R/cloud.rm.R

In DGampe/TriangleMethod: Calculation of NDVI, LST and finally provide an estimation for actual evapotranspiration patterns using remote sensing data (default LANDSAT TM and ETM+ scenes).

cloud.rm<-
  function(BLUE, TEMP,nClus=30,nsample=100,layers=c(1,6),maskmin=5,maskmax=NA,
           outname="clouds-masked.tif", outpath = getwd(), write=F, ...){

    if(class(BLUE)[[1]]!="RasterLayer"){
      BLUE = raster(BLUE)
    }
    if(class(TEMP)[[1]]!="RasterLayer"){
      TEMP = raster(TEMP)
    }
    lstack = stack(BLUE,TEMP)
    lDF=as.data.frame(lstack[[layers]])
    lDF=na.omit(lDF)
    l.cl=clara(lDF, stand=T, metric="euclidean"
               ,k=nClus,trace=T,medoids.x=F,keep.data=F, samples=nsample)
    lDF$clus=l.cl$clustering

    cloud.mask=lstack[[1]]
    cloud.mask[][as.numeric(rownames(lDF))]=lDF$clus
    if(is.null(maskmax)) {
      cloud.mask[][which(cloud.mask[]<=maskmin)] = NA
    } else{
      cloud.mask[][which(cloud.mask[]<=maskmin | cloud.mask[]>=maskmax)] = NA
    }
    cloud.mask[][which(!is.na(cloud.mask[]))] = 1

    setwd(outpath)
    if(write==T){
      writeRaster(cloud.mask , filename = outname , "GTiff", overwrite=T, NAflag = -9999)
    }
    return(cloud.mask)
}