[R-sig-Geo] reading PostGIS table into sp data frame
Edzer Pebesma
edzer.pebesma at uni-muenster.de
Fri Dec 21 12:15:47 CET 2012
On 12/21/2012 11:41 AM, Edward Vanden Berghe wrote:
> The GDAL was installed from www.gisinternals.com/sdk; I installed the 32 bits version, though my Windows version is 64: the table on gisinternals.com stated that there was a build problem with the 64-bits version.
>
> rgdal was installed from CRAN, as a binary, version 0.7-20, build 2.15.1. R version is 2.15.2 (2012-10-26) -- "Trick or Treat", platform x86_64-w64-mingw32/x64 (64-bit).
>
> The output from ogrDrivers() is pasted below.
mine mentions
39 PostgreSQL TRUE
too. http://www.gdal.org/ogr/ogr_formats.html mentions that you'll need
to install the PostgreSQL client library (libpq), then compile gdal
against that, and then you'll have to to install rgdal from source on
top of that.
>
> If I understand you correctly, and since I am using the standard CRAN Windows binary package, I might be out of luck?
On the contrary. You may have arrived at the moment where you realize
that you can work with open source software quite easily in an
environment that is completely open source too. You may want to leave
windows. I can't even remember when I did this, but I do remember the
relief it brought.
You can also stay with windows, and solve the problems there. You might
even make a lot of windows/R/rgdal users happy if you publish the
outcome as a binary distribution, or if you publish instructions how to
install & build things on windows.
>
> Cheers,
>
> Edward
>
> Output from ogrDrivers():
>
> name write
> 1 AeronavFAA FALSE
> 2 ARCGEN FALSE
> 3 AVCBin FALSE
> 4 AVCE00 FALSE
> 5 BNA TRUE
> 6 CSV TRUE
> 7 DGN TRUE
> 8 DXF TRUE
> 9 EDIGEO FALSE
> 10 ESRI Shapefile TRUE
> 11 Geoconcept TRUE
> 12 GeoJSON TRUE
> 13 Geomedia FALSE
> 14 GeoRSS TRUE
> 15 GML TRUE
> 16 GMT TRUE
> 17 GPSBabel TRUE
> 18 GPSTrackMaker TRUE
> 19 GPX TRUE
> 20 HTF FALSE
> 21 Idrisi FALSE
> 22 KML TRUE
> 23 MapInfo File TRUE
> 24 Memory TRUE
> 25 MSSQLSpatial TRUE
> 26 ODBC TRUE
> 27 OpenAir FALSE
> 28 PCIDSK TRUE
> 29 PDS FALSE
> 30 PGDump TRUE
> 31 PGeo FALSE
> 32 REC FALSE
> 33 S57 TRUE
> 34 SDTS FALSE
> 35 SEGUKOOA FALSE
> 36 SEGY FALSE
> 37 SUA FALSE
> 38 SVG FALSE
> 39 TIGER TRUE
> 40 UK .NTF FALSE
> 41 VFK FALSE
> 42 VRT FALSE
> 43 XPlane FALSE
>
> -----Original Message-----
> From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
> Sent: 20 December 2012 20:58
> To: Edward Vanden Berghe
> Cc: r-sig-geo at r-project.org
> Subject: Re: [R-sig-Geo] reading PostGIS table into sp data frame
>
> On Thu, 20 Dec 2012, Edward Vanden Berghe wrote:
>
>> Thanks!
>>
>> Unfortunately I have no luck trying to get readOGR to work directly
>> with the PostGIS database. I tried different variations:
>
> Did you check whether your rgdal/GDAL supports the PostGIS driver? Did you look at the output of ogrDrivers()? If you did not install rgdal as a source package built against a GDAL that has the PostGIS driver on your platform (maybe OSGeo4W??), but are using the standard CRAN Windows binary package, then it is simply the case that the driver is not supported. On OSX using the Kyngchaos frameworks, or on Linux, this would be simple, but it isn't simple on Windows. You need to establish how rgdal was installed and report that.
>
> Hope this clarifies,
>
> Roger
>
>>
>>> sp.object <- readOGR(dsn="PG:dbname=...
>>> sp.object <- readOGR(dsn="my_dsn" ... [where my_dsn is a Windows
>>> system dsn] sp.object <- readOGR(dsn="PG:my_dsn" ...
>>
>> all result in the same error message:
>>
>> Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding = input_field_name_encoding) :
>> Cannot open file
>>
>> Another variation,
>>
>>> sp.object <- readOGR(dsn="ODBC:my_dsn" ...
>>
>> Results in
>>
>> Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding = input_field_name_encoding) :
>> Multiple # dimensions:
>>
>> though all he geometries are 2d, and there is a constraint enforcing
>> this in the database.
>>
>> It seems rgdal is properly installed: I can use readOGR to read shape
>> files (and this, actually, resolves my problem, as I can use this as a
>> work-around); also, ogrDrivers() returns a list of 43 drivers (but PG,
>> PostgreSQL or PostGIS are not among these; ESRI Shapefile and ODBC are).
>>
>> I have no problems connecting to the PostgreSQL database using either
>> DBI/RPostgreSQL, or RODBC (the latter with the same Windows system DSN
>> that I used for the tests above). I am not familiar with GDAL, don't
>> know how to try and connect to the PostgreSQL database from GDAL
>> directly, rather than through rgdal.
>>
>> Again, any insight in what might go wrong would be most appreciated.
>>
>> Cheers,
>>
>> Edward
>>
>> Message: 4
>> Date: Wed, 19 Dec 2012 14:58:52 +0100
>> From: Raffaele Morelli <raffaele.morelli at gmail.com>
>> To: r-sig-geo at r-project.org
>> Subject: Re: [R-sig-Geo] reading PostGIS table into sp data frame
>> Message-ID:
>> <CAD4guxOt5fSUPbK4VbbPuZf-oTBrcY-UvNPcguvUYt4qS0+_kQ at mail.gmail.com>
>> Content-Type: text/plain
>>
>> 2012/12/19 Edward Vanden Berghe <evberghe at gmail.com>
>>
>>> I wanted to create a global map with squares in lat-lon. I have
>>> PostGIS tables to define these squares but I havent been able to
>>> figure out an efficient way of reading those tables into R. The code I am using now is:
>>>
>>> crs <- CRS("+proj=longlat +ellps=WGS84")
>>> s <- paste("select id, st_astext(geom) as geom from
>>> geo.cs10d";",
>>> sep="")
>>> r <- dbGetQuery(con, s)
>>> p <- readWKT(r$geom[1],id=r$id[1],p4s=crs)
>>> for(i in 2:length(r$id)){
>>> p <- rbind(p, readWKT(r$geom[i], id=r$id[i], p4s=crs))
>>> }
>>>
>>> where geo.cs10d is the table with squares, id the primary key of the
>>> table, and geom the binary geometry field.
>>>
>>> The code above works fine for the larger squares, such as 10 degrees,
>>> of which I only need 648 to cover the globe. For finer resolutions,
>>> the above takes just too long I assume because the rbind function
>>> rewrites the whole sp object each time it executes. Ive seen other R
>>> scripts that initiate an empty data frame of the correct length to go
>>> round similar problems with the rbind function; I havent been able
>>> to find an equivalent for spatial polygons. How can I initiate an
>>> empty data frame with the right structure, and the right length?
>>>
>>> A preferable solution would be if there would be a single function to
>>> load a complete PostGIS table, rather than having to load the
>>> polygons one by one in a loop. Is there such a function?
>>>
>>> Im using PostgreSQL 8.4, PostGIS 1.5, R 2.15.2, platform
>>> x86_64-w64-mingw32; IDE is StatET 3.0.1 plugin for Eclipse 3.7.2.
>>>
>>> Any help would be much appreciated.
>>>
>>> Edward
>>>
>>
>> Use postgis st_transfom to convert your table in epsg:4326, I would
>> suggest to use a view for that.
>> Then use readOGR (in package rgdal) to read the table/view (geom and
>> attributes) in a sp object with :
>>
>> sp.object <- readOGR("PG:dbname=your_db host=your_host user=username
>> password=xxx", "geo.cs10d ")
>>
>> regards
>> -r
>>
>>
>>
>
> --
> Roger Bivand
> Department of Economics, NHH Norwegian School of Economics, 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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>
--
Edzer Pebesma
Institute for Geoinformatics (ifgi), University of Münster
Weseler Straße 253, 48151 Münster, Germany. Phone: +49 251
8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de
http://www.52north.org/geostatistics e.pebesma at wwu.de
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