Hello Loïc
Let’s keep the discussion on the list, so others can help and benefit from responses.
BTW, you might want to post to the r-sig-geo list also. If you come across questions specific to R and spatial functions, that’s the best place to ask.
Below,inline, some guesses as to what is happening…
···
On 07/07/2020 0:03, Loïc Valéry wrote:
Dear Micha, As you expected, I should have kept a few thanks in stock ! ;-) because I have a new little problem with rgrass7 ! In fact, when I run the script that you kindly corrected me (as a reminder, our exchange of previous emails is below) , everything goes fine...the first time. If I run the script a second time, I get an error message from Windows and another one from R (see below). For the script to work properly again I have to close and open R (or use the .rs.rstartR() command from RStudio) which is not very convenient because it stops the script. I tried to fix this error but without success. That's why I'm contacting you, hoping you will have an idea on how to "reset" rgrass7 without having to restart a new session. I thank you in advance for your answer and remain at your disposal if you need additional information to find the solution. Kind regards, Loïc ERRORS WHEN I RUN THE SCRIPT FOR A SECOND TIME : - FROM WINDOWS : g.region.exe : the procedure entry point GEOSMakeValid_r could not be located in the dynamic link library C:\Program Files\GRASS GIS 7.8\extrabin\gdal300.dll - FROM R : # Link to GRASS GIS software v.7.8.3initGRASS(gisBase ="C:/Program Files/GRASS GIS 7.8",+ home="temp/GRASS_tmp", use_g.dirseps.exe=F, + gisDbase="temp/GRASS_tmp", mapset="PERMANENT", + remove_GISRC=T, override=T) Error in if (is.na(projstr)) uprojargs <- projstr else uprojargs <- paste(unique(unlist(strsplit(projstr, : l'argument est de longueur nulle De plus : There were 50 or more warnings (use warnings() to see the first 50)
I’m not sure, but I don’t think you want to reruninitGRASS()a second time. In your script, you do initGRASS only once, then if you need to perform several analyses, do them in the same (running) GRASS session.
# Specifying the projection reference for the GRASS working environment p4str<-sp::proj4string(seg_poly)Warning message: In sp::proj4string(seg_poly) : CRS object has comment, which is lost in outputexecGRASS("g.proj", flags = "c", proj4 = p4str) rgrass7::use_sp() # Converting the 'sp' object into a GRASS-readable file format (here, 'vec1.shp') writeVECT(seg_poly,"vec1",v.in.ogr_flags=c("o", "overwrite"),+ driver="ESRI Shapefile")
The driver name is “ESRI_Shapefile” (note the underscore). Perhaps that is the problem here?
Error in writeVECT(seg_poly, "vec1", v.in.ogr_flags = c("o", "overwrite"), : driver %in% candDrivers is not TRUE De plus : Warning message: In system(syscmd, intern = intern, ignore.stderr = ignore.stderr, : l'exécution de la commande 'v.in.ogr.exe -f' renvoie un statut 313# Run the 'v.generalize' function execGRASS("v.generalize",flag=c("overwrite"),+ parameters=list(input="vec1", + output="GRASS_smooth_seg_poly", + error="GRASS_smooth_seg_poly_error", + method="distance_weighting", + threshold=1))# Converting the shapefile 'GRASS_smooth_seg_poly.shp' into a R-readable object # (here, a SpatialPolygonDataFrame named 'smooth_seg_poly') smooth_seg_poly<-readVECT("GRASS_smooth_seg_poly", with_prj=T,+ driver="ESRI Shapefile")
Same here, the driver name for shapefile is wrong.
I would also add that both R and GRASS have switched to the better Geopackage format for exchanging spatial data. You might want to try, the driver name is “GPKG”
See details about Geopackage here:
https://www.gis-blog.com/geopackage-vs-shapefile/
and in French here:
https://www.sigterritoires.fr/index.php/le-format-geopackage-et-qgis-3/
Best, Micha
Error in .read_vect_non_plugin(vname = vname, layer = layer, type = type, : driver %in% candDrivers is not TRUE De plus : Warning message: In system(syscmd, intern = intern, ignore.stderr = ignore.stderr, : l'exécution de la commande 'v.in.ogr.exe -f' renvoie un statut 313 PREVIOUS EMAILS: De : Micha Silver [<tsvibar@gmail.com>](mailto:tsvibar@gmail.com) Envoyé : mardi 9 juin 2020 23:08 À : Loïc Valéry [<lvalery@outlook.fr>](mailto:lvalery@outlook.fr) Objet : Re: [R] Need help using GRASS within R - problem with CRS using the 'v.generalize' command On 09/06/2020 16:22, Loïc Valéry wrote: Dear Micha, A thousand thanks for your help. It works now! Whoa, you'd better save some thanks for the next question. ;-) For your information and following your remark, I also updated rgdal. Thanks again for taking the time to answer me. Kind regards Loïc De : Micha Silver [<tsvibar@gmail.com>](mailto:tsvibar@gmail.com) Envoyé : mardi 9 juin 2020 08:44 À : Loïc Valéry [<lvalery@outlook.fr>](mailto:lvalery@outlook.fr); [r-help@R-project.org](mailto:r-help@R-project.org) [<r-help@R-project.org>](mailto:r-help@R-project.org) Objet : Re: [R] Need help using GRASS within R - problem with CRS using the 'v.generalize' command Hello On 08/06/2020 19:52, Loïc Valéry wrote:Dear all, First of all, this is my first message on the list. Therefore, please be indulgent if my message is not perfectly formatted as it should be. I am currently encountering a difficulty with GRASS 7.8 within R when using the 'v.generalize' command to smooth the contour of polygons after a segmentation step. I tried two different ways to "call" GRASS: 1 - using the RQGIS3 packageMy first suggestion: no need for getting QGIS involved here. That's an extra layer of complication that seems unnecessary, given your goal of using the GRASS module, v.generalize.2 - using the rgrass7 package The first method returns an error message (i.e. "proj_create_from_database: Cannot find proj.db") and therefore does not produce any result. The second method results in a layer of smoothed polygons but the projection reference (i.e. CRS) is lost whereas the input layer has one. Since in both cases the problem seems to be the same (i.e. GRASS fails to access the projection information), I thought it was interesting to deal with these two cases simultaneously. So, below you will find two small examples - each dealing with one of the two procedures - in order to clarify the problem. 1 - Example using the RQGIS3 package :setwd("D:/test") library(sp) library(rgdal)rgdal: version: 1.4-8, (SVN revision 845) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20 Path to GDAL shared files: C:/Users/toto/Documents/R/win-library/3.6/rgdal/gdal GDAL binary built with GEOS: TRUE Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493] Path to PROJ.4 shared files: C:/Users/toto/Documents/R/win-library/3.6/rgdal/proj Linking to sp version: 1.4-1Please note that you have older versions of GDAL (2.2.3 here) and PROJ.4 (4.9 here). These are currently being replaced by GDAL 3.0 and PROJ 6.3. You might (should) want to follow the discussion the the r-sig-geo maillist: [https://stat.ethz.ch/pipermail/r-sig-geo/2020-June/028165.html](https://stat.ethz.ch/pipermail/r-sig-geo/2020-June/028165.html) ....... (skipped all the discussion regarding RQGIS3 as I think it's not relevant)2 - EXAMPLE USING THE RGRASS7 PACKAGE seg_poly = a SpatialPolygonsDataFrame with CRS (cf. below) :setwd("D:/test") library(rgrass7) # characteristics of the SpatialPolygonsDataFrame 'seg_poly' : CRS does exist seg_polyclass : SpatialPolygonsDataFrame features : 31 extent : 477371.3, 477397.6, 5631995, 5632020 (xmin, xmax, ymin, ymax) crs : +proj=utm +zone=32 +datum=WGS84 +units=m +no_defs variables : 1 names : Seg_ID min values : 1 max values : 31 Warning message: In proj4string(x) : CRS object has comment, which is lost in output# initialization of GRASS 7.8 from R initGRASS(gisBase ="C:/Program Files/GRASS GIS 7.8", home="temp/GRASS",gisDbase="temp/GRASS", use_g.dirseps.exe=F,remove_GISRC=T, override=T)gisdbase temp/GRASS location file19685026c56 mapset file196829fa7141 rows 1 columns 1 north 1 south 0 west 0 east 1 nsres 1 ewres 1 projection NA I suspect that the problem comes from 'projection NA' when initializing GRASS (cf. just above)What you need to do here is setup the CRS of your new location. Typically, you would run initGRASS and point to a *previously created* LOCATION, with CRS already defined. In this case, since you are creating a new location, you must define it's coordinate system. (GRASS is very "picky" about that). Here's a GIS Stackexchange post that explains: [https://gis.stackexchange.com/questions/183032/create-a-new-grass-database-in-r-with-crs-projection](https://gis.stackexchange.com/questions/183032/create-a-new-grass-database-in-r-with-crs-projection) You can derive the full proj4 string from your sp object with: p4str = sp::proj4string(seg_poly) Then use that to set the project parameters for the new LOCATION, with execGRASS("g.proj", flags = "c", proj4 = p4str) Now you should be able to continue with...execGRASS("v.generalize",flag=c("overwrite"),parameters=list(input="vec1",+ output="GRASS_smooth_seg_poly", + error="GRASS_smooth_seg_poly_error", + method="distance_weighting", + threshold=1)) As a novice in the field, I would be very grateful for your help. I remain at your entire disposal for any further information you may need to help me in finding a solution to this problem. Yours sincerely, Loïc ______________________________________________ [R-help@r-project.org](mailto:R-help@r-project.org) mailing list -- To UNSUBSCRIBE and more, see [https://stat.ethz.ch/mailman/listinfo/r-help](https://stat.ethz.ch/mailman/listinfo/r-help) PLEASE do read the posting guide [http://www.R-project.org/posting-guide.html](http://www.R-project.org/posting-guide.html) and provide commented, minimal, self-contained, reproducible code.
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Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
[https://orcid.org/0000-0002-1128-1325](https://orcid.org/0000-0002-1128-1325)
