R/fa_crownmetrics.R

In uavRst: Unmanned Aerial Vehicle Remote Sensing Tools

#'calculate morphometric features of polygons.
#'@description calculate morphometric features of polygons. Calculate some crown related metrics, returns the metrics as a spatialpointdataframe/spatialpolygondataframe
#'@seealso  \href{https://CRAN.R-project.org/package=Momocs}{Momocs}
#' \href{https://www.researchgate.net/profile/Paul_Rosin/publication/228382248_Computing_global_shape_measures/links/0fcfd510802e598c31000000.pdf?origin=publication_detail}{Paul Rosin}
#'
#'@param crownarea sp*  spatialpolygon object
#'@param funNames character. names of morphometrics to be calculated
#'available are ("length","elongation","eccentricityboundingbox","solidity","eccentricityeigen",
#'"calliper","rectangularity","circularityharalick","convexity")
#'
#'@return sp* object
#'@export
#'
#'@examples
#'
#'\dontrun{
#' # required packages
#' require(uavRst)
#' require(mapview)
#'
#' # get the rgb image, chm and training data
#' utils::download.file("https://github.com/gisma/gismaData/raw/master/uavRst/data/tutorial_data.zip",
#'                       paste0(tempdir(),"tutorial_data.zip"))
#' unzip(zipfile = paste0(tempdir(),"tutorial_data.zip"), exdir = tempdir())
#' crown<-raster::shapefile(paste0(tempdir(),"rgb_3-3_train2.shp"))
#' ## calculate polygon morpho metrics
#' polymetric <- poly_metrics(crown)
#'
#' # visualize it
#' mapview::mapview(polymetric)
#' ##+}



poly_metrics<- function(crownarea,
                        funNames = c("length","elongation","eccentricityboundingbox","solidity","eccentricityeigen","calliper","rectangularity","circularityharalick","convexity"))
  {
  if (!exists("path_run")) path_run = tempdir()
  message("calculate crown-metrics for ",nrow(crownarea)," polygons... \n")
  polys <- crownarea@polygons

  for(subfun in funNames) {
    message("calculate ",subfun,"\n")
    crownarea@data$subfun <- unlist(lapply(seq(1:length(polys)),function(i){
      f <- eval(parse(text=paste("Momocs::coo_",subfun,sep = "")))(as.matrix(polys[[i]]@Polygons[[1]]@coords))
      assign("comp", f)
      return(unlist(comp))
    }))
    colnames(crownarea@data)[ncol(crownarea@data)]<-subfun
  }
  crownarea@proj4string <- sp::CRS("+proj=utm +zone=32 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs")
  crownarea[is.na(crownarea$chmQ10)]<- 0
  crownarea@data$Area <- rgeos::gArea(crownarea,byid = TRUE)
  return(crownarea)
}