[R-sig-Geo] Processing best quality MODIS pixels only (MODIS package)

[Matteo Mattiuzzi]

Dear Amit,
Thats correct, if you want to use only pixel of 0000 quality you have to set 0 as threshold (everything > than threshold is set to 0 weight). But for what I remember, and this might explains your result with all 0s, is that 0000 does not exist in MODIS data despite the fact that it is described so on the website. You can use the decodeOnly=TRUE option to see the exact values of your quality layers, but I guess you will not find any values lower than 1.
If you run whittaker.raster, you can feed also argument of the makeWeights function. If you use a cluster this step is parallelized automatically.
I gave a short look to makeWeights now, probably I can do some little speed improvements.

It should be possible to do:

library("MODIS")
path=("E:/NDVI/Indonesia")
#stack ndvi images, following MODIS package example
ndvi = preStack(pattern = "*_NDVI.tif", path = path)
timeInfo <- orgTime(ndvi,nDays=16,begin="2000049",end="2015049",pillow=40)
#Restack evi
ndvi <- preStack(files=ndvi,timeInfo=timeInfo)
# You don't need to stack here, it is done with stack(...quick=TRUE) within whittaker.raster.
wt  <- preStack(path=path, pattern="*_VI_Quality.tif$", timeInfo=timeInfo)
inT <- preStack(path=path, pattern="*_composite_day_of_the_year.tif", timeInfo=timeInfo)
nodes <- 4
library(snow)
beginCluster(nodes)
system.time(whittaker.raster(vi=ndvi, wt = wt, inT = inT, timeInfo = timeInfo, lamba = 500, bitShift = 2, bitMask = 15, threshold = 1))
endCluster()

Matteo


>>> Amit Boshale <amit.boshale at yahoo.com> 05/19/15 4:54 PM >>>
Hello!
I use MODIS package to smooth MODIS NDVI raster time series. 
Just wanted to try how would it look like if I used the best qulity pixels only.makeWeights function took about two days and resulted in raster stack of zeros. According to MODIS, the best qulity is 0, hence I used 0 as the threshold, is that correct? Is there a multicore version of makeWeights function?
Best,Amit
library("MODIS")path=("E:/NDVI/Indonesia")
#stack ndvi images, following MODIS package example
ndvi = preStack(pattern = "*_NDVI.tif", path = path)
timeInfo <- orgTime(ndvi,nDays=16,begin="2000049",end="2015049",pillow=40)
#Restack evi
ndvi <- preStack(files=ndvi,timeInfo=timeInfo)
#stack Vegtation index quality layers
VIqual <- stack(preStack(path=path, pattern="*_VI_Quality.tif", timeInfo=timeInfo))
bitShift = 2
bitMask = 15 
threshold=0 # based on MODIS documentation, quality 0 is the best
wt <- makeWeights(VIqual,bitShift,bitMask,threshold,decodeOnly=FALSE)
#stack composite day of the year layers
inT <- stack(preStack(path=path, pattern="*_composite_day_of_the_year.tif", timeInfo=timeInfo))
nodes <- 4
library(snow)
beginCluster(nodes)
system.time(whittaker.raster(vi=ndvi, wt=wt, inT=inT, timeInfo=timeInfo, lambda=500))
endCluster()