Merge pull request #53 from RLumSK/add_set_get_energy_calibration

Add set and get methods for energy calibration

NAMESPACE

@@ -8,6 +8,7 @@ S3method(as.matrix,PeakPosition)
 exportMethods("[")
 exportMethods("[[")
 exportMethods("set_energy<-")
+exportMethods("set_energy_calibration<-")
 exportMethods("set_method<-")
 exportMethods("set_names<-")
 exportMethods(Arith)
@@ -25,6 +26,7 @@ exportMethods(energy_calibrate)
 exportMethods(get_channels)
 exportMethods(get_counts)
 exportMethods(get_energy)
+exportMethods(get_energy_calibration)
 exportMethods(get_hash)
 exportMethods(get_livetime)
 exportMethods(get_method)

NEWS.md

@@ -16,6 +16,8 @@ uncertainty calculation. (PR #42 by @RLumSK)
 workflow once the equipment was calibrated (PR #49 by @RLumSK).
 * Add new argument `use_MC` to `dose_predict()` method. The default is `FALSE` to maintain compatibility with old code and output exceptions. If set to `TRUE` the uncertainty on the gamma dose rate uses a Monte Carlo simulation approach for a more realistic error estimation (PR #46 by RLumSK)
 * Add new function parameter `water_content` to `dose_predict()` to allow for an estimate of the dry gamma dose rate using the correction factor by Aitken (1985). The default is `NULL`, in this case nothing is corrected (PR #48 by @RLumSK)
+* Add two more generics: `set_energy_calibration()` and `get_energy_calibration()` and corresponding methods for `GammaSpectrum` and `GammaSpectra` objects. They build on `energy_calibrate()` but enable a more comprehensible scripting
+(PR XX by RLumSK).
 * Extend `dose_predict()` to work with a `numeric` input for `background` as claimed in the documentary. This value can also be set to `c(0,0)` if no background
 subtraction is wanted (PR #38 by @RLumSK)
 

R/AllGenerics.R

@@ -61,6 +61,20 @@ setGeneric(
   def = function(x, value) standardGeneric("set_names<-")
 )
 
+#' @rdname mutator
+#' @aliases get_energy_calibration-method
+setGeneric(
+  name = "get_energy_calibration",
+  def = function(x) standardGeneric("get_energy_calibration")
+)
+
+#' @rdname mutator
+#' @aliases set_energy_calibration-method
+setGeneric(
+  name = "set_energy_calibration<-",
+  def = function(x, value) standardGeneric("set_energy_calibration<-")
+)
+
 #' @rdname mutator
 #' @aliases get_livetime-method
 setGeneric(

R/mutators.R

@@ -321,6 +321,29 @@ setMethod(
   }
 )
 
+#' @export
+#' @rdname mutator
+#' @aliases set_energy_calibration,GammaSpectrum-method
+setMethod(
+  f = "set_energy_calibration<-",
+  signature = "GammaSpectrum",
+  definition = function(x, value) {
+    x <- energy_calibrate(object = x, lines = value)
+    x
+  }
+)
+
+#' @export
+#' @rdname mutator
+#' @aliases get_energy_calibration,GammaSpectrum-method
+setMethod(
+  f = "get_energy_calibration",
+  signature = "GammaSpectrum",
+  definition = function(x) {
+    x@calibration
+  }
+)
+
 ## Baseline --------------------------------------------------------------------
 #' @export
 #' @rdname mutator
@@ -351,6 +374,30 @@ setMethod(
   }
 )
 
+#' @export
+#' @rdname mutator
+#' @aliases set_energy_calibration,GammaSpectra-method
+setMethod(
+  f = "set_energy_calibration<-",
+  signature = "GammaSpectra",
+  definition = function(x, value) {
+    x <- energy_calibrate(object = x, lines = value)
+    x
+  }
+)
+
+#' @export
+#' @rdname mutator
+#' @aliases get_energy_calibration,GammaSpectra-method
+setMethod(
+  f = "get_energy_calibration",
+  signature = "GammaSpectra",
+  definition = function(x) {
+    lapply(x, function(y) y@calibration)
+  }
+)
+
+
 ## PeakPosition ----------------------------------------------------------------
 #' @export
 #' @rdname mutator

tests/testthat/test-mutator.R

@@ -25,6 +25,24 @@ test_that("GammaSpectrum", {
   # energy
   expect_length(get_energy(spectrum), 1024)
   expect_equal(range_energy(spectrum), c(-7.004032, 3124.914528))
+  ## set energy calibration method
+  lines <- data.frame(
+    channel = c(115, 496, 870),
+    energy = c(238, 1461, 2615)
+  )
+  set_energy_calibration(spectrum) <- lines
+  expect_s4_class(spectrum, class = "GammaSpectrum")
+  expect_true(has_calibration(spectrum))
+
+  spectra <- as(list(spectrum, spectrum), "GammaSpectra")
+  set_energy_calibration(spectra) <- lines
+  expect_s4_class(spectra, class = "GammaSpectra")
+  expect_true(all(has_calibration(spectra)))
+
+  ## check the get method
+  expect_s3_class(get_energy_calibration(spectrum), "lm")
+  expect_s3_class(get_energy_calibration(spectra)[[2]], "lm")
+
 })
 # GammaSpectra =================================================================
 test_that("GammaSpectra", {