Re: [GRASS-user] raster exchange between GRASS and R with nodata
I think I discovered the problem. This was a mistake on my side:
The summary() function in R applied on a raster does subsample the
data in case of very large raster maps. However, this seems to
cause that summary information about NA gets lost and no NA are
mentioned in the summary output although there are NA included
in the raster map.
Here an example output of a map with lots of NA's which are ignored
by summary(rastermap):
> summary(streams[[1]])
Elbe_distance_from_mouth
Min. 0.
1st Qu. 488.7067
Median 789.8560
3rd Qu.1025.4501
Max. 1876.6429
NA's 0.
Warning message:
In .local(object, ...) :
summary is an estimate based on a sample of 1e+05 cells (10.7% of all
cells)
> length(bioclim[[1]][is.na(bioclim[[1]])])
[1] 12688
So there was actually no problem, just some confusion concerning the
information about
NA in the summary.
Best regards,
Johannes
On Thu, Sep 4, 2014 at 6:26 PM, Robert J. Hijmans
wrote:
> Johannes,
>
> raster uses GDAL to access GTiff data. So it seems that there is no,
> or at least GDAL does not see, a no data value in the file.
> I would suggest running GDALinfo to troubleshoot. Can you email me a
> small example file?
>
> By the way, the spgrass6 route has a shortcoming: it may not work with
> very large files as it attempts to load all values into RAM.
>
> Robert
>
> On Thu, Sep 4, 2014 at 6:47 AM, Johannes Radinger
> wrote:
> >
> >
> >
> > On Thu, Sep 4, 2014 at 3:38 PM, Nuno Sá 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 <
> johannesradin...@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 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
> 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 0.000
> >
> > 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 multip
Re: [GRASS-user] raster exchange between GRASS and R with nodata
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
wrote:
>
>
>
> On Thu, Sep 4, 2014 at 3:38 PM, Nuno Sá 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
>> 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 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 <
johannesradin...@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 0.000
>
> 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@lists.osgeo.org
> http://lists.osgeo.org/mailman/listinfo/grass-user
>
>>>
>>> ___
>>> grass-user mailing list
>>> grass-user@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
___
grass-user mailing list
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Re: [GRASS-user] raster exchange between GRASS and R with nodata
On Thu, Sep 4, 2014 at 3:38 PM, Nuno Sá 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
> 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 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 <
>>> johannesradin...@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 0.000
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
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>>>
>>>
>>>
>>>
>>
>> ___
>> grass-user mailing list
>> grass-user@lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-user
>>
>
>
>
> --
>
> Nuno César de Sá
> +351 91 961 90 37
>
>
___
grass-user mailing list
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Re: [GRASS-user] raster exchange between GRASS and R with nodata
Hello!
Did you try this one?
*r.out.gdal etc nodata*=*'NA'*
On 4 September 2014 14:27, Johannes Radinger
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 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 <
>> johannesradin...@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 0.000
>>>
>>> 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@lists.osgeo.org
>>> http://lists.osgeo.org/mailman/listinfo/grass-user
>>>
>>
>>
>>
>>
>
> ___
> grass-user mailing list
> grass-user@lists.osgeo.org
> http://lists.osgeo.org/mailman/listinfo/grass-user
>
--
Nuno César de Sá
+351 91 961 90 37
___
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Re: [GRASS-user] raster exchange between GRASS and R with nodata
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 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 <
> johannesradin...@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 0.000
>>
>> 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@lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-user
>>
>
>
>
>
___
grass-user mailing list
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Re: [GRASS-user] raster exchange between GRASS and R with nodata
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 <
johannesradin...@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 0.000
>
> 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@lists.osgeo.org
> http://lists.osgeo.org/mailman/listinfo/grass-user
>
___
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Re: [GRASS-user] raster exchange between GRASS and R with nodata
You probably have good reasons for your work flow, but just to make sure:
is there a specific reason to export to geotiff first? It seems easier to
import the raster layer directly from GRASS into R using the spgrass6
package (readRAST6)? You can subsequently convert the spatial raster to the
raster format.
On Thu, Sep 4, 2014 at 11:32 AM, Johannes Radinger <
johannesradin...@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 0.000
>
> 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
>
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[GRASS-user] raster exchange between GRASS and R with nodata
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 0.000
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
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