R/mapDistance2Loess.R

In johanez/probaV: Utils for time-series analysis of Proba-V data

#' @title Spatial calculation of temproal outliers distance
#' @description
#' Applies \code{\link{smoothLoess}} spatially using \code{\link{mcCalc}}
#' to derive the distance of outliers to the \code{\link{loess}} smoothed time
#' series spatially.
#' @param x RasterBrick. Input ProbaV data, layer names must be Proba-V filenames!
#' Multiple bands possible, stackign must be chronological.
#' @param QC_band Integer. IWhcih band is the SM band?
#' @param span Numeric. See \code{\link{smoothLoess}}
#' @param res_type Character. "distance" or "sd_distance, see \code{\link{smoothLoess}}.
#' @param mc.cores Integer. See \code{\link{mcCalc}}.
#' @param ... additional agruments to \code{\link{mcCalc}}.
#'
#' @return RasterBrick with distances to loess curve per band and date.
#' @export
#' @import raster
#'

mapDistance2Loess <- function(x, QC_band=NULL, span=0.3,  res_type=c("distance", "sd_distance"), mc.cores=1, ...) {

  s_info <- getProbaVinfo(names(x))
  bands <- s_info[s_info$date == s_info$date[1], 'band']
  dates <- s_info[s_info$band == bands[1], 'date']
  if (nlayers(x) != length(bands) * length(dates)) {
    stop("Stack layers don't fit meta data in layer names!")
  }

  fun <- function(x){
    # smoothloess
    m <- matrix(x, nrow= length(bands), ncol=length(dates))
    if (!is.null(QC_band)){
      qc <- m[QC_band,]
      qc <- qc %in% getProbaVQClist()$clear_all
      m <- m[-QC_band,]
    } else qc <- NULL

    if (!all(is.na(m[1,]))) {
      res <- try({
        d <- apply(m, MARGIN = 1, smoothLoess, QC_good=qc, dates = dates, res_type = res_type, span=span, threshold=NULL)
        as.vector(t(d))
      })
      if(class(res) == 'try-error') {
        res <- rep(NA, length(x))
      }
    } else {
      res <- rep(NA, length(x))
    }
    # no names, because they get lsot in mc.calc anyway
    ### names(res) <- paste0(rep(bands, nrow(coefs)), "_", rownames(coefs))
    return(res)
  }

  out <- mcCalc(x=x, fun=fun, mc.cores=mc.cores, ...)

  return(out)
}