R/vx_extract.R

In juoe/vxr: Fast raster operations with velox and raster

#' Extract values at points
#'
#' @param s Input RasterStack
#' @param points SpatialPoints* or sf-object containing the points at which to extract values
#' @param n_cores Number of cores used for parallel processing. Default is NULL, indicating no parallelization.
#' @param mem_share Share of memory to be used
#' @param mem_of_total Is 'mem_share' specified as share of total memory (instead of currently available)?
#'
#' @return matrix with extracted values
#' @export

vx_extract <- function(s, points, n_cores = NULL,  mem_share = .5, mem_of_total = FALSE){

  # split into memory-safe chunks
  raster_chunk_list <- split_layers(s, mem_share, mem_of_total)

  # process one chunk after the other
  # use parallel processing if specified

  out_list <- lapply(raster_chunk_list, function(r_chunk){

    if(!is.null(n_cores)) {

      cl <- parallel::makeCluster(n_cores)

      v_list <- parallel::parLapply(cl,
                                    raster::unstack(r_chunk),
                                    varlist = c("points"),
                                    fun = function(ri) {

                                      vx <- velox::velox(ri)
                                      vx$extract_points(points)

                                    })

      out_chunk <- do.call(cbind, v_list)
      parallel::stopCluster(cl)

    } else {

      vx <- velox::velox(r_chunk)
      out_chunk <- vx$extract_points(points)


    }

    out_chunk

  })

  out <- do.call(cbind, out_list)
  out

}