[Qgis-developer] QGIS - SEXTANTE - R

[Victor Olaya]

If you are using the latest version, you should have an example R script
called Advanced raster histogram, with the following code

##Classification=group

##Layer = raster|R.raster

##no_data_value = number 0

##showplots

Layer <- raster(Layer, 1)

NAvalue(Layer) = no_data_value

hist(as.matrix(Layer), breaks=100, xlab = basename(filename(Layer)))


It uses the raster package


What do you think of this solution? Leaving the current types "raster" and
"vector", which create the object in R, and then two additional ones
"rasterfile" and "vectorfile", that create the same interface but skip the
process of creating the obejct and pass the filename string to R. That woul
be more flexible, and not to complex.


For the latest docs, have a look at the QGIS doc repo:
http://github.com/qgis/QGIS-Documentation/tree/master/source/docs/user_manual/sextante


Regards

Victor



2013/2/22 Matteo Mattiuzzi <matteo at mattiuzzi.com>

> Sounds great!
> I could imagine to have a default method (for raster/vector) to facilitate
> the transfer of the data into R. I think rgdal is a quite low-level package
> that is also used by the raster package. I think that at least for raster
> data the package raster is the most advanced and most user-friendly package
> at all and also the most diffused in the community.
>
> to load a raster-file it has 3 function:
> raster # used for single layer raster data
> stack # used for multiple single- or multi-layer files loaded as 1
> multilayer file (requires identical extent, proj and resolution for all
> files), comparable with a BSQ file with separate sources
> brick # used for a multi-layer image (tipically BIP, BIL)
> # the problem could be here that the user has to know in advanced which
> one to use. In most of the cases its fairly simple, or the function stack()
> could handle every input, but I'm not sure it it is the best solution.
>
> to write a raster file:
> writeRaster
> Normally the raster package writes everything to a tmp folder, writeRaster
> is basically the function to move the file from the tmp to a definitive
> location handing datatype, filename, driver etc.
>
> For reading and writing vector data it presents some limited facilities,
> but very simple to use, could also be suitable as a default method, and if
> required it will be easy to amplify its functionality.
> shapefile # uses readOGR/writeOGR and can handle only ESRI shapefiles....
>
> From my point of view I could imagine to have such default, but I think it
> has to be easy to modify (as you wrote me!). I will try to mobilitate some
> R-SIG-GEO members for this discussion.
> I have tried:
> ##myraster=raster|R.Raster
> and also
> ##myraster=raster|R.raster
> but I was not successful. I'm using the developer version from git but I
> don't know how to get to the documentation... Actually every time a script
> has some non-conform values it disappears from the list...
>
> Thanks!
> Matteo
>
>
>
>
>
>
> 2013/2/22 Victor Olaya <volayaf at gmail.com>
>
>> Matteo
>>
>> Thanks for your ideas
>>
>> you can tell SEXTANTE to use the raster package by using
>>
>> ##myraster=raster|R.Raster
>>
>> instead of
>>
>> ##myraster=raster
>>
>> This is already documented, but only in the github version of the
>> documentation, as it is something that is implemented only in the
>> development versino of SEXTANTE.
>>
>> Anyway, your proposal seems interesting. I tried to save all the possible
>> effort from users developing R algorithms in SEXTANTE, but it's true that
>> you will have more flexibility by just getting the filename.
>>
>> Honestly, I am not an R expert, so I will implement whatever you the R
>> users think is best. My goal is to make it easier for anyonen with a good
>> knowledge of R to adapt their algorithms to SEXTANTE and be able to call
>> them from QGIS. I am opne to all kind off suggestions, since, as I said, I
>> am not an R user and my knowledge of R is very limited.
>>
>> Let's discuss this here in the list.. Hopefully other people using R and
>> SEXTANTE will give their opinion and we can decide what to do
>>
>> Many thanks again for your help
>>
>> Victor
>>
>>
>>
>>
>> 2013/2/22 Matteo Mattiuzzi <matteo at mattiuzzi.com>
>>
>>> Dear list,
>>>
>>> I have now tested the possibilities to integrate R Processing in Q-GIS.
>>> I think it closes the huge gap in R of interactive visualization and also
>>> gives the possibility to use R-functionality to non-R people!
>>>
>>> I saw that a raster/vector file is loaded through rgdal and there is no
>>> possibility to do it in the own way, such as the almost standard 'raster'
>>> package that handles also out of RAM data!
>>> In order to maintain the flexibility of R I think that arguments should
>>> be passed as they are (path+file) and everybody would be free to benefit
>>> from the entire R repository of functions.
>>> Thanks Matteo
>>>
>>> here an example for extracting and plotting pixels based on vector,
>>> point or polygon shp file:
>>>
>>> ##[MyScr]=group
>>> ##vector=vector
>>> ##raster=raster
>>> library(raster)
>>>
>>> s <- shapefile(vector) % high level function from raster package, the
>>> argument should be only the file path+ name
>>> r <- brick(raster) % high level function from raster package, the
>>> argument should be only the file path+ name
>>>
>>> v <- extract(r,s)
>>> ##showplots
>>> for(u in seq_along(v))
>>> {
>>>     val <- v[[u]]
>>>     if(u>1) X11()
>>>
>>>
>>> plot(x=1:ncol(val),ylim=c(min(val),max(val)),type="n",main=paste("Extraction
>>> line",u),xlab="Band",ylab="Spectral")
>>>
>>>     for(i in 1:nrow(val))
>>>     {
>>>        lines(val[i,],col=i)
>>>     }
>>> }
>>>
>>> ############################
>>> LINUX Ubuntu 12.10
>>> QGIS version1.9.0-MasterQGIS code revision 2a2465eCompiled against Qt
>>> 4.8.1Running against Qt4.8.1Compiled against GDAL/OGR1.9.2Running
>>> against GDAL/OGR1.9.2 GEOS Version3.3.3PostgreSQL Client Version9.1.8SpatiaLite
>>> Version3.1.0-RC2QWT Version5.2.2PROJ.4 Version480QScintilla2 Version This
>>> copy of QGIS writes debugging output.
>>>
>>> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
>>>
>>>
>>> _______________________________________________
>>> Qgis-developer mailing list
>>> Qgis-developer at lists.osgeo.org
>>> http://lists.osgeo.org/mailman/listinfo/qgis-developer
>>>
>>>
>>
>
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