R/clipLevel2AM.R

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

#'Clip GEDI Elevation and Height Metrics by Coordinates
#'
#'@description This function clips GEDI Level2A extracted Elevation and Height Metrics (Level2AM)
#' within a given bounding coordinates
#'
#'@usage clipLevel2AM(level2AM, xmin, xmax, ymin, ymax)
#'
#'@param level2AM A GEDI Level2A object (output of \code{\link[rGEDI:readLevel2A]{readLevel2A}} function).
#'An S4 object of class "gedi.level2a".
#'@param xmin Numeric. West longitude (x) coordinate of bounding rectangle, in decimal degrees.
#'@param xmax Numeric. East longitude (x) coordinate of bounding rectangle, in decimal degrees.
#'@param ymin Numeric. South latitude (y) coordinate of bounding rectangle, in decimal degrees.
#'@param ymax Numeric. North latitude (y) coordinate of bounding rectangle, in decimal degrees.
#'
#'@return Returns an S4 object of class \code{\link[data.table:data.table]{data.table-class}}
#'containing the clipped elevation and relative heights metrics.
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi02_av001/
#'
#'@examples
#'# Specifying the path to GEDI level2A data (zip file)
#'outdir = tempdir()
#'level2A_fp_zip <- system.file("extdata",
#'                   "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",
#'                   package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Apath <- unzip(level2A_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2A data (h5 file)
#'level2a<-readLevel2A(level2Apath=level2Apath)
#'
#'# Extracting GEDI Elevation and Height Metrics
#'level2AM = getLevel2AM(level2a)
#'
#'# Bounding rectangle coordinates
#'xmin = -44.15036
#'xmax = -44.10066
#'ymin = -13.75831
#'ymax = -13.71244
#'
#'# Clipping GEDI data by boundary box extent
#'level2AM_clip <- clipLevel2AM(level2AM,xmin, xmax, ymin, ymax)
#'
#'close(level2a)
#'@import hdf5r stats
#'@export
clipLevel2AM = function(level2AM,xmin, xmax, ymin, ymax){
  # xmin ymin xmax ymax
  mask =
    level2AM$lon_lowestmode >= xmin &
    level2AM$lon_lowestmode <= xmax &
    level2AM$lat_lowestmode >= ymin &
    level2AM$lat_lowestmode <=  ymax &
    level2AM$lon_lowestmode >= xmin &
    level2AM$lon_lowestmode <= xmax &
    level2AM$lat_lowestmode >= ymin &
    level2AM$lat_lowestmode <=  ymax
  mask[!stats::complete.cases(mask)] = FALSE
  mask = (1:length(level2AM$lat_lowestmode))[mask]
  newFile<-level2AM[mask,]
  #newFile<- new("gedi.level1b.dt", dt = level1bdt[mask,])
  return (newFile)
}

#'Clip GEDI Elevation and Height Metrics by Coordinates
#'
#'@description This function clips GEDI Level2A extracted Elevation and Height Metrics (Level2AM)
#' within a given bounding coordinates
#'
#'@usage clipLevel2AMGeometry(level2AM, polygon_spdf, split_by)
#'
#'@param level2AM A GEDI Level2A object (output of \code{\link[rGEDI:readLevel2A]{readLevel2A}} function).
#'An S4 object of class "data.table".
#'@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{raster} package.
#'@param split_by Polygon id. If defined, GEDI data will be clipped by each polygon using the polygon id from table of attribute defined by the user
#'
#'@return Returns an S4 object of class \code{\link[data.table:data.table]{data.table-class}}
#'containing the clipped elevation and relative heights metrics.
#'
#'@examples
#'# Specifying the path to GEDI level2A data (zip file)
#'outdir = tempdir()
#'level2A_fp_zip <- system.file("extdata",
#'                   "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",
#'                   package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Apath <- unzip(level2A_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2A data (h5 file)
#'level2a<-readLevel2A(level2Apath=level2Apath)
#'
#'# Extracting GEDI Elevation and Height Metrics
#'level2AM = getLevel2AM(level2a)
#'
#'# 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 data by Geometry
#'level2AM_clip = clipLevel2AMGeometry(level2AM, polygon_spdf, split_by="id")
#'
#'hasLeaflet = require(leaflet)
#'
#'if (hasLeaflet) {
#'leaflet() %>%
#'  addCircleMarkers(level2AM_clip$lat_lowestmode,
#'                   level2AM_clip$lon_lowestmode,
#'                   radius = 1,
#'                   opacity = 1,
#'                   color = "red")  %>%
#'  addScaleBar(options = list(imperial = FALSE)) %>%
#'  addPolygons(data=polygon_spdf,weight=1,col = 'white',
#'              opacity = 1, fillOpacity = 0) %>%
#'  addProviderTiles(providers$Esri.WorldImagery)
#' }
#'
#'close(level2a)
#'@export
clipLevel2AMGeometry = function(level2AM, polygon_spdf, split_by="id") {
  exshp<-raster::extent(polygon_spdf)
  level2adt<-clipLevel2AM(level2AM, xmin=exshp[1], xmax=exshp[2], ymin=exshp[3], ymax=exshp[4])
  if (nrow(level2adt) == 0) {print("The polygon does not overlap the GEDI data")} else {
    points = sp::SpatialPointsDataFrame(coords=matrix(c(level2adt$lon_lowestmode, level2adt$lat_lowestmode), ncol=2),
                                        data=data.frame(id=1:length(level2adt$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$rowids)
        newFile<-level2adt[mask,]
        newFile$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<-level2adt[mask,]
    }
    #newFile<- new("gedi.level1b.dt", dt = level2adt2@dt[mask,])
    return (newFile)}
}