## ----StateQA, echo=FALSE------------------------------------------------------
table <- read.csv("sur_refl_state.txt", header=TRUE, sep = "\t", colClasses = "character", encoding ="UTF-8")
dm <- data.frame(table, stringsAsFactors = FALSE)
colnames(dm) <- c("bit", "variable", "value", "description")
#dm[,4] = gsub("\n", " ", dm[,4])
knitr::kable(dm, align="l")


## ----qcconst------------------------------------------------------------------
from <- c(1,3,11,14)
to   <- c(2,3,11,14)
reject <- c("01,10", "1", "1", "1")

qa_bits <- cbind(from, to, reject)
qa_bits


## ----mod, message=FALSE-------------------------------------------------------
library(terra)
datadir <- file.path(dirname(tempdir()), "_modis")
mf <- file.path(datadir, "MOD09A1.A2009361.h21v08.061.2021149144347.hdf")

r <- rast(mf)


## ----qc1----------------------------------------------------------------------
qc <- r[[12]]

plot(qc, main = "Quality")


## ----qc2----------------------------------------------------------------------
library(luna)

quality_mask <- modis_mask(qc, 16, qa_bits)

plot(quality_mask, main="Quality mask")  


## ----qcmask-------------------------------------------------------------------
rmask <- mask(r, quality_mask)


## ----qcmaskplot---------------------------------------------------------------
plotRGB(rmask, r = 2, g = 1, b = 4, main='False color composite', stretch="lin")


## ----savefile, echo=FALSE-----------------------------------------------------
mf <- file.path(datadir, "modis_qualmasked.tif")

writeRaster(rmask, mf, overwrite=TRUE)