[Qgis-developer] QGIS - SEXTANTE - R

Fri Feb 22 13:04:09 PST 2013

With the addition of "rasterfile" and "vectorfile" for me personally there
are no more wishes open. I think it is absolutely required as it makes
every individual solution possible. The same for the saving of the files.

Thanks again!

2013/2/22 Victor Olaya <volayaf at gmail.com>

> 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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