Reading hdf files into R and converting them to geoTIFF rasters

Question

I\'m trying to read MODIS 17 data files into R, manipulate them (cropping etc.) and then save them as geoTIFF\'s. The data files come in .hdf format and there

Answer 1

This script has been very useful and I managed to convert a batch of 36 files using it. However, my problem is that the conversion does not seem correct. When I do it using ArcGIS 'Make NetCDF Raster Layer tool', I get different results + I am able to convert the numbers to C from Kelvin using simple formula: RasterValue * 0.02 - 273.15. With the results from R conversion I don't get the right results after conversion which leads me to believe ArcGIS conversion is good, and R conversion returns an error.

library(gdalUtils)
library(raster)

setwd("D:/Data/Climate/MODIS")

# Get a list of sds names
sds <- get_subdatasets('MOD11C3.A2009001.006.2016006051904.hdf')
# Isolate the name of the first sds
name <- sds[1]
filename <- 'Rasterinr.tif'

gdal_translate(sds[1], dst_dataset = filename)
# Load the Geotiff created into R
r <- raster(filename)

# Identify files to read:
rlist=list.files(getwd(), pattern="hdf$", full.names=FALSE)


# Substract last 5 digits from MODIS filename for use in a new .img filename
substrRight <- function(x, n){
        substr(x, nchar(x)-n+1, nchar(x))
}

filenames0 <- substrRight(rlist,9)
# Suffixes for MODIS files for identyfication:
filenamessuffix <- substr(filenames0,1,5)

listofnewnames <- c("2009.01.MODIS_","2009.02.MODIS_","2009.03.MODIS_","2009.04.MODIS_","2009.05.MODIS_",
                    "2009.06.MODIS_","2009.07.MODIS_","2009.08.MODIS_","2009.09.MODIS_","2009.10.MODIS_",
                    "2009.11.MODIS_","2009.12.MODIS_",
                    "2010.01.MODIS_","2010.02.MODIS_","2010.03.MODIS_","2010.04.MODIS_","2010.05.MODIS_",
                    "2010.06.MODIS_","2010.07.MODIS_","2010.08.MODIS_","2010.09.MODIS_","2010.10.MODIS_",
                    "2010.11.MODIS_","2010.12.MODIS_",
                    "2011.01.MODIS_","2011.02.MODIS_","2011.03.MODIS_","2011.04.MODIS_","2011.05.MODIS_",
                    "2011.06.MODIS_","2011.07.MODIS_","2011.08.MODIS_","2011.09.MODIS_","2011.10.MODIS_",
                    "2011.11.MODIS_","2011.12.MODIS_")

# Final new names for converted files:
newnames <- vector()
for (i in 1:length(listofnewnames)) {
        newnames[i] <- paste0(listofnewnames[i],filenamessuffix[i],".img")
}

# Loop converting files to raster from NetCDF
for (i in 1:length(rlist)) {
        sds <- get_subdatasets(rlist[i])
        gdal_translate(sds[1], dst_dataset = newnames[i])
}