R/fa_crownfilter.R

In uavRst: Unmanned Aerial Vehicle Remote Sensing Tools

if (!isGeneric('crown_filter')) {
  setGeneric('crown_filter', function(x, ...)
    standardGeneric('crown_filter'))
}

#'@name crown_filter
#'@title basic filtering of crown polygons using altitude, area and other optional thresholds
#'
#'@description
#' applies basic filtering of crown polygons using altitude, area and other optional thresholds. crown_filter basically returns SPDF with the crown polygons and all calculated parameters.
#'

#'@author Chris Reudenbach
#'
#'
#'@param crownFn filname of OGR compliant vector file
#'@param minTreeAlt minimum height in meter that will be regarded as tree
#'@param minCrownArea minimum area of crowns that is accepted
#'@param maxCrownArea maximum area of crowns that is accepted
#'@param minTreeAltParam parameter that is used for filtering MinTreeAlt, default is Median "chmQ50"
#'@param crownSTDW parameter that optionally filters for the STDV of the crown altitudes, default is NULL
#'@param TAopt optional parameter that might be used for filtering, default is NULL
#'@param opt threshold value for optional filter, default is NULL
#'@param proj4string proj4 string

#'
#'
#'@export crown_filter
#'
#'@examples
#'\dontrun{
#'
#'  require(uavRst)
#'  require(link2GI)
#'
#' # project folder
#'  projRootDir<-tempdir()
#'
#' # create subfolders please mind that the pathes are exported as global variables
#'  paths<-link2GI::initProj(projRootDir = projRootDir,
#'                          projFolders = c("data/","data/ref/","output/","run/","las/"),
#'                          global = TRUE,
#'                          path_prefix = "path_")
#' # overide trailing backslash issue
#'
#' # get the data
#' utils::download.file("https://github.com/gisma/gismaData/raw/master/uavRst/data/crowns.zip",
#'                        file.path(tempdir(),"crowns.zip"))
#' unzip(zipfile = file.path(tempdir(),"crowns.zip"), exdir =".")
#' 
#'  raster::plot(raster::shapefile(file.path(tempdir(),"polyStat.shp")))
#'
#' # start postclassification of segements
#' tree_crowns <- crown_filter(crownFn =  file.path(tempdir(),"polyStat.shp"),
#'                              minTreeAlt = 3,
#'                              minCrownArea = 20,
#'                              maxCrownArea = 50,
#'                              minTreeAltParam = "chmQ20" )
#' # visualize it
#' raster::plot(tree_crowns[[2]])
#'##+}
#'


crown_filter<- function(crownFn,
                        minTreeAlt = 10,
                        minCrownArea = 5,
                        maxCrownArea =100,
                        minTreeAltParam = "chm_Q50",
                        crownSTDW = NULL,
                        opt = NULL,
                        TAopt = NULL,
                        proj4string="+proj=utm +zone=32 +ellps=GRS80 +units=m +no_defs") {
  
  if (!exists("path_run")) path_run = tempdir()
  # read crown vector data set
  if (class(crownFn)=="character")
    crownarea <- rgdal::readOGR(file.path(R.utils::getAbsolutePath(path_run)),
                                tools::file_path_sans_ext(basename(crownFn)), 
                                verbose = FALSE,
                                use_iconv = TRUE)
  else
    crownarea <- crownFn
  range <- grep(pattern = "RANGE", names(crownarea), value = TRUE)
  crownarea@proj4string <- sp::CRS(proj4string)
  # calculate area
  #if (sum(is.na(crownarea$chmQ)) > 0) crownarea[is.na(crownarea$chmQ)]<- 0
  crownarea@data$area <- rgeos::gArea(crownarea,byid = TRUE)
  # filter for min, tree height and min max crown area
  crownarea <- crownarea[eval(parse(text=paste("crownarea@data$",minTreeAltParam,sep = ""))) >= minTreeAlt ,]
  crownarea <- crownarea[crownarea@data$area > minCrownArea,]
  crownarea <- crownarea[crownarea@data$area < maxCrownArea,]
  crownarea <- crownarea[crownarea$VALUE >= 0,]
  # if (!is.null(crownSTDW)) crownarea <- crownarea[crownarea@data$chmSTDDEV > crownSTDW,]
  #  filter for arbitray threshold
  if (!is.null(TAopt)) crownarea <- crownarea[eval(parse(text=paste0("crownarea@data$",TAopt)))  > opt ,]
  crowns <- crownarea
  # calculate centroids as synthetic tree stems of the crowns
  sT <- rgeos::gCentroid(crowns,byid = TRUE)
  crowns@data$xcoord <- sT@coords[,1]
  crowns@data$ycoord <- sT@coords[,2]
  crowns@data$height <- crownarea[eval(parse(text=paste("crownarea@data$",range,sep = ""))),]
  centerTrees <- crowns@data
  sp::coordinates(centerTrees) <- ~xcoord+ycoord
  sp::proj4string(centerTrees) <- sp::CRS(proj4string)


  # save centerTrees and crowns as shapefile
  # export geojson
  #sf::st_write(sf::st_as_sf(centerTrees), "cTr.geojson",delete_dsn=TRUE,driver="GeoJSON")
  # export geojson
  #sf::st_write(sf::st_as_sf(crowns), "cro.geojson",delete_dsn=TRUE,driver="GeoJSON")

  return(list(centerTrees,crowns))
}