perfectPeak: Calculates the perfect peaks

#'@name initEnvironGIS
#'
#'@title Function that initializes RSAGA, GRASS GDAL and the R packages 
#'
#'@description Function that initializes environment pathes, SAGA, GRASS7 and GDAL support.
#'             *NOTE* you probably have to customize some settings in your custom or the demo.ini file
#'@details This concept is somehow not very R-like. You have to provide and control at least the installations pathes of the used SAGA and GRASS executables, root and working folder, epsg code AND correct corresponding proj4 string of the DEM data file (all controlled by the ini file). Finally you need to provide a GDAL conform DEM file.
#' 
#'@usage initEnvironGIS(fname.control)
#'
#'@param fname.control name of the session ini.file
#'@param fname.DEM name of used raster DEM (GDAL format)
#'
#'@author Chris Reudenbach 
#'
#'@details For Further Information look at:\link{INI}
#'
#'@return initEnvironGIS initializes the usage of the GIS packages and other utilities
#'@export initEnvironGIS
#'
#'@examples   
#'#### Example to initialize the enviroment and GIS bindings for use with R
#'#### uses the ini list from an ini file
#'       
#' ini.example=system.file("data","demo.ini", package="perfectPeak")
#' dem.example=system.file("data","deḿo.asc", package="perfectPeak")
#' initEnvironGIS(ini.example,dem.example)
#' gmeta()
#' 

initEnvironGIS <- function(fname.control,fname.DEM){
  
  # check for packages and if necessary install libs 
#  libraries<-c("downloader","sp","maptools","osmar",
#               "RSAGA","rgeos","gdata","Matrix","igraph",
#               "rgdal","gdistance","OpenStreetMap","spgrass6", "rgrass7",
#               "gdalUtils","raster","plotKML","maps","ggplot2","googleVis",
#               "webmaps","mapview","magrittr","devtools","RgoogleMaps")

    libraries<-c("plotKML","maps","ggplot2","googleVis",
                 "webmaps","mapview","magrittr","devtools",
                 "downloader","maptools","osmar",
                 "RSAGA","rgeos","gdata","Matrix","igraph", 
                 "rgdal","gdistance", "rgrass7",
                 "gdalUtils","sp","raster")
  
  # Install CRAN packages (if not already installed)
  inst <- libraries %in% installed.packages()
  if(length(libraries[!inst]) > 0){ 
    install.packages(libraries[!inst]) 
    install_github(repo = "RCura/webmaps")
  }
  # Load packages into session 
  lapply(libraries, require, character.only=TRUE)

  # get environment
  ini<-iniParse(fname.control)  
  
  # (R) assign local vars for working folder 
  root.dir <- ini$Pathes$workhome               # project folder 
  working.dir <- ini$Pathes$runtimedata         # working folder 
  
  ### assign correct projection information
  # To derive the correct proj.4 string for Austria MGI (EPSG:31254) is very NOT straightforward
  # please refer to: http://moc.environmentalinformatics-marburg.de/doku.php?id=courses:msc:advanced-gis:code-examples:ag-ce-09-01
  
  # taget EPSG code
  epsg.code<-ini$Projection$targetepsg
  
  # target projection (actually the projection of the DEM)
  target.proj4<-ini$Projection$targetproj4
  
  # basic latlon wgs84 proj4-string 
  latlon.proj4<-ini$Projection$latlonproj4
  
  # (raster) read GDAL data set
  dem<- raster(fname.DEM)
  
  # (raster) assign projection 
  projection(dem)<-target.proj4
  
  # reproject it to geographical coordinates
  dem.latlon<-projectRaster(dem, crs=latlon.proj4, method="ngb")
  
  # assign extent,col and row names
  extent<-data.frame(cbind(dem.latlon@extent@xmin,dem.latlon@extent@xmax, dem.latlon@extent@ymin, dem.latlon@extent@ymax))
  colnames(extent)<-c('xmin','xmax','ymin', 'ymax')
  rownames(extent)<-c(basename(fname.DEM))
  
  
  ### now starting the setup of the packages bindings
  
  ## (gdalUtils) check for a valid GDAL binary installation on your system
  gdal_setInstallation()
  valid.install<-!is.null(getOption("gdalUtils_gdalPath"))
  if (!valid.install){stop('no valid GDAL/OGR found')} else{print('gdalUtils status is ok')}
  
  #--- set environment variables for RSAGA and GRASS
  
  # (spgrass6/rgrass7) define GRASS 6.x 7.x variables
  grass.epsg.code<- as.numeric(epsg.code)  # grass needs the projection numeric
  grass.loc<- paste0('location',epsg.code)      # define corresponding folder name
  grass.mapset<- 'PERMANENT'                               # NOTE PERMANENT" is the default one and it has to be in upper cases
  
  
  # (R) set pathes  of SAGA/GRASS modules and binaries depending on OS
  if(Sys.info()["sysname"] == "Windows"){
    os.saga.path<-ini$SysPath$wossaga
    saga.modules<-ini$SysPath$wsagamodules
    grass.gis.base<-ini$SysPath$wgrassgisbase
  }else if (Sys.info()["sysname"] == "Linux"){
    os.saga.path<-ini$SysPath$lossaga
    saga.modules<-ini$SysPath$lsagamodules
    grass.gis.base<-ini$SysPath$lgrassgisbase
  }
  if (!file.exists(file.path(root.dir, working.dir))){
    dir.create(file.path(root.dir, 'run'),recursive = TRUE)
    dir.create(file.path(root.dir, 'run',grass.loc),recursive = TRUE)
    dir.create(file.path(root.dir, 'run',grass.loc,grass.mapset),recursive = TRUE)
    
  }  
  # (R) set R working directory
  setwd(file.path(root.dir, working.dir))

  # (RSAGA) set SAGA environment 
  myenv=rsaga.env(check.libpath=FALSE,
                  check.SAGA=FALSE,
                  workspace=file.path(root.dir, working.dir),
                  os.default.path=os.saga.path,
                  modules=saga.modules)
  
  # Create a new grass location with epsg from the data import dataset as a
  # subfolder of the working folder
  ## All users:
  initGRASS(gisBase = grass.gis.base,
            home = file.path(root.dir, working.dir),
            gisDbase=file.path(root.dir, working.dir),
            location=grass.loc,
            mapset = grass.mapset,
            override=TRUE)
  
  execGRASS("g.gisenv", parameters=list(set=paste("'LOCATION_NAME=", grass.loc,"'", sep="")))
  
  # get current extent using the input DEM 
  # BE CAREFULL this works only if the INPUT ASCII FILE CONTAINS TRULY THIS Projection

  # (1) import data in GRASS
  execGRASS('r.in.gdal',  flags=c('o',"overwrite"), input=fname.DEM,  output='rastgrass', band=1)
  # (2) join input file extent and the epsg code
  execGRASS('g.region',raster="rastgrass")
  execGRASS('g.proj', flags=c('c') ,  epsg=grass.epsg.code)
  
  # export myenv and parameterlist for common use
  result=list(ini,myenv,extent)
  names(result)=c('ini','myenv','extent')
  return (result)  
}