makeWeights: Extract Bit-Encoded Information and create Weights Raster

In MODIS: Acquisition and Processing of MODIS Products

Extract Bit-Encoded Information and create Weights Raster

Description

This function applies bitops::bitAnd() and bitops::bitShiftR() to convert bit-encoded information. It is also possible to convert this information to a scale from 0 to 1 in order to use it as weighting information in functions like whittaker.raster() or smooth.spline.raster().

Usage

extractBits(
  x,
  bitShift = 2,
  bitMask = 15,
  filename = "",
  datatype = "INT1U",
  NAflag = 255,
  ...
)

makeWeights(
  x,
  bitShift = 2,
  bitMask = 15,
  threshold = NULL,
  decodeOnly = FALSE,
  filename = "",
  datatype = "INT1U",
  NAflag = 255,
  ...
)

maskWater(
  X,
  bitShift = NULL,
  bitMask = NULL,
  keep = NULL,
  datatype = "INT1U",
  NAflag = 255,
  ...
)

Arguments

x	matrix, vector or Raster* object.
bitShift	integer. Bit starting point, see Examples and detectBitInfo().
bitMask	integer. Bit mask size, see Examples and detectBitInfo().
filename	character passed to raster::writeRaster(). If not specified, output is written to a temporary file.
datatype	character. Default "INT1U" used for Raster* object. Output datatype, see raster::writeRaster().
NAflag	integer. Default 255 used for Raster* object. Set specific NA value, see raster::writeRaster().
...	Other arguments passed to raster::writeRaster().
threshold	integer. Threshold for valid quality.
decodeOnly	logical. If FALSE (default), convert bits to weights from 0 (not used) to 1 (best quality). If TRUE, only extract selected bits and convert to decimal system.
X	Raster* object.
keep	If NULL (default), bits are only encoded, else an integer vector of values you want to keep (becomes TRUE), the rest becomes NA. See Examples.

Value

A Raster* object.

Functions

• extractBits(): Extract bit-encoded information from Raster* file

• maskWater(): Masks water (additional information required)

Note

makeWeights() and extractBits() are identical with the only difference that makeWeights() does additionally convert the data into weighting information.

Author(s)

Matteo Mattiuzzi

See Also

detectBitInfo().

Examples

## Not run: 

# example MOD13Q1 see MODIS Vegetation Index User's Guide (MOD13 Series; 
# https://lpdaac.usgs.gov/sites/default/files/public/product_documentation/mod13_user_guide.pdf)
# enter in Layers
# See in TABLE 5: Descriptions of the VI Quality Assessment Science Data Sets (QA SDS).
# column 1 (bit) row 2 VI usefulness 
bitShift = 2
bitMask = 15 # ('15' is the decimal of the binary '1111')  
# or try to use
detectBitInfo("MOD13Q1") # not all products are available!
viu <- detectBitInfo("MOD13Q1","VI usefulness") # not all products are available!
viu

# simulate bit info
bit <- round(runif(10*10,1,65536))

# extract from vector
makeWeights(bit,bitShift,bitMask,decodeOnly=TRUE)
# the same as
extractBits(bit,bitShift,bitMask)

# create a Raster object
VIqual <- raster(ncol=10,nrow=10)
VIqual[] <- bit

# extract from Raster object
a <- makeWeights(VIqual,bitShift,bitMask,decodeOnly=TRUE)

# linear conversion of 0 (0000) to 15 (1111) to 1 fo 0 
b <- makeWeights(VIqual,bitShift,bitMask,decodeOnly=FALSE)

threshold=6 # every thing < threshold becomes a weight = 0
c <- makeWeights(VIqual,bitShift,bitMask,threshold,decodeOnly=FALSE)

res <- round(cbind(a[],b[],c[]),2)
colnames(res) <- c("ORIG","Weight","WeightThreshold") 
res

#####
# water mask
tif = runGdal(product="MOD13A2",begin="2009001",end="2009001", extent=extent(c(-9,-3 ,54,58)),
              SDSstring="001",job="delme") # 6.4 MB
x <- raster(unlist(tif))

res1 <- maskWater(x)
plot(res1)

res2 <- maskWater(x,keep=1) # 1 = Land (nothing else)
x11()
plot(res2)

# Land (Nothing else but land) + Ocean coastlines and lake shorelines + shallow inland Water,
# the rest becomes NA
x11()
res3 <- maskWater(x,keep=c(1,2,3)) 
plot(res3)

###############

# as on Linux you can read HDF4 directly you can also do:
if(.Platform$OS.type=="unix")
{
  x <- getHdf(HdfName="MOD13A2.A2009001.h17v03.005.2009020044109.hdf", wait=0) # 6.4 MB
  
  detectBitInfo(x) # just info
  getSds(x) # just info
  
  x <- getSds(x)$SDS4gdal[3] # you need 'VI Quality'
  x  <- raster(x) 
  # plot(x)
  # ex <- drawExtent()
  ex <- extent(c(-580779,-200911,5974929,6529959))
  x  <- crop(x,ex) # just for speed-up
  
  res1 <- maskWater(x)
  plot(res1)
  
  res2 <- maskWater(x,keep=1) # 1 = Land (Nothing else but land), the rest becomes NA
  x11()
  plot(res2)
  
  # Land (Nothing else but land) + Ocean coastlines and lake shorelines + shallow inland Water,
  # the rest becomes NA
  res3 <- maskWater(x,keep=c(1,2,3))
  x11()
  plot(res3)
}

## End(Not run)

MODIS documentation built on Jan. 6, 2023, 5:10 p.m.