readRAST6() in {spgrass6}
On Tue, 17 May 2011, Sam Prentice wrote:
Hello,
After resampling down and subsetting my DEM derivatives using g.region, I am
getting the same error. The first input file ("clip1_er1m") is now 550KB,
and the .tmp file in the error is 800KB. Code and output copied below. Am I
correct now in concluding this is not an issue with data size/structure? Any
further thoughts about how to proceed?
Fortunately, you have now given some useful information, suggesting that you have not understood how to use the interface. I do not have your location, so cannot check. It appears that your workflow is highly non-standard - which you have not made clear previously. If you are using spgrass6 to interface R with an existing GRASS location - which seems to be the case, you should not use initGRASS(), and should not use the PERMANENT mapset. The initGRASS() function is for creating one-time, throwaway GRASS locations to use GRASS modules from R when no GISDBASE or LOCATION is required. Under Linux, I cannot reproduce this problem, in addition you seem to be using a Windows server OS, to which I have no access. Start GRASS under Windows from the MSYS/GRASS icon, selecting the location and mapset (not PERMANENT) in the usual way for interactive use. Then start R from the MSYS console prompt - perhaps other possibilities exist for starting R within GRASS for the Windows native build of 6.4.1. R will then be "inside" the GRASS session defined by the GRASS environmental variables and the GISRC file. I do not know if you can run non-interactive on Windows, it isn't a common situation. If you can start GRASS from a Windows console/terminal - interactively, next start R from the GRASS prompt - you will need to be very careful to set PATH variables. Windows by definition is supposed to be run interactively, as its name suggests. Finally, this is not the correct list for detailed R/GRASS questions - you are asking about things which are very specific. Use this list instead: http://lists.osgeo.org/mailman/listinfo/grass-stats Roger
Sam
# PREPEND
require(spgrass6)
require(cluster)
# READ IN SPATIAL DATA FROM GRASS IN R SESSION
initGRASS("C:/Program Files (x86)/GRASS 6.4.1", home = tempdir(),
,"D:/GRASSdata", "Sedgwick2", "PERMANENT", override = "TRUE")
gmeta6 = gmeta6()
gisdbase D:/GRASSdata
location Sedgwick2
mapset PERMANENT
rows 500
columns 402
north -3569501
south -3570001
west -19670403
east -19670001
nsres 1
ewres 1
projection +proj=utm +no_defs +zone=10 +a=6378137 +rf=298.257223563
+towgs84=0.000,0.000,0.000 +to_meter=1
#read in raster files
x =
readRAST6(c("clip1_er1m","clip1_crosC_1m","clip1_longC_1m","clip1_slope5","c
lip1_profC","clip1_miniC_1m","clip1_maxiC_1m"))
D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/clip1_er1m has GDAL driver GTiff
and has 500 rows and 402 columns
Permission denied
Error in deleteDataset(DS) :
GDAL Error 1: Deleting
D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/clip1_er1m failed:
Permission denied
|-----Original Message-----
|From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
|Sent: Monday, May 16, 2011 9:28 PM
|To: Sam Prentice
|Cc: Dylan Beaudette; r-sig-geo at r-project.org
|Subject: Re: [R-sig-Geo] readRAST6() in {spgrass6}
|
|On Mon, 16 May 2011, Dylan Beaudette wrote:
|
|> It is hard to know what the upper-limit is on Windows-- as the memory
|> is usually fragmented by the operating system.
|
|Correct, the upper limit on other OS is higher in practice.
|
|>
|> Since you are using GRASS, I would first try a coarsened version of
|> your terrain-shape rasters via the built-in re-sampling functionality.
|> While this is not ideal, as it is NN-based, it will give a quick way
|> to try out methods.
|>
|> After you have initialized your GRASS connection in R, execute something
|like:
|>
|> system('g.region res=10 -ap')
|>
|> This will align the region along a 10x10 map unit grid. All further
|> interaction with raster data will be automatically re-sampled to this
|> grid system.
|
|Right, for some res=, you will get a systematic sample that will let you
|decimate your data. Randomly shifting the window while resampling will help
|you see whether your classification model boundaries change.
|
|As both Dylan and I have said, there is no good reason for calibrating the
|classification model with more data than necessary, even if it were
possible.
|The only reason to use very much data would be if discrimination between
|very rare classes is your target, but even then you could stratify your
sample
|to get better representation of critical areas.
|
|You seem to be looking for classification signatures, from which you are
going
|to predict. Sampling will give you distributions of these signatures, which
could
|be used for similation by tile. If you are very concerned about the
statistical
|quality of your classification signatures, you could go fuzzy, but your
main goal
|is to get to the distributions of these signatures, IMO. Once you have
them,
|you can predict. You do not need to have GBs of dat in memory to do this
|adequately.
|
|So one could agree that software (OS, R, whatever) is your limitation, but
it is
|only a limitation if you are not able to consider more statistical
approaches to
|your apparent problem, which is finding out how to classify your input, and
|then to predict to output.
|
|Roger
|
|>
|> Dylan
|>
|> On Mon, May 16, 2011 at 2:25 PM, Sam Prentice <sep at umail.ucsb.edu>
|wrote:
|>> Thanks you for your suggestions. This error is not affected by choice
|>> of mapset, and is not limited by my hardware.
|>>
|>> Further info: I'm running 64-bit windows, 16MB memory, w/multiple cores.
|>> GRASS 6.4.1, R 2.12.2. I'm running standalone R using initGRASS() to
|>> set GRASS env parameters. The GRASS files I'm trying to read-in are
|>> DEM derivatives, each ~170MB. The intermediate .tmp file in the error
|>> message is 300MB.
|>>
|>> It's been suggested that I am "likely trying to import too much data
|>> into R". Assuming non-limiting computer power, what is the upper
|>> bound on amount of data that can be read into R from GRASS? If not a
|>> fixed amount, what are the main conditions that cause it to vary? I
|>> did not see this addressed in the {spgrass6} documentation, so I'm
|>> assuming it's a base R limitation, but maybe not? Quantifying this
|>> limitation will help determined how to move forward (e.g, resampling
|>> at smaller scale versus subsetting my DEM derivatives).
|>>
|>> Thanks,
|>> Sam
|>>
|>> |-----Original Message-----
|>> |From: Pierre Roudier [mailto:pierre.roudier at gmail.com]
|>> |Sent: Tuesday, May 10, 2011 3:40 PM
|>> |To: Sam Prentice
|>> |Cc: r-sig-geo at r-project.org
|>> |Subject: Re: [R-sig-Geo] readRAST6() in {spgrass6}
|>> |
|>> |Could that message have anything to do with the fact that this is a
|>> |layer
|>> from
|>> |the PERMANENT mapset?
|>> |
|>> |My two cents,
|>> |
|>> |Pierre
|>> |
|>> |2011/5/11 Sam Prentice <sep at umail.ucsb.edu>:
|>> |> Hi,
|>> |>
|>> |>
|>> |>
|>> |> I'm running R 2.12.2 via Tinn-R on Windows Server 2008. I'm using
|>> |> R for cluster analysis for terrain classification and I'm getting
|>> |> the following error when parsing GRASS data into R:
|>> |>
|>> |>
|>> |>
|>> |>> x =
|>> |>
|>>
||readRAST6(c("param_elev3","param_crosC_1m","param_longC_1m","para
|m
|>> |_slope5","
|>> |> param_profC","param_miniC_1m","param_maxiC_1m"))
|>> |>
|>> |> D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/param_elev3 has GDAL
|driver
|>> |> GTiff
|>> |>
|>> |> and has 6224 rows and 6242 columns
|>> |>
|>> |>
|>> |>
|>> |> Error in deleteDataset(DS) :
|>> |>
|>> |> GDAL Error 1: Deleting
|>> |> D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/param_elev3 failed:
|>> |>
|>> |> Permission denied
|>> |>
|>> |>
|>> |>
|>> |> On the surface this looked like an issue with user privileges,
|>> |> since I do not have admin-level user privileges on this machine.
|>> |> However, this has been corrected - I now have permissions on the
|>> |> .tmp directory listed in the error, and I can create, append, and
|>> |> delete any file in that location, but the error is still occurring.
|>> |>
|>> |>
|>> |>
|>> |> Thoughts?
|>> |>
|>> |>
|>> |>
|>> |> Thanks,
|>> |>
|>> |> Sam
|>> |>
|>> |>
|>> |> [[alternative HTML version deleted]]
|>> |>
|>> |> _______________________________________________
|>> |> R-sig-Geo mailing list
|>> |> R-sig-Geo at r-project.org
|>> |> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|>> |>
|>> |
|>> |
|>> |
|>> |--
|>> |Scientist
|>> |Landcare Research, New Zealand
|>>
|>> _______________________________________________
|>> R-sig-Geo mailing list
|>> R-sig-Geo at r-project.org
|>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|>>
|>
|> _______________________________________________
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|> 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