R/run.process.HOCR.batch.R

In belasi01/HyperocR: Hyperspectral OCR data processing

#'
#' Run batch processing for surface in-water HyperOCR measurements
#'
#' This programe reads a log file in which *L2.dat files coming for prosoft are listed for processing.
#' Each file will be processed using the parameters provided in the log file. The files must be put in the same folders
#' (e.g., ../dat/). The output will be save as PNG and RData.
#' The user can provide IOPs to estimate the K_Lu or K_u in order to make
#' the extrapolation of the Lu0- measured near the sea surface
#' (typically around 10 to 15 cm from the sea surface).
#'
#' No shadow correction is applied yet.
#'
#'
#'@param log.file is the name of the ASCII file containing the
#' list of L2 data to processed with parameters
#' (see process.HOCR for details).
#'@param data.path is the full path where the L2 data folder is stored (./dat/*.dat).
#' Note that the path should not include the "dat" folder name. On the parent folder is needed.
#'@param Ag.path is the full path where the CDOM  absorption files (RData format) are stored
#'@param Ap.path is the full path where the particulate absorption files (RData format) are stored
#'@param Bbp.path is the full path where the particulate backscattering files (RData format) are stored
#'
#'@details
#'The HOCR radiometers can be deployed from small boats to estime hyperspectral remote sensing reflectance.
#'Diffent setup are supported but the minimum is to heve one reference sensor in the air for Ed0+ and
#'at least one sensor in-water for either Eu, Lu or Ed.  The depth at which the in-water sensor is emerged
#'is given in the processing parameters in the log file. For example, if the Lu sensor near was lowered at 10cm below the
#'surface, Lu0.Depth = 0.1. If the set up uses a Eu0 sensor, then Eu0.Depth must be provided.
#'More accurate Rrs can be obtained using two Lu sensors emerged near the surface at two different depths,
#'which allow a direct assessment of the diffuse attenuation coefficient for upwelling radiance (K_Lu).
#'
#'See \code{\link{process.HOCR}} for more details.
#'
#' @author Simon Bélanger
#' @export
#' @name run.process.HOCR.batch
run.process.HOCR.batch <- function(log.file="log.txt",
                                   data.path="./",
                                   Ag.path="./",
                                   Ap.path="./",
                                   Bbp.path="./") {
  if (file.exists(data.path)) {
    print("Data path exists")
    print(data.path)
  } else {
    print("data.path does not exist!")
    print("STOP processing")
    return(0)
  }

  # Check the output directories and Create them if they are not available.
  path.png = file.path(data.path,"png/") #paste(data.path,"/png/", sep="")
  path.out = file.path(data.path,"RData/") #paste(data.path,"/RData/", sep="")
  path.raw = file.path(data.path,"dat/")
  if (!file.exists(path.raw)) {
    print("No folder named raw found")
    print("STOP processing")
    print("Create a folder:")
    print(path.raw)
    print("and put your data files in it")
    return(0)
  } else print(paste("Raw data in :",path.raw))

  if (!file.exists(path.png)) dir.create(path.png)
  if (!file.exists(path.out)) dir.create(path.out)

  # Lecture des informations dans un fichier texte
  ext = unlist(strsplit(log.file, "[.]"))[2]
  if (ext == "csv") {
    log = read.table(file=log.file, header=T, sep=",")
  } else {
    log = read.table(file=log.file, header=T)
  }

  # Check for missing columns in the log file and added if needed
  if (is.null(log$Lu0.Depth)) log$Lu0.Depth = NA
  if (is.null(log$Eu0.Depth)) log$Eu0.Depth = NA
  if (is.null(log$Ed.Depth)) log$Ed.Depth = NA
  if (is.null(log$Ag.file)) log$Ag.file = NA
  if (is.null(log$Ap.file)) log$Ap.file = NA
  if (is.null(log$Bbp.file)) log$Bbp.file = NA

  nfiles = length(log$HOCR.filename)
  print(paste(nfiles, "files to process."))
  for (i in 1:nfiles) {
    #print(paste("Processing ", log$HOCR.filename[i]))

    raw.file <- paste(path.raw,log$HOCR.filename[i], sep="/")
    Ag.file <- paste(Ag.path,log$Ag.file[i], sep="/")
    if (!file.exists(Ag.file)) {
      print("WARNING no CDOM file found")
      Ag.file = NA
    }
    Ap.file <- paste(Ap.path,log$Ap.file[i], sep="/")
    if (!file.exists(Ap.file)) {
      print("WARNING no Ap file found")
      Ap.file = NA
    }

    Bbp.file <- paste(Bbp.path,log$bbp.file[i], sep="/")
    if (!file.exists(Bbp.file)) {
      print("WARNING no Bbp file found")
      Bbp.file = NA
    }
    if (file.exists(raw.file)) {
      print(paste("Processing ", raw.file))

      #### Check if Lu0 or Eu0 is used
      HOCR <- process.HOCR(filen=raw.file,
                           Station=log$Station[i],
                           Lu0.Depth = log$Lu0.Depth[i],
                           Eu0.Depth = log$Eu0.Depth[i],
                           EdZ.Depth = log$Ed.Depth[i],
                           Delta.LuZ.Depth = log$Delta.Depth[i],
                           Ag.file =  Ag.file,
                           Ap.file =  Ap.file,
                           Bbp.file = Bbp.file)

      # Plot data
      time <- paste(unlist(str_split(log$UTCTime[i],":"))[1],
                    unlist(str_split(log$UTCTime[i],":"))[2],sep="")
      png(file=file.path(path.png,paste(log$Station[i],"_",log$Date[i],"_",time,".png", sep="")),
          width=6, height=6, units="in", res=300)

      par(mfrow=c(2,1))
      par(mar=c(4,5,1,1))

      if (!is.na(log$Eu0.Depth[i])) {
        plot(HOCR$waves, HOCR$R,
             type="l", lwd=2,
             main=paste(HOCR$Station, HOCR$DateTime),
             ylab=expression(R),
             xlab=expression(lambda))
        lines(HOCR$waves,HOCR$uR, col=2, lwd=1)
      } else if (!is.na(log$Lu0.Depth[i])) {
        plot(HOCR$waves, HOCR$Rrs,
             type="l", lwd=2,
             main=paste(HOCR$Station, HOCR$DateTime),
             ylab=expression(R[rs](sr^-1)),
             xlab=expression(lambda))
        lines(HOCR$waves,HOCR$uRrs, col=2, lwd=1)
      }


      legend("topleft", c("uncorrected", "corrected"), lwd=c(1,2), col=c(2,1))

      if (!is.na(HOCR$K.CORRECTION)) {
        if (HOCR$K.CORRECTION == "Kd") {
          plot(HOCR$waves, HOCR$Kd,
               type="l", lwd=2,
               ylab=expression(K[d](m^-1)),
               xlab=expression(lambda))
        }
        if (HOCR$K.CORRECTION == "KLu") {
          plot(HOCR$waves, HOCR$KLu,
               type="l", lwd=2,
               ylab=expression(K[Lu](m^-1)),
               xlab=expression(lambda))
        }
        if (HOCR$K.CORRECTION == "Kd.modeled") {
          plot(HOCR$waves, HOCR$Kd.mod,
               type="l", lwd=2,
               ylab=expression(paste("Modeled",K[d](m^-1))),
               xlab=expression(lambda))
        }
      }

      dev.off()

      # Saving data in RData format
      save(HOCR, file=file.path(path.out,paste(log$Station[i],"_",log$Date[i],"_",time,".RData", sep="")))


    } else {
      print("WARNING no data file")
      print(paste("Skipping", raw.file))
    }
  }

}