Reading JPEG2000 in R using gdal (installing gdal driver)

Question

I currently write a code for automatic reading sentinel 2 data (JPEG2000 format), clipping it and save it a .tif. I use the language R and my system is Windows 10.

My problem is to install properly a gdal driver for JPEG2000. I tried to install the OpenJpeg library, but the installation is very poorly documented.

Can someone explain how to install the OpenJpeg library to use in R or has another suggestion how to read the JPEG2000 in R ?

Answer 1

Here are a couple of examples of using gdal from R but without rgdal (this is assuming Windows OS):

This is a really simple example, with just one image. You can use a vector of images (for instance as returned by list.files) and build multiple calls at once.

# your image is 'C:/Sentinelbands/B01.jp2'

Case 1: you have your gdal distribution available in your path:

cmd <- 'gdal_translate C:/Sentinelbands/B01.jp2 C:/Sentinelbands/B01.tif'

shell(cmd) #Linux use system()

Case 2: using the OSGEO distribution

# assume your OSGEO distribution is at C:/OSGeo4W64

cmd <- 'C:/OSGeo4W64/OSGeo4W.bat; gdal_translate C:/Sentinelbands/B01.jp2 C:/Sentinelbands/B01.tif'
shell(cmd)

Answer 2

You are correct in your comment, recommend you install GDAL via the OSGeo4W package manager. It comes with JP2OpenJPG, which should be able to handle Sentinel data (plus a couple of others).

Once its installed, a simple call would be like

system2('C:/OSgeo4w64/bin/gdal_translate.exe', args = c('--formats'))

(even simpler if the GDAL install is on your PATH properly!)

If the above works, you can call any GGAL/OGR tool in R with system2(), for instance something like

allthefiles <- list.files(dir, pattern = '\\.jp2$', full.names = TRUE)
sapply(allthefiles, function(x) {
    system2('C:/OSgeo4W64/bin/gdalwarp.exe', 
            args = c('-crop_to_cutline', '"path/to/cutlinefile.shp"', 
                     paste0('"', x, '"'),
                     paste0('"', tools::file_path_sans_ext(basename(x)), '.tif"')
})

It can just take a little bit of mucking around to make the system2() output match a valid shell command exactly.