From c81fa8357461b38b8e3b59d977b686797a01c026 Mon Sep 17 00:00:00 2001
From: "Win Cowger, PhD" <wincowger@gmail.com>
Date: Thu, 4 Jan 2024 14:08:54 -0800
Subject: [PATCH] add csv writing.

---
 R/io_spec.R  | 17 +++++++++++++++--
 R/read_ext.R | 20 ++++++++++++++++----
 2 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/R/io_spec.R b/R/io_spec.R
index 278740bb..52b9e0ea 100644
--- a/R/io_spec.R
+++ b/R/io_spec.R
@@ -41,6 +41,7 @@
 #' write_spec(raman_hdpe, "raman_hdpe.yml")
 #' write_spec(raman_hdpe, "raman_hdpe.json")
 #' write_spec(raman_hdpe, "raman_hdpe.rds")
+#' write_spec(raman_hdpe, "raman_hdpe.csv")
 #'
 #' # Convert an OpenSpecy object to a hyperSpec object
 #' hyper <- as_hyperSpec(raman_hdpe)
@@ -61,7 +62,7 @@
 #'
 #' @importFrom yaml write_yaml read_yaml
 #' @importFrom jsonlite write_json read_json
-#' @importFrom data.table as.data.table
+#' @importFrom data.table as.data.table fwrite
 #'
 #' @export
 write_spec <- function(x, ...) {
@@ -88,7 +89,19 @@ write_spec.OpenSpecy <- function(x, file, method = NULL,
       write_json(x, path = file, dataframe = "columns", digits = digits, ...)
     } else if (grepl("\\.rds$", file, ignore.case = T)) {
       saveRDS(x, file = file, ...)
-    } else {
+    }
+      else if (grepl("\\.csv$", file, ignore.case = T)){
+          wave_names <- round(x$wavenumber, 0)
+          
+          spectra <- t(x$spectra)
+          
+          colnames(spectra) <- wave_names
+          
+          flat_specy <- cbind(spectra, x$metadata)
+          
+          fwrite(flat_specy, file = file)
+    }
+      else {
       stop("unknown file type: specify a method to write custom formats or ",
            "provide one of the supported .yml, .json, or .rds formats as ",
            "file extension", call. = F)
diff --git a/R/read_ext.R b/R/read_ext.R
index 4602cf39..3c6b6d35 100644
--- a/R/read_ext.R
+++ b/R/read_ext.R
@@ -53,7 +53,7 @@
 #' \code{\link{read_zip}()} and \code{\link{read_any}()} for wrapper functions;
 #' \code{\link[hyperSpec]{read.jdx}()}; \code{\link[hyperSpec]{read.spc}()}
 #'
-#' @importFrom data.table data.table as.data.table fread
+#' @importFrom data.table data.table as.data.table fread transpose
 #' @export
 read_text <- function(file, colnames = NULL, method = "fread",
                       share = NULL,
@@ -91,9 +91,21 @@ read_text <- function(file, colnames = NULL, method = "fread",
                                               "use 'header = FALSE' or an ",
                                               "alternative read method",
                                               call. = F)
-
-  os <- as_OpenSpecy(dt, colnames = colnames, metadata = metadata,
-                     session_id = T)
+  if(sum(grepl("^[0-9]{1,}$",colnames(dt))) > 4){
+      wavenumbers <- colnames(dt)[grepl("^[0-9]{1,}$",colnames(dt))]
+      
+      spectra <- transpose(dt[,..wavenumbers])
+      
+      metadata_names <- colnames(dt)[!grepl("^[0-9]{1,}$",colnames(dt))]
+      
+      metadata <- dt[,..metadata_names]
+      
+      os <- as_OpenSpecy(as.numeric(wavenumbers), spectra = spectra, metadata = metadata)
+  }
+  else{
+      os <- as_OpenSpecy(dt, colnames = colnames, metadata = metadata,
+                         session_id = T)      
+  }
 
   if (!is.null(share)) share_spec(os, file = file, share = share)