Script_R_2018/SIGNE_load.R

In martinEcarnot/signe: Useful functions to handle spectra

#' Function to import ASD spectra
#'
#' @param d character
#'
#' @return matrix
#' @author Martin Ecarnot
#' @export
#'
#'

user="ME"
if (user=="NL") {source('C:/Users/Noémie/Desktop/SFE/Script_R/asd_read.R')} else {source('/home/ecarnot/Documents/INRA/R/asd_read.R')}


SIGNE_load <- function (d) {
  library(asdreader)
  #d=choose.dir()
  #d="C:\\Users\\No?mie\\Desktop\\SFE\\Pour_Nathan\\Documents_finaux\\test_spectres\\"
  l=Sys.glob(file.path(d, "*.asd"))
  l=sort(l)

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

  for (i in 1:length(l)) {
    #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)

}