[GRASS-user] raster exchange between GRASS and R with nodata

[Nuno Sá]

Ok, didn't check that before since I didn't have the same problem before.

Try exporting with a "crazy value" as NA such as in a 16bit unsigned

r.out.gdal etc nodata=65535

Then on R use the mask function such as:

mask(x, mask, filename="", inverse=FALSE, maskvalue=65535,
updatevalue='NA', ...)

might work but its very, you know, hurtful to see :P but I'm like you, I
prefer .tif.





On 4 September 2014 14:47, Johannes Radinger <johannesradinger at gmail.com>
wrote:

>
>
>
> On Thu, Sep 4, 2014 at 3:38 PM, Nuno Sá <nunocesardesa at gmail.com> wrote:
>
>> Hello!
>>
>> Did you try this one?
>>
>> *r.out.gdal etc nodata*=*'NA'*
>>
>
> As mentioned in the manual of r.out.gdal, the no data parameter takes only
> float values
> and no strings like 'NA'. Without stating as specific value in GRASS, this
> nodata-value is
> automatically set to e.g. 65535 for DCELL rasters if I remember correctly
> and to 255
> for BYTE rasters. However, this seems not to be recognized when imported
> into R with
> the package 'raster'.
>
> /Johannes
>
>
>>
>>
>>
>> On 4 September 2014 14:27, Johannes Radinger <johannesradinger at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> of course it is possible to load the raster maps directly via spgrass6.
>>> However, we use this work
>>> flow also to exchange some of the maps between different users (e.g. via
>>> email) and to permanently
>>> store single files (geotiffs that contain the proj information within
>>> the file). So, I agree that using spgrass6 would be much more efficient,
>>> but I'll stick to exporting to geotiffs and so I need to solve the issues
>>> with NA's.
>>>
>>> /Johannes
>>>
>>>
>>> On Thu, Sep 4, 2014 at 2:31 PM, Thomas Adams <tea3rd at gmail.com> wrote:
>>>
>>>> Johannes,
>>>>
>>>> If you want to read your file into R, there is no need to export your
>>>> map from GRASS to do this. Simply install and use the R contributed package
>>>> 'spgrass6' (spgrass6 has R dependencies that need to be installed first);
>>>> it works wonderfully:
>>>>
>>>> Within GRASS, at the GRASS terminal prompt...
>>>>
>>>> > library(spgrass6)
>>>> Loading required package: sp
>>>> Loading required package: XML
>>>> GRASS GIS interface loaded with GRASS version: GRASS 7.0.0beta3 (2014)
>>>> and location: ohrfc_mpe
>>>> > dat<-readRAST6("xmrg0101200306z")
>>>> > image(dat)
>>>>
>>>> This is far more efficient.
>>>>
>>>> Tom
>>>>
>>>>
>>>>  On Thu, Sep 4, 2014 at 5:32 AM, Johannes Radinger <
>>>> johannesradinger at gmail.com> wrote:
>>>>
>>>>>  Hi,
>>>>>
>>>>> I want to export a raster map (FCELL) from GRASS70 to the geotiff
>>>>> format using r.out.gdal and to import it later on in R. The map contains
>>>>> many no data values.
>>>>>
>>>>> Here some details about the raster:
>>>>> Type of Map:  raster               Number of Categories: 0
>>>>> Data Type:    FCELL
>>>>> Rows:         750
>>>>> Columns:      750
>>>>> Total Cells:  562500
>>>>> total null and non-null cells: 15105636
>>>>> total null cells: 15105047
>>>>>
>>>>> So when I export the map, r.out.gdal reports: "Input raster map
>>>>> contains cells with NULL-value (no-data). The value -nan will be used to
>>>>> represent no-data values in the input map. You can specify a nodata value
>>>>> with the nodata option."
>>>>>
>>>>> When I subsequently try to import the geotiff into R (using the
>>>>> package 'Raster') the nodata values are not recognised as NA's:
>>>>>
>>>>> a <- raster("*.tif")
>>>>> summary(a)
>>>>> Min.     0.5294496
>>>>> 1st Qu.  0.7171210
>>>>> Median   0.7871540
>>>>> 3rd Qu.  1.1581826
>>>>> Max.     1.5494517
>>>>> NA's     0.0000000
>>>>>
>>>>> So I am wondering if I need to set any specific parameter during the
>>>>> export (r.out.gdal) or import (raster()).
>>>>>
>>>>> As I am not only exporting FCELL (Float32) raster but also multiple
>>>>> (N=500) other rasters to R I would be interested in a solution also for
>>>>> DCELL (Float64). Of course I can export all of as Float64 as the file size
>>>>> should not be a problem.
>>>>>
>>>>> Any suggestions or experiences of handling NA's during raster exchange
>>>>> between GRASS and R?
>>>>>
>>>>> /Johannes
>>>>>
>>>>> _______________________________________________
>>>>> grass-user mailing list
>>>>> grass-user at lists.osgeo.org
>>>>> http://lists.osgeo.org/mailman/listinfo/grass-user
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> grass-user mailing list
>>> grass-user at lists.osgeo.org
>>> http://lists.osgeo.org/mailman/listinfo/grass-user
>>>
>>
>>
>>
>> --
>>
>> Nuno César de Sá
>> +351 91 961 90 37
>>
>>
>


-- 

Nuno César de Sá
+351 91 961 90 37
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