add wavenumber adjustments

NAMESPACE

@@ -2,6 +2,8 @@
 
 S3method(adj_intens,OpenSpecy)
 S3method(adj_intens,default)
+S3method(adj_wave,OpenSpecy)
+S3method(adj_wave,default)
 S3method(ai_classify,OpenSpecy)
 S3method(ai_classify,default)
 S3method(as.data.frame,OpenSpecy)
@@ -76,6 +78,7 @@ export(OpenSpecy)
 export(adj_intens)
 export(adj_neg)
 export(adj_res)
+export(adj_wave)
 export(ai_classify)
 export(as_OpenSpecy)
 export(as_hyperSpec)

R/adj_wave.R

@@ -0,0 +1,44 @@
+#' @rdname adj_wave
+#' @title Adjust wavelength to wavenumbers for Raman
+#'
+#' @description
+#' Functions for converting between wave* units. 
+#'
+#' @return
+#' An \code{OpenSpecy} object with new units converted from wavelength 
+#' to wavenumbers or a vector with the same conversion. 
+#'
+#' @examples
+#' data("raman_hdpe")
+#' raman_wavelength <- raman_hdpe
+#' raman_wavelength$wavenumber <- (-1*(raman_wavelength$wavenumber/10^7-1/530))^(-1)
+#' adj_wave(raman_wavelength, laser = 530)
+#' adj_wave(raman_wavelength$wavenumber, laser = 530)
+#'
+#' @param x an \code{OpenSpecy} object with wavenumber units specified as 
+#' wavelength in nm or a wavelength vector.
+#' @param laser the wavelength in nm of the Raman laser.
+#' @param \ldots additional arguments passed to submethods.
+#' 
+#' @author
+#' Win Cowger, Zacharias Steinmetz
+#'
+#' @export
+adj_wave <- function(x, ...) {
+    UseMethod("adj_wave")
+}
+
+#' @rdname adj_wave
+#'
+#' @export
+adj_wave.default <- function(x, laser, ...) {
+    10^7*(1/laser - 1/x)
+}
+
+#' @rdname adj_wave
+#'
+#' @export
+adj_wave.OpenSpecy <- function(x, laser, ...) {
+    x$wavenumber <- adj_wave(x$wavenumber, laser)
+    return(x)
+}

tests/testthat/test-adj_wave.R

@@ -0,0 +1,17 @@
+ data("raman_hdpe")
+ raman_wavelength <- raman_hdpe
+ raman_wavelength$wavenumber <- (-1*(raman_wavelength$wavenumber/10^7-1/530))^(-1)
+
+ test_that("adj_wave() handles input errors and inputs correctly", {
+     adj_wave(1:1000) |> expect_error()
+     adj_wave(raman_wavelength, laser = 530) |> expect_silent()
+     adj_wave(raman_wavelength$wavenumber, laser = 530) |> expect_silent()
+     #identical with different structured inputs. 
+     expect_identical(adj_wave(raman_wavelength, laser = 530)$wavenumber, 
+                      adj_wave(raman_wavelength$wavenumber, laser = 530)) 
+     #expected values.
+     expect_identical(round(adj_wave(raman_wavelength, laser = 530)$wavenumber)[1:2], c(301,305))
+     #minimal shifts in wavenumbers
+     expect_true(all(abs(round(adj_wave(raman_wavelength, laser = 530)$wavenumber) - round(raman_hdpe$wavenumber))<=1))
+ })
+