From 6fd4dccc0ba21afc678d7ff45a634ed49dc32a59 Mon Sep 17 00:00:00 2001
From: RLumSK <sebastian.kreutzer@uni-heidelberg.de>
Date: Thu, 22 Aug 2024 12:47:37 +0200
Subject: [PATCH 1/2] Implement request from #22 for GammaSpectra-class objects
 + ad method in energy_calibrate() + up docu + ad tests + ad NEWS

---
 NEWS.md                         |  1 +
 R/energy_calibrate.R            | 22 ++++++++++++++++++++++
 man/energy.Rd                   |  3 +++
 tests/testthat/test-calibrate.R | 18 ++++++++++++++++++
 4 files changed, 44 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 1f51e238..e0e259a5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 # gamma 1.0.5
 ## Bugfixes & changes
 * Add support for Kromek SPE files to `read()`(#28 by @RLumSK)
+* Add support for `GammaSpectra-class` objects for `energy_calibrate()`(issue: #22)
 
 ## Internals
 * Fix unicode character in plot axis labels.
diff --git a/R/energy_calibrate.R b/R/energy_calibrate.R
index 6cbeceef..cfee9f74 100644
--- a/R/energy_calibrate.R
+++ b/R/energy_calibrate.R
@@ -61,6 +61,28 @@ setMethod(
   }
 )
 
+#' @export
+#' @rdname energy
+#' @aliases energy_calibrate,GammaSpectra,PeakPosition-method
+setMethod(
+  f = "energy_calibrate",
+  signature = signature(object = "GammaSpectra", lines = "PeakPosition"),
+  definition = function(object, lines, ...) {
+    # Get data
+    peaks <- as.data.frame(lines)
+    peaks$energy <- peaks$energy_expected
+
+    # Adjust spectrum for energy shift using the same set of peask for
+    # the entire set of gamma spectra
+    # Return a new gamma spectrum with adjusted energy
+    spc <- lapply(unlist(object), energy_calibrate, peaks)
+
+    ## make create GammaSpectra class
+    methods::as(spc, "GammaSpectra")
+
+  }
+)
+
 # Predicates ===================================================================
 #' @export
 #' @rdname energy
diff --git a/man/energy.Rd b/man/energy.Rd
index 99948892..833139b1 100644
--- a/man/energy.Rd
+++ b/man/energy.Rd
@@ -9,6 +9,7 @@
 \alias{has_calibration}
 \alias{energy_calibrate,GammaSpectrum,list-method}
 \alias{energy_calibrate,GammaSpectrum,PeakPosition-method}
+\alias{energy_calibrate,GammaSpectra,PeakPosition-method}
 \alias{has_energy,GammaSpectrum-method}
 \alias{has_energy,GammaSpectra-method}
 \alias{has_calibration,GammaSpectrum-method}
@@ -25,6 +26,8 @@ has_calibration(object)
 
 \S4method{energy_calibrate}{GammaSpectrum,PeakPosition}(object, lines, ...)
 
+\S4method{energy_calibrate}{GammaSpectra,PeakPosition}(object, lines, ...)
+
 \S4method{has_energy}{GammaSpectrum}(object)
 
 \S4method{has_energy}{GammaSpectra}(object)
diff --git a/tests/testthat/test-calibrate.R b/tests/testthat/test-calibrate.R
index d8c2fef5..06e5fdfd 100644
--- a/tests/testthat/test-calibrate.R
+++ b/tests/testthat/test-calibrate.R
@@ -58,6 +58,24 @@ test_that("Calibrate a GammaSpectrum object with a PeakPosition object", {
   expect_length(spectrum@energy, 0)
   expect_length(calib@energy, 1024)
 })
+test_that("Calibrate a GammaSpectra object with a PeakPosition object", {
+  spc_file <- system.file("extdata/LaBr.TKA", package = "gamma")
+  spectrum_1 <- spectrum_2 <- read(spc_file)
+  spectra <- methods::as(list(spectrum_1, spectrum_2), "GammaSpectra")
+
+  peaks <- .PeakPosition(
+    hash = spectrum_1@hash,
+    channel = c(76L, 459L, 816L),
+    energy_expected = c(NA_real_, NA_real_, NA_real_)
+  )
+
+  set_energy(peaks) <- c(238, 1461, 2614.5)
+  calib <- energy_calibrate(spectra, lines = peaks)
+
+  expect_s4_class(calib, "GammaSpectra")
+
+})
+
 test_that("the energy scale of a GammaSpectrum is set", {
   cnf_file <- system.file("extdata/LaBr.CNF", package = "gamma")
   cnf_spc <- read(cnf_file)

From 5378febc07ec533edb55e8c6ac8289b55ad37a96 Mon Sep 17 00:00:00 2001
From: RLumSK <sebastian.kreutzer@uni-heidelberg.de>
Date: Thu, 22 Aug 2024 12:50:20 +0200
Subject: [PATCH 2/2] Add PR ID

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index e0e259a5..19130c27 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,7 +3,7 @@
 # gamma 1.0.5
 ## Bugfixes & changes
 * Add support for Kromek SPE files to `read()`(#28 by @RLumSK)
-* Add support for `GammaSpectra-class` objects for `energy_calibrate()`(issue: #22)
+* Add support for `GammaSpectra-class` objects for `energy_calibrate()`(issue: #22, PR #31 by @RLumSK)
 
 ## Internals
 * Fix unicode character in plot axis labels.