R/otbControls.R

In link2GI: Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

#'@title  Usually for internally usage, initializes and set up  access to the 'OTB' command line interface
#'@name setenvOTB
#'@description  Initializes and set up  access to the 'OTB' command line interface
#'  
#'@param bin_OTB  string contains the path to the 'OTB' binaries
#'@param root_OTB string contains the full string to the root folder
#'  containing the 'OTB' installation'
#'@return Adds 'OTB' pathes to the enviroment and creates the variable global string variable \code{otbCmd}, that contains the path to the 'OTB' binaries.
#'@export setenvOTB
#'  
#'@examples
#' \dontrun{
#'## example for the most common default OSGeo4W64 installation of OTB
#'setenvOTB(bin_OTB = "C:\\OSGeo4W64\\bin\\",
#'           root_OTB = "C:\\OSGeo4W64")
#'}

setenvOTB <- function(bin_OTB = NULL, root_OTB = NULL){
  
    
    # (R) set pathes  of otb modules and binaries depending on OS  
    if (Sys.info()["sysname"] == "Windows") {
      if (!exists("GiEnv")) GiEnv <- new.env(parent=globalenv()) 
      #makGlobalVar("otbPath", bin_OTB)
      add2Path(bin_OTB)
      Sys.setenv(OSGEO4W_ROOT = root_OTB)
      Sys.setenv(GEOTIFF_CSV = paste0(Sys.getenv("OSGEO4W_ROOT"),"\\share\\epsg_csv"),envir = GiEnv)
    }
    #else {
    #  makGlobalVar("otbPath", "(usr/bin/")
    #}
  
  return(bin_OTB)
}

#'@title Search recursively for valid 'OTB' installation(s) on a 'Windows' OS
#'@name searchOTBW
#'@description  Search for valid 'OTB' installations on a 'Windows' OS
#'@param DL drive letter default is "C:"
#'@param quiet boolean  switch for supressing console messages default is TRUE
#'@return A dataframe with the 'OTB' root folder(s) the version name(s) and the installation type(s).
#'@author Chris Reudenbach
#'@export searchOTBW
#'@keywords internal
#'
#'@examples
#' \dontrun{
#' # get all valid OTB installation folders and params
#' searchOTBW()
#' }

searchOTBW <- function(DL = "default",
                       quiet=TRUE) {
  if (DL=="default") DL <- "C:"
  if (Sys.info()["sysname"] == "Windows") {
    if (!exists("GiEnv")) GiEnv <- new.env(parent=globalenv()) 

      # trys to find a osgeo4w installation on the whole C: disk returns root directory and version name
      # recursive dir for otb*.bat returns all version of otb bat files
      if (!quiet) cat("\nsearching for Orfeo Toolbox installations - this may take a while\n")
      if (!quiet) cat("For providing the path manually see ?searchOTBW \n")
      
      
      options(show.error.messages = FALSE)
      options(warn=-1)
      # switch backslash to slash and expand path to full path
      DL <- gsub("/","\\\\" ,DL)  
      raw_OTB  <- try(system(paste0("cmd.exe"," /c dir /B /S ",DL,"\\","otbcli.bat"),intern=TRUE))
      if (identical(raw_OTB, character(0))) raw_OTB <- "File not found"
      if (grepl(raw_OTB,pattern = "File not found") | grepl(raw_OTB,pattern = "Datei nicht gefunden")) {

        class(raw_OTB) <- c("try-error", class(raw_OTB))
      }
      options(show.error.messages = TRUE)
      options(warn=0)
      
      if(!class(raw_OTB)[1] == "try-error")  {
      #if (!grepl(DL,raw_OTB)) stop("\n At ",DL," no OTB installation found")
      
      # trys to identify valid otb installations and their version numbers
      otbInstallations <- lapply(seq(length(raw_OTB)), function(i){
        # convert codetable according to cmd.exe using type
        batchfile_lines <- raw_OTB[i]
        installerType <- ""
        # if the the tag "OSGEO4W64" exists set installation_type
        if (length(unique(grep(paste("OSGeo4W64", collapse = "|"), raw_OTB[i], value = TRUE))) > 0) {
          root_dir <- unique(grep(paste("OSGeo4W64", collapse = "|"), raw_OTB[i], value = TRUE))
          root_dir <- substr(root_dir,1, gregexpr(pattern = "otbcli.bat", root_dir)[[1]][1] - 1)
          installDir <- substr(root_dir,1, gregexpr(pattern = "bin", root_dir)[[1]][1] - 2)
          installerType <- "osgeo4w64OTB"
        }    
        
        # if the the tag "OSGEO4W" exists set installation_type
        else if (length(unique(grep(paste("OSGeo4W", collapse = "|"), raw_OTB[i], value = TRUE))) > 0) {
          root_dir <- unique(grep(paste("OSGeo4W", collapse = "|"), raw_OTB[i], value = TRUE))
          root_dir <- substr(root_dir,1, gregexpr(pattern = "otbcli.bat", root_dir)[[1]][1] - 1)
          installDir <- substr(root_dir,1, gregexpr(pattern = "bin", root_dir)[[1]][1] - 2)
          installerType <- "osgeo4wOTB"
        }
        # if the the tag "QGIS" exists set installation_type
        else if (length(unique(grep(paste("QGIS", collapse = "|"), batchfile_lines, value = TRUE))) > 0) {
          root_dir <- unique(grep(paste("QGIS", collapse = "|"), raw_OTB[i], value = TRUE))
          root_dir <- substr(root_dir,1, gregexpr(pattern = "otbcli.bat", root_dir)[[1]][1] - 1)
          installDir <- substr(root_dir,1, gregexpr(pattern = "bin", root_dir)[[1]][1] - 2)
          installerType <- "qgisOTB"
        }
        # if the the tag "OTB-" exists set installation_type
        else if (length(unique(grep(paste("OTB", collapse = "|"), batchfile_lines, value = TRUE))) > 0) {
          root_dir <- unique(grep(paste("OTB", collapse = "|"), raw_OTB[i], value = TRUE))
          root_dir <- substr(root_dir,1, gregexpr(pattern = "otbcli.bat", root_dir)[[1]][1] - 1)
          installDir <- substr(root_dir,1, gregexpr(pattern = "bin", root_dir)[[1]][1] - 2)
          installerType <- "OTB"
        }
        # put the existing binary root directory in a data frame
        #data.frame(binDir = root_dir, baseDir = installDir, installation_type = installerType, stringsAsFactors = FALSE)
        data.frame(binDir = root_dir, baseDir = installDir, otbCmd = paste0(root_dir,"otbcli"), stringsAsFactors = FALSE)
      }) # end lapply
      # bind the df lines
      otbInstallations <- do.call("rbind", otbInstallations)
      
      } else {
        if(!quiet) cat("Did not find any valid OTB installation at mount point",DL)
        return(otbInstallations <- FALSE)}
    
  } else {
    otbInstallations <- NULL
    cat("Sorry no Windows system..." )
  
  }
  return(otbInstallations)
}

#'@title Search recursively for valid 'OTB' installation(s) on a 'Linux' OS
#'@name searchOTBX
#'@description  Search for valid 'OTB' installations on a 'Linux' OS
#'@param MP default mount point is the home directory "~" (as suggested by the OTB team) 
#'@param quiet boolean  switch for supressing messages default is TRUE
#'@return A dataframe with the 'OTB' root folder(s) the version name(s) and the installation type(s).
#'@author Chris Reudenbach
#'@export searchOTBX
#'@keywords internal
#'
#'@examples
#' \dontrun{
#' # get all valid OTB installation folders and params
#' searchOTBX()
#' }

searchOTBX <- function(MP = "default",
                       quiet=TRUE) {
  if (MP=="default") MP <- "/usr/bin"
    if (!exists("GiEnv")) GiEnv <- new.env(parent=globalenv()) 
      # trys to find a osgeo4w installation at the mounting point  disk returns root directory and version name
      # recursive dir for otb*.bat returns all version of otb bat files
      if (!quiet) cat("\nsearching for Orfeo Toolbox installations - this may take a while\n")
      if (!quiet) cat("For providing the path manually see ?searchOTBX \n")

      raw_OTB <- 
      options(show.error.messages = FALSE)
      options(warn=-1)
      raw_OTB  <- try(system2("find", paste(MP," ! -readable -prune -o -type f -executable -iname 'otbcli' -print"),stdout = TRUE))
      if (identical(raw_OTB, character(0))){ # raw_OTB <- "File not found"
      #if (grepl(raw_OTB,pattern = "File not found") | grepl(raw_OTB,pattern = "Datei nicht gefunden")) {

        class(raw_OTB) <- c("try-error", class(raw_OTB))
      }
      options(show.error.messages = TRUE)
      options(warn=0)
      
      if(!class(raw_OTB)[1] == "try-error") {
      #if (!grepl(MP,raw_OTB)) stop("\n At ",MP," no OTB installation found")
      # trys to identify valid otb installations and their version numbers
      otbInstallations <- lapply(seq(length(raw_OTB)), function(i){
        
       # TODO strip version from OTB /usr/bin/otbcli_BandMath -version
        # "This is the BandMath application, version 6.0.0"
        
      # if the the tag "OSGEO4W64" exists set installation_type
          root_dir <- substr(raw_OTB[i],1, gregexpr(pattern = "otbcli", raw_OTB[i])[[1]][1] - 1)
        # put the existing GISBASE directory, version number  and installation type in a data frame
        data.frame(binDir = root_dir,otbCmd = paste0(root_dir,"otbcli"), stringsAsFactors = FALSE)
      }) # end lapply
      # bind the df lines
      otbInstallations <- do.call("rbind", otbInstallations)
      } else {
        if(!quiet) cat("Did not find any valid OTB installation at mount point",MP)
        return(otbInstallations <- FALSE)}
  
  return(otbInstallations)
}

#'@title Search recursivly existing 'Orfeo Toolbox' installation(s) at a given drive/mountpoint 
#'@name findOTB
#'@description  Provides an  list of valid 'OTB' installation(s) 
#'on your 'Windows' system. There is a major difference between osgeo4W and 
#'stand_alone installations. The functions trys to find all valid 
#'installations by analysing the calling batch scripts.
#'@param searchLocation drive letter to be searched, for Windows systems default
#' is \code{C:}, for Linux systems default is \code{/usr}.
#'@param quiet boolean  switch for supressing console messages default is TRUE
#'@return A dataframe with the 'OTB' root folder(s),  and command line executable(s)
#'@author Chris Reudenbach
#'@export findOTB
#'
#'@examples
#' \dontrun{
#' # find recursively all existing 'Orfeo Toolbox' installations folders starting 
#' # at the default search location
#' findOTB()
#' }
findOTB <- function(searchLocation = "default",
                    quiet=TRUE) {
  
  if (Sys.info()["sysname"] == "Windows") {
    if (searchLocation=="default") searchLocation <- "C:"
    if (grepl(paste0(LETTERS, ":", collapse="|"), searchLocation))
      link = link2GI::searchOTBW(DL = searchLocation,                     
                                 quiet=TRUE)  
    else stop("You are running Windows - Please choose a suitable searchLocation argument that MUST include a Windows drive letter and colon" )
  } else {
    if (searchLocation=="default") searchLocation <- "/usr/bin/"
    if (grepl(searchLocation,pattern = ":"))  stop("You are running Linux - please choose a suitable searchLocation argument" )
    else link = link2GI::searchOTBX(MP = searchLocation,
                                    quiet=TRUE)
  } 
  return(link)
}

getrowotbVer<- function (paths){

  scmd = ifelse(Sys.info()["sysname"]=="Windows", "otbcli_LocalStatisticExtraction.bat", "otbcli_LocalStatisticExtraction")
  #sep = ifelse(Sys.info()["sysname"]=="Windows", "\\", "/")
  oldversion<-"0.0.0"
  ver <- 1
  for (i in 1:length(paths)){
    if (file.exists(paste0(paths[i],"../VERSION"))) tmp = strsplit(grep("OTB Version",readLines(paste0(paths[i],"../VERSION")),value = TRUE),"OTB Version: ")[[1]][2]
    else if (grep("OTB-",paths[i]) >0)  tmp = substr(strsplit(paths[i],"OTB-")[[1]][2],start = 1,stop = 5)
    #highestVer <- max(tmp,highestVer)
    if (oldversion < tmp) {ver=i
   oldversion<-tmp}

  }
  
  return (ver)
}


getotbVer<- function (paths){
  scmd = ifelse(Sys.info()["sysname"]=="Windows", "otbcli_LocalStatisticExtraction.bat ", "otbcli_LocalStatisticExtraction ")
  sep = ifelse(Sys.info()["sysname"]=="Windows", "\\", "/")
  
  otbVersion<-  strsplit(x = system(paste0(paste0(shQuote(paths),sep,scmd)," -version"),intern = FALSE),split = " version ")[[1]][2]
  otbVersion<-  strsplit(x = otbVersion,split = "version ")[[1]][2]
  
  return (otbVersion)
}