[R-sig-Geo] Sentienl 2 gdal translate

[Miguel Castro Gómez]

Hi Loïc,

I have tried your code but it does not work yet. It just produces one tif file for the first band but this file is not correct (8 kb just). The R process keep working for a long time without any other output

Here are the versions I’m using

R version: 3.3.2
gdalUtils: v 2.0.1.7
raster: 2.5-8
gdal: 2.1.2, released 2016/10/24

When checking for the sentinel 2 driver in gdal (see red)

 gdal-config --formats | grep sentinel2
gxf gtiff hfa aigrid aaigrid ceos ceos2 iso8211 xpm sdts raw dted mem jdem envisat elas fit vrt usgsdem l1b nitf bmp airsar rs2 ilwis rmf leveller sgi srtmhgt idrisi gsg ingr ers jaxapalsar dimap gff cosar pds adrg coasp tsx terragen blx msgn til r northwood saga xyz hf2 kmlsuperoverlay ctg e00grid zmap ngsgeoid iris map cals safe sentinel2 mrf webp wcs wms plmosaic wmts dods grib bsb openjpeg jpeg2000 netcdf hdf5 hdf4 ogdi gif jpeg gta png pcraster fits pcidsk rik ozi rasterlite mbtiles postgisraster arg

I think the problem is the driver that is used to manage the jp2 file. Any idea how can I include in the R code the --config GDAL_SKIP JP2ECW option. 

Cheers,
M

> El 15 mar 2017, a las 23:13, Loïc Dutrieux <loic.dutrieux at conabio.gob.mx> escribió:
> 
> Hi,
> 
> I tried your code with some S2 images I had lying around, and it works
> on my system. I modified it a bit to write the output layers to the same
> directory and not to my working directory.
> 
> library(gdalUtils)
> library(raster)
> 
> Image_Path<-'/path/to/images/'
> 
> S2_JP2_List <- list.files(Image_Path, full.names = TRUE, pattern = ".jp2$")
> 
> for (file in S2_JP2_List) {
>  out_file <- extension(file, 'tif')
>  gdal_translate(src_dataset = file, dst_dataset = out_file, ot =
> "UInt16", of = "GTiff")
> }
> 
> gdal has a sentinel 2 driver, but it's not extremely old, therefore it's
> possible that your installation doesn't have it; you can check with:
> 
> gdal-config --formats | grep sentinel2
> 
> Cheers,
> Loïc
> 
> 
> 
> On 15/03/17 12:49, Miguel Castro Gómez wrote:
>> Hi,
>> 
>> I have Sentinel 2 images (jp2) that I want to convert to GTiff using gdal_translate in R (from gdalutils package). Here is the code I’m using
>> 
>> Image_Path<-“/path/to/wd“
>> 
>> S2_JP2_List <- list.files(Image_Path, full.names = TRUE, pattern = ".jp2$")
>> 
>> for (i in 1:length(S2_JP2_List)) {
>> gdal_translate(src_dataset = S2_JP2_List[[i]], dst_dataset = paste("Band", i , "tif"), ot = "UInt16", of = “GTiff")
>>    }
>> 
>> When running this code, the process starts without any error but its never ending neither producing any output
>> 
>> I've tried to do it in gdal and the same code works, except that it is necessary to skip  the default driver since it cannot manage large jp2 files. 
>> 
>> gdal_translate -of GTiff /path/to/input/S2_b1.jp2  /path/to/output/S2_b1converted.tif --config GDAL_SKIP JP2ECW
>> 
>> Any idea how could I run this in R?
>> 
>> Thanks 
>> M
>> 
>> 
>> 
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>> 
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> 
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