R/poligonize.R

In MartinezLaura/CanHeMonR.MaxEnt: Application of MaxEnt for canopy health monitoring through airbone image analysis.

#' @title Poligonize Raster
#' @description Poligonize a raster with values between 0 and 1.
#' @param rast Path to the raster to polyginze
#' @return A SpatialDataFrame object
#' @export
Poligonize <- function(rast, rastpath){
  
  gdalformat = 'ESRI Shapefile'
  quiet=TRUE
  require(rgdal)
  require(sf)
  pypath <- Sys.which('gdal_polygonize.py')
  owd <- getwd()
  readpoly <- TRUE
  on.exit(setwd(owd))
  setwd(dirname(pypath))
  
  
  
  ##############
  #Creation of the shapefile to extract the radius to work with
  ##############
  tempdir =  tempdir()
  outshape <- paste0(tempdir,'/',basename(rastpath))
  outshape <- sub('.tif', '.shp', outshape)
  f.exists <- file.exists(outshape)
  if (any(f.exists)){
    #cat('File already exists: %s',outshape)
    return( NULL)
  }else{
    rastpath <- normalizePath(rastpath)
    system2('python', args=(sprintf('"%1$s" -mask "%2$s" "%2$s" -f "%3$s" "%4$s"',
                                    pypath, rastpath, gdalformat, outshape)))
    
    if (isTRUE(readpoly)) {
      shp <- sf::st_read(outshape)
      return(shp)
    }
  }
  
  
}