R/clipLevel2BPAVDProfile.R

In rGEDI: NASA's Global Ecosystem Dynamics Investigation (GEDI) Data Visualization and Processing

#'Clip GEDI Plant Area Volume Density profile by Coordinates
#'
#'@description This function clips GEDI level2B derived
#'Plant Area Volume Density profile within a given bounding coordinates
#'
#'@usage clipLevel2BPAVDProfile(level2BPAVDProfile, xmin, xmax, ymin, ymax)
#'
#'@param level2BPAVDProfile A GEDI Level2B object (output of \code{\link[rGEDI:getLevel2BPAVDProfile]{getLevel2BPAVDProfile}} function).
#'An S4 object of class "data.table".
#'@param xmin Numeric. West longitude (x) coordinate of the bounding rectangle, in decimal degrees.
#'@param xmax Numeric. East longitude (x) coordinate of the bounding rectangle, in decimal degrees.
#'@param ymin Numeric. South latitude (y) coordinate of the bounding rectangle, in decimal degrees.
#'@param ymax Numeric. North latitude (y) coordinate of the bounding rectangle, in decimal degrees.
#'
#'@return Returns an S4 object of class \code{\link[data.table:data.table]{data.table-class}}
#'containing the Plant Area Volume Density profile data.
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi02_bv001/
#'
#'@examples
#'# specify the path to GEDI level2B data (zip file)
#'outdir = tempdir()
#'level2B_fp_zip <- system.file("extdata",
#'                   "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip",
#'                   package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Bpath <- unzip(level2B_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2B data (h5 file)
#'level2b<-readLevel2B(level2Bpath=level2Bpath)
#'
#'# Extracting GEDI Plant Area Volume Density profile
#'level2BPAVDProfile<-getLevel2BPAVDProfile(level2b)
#'
#'# Bounding rectangle coordinates
#'xmin = -44.15036
#'xmax = -44.10066
#'ymin = -13.75831
#'ymax = -13.71244
#'
#'# Clipping GEDI Plant Area Volume Density profile by boundary box extent
#'level2BPAVDProfile_clip <- clipLevel2BPAVDProfile(level2BPAVDProfile,xmin, xmax, ymin, ymax)
#'
#'close(level2b)
#'@export
clipLevel2BPAVDProfile = function(level2BPAVDProfile,xmin, xmax, ymin, ymax){
  # xmin ymin xmax ymax
  mask =
    level2BPAVDProfile$lon_lowestmode >= xmin &
    level2BPAVDProfile$lon_lowestmode <= xmax &
    level2BPAVDProfile$lat_lowestmode >= ymin &
    level2BPAVDProfile$lat_lowestmode <=  ymax

  mask[!stats::complete.cases(mask)] = FALSE
  mask = (1:length(level2BPAVDProfile$lon_lowestmode))[mask]
  newFile<-level2BPAVDProfile[mask,]
  #newFile<- new("gedi.level1b.dt", dt = level2bdt[mask,])
  if (nrow(newFile) == 0) {print("The polygon does not overlap the GEDI data")} else {
    return (newFile)
  }

}

#'Clip GEDI Plant Area Volume Density profile by geometry
#'
#'@description This function clips GEDI level2B derived
#'Plant Area Index profile within a given geometry
#'
#'@usage clipLevel2BPAVDProfileGeometry(level2BPAVDProfile, polygon_spdf, split_by)
#'
#'@param level2BPAVDProfile A GEDI Level2B object (output of \code{\link[rGEDI:getLevel2BPAIProfile]{getLevel2BPAIProfile}} function).
#'An S4 object of class "gedi.level2b".
#'@param polygon_spdf Polygon. An object of class \code{\link[sp]{SpatialPolygonsDataFrame-class}},
#'which can be loaded as an ESRI shapefile using \code{\link[raster:shapefile]{raster::shapefile()}} function in the \emph{shapefile} package.
#'@param split_by Polygon id. If defined, GEDI data will be clipped by each polygon using the attribute specified by \code{split_by} from the attribute table.
#'
#'@return Returns an S4 object of class \code{\link[data.table:data.table]{data.table-class}}
#'containing the Plant Area Volume Density profile data.
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi02_bv001/
#'
#'@examples
#'# Specifying the path to GEDI level2B data (zip file)
#'outdir = tempdir()
#'level2B_fp_zip <- system.file("extdata",
#'                   "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip",
#'                   package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Bpath <- unzip(level2B_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2B data (h5 file)
#'level2b<-readLevel2B(level2Bpath=level2Bpath)
#'
#'# Extracting GEDI Plant Area Volume Density profile
#'level2BPAVDProfile<-getLevel2BPAVDProfile(level2b)
#'
#'# Specifying the path to shapefile
#'polygon_filepath <- system.file("extdata", "stands_cerrado.shp", package="rGEDI")
#'
#'# Reading shapefile as SpatialPolygonsDataFrame object
#'library(raster)
#'polygon_spdf<-shapefile(polygon_filepath)
#'
#'# Clipping GEDI Plant Area Volume Density profile by geometry
#'level2BPAVDProfile_clip <- clipLevel2BPAVDProfileGeometry(
#'                                                          level2BPAVDProfile,
#'                                                          polygon_spdf,
#'                                                          split_by="id")
#'
#'close(level2b)
#'@export
clipLevel2BPAVDProfileGeometry = function(level2BPAVDProfile, polygon_spdf, split_by=NULL) {
  exshp<-raster::extent(polygon_spdf)
  level2bdt<-clipLevel2BPAIProfile(level2BPAVDProfile, xmin=exshp[1], xmax=exshp[2], ymin=exshp[3], ymax=exshp[4])

  if (nrow(level2bdt) == 0) {print("The polygon does not overlap the GEDI data")} else {
    points = sp::SpatialPointsDataFrame(coords=matrix(c(level2bdt$lon_lowestmode, level2bdt$lat_lowestmode), ncol=2),
                                        data=data.frame(id=1:length(level2bdt$lon_lowestmode)), proj4string = polygon_spdf@proj4string)
    pts = raster::intersect(points, polygon_spdf)
    colnames(pts@data)<-c("rowids",names(polygon_spdf))

    if (!is.null(split_by)){

      if ( any(names(polygon_spdf)==split_by)){

        mask = as.integer(pts@data$rowids)
        newFile<-level2bdt[mask,]
        newFile$poly_id<-pts@data[,split_by]
      } else {stop(paste("The",split_by,"is not included in the attribute table.
                       Please check the names in the attribute table"))}

    } else {
      mask = as.integer(pts@data$rowids)
      newFile<-level2bdt[mask,]
    }
    #newFile<- new("gedi.level1b.dt", dt = level2bdt2@dt[mask,])
    return (newFile)}
}