Improve conform_spec()

- renamed `new_wavenumbers` argument to `range`
- updated docs
- added tests

R/adj_range.R

@@ -37,8 +37,10 @@
 #' Win Cowger, Zacharias Steinmetz
 #'
 #' @seealso
-#' \code{\link[base]{min}()} and \code{\link[base]{round}()};
-#' \code{\link{adj_intens}()} for log transformation functions
+#' \code{\link{conform_spec}()} for conforming wavenumbers to be matched with
+#' a reference library;
+#' \code{\link{adj_intens}()} for log transformation functions;
+#' \code{\link[base]{min}()} and \code{\link[base]{round}()}
 #'
 #' @importFrom data.table as.data.table .SD
 #' @export

R/conform_spec.R

@@ -1,17 +1,19 @@
 #' @rdname conform_spec
-#'
 #' @title Conform spectra to a standard wavenumber series
 #'
 #' @description
-#' Spectra can be conformed to a standard suite of wavenumbers to be compared with a reference library or to be merged to other spectra.
+#' Spectra can be conformed to a standard suite of wavenumbers to be compared
+#' with a reference library or to be merged to other spectra.
 #'
 #' @param x a list object of class \code{OpenSpecy}.
-#' @param new_wavenumbers a vector of new wavenumber values, can be just supplied as a min and max value.
+#' @param range a vector of new wavenumber values, can be just supplied as a
+#' min and max value.
 #' @param res spectral resolution adjusted to.
+#' @param \ldots further arguments passed to \code{\link[stats]{approx}()}
 #'
 #' @return
 #' \code{adj_intens()} returns a data frame containing two columns
-#' named \code{"wavenumber"} and \code{"intensity"}.
+#' named \code{"wavenumber"} and \code{"intensity"}
 #'
 #' @examples
 #' data("raman_hdpe")
@@ -21,34 +23,37 @@
 #' Win Cowger, Zacharias Steinmetz
 #'
 #' @seealso
-#' \code{\link{subtr_bg}()} for spectral background correction.
+#' \code{\link{restrict_range}()} and  \code{\link{flatten_range}()} for
+#' adjusting wavenumber ranges;
+#' \code{\link{subtr_bg}()} for spectral background correction
 #'
 #' @importFrom data.table .SD
 #' @export
-conform_spec <- function(x, new_wavenumbers, res = 5) {
+conform_spec <- function(x, ...) {
   UseMethod("conform_spec")
 }
 
 #' @rdname conform_spec
 #'
 #' @export
-conform_spec.default <- function(x, new_wavenumbers, res = 5) {
+conform_spec.default <- function(x, ...) {
   stop("object 'x' needs to be of class 'OpenSpecy'", call. = F)
 }
 
 #' @rdname conform_spec
 #'
 #' @export
-conform_spec.OpenSpecy <- function(x, new_wavenumbers, res = 5) {
-  if(is.null(new_wavenumbers)){
-      new_wavenumbers <- x$wavenumber
-  }
+conform_spec.OpenSpecy <- function(x, range = NULL, res = 5, ...) {
+  if(is.null(range)) range <- x$wavenumber
+  range <- c(max(min(range), min(x$wavenumber)),
+             min(max(range), max(x$wavenumber))
+  )
 
-  wn <- conform_res(x = new_wavenumbers[new_wavenumbers <= max(x$wavenumber) & new_wavenumbers >= min(x$wavenumber)], res = res)
+  wn <- conform_res(range, res = res)
 
   spec <- x$spectra[, lapply(.SD, .conform_intens,
                              x = x$wavenumber,
-                             xout = wn)]
+                             xout = wn, ...)]
 
   x$wavenumber <- wn
   x$spectra <- spec

R/data_norm.R

@@ -49,7 +49,9 @@
 #'
 #' @seealso
 #' \code{\link[base]{min}()} and \code{\link[base]{round}()};
-#' \code{\link{adj_intens}()} for log transformation functions
+#' \code{\link{adj_intens}()} for log transformation functions;
+#' \code{\link{conform_spec}()} for conforming wavenumbers of an
+#' \code{OpenSpecy} object to be matched with a reference library
 #'
 #' @export
 adj_res <- function(x, res = 1, fun = round) {

R/interactive_plots.R

@@ -23,7 +23,7 @@
 #' plotly_spec(raman_hdpe)
 #'
 #' correlation <- cor_spec(
-#'   conform_spec(raman_hdpe, new_wavenumbers = raman_hdpe$wavenumber, res = 5),
+#'   conform_spec(raman_hdpe, range = raman_hdpe$wavenumber, res = 5),
 #'   conform_spec(tiny_map, tiny_map$wavenumbers, res = 5)
 #' )
 #' heatmap_spec(tiny_map, z = tiny_map$metadata$y)

R/manage_spec.R

@@ -53,7 +53,7 @@ c_spec <- function(objects, wavenumber_transform = NULL, res = 5){
     }
         objects <- lapply(objects, function(x) {
             conform_spec(x,
-                         new_wavenumbers = new_wavenumbers, 
+                         range = new_wavenumbers, 
                          res = res)})
     }
 

R/match_spec.R

@@ -27,7 +27,7 @@
 #' @examples
 #' data("test_lib")
 #' unknown <- read_any(read_extdata("ftir_ldpe_soil.asp")) |>
-#'   conform_spec(new_wavenumbers = test_lib$wavenumber,
+#'   conform_spec(range = test_lib$wavenumber,
 #'                res = spec_res(test_lib)) |>
 #'   process_spec()
 #' matches <- cor_spec(unknown, test_lib)

R/process_spec.R

@@ -121,7 +121,7 @@ process_spec.OpenSpecy <- function(x,
     if(adj_intensity_decision)
       x <- adj_intens(x, type = type, make_rel = F)
     if(conform_decision)
-      x <- conform_spec(x, new_wavenumbers = new_wavenumbers, res = res)
+      x <- conform_spec(x, range = new_wavenumbers, res = res)
     if(range_decision)
       x <- restrict_range(x, min_range = min_range, max_range = max_range,
                           make_rel = F)

tests/testthat/test-conform_spec.R

@@ -1,36 +1,42 @@
-spectrum <- read_extdata("raman_hdpe.csv") |> read_any()
-
-test_that("check that conforming spectra doesn't produce errors", {
-    expect_true(is_OpenSpecy(conform_spec(spectrum, c(min(spectrum$wavenumber + 10), max(spectrum$wavenumber)))))
-    expect_equal(conform_spec(spectrum, c(1000, 2000))$wavenumber, seq(1000, 2000, by = 5))
-    expect_error(is_OpenSpecy(conform_spec(spectrum, c(min(spectrum$wavenumber + 10)))))
-    expect_error(is_OpenSpecy(conform_spec(spectrum)))
-    expect_error(is_OpenSpecy(conform_spec(spectrum, c(min(spectrum$wavenumber + 10), max(spectrum$wavenumber)), res = 0)))
-})
+library(data.table)
+
+data("raman_hdpe")
 
-test_that("conform_spec.default throws an error for non-OpenSpecy objects", {
+test_that("conform_spec() throws an error for non-OpenSpecy objects", {
   # Create a non-OpenSpecy object
-  non_open_specy_object <- data.frame(wavenumber = c(1000, 1100, 1200),
-                                      intensity = c(0.1, 0.2, 0.3))
+  non_OpenSpecy <- data.frame(wavenumber = c(1000, 1100, 1200),
+                              intensity = c(0.1, 0.2, 0.3))
+
+  conform_spec(non_OpenSpecy, c(1000, 2000)) |>
+    expect_error()
+})
 
-  # Test if the function throws an error for non-OpenSpecy object
-  expect_error(conform_spec(non_open_specy_object, c(1000, 2000)))
+test_that("conform_spec() handles errors correctly", {
+  conform_spec(raman_hdpe, range = c(min(raman_hdpe$wavenumber + 10),
+                                     max(raman_hdpe$wavenumber))) |>
+    expect_silent()
+  conform_spec(raman_hdpe, range = c(0,5000)) |>
+    expect_silent()
+  expect_equal(conform_spec(raman_hdpe, c(1000, 2000))$wavenumber,
+               seq(1000, 2000, by = 5))
+  conform_spec(raman_hdpe, c(min(raman_hdpe$wavenumber + 10))) |>
+    expect_error()
+  conform_spec(raman_hdpe, c(min(raman_hdpe$wavenumber + 10),
+                             max(raman_hdpe$wavenumber)), res = 0) |>
+    expect_error()
 })
 
-test_that("conform_spec.OpenSpecy conforms wavenumbers correctly", {
-  # Create a sample OpenSpecy object
-  wavenumber <- seq(1000, 2000, 5)
-  intensity <- rnorm(length(wavenumber))
-  open_specy_object <- as_OpenSpecy(wavenumber, data.table(intensity = intensity))
+test_that("conform_spec() conforms wavenumbers correctly", {
+  sam <- as_OpenSpecy(wn <- seq(1000, 2000, 5),
+                      data.table(intensity = rnorm(length(wn))))
 
-  # Conform the wavenumbers to a new range
   new_wavenumbers <- c(1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900)
-  conform_result <- conform_spec(open_specy_object, new_wavenumbers)
+  conf_spec <- conform_spec(sam, new_wavenumbers)
 
-  # Test if the wavenumber and intensity vectors have the same length after conforming
-  expect_equal(length(conform_result$wavenumber), length(conform_result$spectra[[1]]))
+  expect_equal(length(conf_spec$wavenumber), length(conf_spec$spectra[[1]]))
+  expect_equal(range(conf_spec$wavenumber), range(new_wavenumbers))
 
-  # Test if the wavenumber range matches the new_wavenumbers vector
-  expect_equal(min(conform_result$wavenumber), min(new_wavenumbers))
-  expect_equal(max(conform_result$wavenumber), max(new_wavenumbers))
+  conform_spec(raman_hdpe)$spectra$intensity[c(63, 143, 283, 325, 402)] |>
+    round(2) |>
+    expect_equal(c(78.84, 65.00, 105.73, 109.41, 116.00))
 })

tests/testthat/test-match_spec.R

@@ -1,7 +1,7 @@
 # Create test data for cor_spec function
 data("test_lib")
 unknown <- read_any(read_extdata("ftir_ldpe_soil.asp")) |>
-    conform_spec(new_wavenumbers = test_lib$wavenumber, res = spec_res(test_lib)) |>
+    conform_spec(range= test_lib$wavenumber, res = spec_res(test_lib)) |>
     process_spec()
 
 # Create a subset of test_lib for filtering

tests/testthat/test-workflows.R

@@ -16,7 +16,7 @@ test_that("Raman batch analysis with test library", {
   expect_silent(lib <- load_lib(type = "test", path = tmp))
 
   expect_silent(filter_spec(lib, lib$metadata$SpectrumType == "Raman"))
-  expect_silent(batch2 <- conform_spec(batch, new_wavenumbers = lib$wavenumber,
+  expect_silent(batch2 <- conform_spec(batch, lib$wavenumber,
                                        res = spec_res(lib$wavenumber)))
 
   expect_silent(plotly_spec(batch2))
@@ -48,7 +48,7 @@ test_that("Raman batch analysis with complete library", {
   expect_silent(lib <- load_lib(type = "nobaseline", path = tmp))
 
   expect_silent(filter_spec(lib, lib$metadata$SpectrumType == "Raman"))
-  expect_silent(batch2 <- conform_spec(batch, new_wavenumbers = lib$wavenumber,
+  expect_silent(batch2 <- conform_spec(batch, range = lib$wavenumber,
                                        res = spec_res(lib$wavenumber)))
 
   expect_silent(plotly_spec(batch2))