Configurazione di applicazioni esterne¶

SAGA¶

Gli algoritmi di SAGA possono essere lanciati da QGIS se avete SAGA installato nel vostro sistema e se configurate l’ambiente di processing in modo che possa ritrovare l’eseguibile SAGA. In particolare, è necessario l’eseguibile SAGA da riga di comando, per lanciare gli algoritmi SAGA.

If you are running Windows, both the stand-alone installer and the OSGeo4W installer include SAGA along with QGIS, and the path is automatically configured, so there is no need to do anything else.

If you have installed SAGA yourself (remember, you need version 2.1), the path to the SAGA executable must be configured. To do this, open the configuration dialog. In the SAGA block, you will find a setting named SAGA Folder. Enter the path to the folder where SAGA is installed. Close the configuration dialog, and now you are ready to run SAGA algorithms from QGIS.

If you are running Linux, SAGA binaries are not included with SEXTANTE, so you have to download and install the software yourself. Please check the SAGA website for more information. SAGA 2.1 is needed.

In this case, there is no need to configure the path to the SAGA executable, and you will not see those folders. Instead, you must make sure that SAGA is properly installed and its folder is added to the PATH environment variable. Just open a console and type saga_cmd to check that the system can find where the SAGA binaries are located.

R. Creating R scripts¶

R integration in QGIS is different from that of SAGA in that there is not a predefined set of algorithms you can run (except for a few examples). Instead, you should write your scripts and call R commands, much like you would do from R, and in a very similar manner to what we saw in the section dedicated to processing scripts. This section shows you the syntax to use to call those R commands from QGIS and how to use QGIS objects (layers, tables) in them.

The first thing you have to do, as we saw in the case of SAGA, is to tell QGIS where your R binaries are located. You can do this using the R folder entry in the processing configuration dialog. Once you have set that parameter, you can start creating and executing your own R scripts.

Ancora una volta, la cosa è diversa in Linux e dovete solo assicurarvi che la cartella di R sia inclusa nella variabile di ambiente PATH; se eseguendo il comando R in una console, R si avvia, allora siete pronti per partire.

Per aggiungere un nuovo algoritmo che chiama una funzione di R (o un più complesso script che avete sviluppato e vorreste averlo disponibile in QGIS) dovete creare uno script che dica a QGIS come eseguire quell’operazione ed attivare i corrispondenti comandi di R.

R script files have the extension .rsx, and creating them is pretty easy if you just have a basic knowledge of R syntax and R scripting. They should be stored in the R scripts folder. You can set this folder in the R settings group (available from the processing settings dialog), just like you do with the folder for regular processing scripts.

Let’s have a look at a very simple script file, which calls the R method spsample to create a random grid within the boundary of the polygons in a given polygon layer. This method belongs to the maptools package. Since almost all the algorithms that you might like to incorporate into QGIS will use or generate spatial data, knowledge of spatial packages like maptools and, especially, sp, is mandatory.

##polyg=vector
##numpoints=number 10
##output=output vector
##sp=group
pts=spsample(polyg,numpoints,type="random")
output=SpatialPointsDataFrame(pts, as.data.frame(pts))

The first lines, which start with a double Python comment sign (##), tell QGIS the inputs of the algorithm described in the file and the outputs that it will generate. They work with exactly the same syntax as the SEXTANTE scripts that we have already seen, so they will not be described here again.

When you declare an input parameter, QGIS uses that information for two things: creating the user interface to ask the user for the value of that parameter and creating a corresponding R variable that can later be used as input for R commands.

In the above example, we are declaring an input of type vector named polyg. When executing the algorithm, QGIS will open in R the layer selected by the user and store it in a variable also named polyg. So, the name of a parameter is also the name of the variable that we can use in R for accesing the value of that parameter (thus, you should avoid using reserved R words as parameter names).

Spatial elements such as vector and raster layers are read using the readOGR() and brick() commands (you do not have to worry about adding those commands to your description file – QGIS will do it), and they are stored as Spatial*DataFrame objects. Table fields are stored as strings containing the name of the selected field.

Tables are opened using the read.csv() command. If a table entered by the user is not in CSV format, it will be converted prior to importing it into R.

Additionally, raster files can be read using the readGDAL() command instead of brick() by using the ##usereadgdal.

Se siete degli utenti avanzati e non volete che sia QGIS a creare l’oggetto che rappresenta il layer, potete usare l’etichetta ``##passfilename``per indicare che invece, preferite una stringa con il nome del file. In questo caso è di vostra competenza l’apertura del file prima di eseguire le operazioni sui dati in esso contenuti.

Dalla precedente informazione, è possibile capire la prima riga del nostro primo file script di esempio (prima riga che non inizia con un commento Python).

pts=spsample(polyg,numpoints,type="random")

La variabile polygon contiene un oggetto SpatialPolygonsDataFrame che può essere usato per chiamare la funzione spsample o similmente la funzione numpoints che indica il numero di punti da aggiungere alla griglia creata.

Since we have declared an output of type vector named out, we have to create a variable named out and store a Spatial*DataFrame object in it (in this case, a SpatialPointsDataFrame). You can use any name for your intermediate variables. Just make sure that the variable storing your final result has the same name that you used to declare it, and that it contains a suitable value.

In questo caso il risultato ottenuto dal metodo spsample` deve essere convertito esplicitamente in un oggetto SpatialPointsDataFrame, poichè è esso stesso un oggetto di classe ppp, che non è una classe adatta ad essere restituita a QGIS.

If your algorithm generates raster layers, the way they are saved will depend on whether or not you have used the #dontuserasterpackage option. In you have used it, layers are saved using the writeGDAL() method. If not, the writeRaster() method from the raster package will be used.

Se avete usato l’opzione #passfilename, gli output sono generati usando il pacchetto raster (con writeRaster()), anche se non esso non è usato per gli input.

If your algorithm does not generate any layer, but rather a text result in the console instead, you have to indicate that you want the console to be shown once the execution is finished. To do so, just start the command lines that produce the results you want to print with the > (‘greater’) sign. The output of all other lines will not be shown. For instance, here is the description file of an algorithm that performs a normality test on a given field (column) of the attributes of a vector layer:

##layer=vector
##field=field layer
##nortest=group
library(nortest)
>lillie.test(layer[[field]])

The output of the last line is printed, but the output of the first is not (and neither are the outputs from other command lines added automatically by QGIS).

Se il vostro algoritmo produce qualche tipo di risultato grafico (usando la funzione plot()) dovete aggiungere la linea seguente:

##showplots

This will cause QGIS to redirect all R graphical outputs to a temporary file, which will be opened once R execution has finished.

Sia i risultati grafici che quelli da console saranno mostrati nel gestore risultati di processing.

For more information, please check the script files provided with SEXTANTE. Most of them are rather simple and will greatly help you understand how to create your own scripts.

GRASS¶

La configurazione di GRASS non è molto differente da quella di SAGA. Per prima cosa occorre definire, ma solo nel caso di Windows, il percorso della cartella di GRASS; Inoltre occorre definire la shell di interfaccia normalmente msys.exe che si trova in molte distribuzioni di GRASS per Windows) ed il suo percorso.

By default, the processing framework tries to configure its GRASS connector to use the GRASS distribution that ships along with QGIS. This should work without problems in most systems, but if you experience problems, you might have to configure the GRASS connector manually. Also, if you want to use a different GRASS installation, you can change that setting and point to the folder where the other version is installed. GRASS 6.4 is needed for algorithms to work correctly.

Se state usando Linux dovete solo assicurarvi che GRASS è correttamente installato e che può essere attivato senza problemi da una console.

GRASS algorithms use a region for calculations. This region can be defined manually using values similar to the ones found in the SAGA configuration, or automatically, taking the minimum extent that covers all the input layers used to execute the algorithm each time. If the latter approach is the behaviour you prefer, just check the Use min covering region option in the GRASS configuration parameters.

The last parameter that has to be configured is related to the mapset. A mapset is needed to run GRASS, and the processing framework creates a temporary one for each execution. You have to specify if the data you are working with uses geographical (lat/lon) coordinates or projected ones.

GDAL¶

No additional configuration is needed to run GDAL algorithms. Since they are already incorporated into QGIS, the algorithms can infer their configuration from it.

Orfeo Toolbox¶

Orfeo Toolbox (OTB) algorithms can be run from QGIS if you have OTB installed in your system and you have configured QGIS properly, so it can find all necessary files (command-line tools and libraries).

As in the case of SAGA, OTB binaries are included in the stand-alone installer for Windows, but they are not included if you are runing Linux, so you have to download and install the software yourself. Please check the OTB website for more information.

Once OTB is installed, start QGIS, open the processing configuration dialog and configure the OTB algorithm provider. In the Orfeo Toolbox (image analysis) block, you will find all settings related to OTB. First, ensure that algorithms are enabled.

Then, configure the path to the folder where OTB command-line tools and libraries are installed:

• Usually OTB applications folder points to /usr/lib/otb/applications and OTB command line tools folder is /usr/bin.
• If you use the OSGeo4W installer, then install otb-bin package and enter C:\OSGeo4W\apps\orfeotoolbox\applications as OTB applications folder and C:\OSGeo4W\bin as OTB command line tools folder. These values should be configured by default, but if you have a different OTB installation, configure them to the corresponding values in your system.

TauDEM¶

To use this provider, you need to install TauDEM command line tools.