#' Reads the parameters and instrument files and launch processing
#'
#' It call the reading functions for cast.info.dat and cal.info.dat,
#' instruments.dat. If they are not present in the directory, it
#' creates a copy of the templates proveded with the package.
#' Finaly it calls \code{\link{correct.merge.IOP.profile}}.
#'
#' @param dirdat is the directory where the instrument files are stored.
#'
#' @seealso \code{\link{correct.merge.IOP.profile}} and
#' \code{\link{IOPs.go}}
#'
#' @author Simon B\elanger
#' @export
process.IOPs <- function(dirdat) {
# Cast info file
default.cast.info.file <- paste( Sys.getenv("R_IOPs_DATA_DIR"), "cast.info.dat", sep = "/")
cast.info.file <- paste(dirdat, "cast.info.dat", sep = "/")
if(!file.exists(cast.info.file)) {
file.copy(from = default.cast.info.file, to = cast.info.file)
cat("EDIT file", cast.info.file, "and CUSTOMIZE IT\n")
}
# List of instrument to process for the profile
default.instrument.file <- paste( Sys.getenv("R_IOPs_DATA_DIR"), "instrument.dat", sep = "/")
instrument.file <- paste(dirdat, "instrument.dat", sep = "/")
if(!file.exists(instrument.file)) {
file.copy(from = default.instrument.file, to = instrument.file)
cat("EDIT file", instrument.file, "and CUSTOMIZE IT\n")
stop()
}
cast.info <- read.cast.info(cast.info.file)
instrument <- read.instrument(instrument.file)
# Span parameters for calibration and blank correction
default.cal.info.file <- paste( Sys.getenv("R_IOPs_DATA_DIR"), "cal.info.dat", sep = "/")
cal.info.file <- paste(dirdat, "cal.info.dat", sep = "/")
if(!file.exists(cal.info.file)) {
file.copy(from = default.cal.info.file, to = cal.info.file)
cat("USING DEFAULT CALIBRATION PARAMETERS\n")
cat("File", cal.info.file, "CAN BE EDITED\n")
cal.info <- read.cal.info(cal.info.file)
}
cal.info <- read.cal.info(cal.info.file)
parameters = c(list(path=dirdat), cast.info,cal.info)
str(parameters)
str(instrument)
# Launch the processing
print("BEGIN PROCESSING")
IOP = correct.merge.IOP.profile(instrument, parameters)
return(IOP)
}
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