spgrass6, readVECT and overwriting ?

Mr Krug,


It is difficult to reproduce an example from the spearfish dataset as it
doesn't natively contain data in it close to the one I used.

To give you th context, my goal is to detect all blue features : rivers
from a topographic map, ie 3-band RGB raster.

With RStoolbox, I perform a Spectral Angle Classification of my data using
sample points located on (near)blue pixels

With GRASS, I then thin, vectorize and clean the result.

As the process must be performed on a very large scale, I split it using
grids where sample RGB parts of the topo map are extracted with
gdal_translate. Everything is executed within a loop. At the end of the
loop, I export the resulted cleant shapefile in a folder. At the end, I
have as many shapefiles as processing grids.

That's why I use temporary vector datasets inside GRASS that are
overwritten at each loop instead of storing each individual result. I
noticed that in my process, the vector data read in the grass database was
not correct : always the first one. Because in fact, it didn't manage to
delete the temporary file before writing the new one..

The best I can do, is give you part of the code as as you can see the
context.

Thanks for the code improvements with file.remove and unlink !

Cheers,

Mathieu

for (id in 1:length(grids)) {

(...)

## SMOOTH
  print(">> SMOOTH")
  smoothed = smooth(sieved, 9)
  values(smoothed)[values(smoothed) > 0] = 1
  values(smoothed)[values(smoothed)==0] = NA

  ## THIN
  # WRITE TO GRASS
  writeRAST(as(smoothed, "SpatialGridDataFrame"), "bdtopo", zcol="layer",
flags=c("overwrite"))
  execGRASS("g.region", rast="bdtopo")
  execGRASS("r.thin", parameters=list(input="bdtopo", output="thin"),
flags=c("overwrite"))
  thin = raster(readRAST("thin"))

  ## CLEAN
  execGRASS("r.to.vect", parameters=list(input="thin", output="thin",
feature="line"), flags=c("overwrite"))
  execGRASS("v.clean", parameters=list(input="thin", tool="rmdangle",
output="clean", thresh=20), flags=c("overwrite"))

  # REMOVE FILES
  G = gmeta()
  tmpDir = file.path(G$GISDBASE, G$LOCATION_NAME, G$MAPSET, ".tmp")
  file.remove( list.files(path = tmpDir, Pattern ="^clean.*$", full.names
= TRUE))

  # READ TO SPDF
  execGRASS("v.out.ogr", parameters=list(input="clean", type="line",
dsn=tmpDir, olayer="clean", format="ESRI_Shapefile"))
  cleaned = readOGR(tmpDir, "clean")

  ## EXPORT
  writeOGR(cleaned, "OUT/CLEANED", id, "ESRI Shapefile")
}

2015-10-27 14:11 GMT+01:00 Rainer M Krug <Rainer at krugs.de>:

Mathieu Rajerison <mathieu.rajerison at gmail.com> writes:

Dear Mr Krug,

I'll Cc the R-sig-geo list in to keep the conversation there for future
reference and for other users who might have the same problem.

Sorry in advance for my english.

Don't worry abut your English - it is perfectly fine.

My question was not about debugging, but about a potentiel generic
behaviour of spgrass6.

I should have reformulated my question in a simpler manner : does

spgrass6

allow overwriting an existing dataset when using readVECT function ?

The functions readVect / RAST are using temporary files - you are right,
but they should delete these upon exit. So if they do nbot do this, it
is a bug.

1) no version information about R and GRASS (there are several GRASS 6
versions)
I've just put it at the end of this post.
2) no session information i.e. package versions used
the latest spgrass6
3) no information about the OS (I guess it is windows based on the
Source path above)
you're right

OK - thanks.

4) no reproducible example which could be easily done by using the GRASS

As I said - if you manually have to delete the temporary files, then
there is a bug in the package. Could you please provide a reproducible
example, using one of the example data sets from GRASS, so that I can
look at it?

5) as far as I can see, in the newest version of spgrass6 there is no
function readVECT()
Yes, there is, as you will see on page 14 of the documentation.

Sorry - overlooked it.

Finally, I solved the problem by using the following hint, "clean" being
the name of my temporary shapefile dataset :
  l = list.files("D:/GRASSDB/paca/mapset/.tmp", "^clean.*$"); l =
file.path("D:/GRASSDB/paca/mapset/.tmp", l)
  lapply(l,  file.remove)
  execGRASS("v.out.ogr", parameters=list(input="clean", type="line",
dsn="D:/GRASSDB/paca/mapset/.tmp", olayer="clean",

format="ESRI_Shapefile"))

OK - reformated, the code looks as follow:

--8<---------------cut here---------------start------------->8---
l = list.files("D:/GRASSDB/paca/mapset/.tmp", "^clean.*$")
l = file.path("D:/GRASSDB/paca/mapset/.tmp", l)
lapply(l,  file.remove)
execGRASS( "v.out.ogr",
           parameters=list(input="clean",
type="line",dsn="D:/GRASSDB/paca/mapset/.tmp", olayer="clean",
format="ESRI_Shapefile"))
--8<---------------cut here---------------end--------------->8---

as a side note, you should be able to do

file.remove( list.files(path = "D:/GRASSDB/paca/mapset/.tmp", Pattern =
"^clean.*$", full.names = TRUE) )

or

unlink("D:/GRASSDB/paca/mapset/.tmp/clean.*")

instead of the first three commands.

Now - in your example, you don't use the readVECT() function?

If you check in the GRASS help for v.out.ogr, you can specify the
overwrite flag and the exported layer will be overwritten.

But I have the feeling you are doing something in a to complicated way.

What is it you want to do, and e=what is the problem you have or the
error message you get?

Cheers,

Rainer

R.Version()

$platform
[1] "x86_64-w64-mingw32"
$arch
[1] "x86_64"
$os
[1] "mingw32"

$system
[1] "x86_64, mingw32"
(...)
$version.string
[1] "R version 3.1.2 (2014-10-31)"
$nickname
[1] "Pumpkin Helmet"

I will happily look int this if you can provide the necessary info.

Cheers,

Mathieu

2015-10-24 13:34 GMT+02:00 Rainer M Krug <Rainer at krugs.de>:

Mathieu Rajerison <mathieu.rajerison at gmail.com> writes:

Hi,

I'm using spgrass6 and I use readVECT function in a loop.

Using it causes an error because it doesn't overwrite the the

temporary

shapefile..

thin = readVECT(vname="zoneBDTOPOthin")

with_c: argument reversed from version 0.7-11 and in GRASS 6
ERROR :Layer <zoneBDTO> already exists in OGR data source
        'D:/GRASSDB/paca/mapset/.tmp'
OGR data source with driver: ESRI Shapefile
Source: "D:/GRASSDB/paca/mapset/.tmp", layer: "zoneBDTO"
with 770 features
It has 3 fields
Warning message:
running command 'v.out.ogr.exe -e -c input=zoneBDTOPOthin2 type=line
layer=1 dsn=D:/GRASSDB/paca/mapset/.tmp olayer=zoneBDTO
format=ESRI_Shapefile' had status 1


I wonder how to specify to spgrass that I want to overwrite the file

in

readVECT, although I know using execGRASS and v.out.ogr with the
appropriate overwrite flags would do the job.

Thanks in advance for the answer..

One reason why probably nobody replied is that

1) no version information about R and GRASS (there are several GRASS 6
versions)
2) no session information i.e. package versions used
3) no information about the OS (I guess it is windows based on the
Source path above)
4) no reproducible example which could be easily done by using the

GRASS

5) as far as I can see, in the newest version of spgrass6 there is no
function readVECT()

So I would suggest to provide the info and give a reproducible example
using a GRASS sample dataset
(see https://grass.osgeo.org/download/sample-data/ - the Spearfish
dataset is probably the best)

I will happily look int this if you can provide the necessary info.

Cheers,

Rainer

Mathieu

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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

PGP: 0x0F52F982