cercoBanana:

#' Function to import ASD spectra
#'
#' @param d character
#'
#' @return matrix
#' @author Martin Ecarnot
#' @export
#'
source('/home/ecarnot/Documents/INRA/R/cercoBanana/R/asd_read.R')


SIGNE_load <- function (d) {
library(asdreader)
#d=choose.dir()
l=Sys.glob(file.path(d, "*.asd"))
l=sort(l)

sp=matrix(nrow=length(l),ncol=2151)

for (i in 1:length(l)) {
  # print(i)
  # sp1=get_spectra(l[i], type = "reflectance") # Fonction pour lire les fichiers .asd
  sp1=asd_read(l[i])
  sp1=sp1$spectrum/sp1$reference
  sp[i,]=sp1
}


l1=basename(l)
l1=gsub(".asd","",l1)
# l1=gsub("000","-",l1)
# Look for wavelength
md=get_metadata(l[i])
wl=seq(from=md$ch1_wavel, to=md$ch1_wavel+md$channels-1)

colnames(sp)=wl
row.names(sp)=l1

# Create class file
# clas=substr(l1,1,3)
#
# uclas=unique(clas)
# for (i in 1:length(uclas)) {
#   iok=which(clas==uclas[i])
#   clas[iok]=i
# }
#
# clas=data.frame(clas)
# row.names(clas)=l1
# colnames(clas)="clone"
# sp=sp[,50:2121] # Remove noisy part of the spectra

return(sp)
# setwd(d)
# write.table(sp,file=paste(basename(d),"_sp.csv",sep=""),sep=';', quote=FALSE,col.names = NA)
# write.table(clas,file=paste(basename(d),"_clon.csv",sep=""),sep=';', quote=FALSE,col.names = NA)

}