R/create.HyperSAS.report.R

In belasi01/HyperocR: Hyperspectral OCR data processing

#'@title Create a PDF report for the HyperSAS data collection for a station or a transit
#'
#'@description
#'A PDF report is generated using knitr package facilities and a *.Rnw
#'template. It provides an efficent mean to visualise the data.
#'It can be called from the higher level function \code{\link{HyperSAS.go}}, or
#'run in the command line as along as SAS.raw.RData and RRS.RData have been
#'generated by \code{\link{process.HyperSAS}}.
#'
#'@param dirdat is the current directory path contaning the files to process.
#'@param TYPE is either equal to "STATION" or "TRANSIT" depending
#'whether the folder gather replicate Rrs of the same station, or the data
#'collected during the course of a ship transit. If the function is
#'called from \code{\link{HyperSAS.go}}, the TYPE will be read in the file named
#'directories.for.HyperSAS.dat. Otherwise the default is "STATION".
#'@param  DIAGNOSTIC.PLOTS is a logical parameter indicating whether or not diagnostic plots are saved in PNG format.
#'It is used only when TYPE="TRANSIT".
#'The plots shows the temporal variability in Ed and tilt,
#'as well as the spectra for each Ed, Li and Lt recorded during the data acquisition.
#'Default is FALSE.
#'
#'@details
#'There is two templates located in the package data folder:
#'"HyperSAS_Station_TEMPLATE.Rnw" and "HyperSAS_Transit_TEMPLATE.Rnw".
#'This function will extract a number of informations from the current
#'data directory and RData files. Next it uses the brew package to update the Rnw files.
#'The Rnw files are converted into PDF using knitr package.
#'
#'@seealso \code{\link{process.HyperSAS}}, \code{\link{HyperSAS.go}}
#'@author Simon Bélanger
#'@export
#'@name create.HyperSAS.report
create.HyperSAS.report <- function(dirdat,
                                   TYPE="STATION",
                                   DIAGNOSTIC.PLOTS=FALSE){

  if (TYPE == "STATION") {
    report.template  <- paste( Sys.getenv("R_HOCR_DATA_DIR"), "HyperSAS_Station_TEMPLATE.Rnw", sep = "/")

    print("Use knirt report template located at:")
    print(report.template)


    # get information for the report
    # extract Station name and date from the directory name
    res=unlist(strsplit(dirdat, "/"))
    for (i in 1:length(res)){
      xx = str_locate(res[i], "_Station")
      if (!is.na(xx[1])) {
        datestation=unlist(strsplit(res[i], "_Station"))
        # Remove "_" from station name to avoid error with Latex
        if (str_detect(datestation[2], "_")) {
          yy = unlist(strsplit(datestation[2], "_"))

          Station = paste(yy, collapse=" ")
        }   else Station =   datestation[2]
        Date = datestation[1]
      }
    }
  }

  if (TYPE == "TRANSIT") {
    report.template  <- paste( Sys.getenv("R_HOCR_DATA_DIR"), "HyperSAS_Transit_TEMPLATE.Rnw", sep = "/")

    print("Use knirt report template located at:")
    print(report.template)


    # get information for the report
    # extract Station name and date from the directory name
    res=unlist(strsplit(dirdat, "/"))
    for (i in 1:length(res)){
      xx = str_locate(res[i], "_Transit")
      if (!is.na(xx[1])) {
        datestation=unlist(strsplit(res[i], "_Transit"))
        # Remove "_" from station name to avoid error with Latex
        if (str_detect(datestation[2], "_")) {
          yy = unlist(strsplit(datestation[2], "_"))

          Transit = paste(yy, collapse=" ")
        }   else Transit =   datestation[2]
        Date = datestation[1]
      }
    }

  }


  reportname <- "RRS.plot.Rnw"
  brew(report.template,reportname)

  knit2pdf(reportname, quiet = T)

  file.remove("RRS.plot.log")
  file.remove("RRS.plot.aux")
  file.remove("RRS.plot.tex")
}