create conversion to and from hyperspec

NAMESPACE

@@ -5,6 +5,7 @@ S3method(adj_intens,default)
 S3method(as_OpenSpecy,OpenSpecy)
 S3method(as_OpenSpecy,data.frame)
 S3method(as_OpenSpecy,default)
+S3method(as_OpenSpecy,hyperSpec)
 S3method(as_OpenSpecy,list)
 S3method(flatten_range,default)
 S3method(head,OpenSpecy)
@@ -27,7 +28,9 @@ export(adj_intens)
 export(adj_neg)
 export(adj_res)
 export(as_OpenSpecy)
+export(characterize_particles)
 export(check_lib)
+export(collapse_particles)
 export(combine_OpenSpecy)
 export(conform_res)
 export(conform_spec)
@@ -59,7 +62,9 @@ export(share_spec)
 export(smooth_intens)
 export(spec_res)
 export(subtr_bg)
+export(to_hyperspec)
 export(write_spec)
+import(hyperSpec)
 importFrom(data.table,.SD)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
@@ -77,6 +82,8 @@ importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(hyperSpec,read.jdx)
 importFrom(hyperSpec,read.spc)
+importFrom(imager,as.cimg)
+importFrom(imager,label)
 importFrom(jsonlite,read_json)
 importFrom(jsonlite,write_json)
 importFrom(magrittr,"%>%")

R/as_OpenSpecy.R

@@ -150,6 +150,13 @@ as_OpenSpecy.list <- function(x, ...) {
   do.call("as_OpenSpecy", unname(x))
 }
 
+#' @rdname as_OpenSpecy
+#'
+#' @export
+as_OpenSpecy.hyperSpec <- function(x, ...) {
+    do.call("as_OpenSpecy", list(x = x@wavelength, spectra = as.data.table(t(x$spc)), ...))
+}
+
 #' @rdname as_OpenSpecy
 #'
 #' @export

R/io_spec.R

@@ -128,13 +128,14 @@ read_spec <- function(file, share = NULL, method = NULL, ...) {
 
 #' @rdname io_spec
 #' 
-#' @importFrom hyperSpec new
+#' @import hyperSpec
 #' @importFrom data.table transpose
 #' @examples
+#' library("hyperSpec")
 #' data(raman_hdpe)
 #' hyperOpenSpecy <- to_hyperspec(raman_hdpe)
 #' 
 #' @export
 to_hyperspec <- function(object) {
-    new("hyperSpec", spc = as.matrix(transpose(object$spectra)), wavelength = object$wavenumber, data, labels)
+    new("hyperSpec", spc = as.matrix(transpose(object$spectra)), wavelength = object$wavenumber)
 }

tests/testthat/test-as_OpenSpecy.R

@@ -67,3 +67,15 @@ test_that("OpenSpecy objects are read correctly", {
   expect_equal(os$metadata$y, 1)
   expect_equal(os$metadata$license, "CC BY-NC")
 })
+
+
+test_that("OpenSpecy objects are transcribed to and from hyperSpec objects", {
+    os <- as_OpenSpecy(df)
+    hyperOpenSpecy <- to_hyperspec(os)
+    expect_true(is(hyperOpenSpecy, "hyperSpec"))
+    OpenHyper <- as_OpenSpecy(hyperOpenSpecy)
+    expect_true(is_OpenSpecy(OpenHyper))
+    expect_equal(OpenHyper$wavenumber,hyperOpenSpecy@wavelength)
+    expect_equal(unlist(OpenHyper$spectra$V1),unname(t(hyperOpenSpecy$spc)[,1]))
+
+})