[R-sig-Geo] readOGR and PostGIS: "Error getting field 0"
Roger Bivand
Roger.Bivand at nhh.no
Fri Nov 30 17:27:52 CET 2012
On Fri, 30 Nov 2012, Mathieu Basille wrote:
> Dear Roger,
>
> Thanks a lot for your very fast answer! Here are the requested outputs:
>
> Le 30/11/2012 10:39, Roger Bivand a écrit :
>> On Fri, 30 Nov 2012, Mathieu Basille wrote:
>>
>>> Dear R users,
>>>
>>> I have a working PostGIS database that I routinely access through R,
>>> using readOGR or readGDAL. I have this point layer, however, that I can't
>>> read in R:
>>>
>>>> ctrdcoast <- readOGR("PG:dbname=florida host=localhost user=pguser",
>>>> layer
>>> = "gis.world_ctrdcoast")
>>> OGR data source with driver: PostgreSQL
>>> Source: "PG:dbname=florida host=localhost user=pguser", layer:
>>> "gis.world_ctrdcoast"
>>> with 35398 features and 2 fields
>>> Error in readOGR("PG:dbname=florida host=localhost user=pguser", layer =
>>> "gis.world_ctrdcoast") :
>>> Error getting field 0
>>>
>>> The layer is basically a table with just 2 fields: geom (a point feature)
>>> and gid (a serial primary key). I can export this layer without any
>>> problem using ogr2ogr, and the layer looks fine to me (it displays fine
>>> in QGIS):
>>>
>>> ogr2ogr -f "ESRI Shapefile" ctrd.shp PG:"dbname=florida host=localhost
>>> user=pguser" "gis.world_ctrdcoast"
>>>
>>> Any idea where this is going wrong? Thanks in advance for any suggestion.
>>> Mathieu.
>>
>> The error message is from ogrReadColumn(), line 221 in src/ogrsource.cpp,
>> for example here:
>>
>> https://r-forge.r-project.org/scm/viewvc.php/pkg/src/ogrsource.cpp?view=markup&root=rgdal
>>
>>
>> What does ogrInfo() report?
>
> $ ogrinfo "PG:dbname=florida host=localhost user=pguser" gis.world_ctrdcoast
> -summary
> INFO: Open of `PG:dbname=florida host=localhost user=pguser'
> using driver `PostgreSQL' successful.
>
> Layer name: gis.world_ctrdcoast
> Geometry: Unknown (any)
> Feature Count: 35398
> Extent: (-179.916500, -59.083000) - (179.968500, 83.535000)
> Layer SRS WKT:
> (unknown)
> FID Column = gid
> Geometry Column = geom
>
> I noticed there was a call to ogrInfo in the readOGR function. After this
> line, here is what's reported:
>
> Browse[2]> ogr_info
> Source: "PG:dbname=florida host=localhost user=pguser", layer:
> "gis.world_ctrdcoast"
> Driver: PostgreSQL number of rows 35398
> Feature type: wkbPoint with 2 dimensions
> NA
> Number of fields: 0
> [1] name type length typeName
> <0 rows> (or 0-length row.names)
>
Thanks very much, this is the information needed, that there are no
fields. It appears that at least in this driver, readOGR() needs to be
able to return a geometry-only object, or to create a GID column in the
data.frame. I'll let you know when I've committed to R-forge, and will be
very grateful if you can check out the source package, install, and test
whether the changes have helped. It may take a little time to get there,
but I'll give it priority.
Roger
>
>> Does it make a difference if you add an extra
>> field?
>
> As a matter of fact, it does! If I add a serial field named 'bla', it works
> perfectly:
>
>> ctrdcoast <- readOGR("PG:dbname=florida host=localhost user=pguser", layer
> = "gis.world_ctrdcoast")
> OGR data source with driver: PostgreSQL
> Source: "PG:dbname=florida host=localhost user=pguser", layer:
> "gis.world_ctrdcoast"
> with 35398 features and 1 fields
> Feature type: wkbPoint with 2 dimensions
>
>> summary(ctrdcoast)
> Object of class SpatialPointsDataFrame
> Coordinates:
> min max
> coords.x1 -179.9165 179.9685
> coords.x2 -59.0830 83.5350
> Is projected: NA
> proj4string : [NA]
> Number of points: 35398
> Data attributes:
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> 1 8850 17700 17700 26550 35400
>
>> head(ctrdcoast at data)
> bla
> 1 1
> 2 2
> 3 3
> 4 4
> 5 5
> 6 6
>
>
>> I'm wondering whether in this case the GID is not being seen as a
>> field as such, but the FID of the point. Possibly ogr2ogr steps round this.
>
> It looks like a correct guess, given the output of ogrinfo. In addition, the
> exported shapefile from ogr2ogr present one field (named FID), while if I
> load the table into QGIS, I can see the field with its correct name (gid).
> Admittedly, while I'm pretty sure that QGIS uses GDAL to load tables, I have
> no idea how it deals with it.
>
>
>> I don't have a PostGIS system running, so may need help debugging. If you
>> debug(readOGR), what happens here:
>>
>> if (drop_unsupported_fields) {
>> iflds <- as.integer((1:ogr_info$nitems)-1)
>> iflds <- iflds[keep]
>> fldnms <- ogr_info$iteminfo$name[keep]
>> if (any(!keep)) warning(paste("Fields dropped:",
>> paste(ogr_info$iteminfo$name[!keep], collapse=" ")))
>> } else {
>> if (any(!keep)) stop(paste("Unsupported field type:",
>> paste(ogr_info$iteminfo$typeName[!keep], collapse=" ")))
>> iflds <- as.integer((1:ogr_info$nitems)-1)
>> fldnms <- ogr_info$iteminfo$name
>> }
>
> Browse[2]> ogr_info$nitems
> [1] 0
> Browse[2]> iflds
> [1] 0 -1
> Browse[2]> fldnms
> character(0)
>
>
>> I think ogr_info$nitems is 1, so we get 0, but if ogr_info$nitems is 0, (0,
>> -1).
>
> Does that mean that we necessarily need a field in the table (in addition to
> geom + gid)? It's not hard to 'fix' by adding a nonsensical field, but I find
> it quite counterintuitive.
>
> Thanks again for the help!
> Mathieu.
>
>
>> Roger
>>
>>
>>
>>
>>>
>>>
>>>> sessionInfo()
>>> R version 2.15.1 (2012-06-22)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8
>>> [4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8
>>> LC_MESSAGES=fr_FR.UTF-8
>>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
>>> [10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] raster_2.0-31 rgdal_0.7-22 sp_1.0-2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_2.15.1 grid_2.15.1 lattice_0.20-6 tools_2.15.1
>>>
>>>
>>> # SELECT PostGIS_Full_Version();
>>>
>>> postgis_full_version
>>> -------------------------------------------------------------------------
>>> POSTGIS="2.1.0SVN r10597" GEOS="3.3.3-CAPI-1.7.4" PROJ="Rel. 4.7.1, 23
>>> September 2009" GDAL="GDAL 2.0dev, released 2011/12/29" LIBXML="2.8.0"
>>> LIBJSON="UNKNOWN" TOPOLOGY RASTER
>>>
>>>
>>>
>>>
>>
>
>
--
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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