[GRASS-stats] Re: [R-sig-Geo] Fail to load a vector layer using
spgrass6
Roger Bivand
Roger.Bivand at nhh.no
Thu Dec 16 05:04:17 EST 2010
On Wed, 15 Dec 2010, Dylan Beaudette wrote:
> 2010/12/15 Roger Bivand <Roger.Bivand at nhh.no>:
>> On Wed, 15 Dec 2010, Pierre Roudier wrote:
>>
>>> Roger,
>>>
>>>> The latest (0.6-23) spgrass6 has a fix for a specific problem in the
>>>> layer
>>>> parameter of v.out.ogr in GRASS7 - I see that you are using the previous
>>>> spgrass6. Could you try updating spgrass6?
>>>>
>>>
>>> I did update and got the same error on both GRASS 6.4 and GRASS 7.0
>>
>> Pierre,
>>
>> Please use a toy example, with a common data set such as spearfish. You have
>> 355021 areas, which must be getting close to maxing out what a shapefile can
>> take.
>>
>> Using GML is almost certainly a bad idea, as everything gets converted to
>> text.
>>
>> The main problem of trying to use other drivers than "ESRI Shapefile" is
>> that each driver has very specific requirements of the dsn and olayer
>> strings. The interface functions for vector data presuppose "ESRI
>> Shapefile", so dsn is a directory, and olayer is the shared file name within
>> the directory. This is what you are seeing in the error messages below. ESRI
>> Shapefile works with a directory as dsn, GML doesn't; ESRI Shapefile doesn't
>> work with a file as dsn, GML does. For GML, KML, and some others, the dsn is
>> a file name, and olayer is a placeholder. Providing the driver-specific
>> modifications is arguably not a robust way to proceed.
>>
>> I'm unsure about the advisability of persisting with a driver= argument. I'd
>> welcome arguments for or against, and if for, some R code to match the
>> drivers to the dsn/olayer formats, that does not presuppose the presence of
>> drivers that have external dependencies.
>
> Thanks for taking time to tinker with this possibility. I know this is
> asking a lot, but how about providing 2 well-supported drivers: say
> shapefiles and sqlite? Then, a simple switch statement could be used
> to describe the dsn, as opposed to a more generic option. Maybe this
> would introduce too many branches in the code-- but sometimes it would
> be really nice to have an alternative to shapefiles during this
> process.
This draft:
spgrass6_0.6-25.tar.gz
(also committed on CVS) provides ESRI Shapefile, MapInfo File, GML, and
SQLite intermediate formats. Could you please try it, to see if SQLite
handles the specific attribute data concerns you mentioned? The main
shapefile <> sqlite difference I see is that the shapefiles have 0-based
FIDs, the sqlite 1-based, and the sqlite files insist more forcefully on
having 3D coordinates, I think.
Best wishes,
Roger
>
>> I would suggest that you try to install the GRASS plugin for GDAL/OGR, and
>> try to use that, since an intermediate file solution with the standard
>> driver seems undesirable.
>
> I would second this.
>
> Cheers,
> Dylan
>
>
>> I'm also very unsure about what you want to do with the data in R.
>> Visualising will be painfully slow, and if you need to do analysis on the
>> attribute data alone, you may as well transfer just that, not the
>> geometries.
>>
>> Have you considered using a database back-end?
>>
>> Note that you have problems in ph_cl which require the c flag.
>>
>> Roger
>>
>>>
>>>> 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
>>
>> _______________________________________________
>> grass-stats mailing list
>> grass-stats at lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>>
>>
>
--
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
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