Configurar aplicaciones externas¶

SAGA¶

SAGA algorithms can be run from QGIS if you have SAGA installed in your system and you configure the processing framework properly so it can find SAGA executables. In particular, the SAGA command-line executable is needed to run SAGA algorithms.

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.

De nuevo, esto es diferente en Linux, dónde sólo hay que asegurarse de que el directorio de R está correctamente incluido en la variable de entorno PATH. Si R puede iniciarse simplemente escribiendo R en una consola, entonces la configuración es correcta.

To add a new algorithm that calls an R function (or a more complex R script that you have developed and you would like to have available from QGIS), you have to create a script file that tells the processing framework how to perform that operation and the corresponding R commands to do so.

Los archivos de script de R tienen la extensión .rsx, y crearlos es bastante sencillo si sólo tiene un conocimiento básico de la sintaxis y script de R. Deben ser almacenados en la carpeta de scripts de R. Se puede establecer esta carpeta en el grupo de ajustes R (disponible desde el diálogo de Configuración de procesamiento), al igual que se hace con la carpeta para scripts de procesamiento regular.

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.

Las tablas se abren con el comando read.csv(). Sin una tabla introducida por el usuario no esta en formato CSV, será convertirá antes de importarlo en R.

Además, los ráster se pueden leer con el comando readGDAL()` en lugar de ``brick() utilizando el ##usereadgdal.

If you are an advanced user and do not want QGIS to create the object representing the layer, you can use the ##passfilename tag to indicate that you prefer a string with the filename instead. In this case, it is up to you to open the file before performing any operation on the data it contains.

Con la información anterior, se puede comprender la primera línea de nuestro primer script de ejemplo (la primera línea que no comienza con un comentario de Python).

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

La variable polygon ya contiene un objeto SpatialPolygonsDataFrame, por lo que se puede utilizar para llamar al método spsample, al igual que numpoints, que indica el número de puntos a añadir a la rejilla de ejemplo creada.

Como hemos declarado una salida de tipo vectorial llamada salida, tenemos que crear una variable llamada salida y almacenar un objeto Spatial*DataFrame en ella (en este caso, un SpatialPointsDataFrame). Se puede utilizar cualquier nombre para sus variables intermedias. Sólo asegúrese de que la variable almacena su resultado final y que tiene el mismo nombre que utilizó al declararla, y que contiene un valor adecuado.

In this case, the result obtained from the spsample method has to be converted explicitly into a SpatialPointsDataFrame object, since it is itself an object of class ppp, which is not a suitable class to be returned to QGIS.

Si el algoritmo genera capas raster, la forma en que se guardan dependerá de si o no han utilizado la opción #dontuserasterpackage. En que lo ha usado, las capas se guardan utilizando el método writeGDAL (). Si no, se utilizará el método writeRaster() del paquete ráster.

Si ha utilizado la opción #passfilename, las salidas se generan utilizando el paquete raster (mediante writeRaster()), incluso cuando no se utiliza para las entradas.

Si el algoritmo no genera ninguna capa, sino más bien en su lugar regresa un texto en la consola, tiene que indicar lo que desea que la consola mostrará una vez finalizada la ejecución. Para ello, basta con iniciar la línea de comandos que producen los resultados que desea imprimir con el signo > `(‘mayor’). La salida de todas las otras líneas no se mostrará. Por ejemplo, aquí está el archivo de descripción de un algoritmo que realiza una prueba normalmente en un determinado campo (columna) de los atributos de una capa vectorial:

##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).

Si su algoritmo crea algún tipo de gráficos (utilizando el método plot()), añada la siguiente línea:

##showplots

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

Tanto los resultados gráficos como de consola, se mostrará en el gesto de resultados de procesamiento.

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¶

Configuring GRASS is not much different from configuring SAGA. First, the path to the GRASS folder has to be defined, but only if you are running Windows. Additionaly, a shell interpreter (usually msys.exe, which can be found in most GRASS for Windows distributions) has to be defined and its path set up as well.

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.

Si se utiliza Linux, hay que asegurarse de que GRASS está correctamente instalado y que se puede ejecutar sin problemas desde una consola.

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.

Caja de Herramientas de Orfeo¶

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.

Entonces, configurar la ruta al directorio donde las aplicaciones de línea de comandos y las librerías de OTB se encuentran instaladas:

• Normalmente, el directorio de aplicaciones de OTB apunta a `/usr/lib/otb/applications`` y el directorio con los programas de línea de comandos de OTB es `/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.