[R-sig-Geo] Sentienl 2 gdal translate
Loïc Dutrieux
loic.dutrieux at conabio.gob.mx
Fri Mar 17 18:12:45 CET 2017
Hi Miguel,
Do you have more than one installation of gdal? That could potentially
explain why your first try with gdal_translate() did not work.
library(gdalUtils)
length(getOption("gdalUtils_gdalPath"))
should give you the number of installations you have on your system.
If more than 1, gdal_chooseInstallation(hasDrivers=c("SENTINEL2"))
should set the correct path for gdal_translate().
Cheers,
Loïc
On 17/03/17 05:45, Miguel Castro Gómez wrote:
> Hi Loïc,
>
> Thanks for your help,
>
> When trying the system2 option this is what happens:
>
> Image_Path<- “path/to/images/"
>
> S2_JP2_List <- list.files(Image_Path, full.names = TRUE, pattern = ".jp2$")
>
> for (file in S2_JP2_List) {
> out_file <- extension(file, 'tif')
> system2('gdal_translate', args = c('-of GTiff', file, out_file,
> '--config GDAL_SKIP JPECW'))
> }
>
> sh: gdal_translate: command not found
>
>
> I have been checking and the problem may be that R cannot find the
> gdal_translate command. Here are the paths:
>
> Sys.getenv('R_HOME’)
> "/Library/Frameworks/R.framework/Resources"
> Sys.getenv('PATH')
> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin”
>
> In terminal:
> user$ echo $PATH
> /Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/GDAL.framework/Programs:/Users/Miguel/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
>
>
> I think it has to match but not sure how can I change the path that R is
> using to find the command gdal_translate
>
> Regarding sentinel2 driver, any idea why is not working? Any help on that
>
> Cheers
> M
>
>
>> El 16 mar 2017, a las 19:21, Loïc Dutrieux
>> <loic.dutrieux at conabio.gob.mx <mailto:loic.dutrieux at conabio.gob.mx>>
>> escribió:
>>
>> Hi Miguel,
>>
>> Briefly looking at the help and source code of
>> gdalUtils::gdal_translate(), I don't see any way to pass additional
>> options. Your best shot is therefore probably to build the expression
>> yourself and pass it via a system call.
>>
>> library(raster)
>>
>> Image_Path<-'/path/to/images/'
>>
>> S2_JP2_List <- list.files(Image_Path, full.names = TRUE, pattern =
>> ".jp2$")
>>
>> for (file in S2_JP2_List) {
>> out_file <- extension(file, 'tif')
>> system2('gdal_translate', args = c('-of GTiff', file, out_file,
>> '--config GDAL_SKIP JPECW'))
>> }
>>
>> But the real question here is why the simple gdal_translate call without
>> --config GDAL_SKIP JPECW did not work for you while you clearly have the
>> sentinel2 driver...
>>
>> Cheers,
>> Loïc
>>
>> On 16/03/17 06:02, Miguel Castro Gómez wrote:
>>> 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
>>>> <mailto:loic.dutrieux at conabio.gob.mx> <mailto: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
>>>>>
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
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