On Thu, 16 Dec 2010, Pierre Roudier wrote:
Thanks for your answer Roger - many interesting points for a GRASS
newbie like I am,
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 actually got the GRASS plugin for OGR - I just realized ogrDrivers()
displays the writing capabilities. As it is read-only, it shows FALSE.
As a result, foo <- readVECT6('ph_cl', plugin=F) works:
foo <- readVECT6('ph_cl', plugin=F)
Exporting 355021 areas (may take some time)...
100%
118174 features found without category were skipped
v.out.ogr complete. 236847 features written to <ph_cl> (ESRI_Shapefile).
OGR data source with driver: ESRI Shapefile
Source:
"/home/roudierp/Documents/GRASSDATA/NZTM2000/nitrif_inhib/.tmp/A208_RoudierP",
layer: "ph_cl"
with 236847 features and 14 fields
Feature type: wkbPolygon with 2 dimensions
Sorry about that - my bad :(
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).
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.
This is a very good point. I do not want to plot that data in R (I'm
not sure anybody would want to do that!), just some statistics on the
attributes. So, I guess loading the full geometry is a waste of time
and resources.
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?
Roger
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
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--
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: [email protected]
--
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: [email protected]
--
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: [email protected]
--
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: [email protected]
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