Merge pull request #52 from RLumSK/add_methods_energy_calibrate

Add more methodsw for the energy calibration

NEWS.md

@@ -11,7 +11,7 @@ uncertainty calculation. (PR #42 by @RLumSK)
 * Add support for `GammaSpectra-class` objects for `energy_calibrate()`(issue: #22, PR #31 by @RLumSK).
 * Add coercion method for `PeakPosition-class` to `list` (exported as `as.list()`) and from `list` to `PeakPosition-class`. This enables better plotting functionality if the peak positions for where provided manually as `list` and not via, e.g., `peak_find()` (PR #37 by @RLumSK).
 * Add additional columns to the output object of `dose_predict()` and calculate a "final" dose based on the mean of the findings from the count and the energy threshold (PR #43 by @RLumSK) 
-* Add new methods for signatures `lm` and `GammaSpectrum-class` to`energy_calibrate()` for `GammaSpectrum-class` and `GammaSpectra-class()` objects for the argument `lines`. In simple words, instead of providing data for an energy/channel calibration such calibration can be copied over from another already calibrated spectrum (PR #49 by @RLumSK).  
+* Add new methods for signatures `lm`, `CalibrationCurve-class`, and `GammaSpectrum-class` to`energy_calibrate()` for `GammaSpectrum-class` and `GammaSpectra-class()` objects for the argument `lines`. In simple words, instead of providing data for an energy/channel calibration such calibration can be copied over from another already calibrated spectrum (PR #49, #52 by @RLumSK).  
 * Add support for the energy calibration model to `dose_fit()` and `dose_predict()`. What does it mean? (1) If an energy calibration was performed on the spectra used for the dose rate model fitting, the model information is forwarded to the info slot of the model. (2) The function `dose_fit()` can read this information and double-check whether the user tries to predict the dose with calibrated or uncalibrated data. If the calibration has data but the spectrum does not, the function tries to use the available calibration. Given that the energy calibration often does not change considerably, this should dramatically simplify the 
 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)

R/energy_calibrate.R

@@ -39,6 +39,30 @@ setMethod(
 
 })
 
+#' @export
+#' @rdname energy
+#' @aliases energy_calibrate,GammaSpectrum,CalibrationCurve-method
+setMethod(
+  f = "energy_calibrate",
+  signature = signature(object = "GammaSpectrum", lines = "CalibrationCurve"),
+  definition = function(object, lines, ...) {
+    if (is.null(lines@details$energy_calibration) || any(is.na(lines@details$energy_calibration)))
+      stop("The CalibrationCurve-class object provided via 'lines' does not have any energy calibration!",
+           call. = FALSE)
+
+    ## check for multiple calibrations
+    if (length(lines@details$energy_calibration) > 1)
+      stop("Found more than one energy calibration in the CalibrationCurve-class object! Could not decide which one to take!",
+           call. = FALSE)
+
+    ## get calibration
+    lines <- lines@details$energy_calibration[[1]]
+
+    ## call the regular function
+    energy_calibrate(object, lines)
+
+})
+
 #' @export
 #' @rdname energy
 #' @aliases energy_calibrate,GammaSpectrum,list-method
@@ -169,6 +193,21 @@ setMethod(
   }
 )
 
+#' @export
+#' @rdname energy
+#' @aliases energy_calibrate,GammaSpectra,CalibrationCurve-method
+setMethod(
+  f = "energy_calibrate",
+  signature = signature(object = "GammaSpectra", lines = "CalibrationCurve"),
+  definition = function(object, lines, ...) {
+    spc <- lapply(unlist(object), energy_calibrate, lines)
+
+    ## make create GammaSpectra class
+    methods::as(spc, "GammaSpectra")
+
+  }
+)
+
 # Predicates ===================================================================
 #' @export
 #' @rdname energy

tests/testthat/test-calibrate.R

@@ -152,3 +152,55 @@ test_that("Calibrate a GammaSpectrum and GammaSpectra object with a lm object",
                regexp = "The spectrum provided via 'lines' does not have any calibration!")
 
 })
+
+test_that("Calibrate a GammaSpectrum/GammaSpectra object with a CalibrationCurve object", {
+  ##load calibration dataset
+  data("BDX_LaBr_1")
+
+  ## load spectrum
+  cnf_file <- system.file("extdata/LaBr.CNF", package = "gamma")
+  cnf_spc <- read(cnf_file)
+  cnf_spectra <- as(list(cnf_spc, cnf_spc), "GammaSpectra")
+
+  ## make an energy calibration
+  lines <- list(
+    channel = c(76, 459, 816),
+    energy = c(238, 1461, 2614.5)
+  )
+  calib <- energy_calibrate(cnf_spc, lines = lines)
+
+  ## manually add energy calibration
+  BDX_LaBr_1@details[["energy_calibration"]] <- list(calib@calibration)
+
+  ## assign energy calibration
+  t <- expect_s4_class(energy_calibrate(cnf_spectra, BDX_LaBr_1), "GammaSpectra")
+  expect_true(all(has_calibration(t)))
+  t <- expect_s4_class(energy_calibrate(cnf_spc, BDX_LaBr_1), "GammaSpectrum")
+  expect_true(has_calibration(t))
+
+  ## make sure we get an error for no calibration
+  BDX_LaBr_1@details[["energy_calibration"]] <- NULL
+  expect_error(
+    object = energy_calibrate(cnf_spc, BDX_LaBr_1),
+    regexp = "The CalibrationCurve-class object provided via 'lines' does not have any energy calibration!")
+
+  BDX_LaBr_1@details[["energy_calibration"]] <- NULL
+  expect_error(
+    object = energy_calibrate(cnf_spectra, BDX_LaBr_1),
+    regexp = "The CalibrationCurve-class object provided via 'lines' does not have any energy calibration!")
+
+  ## for NA
+  BDX_LaBr_1@details[["energy_calibration"]] <- NA
+  expect_error(
+    object = energy_calibrate(cnf_spc, BDX_LaBr_1),
+    regexp = "The CalibrationCurve-class object provided via 'lines' does not have any energy calibration!")
+
+  ## for NA
+  BDX_LaBr_1@details[["energy_calibration"]] <- list(t@calibration, t@calibration)
+  expect_error(
+    object = energy_calibrate(cnf_spc, BDX_LaBr_1),
+    regexp = "Found more than one energy calibration in the CalibrationCurve-class object! Could not decide which one to take!")
+
+
+})
+