The energy calibration of a spectrum is the most tricky part. To do this, the user must specify the position of at least three observed peaks and the corresponding energy value (in keV). A second order polynomial model is fitted on these energy vs channel values, then used to predict the new energy scale of the spectrum.

The package allows to provide the channel-energy pairs to be use. However, the spectrum can be noisy so it is difficult to properly determine the peak channel. In this case, a better approach may be to pre-process the spectrum (variance-stabilization, smoothing and baseline correction) and perform a peak detection. Once the identified peaks are satisfactory, you can set the corresponding energy values (in keV) and use these lines to calibrate the energy scale of the spectrum.

Regardless of the approach you choose, it is strongly recommended to check the result before proceeding.

N. Frerebeau

## Examples

## Import a CNF file
spc_file <- system.file("extdata/LaBr.TKA", package = "gamma")
#> Gamma spectrum:
#> *  name: LaBr
#> *  date: 2022-09-15 09:21:39
#> *  live_time: 3385.54
#> *  real_time: 3403.67
#> *  channels: 1024
#> *  energy_min: NA
#> *  energy_max: NA

## Set peak positions (channel) and expected energy values
calib_lines <- list(
channel = c(86, 495, 879),
energy = c(238, 1461, 2615)
)

(spc1 <- energy_calibrate(spc, lines = calib_lines))
#> Gamma spectrum:
#> *  name: LaBr
#> *  date: 2022-09-15 09:21:39
#> *  live_time: 3385.54
#> *  real_time: 3403.67
#> *  channels: 1024
#> *  energy_min: -15.38
#> *  energy_max: 3052.2

## Inspect results
plot(spc1, xaxis = "energy", yaxis = "count") +
ggplot2::geom_vline(xintercept = c(238, 1461, 2615), linetype = 3)