[GRASS-stats] Re: [R-sig-Geo] Fail to load a vector layer using
spgrass6
Pierre Roudier
pierre.roudier at gmail.com
Thu Dec 16 16:28:35 EST 2010
Thanks Roger,
> OK, so we know now that the use of intermediate files with the "ESRI
> Shapefile" driver works, but the plugin does not work for you. We don't know
> why your plugin doesn't work (and I'm not sure which versions of GRASS,
> GDAL, or the plugin are involved).
>
The GRASS version is 7svn, however I had the same problem on the 6.4.
I can't manage to check the plugin version, but it is here:
roudierp at A208_RoudierP:~> ls /usr/lib/gdalplugins/
gdal_GRASS.so ogr_GRASS.so
roudierp at A208_RoudierP:~> gdalinfo --formats | grep -i grass
GRASS (ro): GRASS Database Rasters (5.7+)
My GDAL version is 1.7.1:
roudierp at A208_RoudierP:~> gdalinfo --version
GDAL 1.7.1, released 2010/02/08
Form your post I understand I should remove my binaries and compile
GDAL and the GRASS plugin from source.
>> Is there a way for spgrass6 to read the attribute table of a layer as
>> a data.frame, modify it in R and then write it back in GRASS?
>
> res <- execGRASS("v.db.select", parameters=list(map="bugsites",
> layer="1"), intern=TRUE)
> con <- textConnection(res)
> df <- read.table(con, header=TRUE, sep="|")
> close(con)
> str(df)
>
> for reading. This may not scale well, in which case try:
>
> execGRASS("v.out.ogr", parameters=list(input="bugsites", layer="1",
> dsn=paste(td, "bugsites.csv", sep="/"), format="CSV"))
> df <- read.csv(paste(td, "bugsites.csv", sep="/"))
> str(df)
>
> Could others with more experience of updating vector attribute tables add
> the return trip? I suspect that using a database back-end which both R and
> GRASS can update is the cleanest solution, but is there a way of inputting
> hundreds of thousands of values into a column of a vector attribute table?
> Should one create a new table and join it?
>
Thanks, I will use that then,
Pierre
>>> Have you considered using a database back-end?
>>>
>>
>> Another very good point. I guess that would speed up things.
>> Unfortunately, I have no experience whatsoever in DB. I'd be glad to
>> learn though! Dylan's blog has a nice entry about that [1].
>>
>> I think the readVECT6() worked out because I got 7Gb RAM on my
>> workstation. I wouldn't try the same thing on my laptop. BTW, I'm
>> lacking memory when I'm trying to write my result:
>>>
>>> writeVECT6(foo, 'deleteme')
>>
>> Error in system(syscmd, intern = intern, ignore.stderr = ignore.stderr, :
>> cannot popen 'g.tempfile pid=999', probable reason 'Cannot allocate
>> memory'
>>
>>> Note that you have problems in ph_cl which require the c flag.
>>>
>>
>> BTW, I got that problem on GRASS 6.4 but not on GRASS 7svn.
>>
>> Thanks again - and sorry for the misunderstanding on the GRASS plugin,
>>
>> Pierre
>>
>> [1] http://casoilresource.lawr.ucdavis.edu/drupal/node/733
>>
>>>>> If that doesn't work, please move thread only to grass-stats, and try
>>>>> using
>>>>> v.out.ogr to export the vector to the GRASS mapset temporary directory
>>>>> manually - use g.tempfile to find out what the path to that directory
>>>>> is.
>>>>> If
>>>>> v.out.ogr appears to complete without problems, do check the temporary
>>>>> directory to be sure.
>>>>>
>>>>
>>>> The output of g.tempfile is:
>>>>
>>>>
>>>>
>>>> /home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/18058.0
>>>>
>>>> When using that tempfile for export as Shapefile it fails:
>>>>
>>>> v.out.ogr in=ph_cl
>>>>
>>>>
>>>> dsn='/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/18058.0'
>>>> format=ESRI_Shapefile
>>>> WARNING: The map contains islands. To preserve them in the output map,
>>>> use
>>>> the -c flag
>>>> ERROR 1:
>>>>
>>>> /home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/18058.0
>>>> is not a directory.
>>>>
>>>> ERROR: Unable to open OGR data source
>>>>
>>>>
>>>> '/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/18058.0'
>>>>
>>>> However, if I specify the tmp folder that works:
>>>> v.out.ogr in=ph_cl
>>>>
>>>>
>>>> dsn='/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/'
>>>> format=ESRI_Shapefile
>>>>
>>>> BUT - and that's where it gets tricky, if I want to use the GML
>>>> driver, this is the opposite situation:
>>>>
>>>> v.out.ogr in=ph_cl
>>>>
>>>>
>>>> dsn='/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/'
>>>> format=GML
>>>> ERROR 4: Failed to create GML file
>>>>
>>>>
>>>> /home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/.
>>>> ERROR: Unable to open OGR data source
>>>>
>>>>
>>>> '/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/'
>>>>
>>>> While this works:
>>>>
>>>> v.out.ogr in=ph_cl
>>>>
>>>>
>>>> dsn='/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP/18628.0'
>>>> format=GML
>>>> Exporting 355021 areas (may take some time)...
>>>>
>>>> Any idea?
>>>>
>>>> Pierre
>>>>
>>>>> Roger
>>>>>
>>>>>>
>>>>>>> And GDAL 1.7.1 is not the current
>>>>>>> version, which is 1.7.3. Did you install GDAL and/or GRASS from
>>>>>>> source,
>>>>>>> or
>>>>>>> from binaries (in my experience, installing from source ensures more
>>>>>>> consistency, and the GDAL/OGR GRASS plugins are often the source of
>>>>>>> problems
>>>>>>> because of version mismatch).
>>>>>>
>>>>>> I installed both GRASS 6.4 and GDAL/OGR from binaries, yes.
>>>>>>
>>>>>>> PS. The best list is probably:
>>>>>>>
>>>>>>> http://grass.osgeo.org/statsgrass/index.php
>>>>>>
>>>>>> OK. I am sending that message to that list, and keep R-sig-geo for
>>>>>> consistency. Sorry for cross-posting.
>>>>>>
>>>>>> Thanks again,
>>>>>>
>>>>>> Pierre
>>>>>>
>>>>>>>
>>>>>>> Roger
>>>>>>>
>>>>>>>
>>>>>>> as it is more specific, and also seen by GRASS developers.
>>>>>>>
>>>>>>>>
>>>>>>>> I tried to play with the different options but I did not succeed>
>>>>>>>> Here's more info about my data and platform:
>>>>>>>>
>>>>>>>> Here is the output of v.info for the data I want to load:
>>>>>>>> GRASS 7.0.svn (NZTM2000):~ > v.info ph_cl
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> +----------------------------------------------------------------------------+
>>>>>>>> | Name: ph_cl
>>>>>>>> |
>>>>>>>> | Mapset: nitrif_inhib
>>>>>>>> |
>>>>>>>> | Location: NZTM2000
>>>>>>>> |
>>>>>>>> | Database: /home/roudierp/Documents/GRASSDATA
>>>>>>>> |
>>>>>>>> | Title:
>>>>>>>> |
>>>>>>>> | Map scale: 1:1
>>>>>>>> |
>>>>>>>> | Map format: native
>>>>>>>> |
>>>>>>>> | Name of creator: roudierp
>>>>>>>> |
>>>>>>>> | Organization:
>>>>>>>> |
>>>>>>>> | Source date: Mon Dec 13 11:30:11 2010
>>>>>>>> |
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> |----------------------------------------------------------------------------|
>>>>>>>> | Type of map: vector (level: 2)
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>> | Number of points: 0 Number of centroids:
>>>>>>>> 236847
>>>>>>>> |
>>>>>>>> | Number of lines: 0 Number of boundaries:
>>>>>>>> 892041
>>>>>>>> |
>>>>>>>> | Number of areas: 355021 Number of islands:
>>>>>>>> 79124
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>> | Map is 3D: No
>>>>>>>> |
>>>>>>>> | Number of dblinks: 1
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>> | Projection: Transverse Mercator
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>> | N: 6190887.80270169 S: 4823266.04395524
>>>>>>>> |
>>>>>>>> | E: 2091804.65744429 W: 1170289.3071784
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>> | Digitization threshold: 0
>>>>>>>> |
>>>>>>>> | Comment:
>>>>>>>> |
>>>>>>>> |
>>>>>>>> |
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> +----------------------------------------------------------------------------+
>>>>>>>>
>>>>>>>> And finally some metadata about the software packages I used:
>>>>>>>>
>>>>>>>> here's the sessionInfo():
>>>>>>>>
>>>>>>>>> sessionInfo()
>>>>>>>>
>>>>>>>> R version 2.12.0 (2010-10-15)
>>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>>>>>
>>>>>>>> locale:
>>>>>>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>>>>>>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
>>>>>>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>>>>>>
>>>>>>>> attached base packages:
>>>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>>>
>>>>>>>> other attached packages:
>>>>>>>> [1] spgrass6_0.6-21 XML_3.2-0 rgdal_0.6-31 sp_0.9-74
>>>>>>>>
>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>> [1] grid_2.12.0 lattice_0.19-13
>>>>>>>>
>>>>>>>>> library(spgrass6)
>>>>>>>>
>>>>>>>> Loading required package: sp
>>>>>>>> Loading required package: rgdal
>>>>>>>> Geospatial Data Abstraction Library extensions to R successfully
>>>>>>>> loaded
>>>>>>>> Loaded GDAL runtime: GDAL 1.7.1, released 2010/02/08
>>>>>>>> Path to GDAL shared files: /usr/share/gdal
>>>>>>>> Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
>>>>>>>> Path to PROJ.4 shared files: /usr/share/proj/
>>>>>>>> Loading required package: XML
>>>>>>>> GRASS GIS interface loaded with GRASS version: 7.0.svn
>>>>>>>> and location: NZTM2000
>>>>>>>>
>>>>>>>> I got the last CRAN version of sp.
>>>>>>>>
>>>>>>>> This runs on a linux machine:
>>>>>>>> GRASS 7.0.svn (NZTM2000):~ > uname -a
>>>>>>>> Linux A208_RoudierP 2.6.34.7-0.5-xen #1 SMP 2010-10-25 08:40:12
>>>>>>>> +0200
>>>>>>>> x86_64 x86_64 x86_64 GNU/Linux
>>>>>>>>
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Pierre
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-sig-Geo mailing list
>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Roger Bivand
>>>>>>> Economic Geography Section, Department of Economics, Norwegian School
>>>>>>> of
>>>>>>> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>>>>>>> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>>>>>>> e-mail: Roger.Bivand at nhh.no
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Roger Bivand
>>>>> Economic Geography Section, Department of Economics, Norwegian School
>>>>> of
>>>>> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>>>>> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>>>>> e-mail: Roger.Bivand at nhh.no
>>>>
>>>
>>> --
>>> Roger Bivand
>>> Economic Geography Section, Department of Economics, Norwegian School of
>>> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>>> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>>> e-mail: Roger.Bivand at nhh.no
>>>
>>
>
> --
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
>
--
Scientist
Landcare Research, New Zealand
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