linux_raster_raster_MODIS.r

stack_MODIS_MOD13Q1=function(x,pixelreliab=0,file.remove=F) {

require(MODIS)
require(gdalUtils)
require(rgdal)

mod <- getSds(x,method="gdal")

names=list(gsub(".hdf","_NDVI.tif",x),gsub(".hdf","_EVI.tif",x),gsub(".hdf","_RELIAB.tif",x),gsub(".hdf","_NDVI_Q.tif",x),gsub(".hdf","_EVI_Q.tif",x))
ndvi <- raster(readGDAL(mod$SDS4gdal[1], as.is=TRUE))*0.0001
evi <- raster(readGDAL(mod$SDS4gdal[2], as.is=TRUE))*0.0001 
reliab <-raster(readGDAL(mod$SDS4gdal[12], as.is=TRUE)) 
m=reliab
m[m != pixelreliab]<-NA
ndvi_qa=mask(ndvi,m)
evi_qa=mask(evi,m)
writeRaster(ndvi, filename=names[[1]], overwrite=TRUE)
writeRaster(evi, filename=names[[2]], overwrite=TRUE)
writeRaster(reliab, filename=names[[3]], datatype='INT4S', overwrite=TRUE)
writeRaster(ndvi_qa, filename=names[[4]], overwrite=TRUE)
writeRaster(evi_qa, filename=names[[5]], overwrite=TRUE)

if ( file.remove==T) { file.remove(x)}


}

stack_MODIS_MOD11A2=function(x,pixelreliab=81,file.remove=F) {

require(MODIS)
require(gdalUtils)
require(rgdal)

mod <- getSds(x,method="gdal")

names=list(gsub(".hdf","_LSTday.tif",x),
           gsub(".hdf","_QC_day.tif",x),
           gsub(".hdf","_LSTnight.tif",x),
           gsub(".hdf","_QC_night.tif",x), 
           gsub(".hdf","_LSTdayQA.tif",x),
           gsub(".hdf","_LSTnightQA.tif",x))


lstday <- raster(readGDAL(mod$SDS4gdal[1], as.is=TRUE))
lstday[lstday==0]<-NA
lstday=lstday*0.02-273.16

DayQC <-raster(readGDAL(mod$SDS4gdal[2], as.is=TRUE)) 
lstnight <- raster(readGDAL(mod$SDS4gdal[5], as.is=TRUE))*0.02-273.16
lstnight[lstnight==0]<-NA
lstnight=lstnight*0.02-273.16
NightQC <-raster(readGDAL(mod$SDS4gdal[6], as.is=TRUE)) 

m <- DayQC
m[m > pixelreliab]<-NA
#m[ m == 2 | m== 3]<-NA
lstdayQA <- mask(lstday, m)

m <- NightQC
m[m > pixelreliab]<-NA
# m[ m == 2 | m== 3]<-NA

lstnightQA <- mask(lstnight, m)

writeRaster(lstday, filename=names[[1]], overwrite=TRUE)
writeRaster(DayQC, filename=names[[2]], datatype='INT4S', overwrite=TRUE)
writeRaster(lstnight, filename=names[[3]],  overwrite=TRUE)
writeRaster(NightQC, filename=names[[4]], datatype='INT4S', overwrite=TRUE)
writeRaster(lstdayQA, filename=names[[5]], d overwrite=TRUE)
writeRaster(lstnightQA, filename=names[[6]], overwrite=TRUE)

if ( file.remove==T) { file.remove(x)}
}

On WIN32 or WIN64 systems must be installed FWtools gdal or other ones to read HDF4 modis format.

reference https://stevemosher.wordpress.com/2012/12/05/modis-qc-bits/bitsin-hdf/