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Настройка сторонних приложений

The processing framework can be extended using additional applications. Currently, SAGA, GRASS, OTB (Orfeo Toolbox) and R are supported, along with some other command-line applications that provide spatial data analysis functionalities. Algorithms relying on an external application are managed by their own algorithm provider.

This section will show you how to configure the processing framework to include these additional applications, and it will explain some particular features of the algorithms based on them. Once you have correctly configured the system, you will be able to execute external algorithms from any component like the toolbox or the graphical modeler, just like you do with any other geoalgorithm.

По умолчанию, все алгоритмы, зависящие от внешних приложений, которые не поставляются с QGIS, деактивированы. Вы можете активировать их в диалоге настройки платформы геообработки. Убедитесь, что соответствующее приложение уже установлено в системе. Активация провайдера алгоритмов без установки приложения, которое ему требуется, приведет к появлению алгоритмов в панели инструментов, но при попытке запуска алгоритма вы получите ошибку.

This is because the algorithm descriptions (needed to create the parameters dialog and provide the information needed about the algorithm) are not included with each application, but with QGIS instead. That is, they are part of QGIS, so you have them in your installation even if you have not installed any other software. Running the algorithm, however, needs the application binaries to be installed in your system.

Примечание для пользователей Windows

If you are not an advanced user and you are running QGIS on Windows, you might not be interested in reading the rest of this chapter. Make sure you install QGIS in your system using the OSGeo4W application. That will automatically install SAGA, GRASS and OTB in your system and configure them so they can be run from QGIS. All the algorithms in the simplified view of the toolbox will be ready to be run without needing any further configuration.

If you want to know more about how these providers work, or if you want to use some algorithms not included in the simplified toolbox (such as R scripts), keep on reading.

О форматах файлов

When using an external software, opening a file in QGIS does not mean that it can be opened and processed as well in that other software. In most cases, other software can read what you have opened in QGIS, but in some cases, that might not be true. When using databases or uncommon file formats, whether for raster or vector layers, problems might arise. If that happens, try to use well-known file formats that you are sure are understood by both programs, and check the console output (in the history and log dialog) to know more about what is going wrong.

Использование растровых данных GRASS является одним из случаев, когда у вас могут возникнуть проблемы, мешающие завершить анализ, если внешний алгоритм использует такой слой в качестве исходного. Поэтому такие слои не отображаются в качестве доступных для алгоритмов.

You should, however, find no problems at all with vector layers, since QGIS automatically converts from the original file format to one accepted by the external application before passing the layer to it. This adds extra processing time, which might be significant if the layer has a large size, so do not be surprised if it takes more time to process a layer from a DB connection than it does to process one of a similar size stored in a shapefile.

Провайдеры, не использующие внешние приложения, могут обрабатывать любые слои, открытые в QGIS, так как они открыты для анализа самой QGIS.

Regarding output formats, all formats supported by QGIS as output can be used, both for raster and vector layers. Some providers do not support certain formats, but all can export to common raster layer formats that can later be transformed by QGIS automatically. As in the case of input layers, if this conversion is needed, that might increase the processing time.

If the extension of the filename specified when calling an algorithm does not match the extension of any of the formats supported by QGIS, then a suffix will be added to set a default format. In the case of raster layers, the .tif extension is used, while .shp is used for vector layers.

О выделении в векторных слоях

External applications may also be made aware of the selections that exist in vector layers within QGIS. However, that requires rewriting all input vector layers, just as if they were originally in a format not supported by the external application. Only when no selection exists, or the Use only selected features option is not enabled in the processing general configuration, can a layer be directly passed to an external application.

Во всех остальных случаях необходим экспорт выбранных объектов, что увеличивает время обработки.


Алгоритмы SAGA могут использоваться из QGIS, если SAGA установлена в системе, а платформа геообработки правильно настроена и может найти исполнимые файлы SAGA. Для запуска алгоритмов SAGA необходимы консольные приложения 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.

Ограничения системы покрытий SAGA

Most SAGA algorithms that require several input raster layers require them to have the same grid system. That is, they must cover the same geographic area and have the same cell size, so their corresponding grids match. When calling SAGA algorithms from QGIS, you can use any layer, regardless of its cell size and extent. When multiple raster layers are used as input for a SAGA algorithm, QGIS resamples them to a common grid system and then passes them to SAGA (unless the SAGA algorithm can operate with layers from different grid systems).

The definition of that common grid system is controlled by the user, and you will find several parameters in the SAGA group of the settings window to do so. There are two ways of setting the target grid system:

  • Setting it manually. You define the extent by setting the values of the following parameters:

    • Resampling min X
    • Resampling max X
    • Resampling min Y
    • Resampling max Y
    • Resampling cellsize

    Имейте ввиду, что QGIS выполнит пересчет исходных слоёв к этому охвату даже если они не пересекают его.

  • Setting it automatically from input layers. To select this option, just check the Use min covering grid system for resampling option. All the other settings will be ignored and the minimum extent that covers all the input layers will be used. The cell size of the target layer is the maximum of all cell sizes of the input layers.

При вызове алгоритмов, которые не используют несколько исходных слоёв или не требуют единой системы покрытия, пересчет перед запуском SAGA не выполняется и все эти настройки ингорируются.

Ограничения многоканальных слоёв

Unlike QGIS, SAGA has no support for multi-band layers. If you want to use a multiband layer (such as an RGB or multispectral image), you first have to split it into single-banded images. To do so, you can use the ‘SAGA/Grid - Tools/Split RGB image’ algorithm (which creates three images from an RGB image) or the ‘SAGA/Grid - Tools/Extract band’ algorithm (to extract a single band).

Limitations in cell size

SAGA assumes that raster layers have the same cell size in the X and Y axis. If you are working with a layer with different values for horizontal and vertical cell size, you might get unexpected results. In this case, a warning will be added to the processing log, indicating that an input layer might not be suitable to be processed by SAGA.


When QGIS calls SAGA, it does so using its command-line interface, thus passing a set of commands to perform all the required operations. SAGA shows its progress by writing information to the console, which includes the percentage of processing already done, along with additional content. This output is filtered and used to update the progress bar while the algorithm is running.

Both the commands sent by QGIS and the additional information printed by SAGA can be logged along with other processing log messages, and you might find them useful to track in detail what is going on when QGIS runs a SAGA algorithm. You will find two settings, namely Log console output and Log execution commands, to activate that logging mechanism.

Большинство провайдеров, использующих сторонние приложения и взаимодействующие с ними через командную строку, имеют схожие параметры, так что вы можете встретить их и в других местах диалога настройки.

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.

И снова, в Linux всё значительно проще: достаточно убедиться, что R доступен в PATH. Если ыв можете запустить R просто введя в консоли R, значит всё в порядке.

Чтобы добавить новый алгоритм, вызывающий функицю R (или более сложный скрипт R, который вы написали и хотите сделать доступным из QGIS), необходимо создать файл скрипта, объясняющий платформе геообработки как выполнить операцию и содержащий соответствующие команды 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.

##numpoints=number 10
##output=output vector
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. Check the processing_scripts section for more information.

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.

Если вы опытный пользователь и не хотите чтобы QGIS создавала объект, представляющий слой, используйте директиву ##passfilename. Эта директива указывает, что необходимо вернуть строку с именем файла. В этом случае, перед выполнением любых операций с файлом, вам необходимо позаботиться о его открытии.

Теперь, используя вышеприведённые сведения, мы легко можем разобрать первую строку скрипта (первую строку без символа комментария в начале).


Переменная polygon уже содержит объект SpatialPolygonsDataFrame и может использоваться для вызова метода spsample, как и переменная numpoints, которая содержит число точек для создания сетки.

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.

В нашем случае результат полученный от метода spsample необходимо явно преобразовать в объект SpatialPointsDataFrame, так как изначально это экземпляр класса ppp, который не подходит для возвращения в 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.

Если указана директива #passfilename, выходные растры будут созданы при помощи пакета raster (методом writeRaster()), даже если он не использовался для загрузки исходных данных.

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:

##field=field layer

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).

Если алгоритм создаёт какие-либо графические объекты (используя метод plot()), добавьте следующую строку:


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

И консольные и графические результаты будут доступны в окне Просмотр результатов.

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.


rgdal and maptools libraries are loaded by default, so you do not have to add the corresponding library() commands (you just have to make sure that those two packages are installed in your R distribution). However, other additional libraries that you might need have to be explicitly loaded. Just add the necessary commands at the beginning of your script. You also have to make sure that the corresponding packages are installed in the R distribution used by QGIS. The processing framework will not take care of any package installation. If you run a script that requires a package that is not installed, the execution will fail, and SEXTANTE will try to detect which packages are missing. You must install those missing libraries manually before you can run the algorithm.


Настройка GRASS мало чем отличается от настройки SAGA. Прежде всего необходимо указать путь к каталогу установки GRASS, но только в том случае, если вы использует Windows. Дополнительно требуется указать используемый интерпретатор командной строки (обычно это msys.exe, который имеется в большинстве дистрибутивов GRASS для Windows) и его расположение.

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.

Если вы используете Linux, просто убедитесь, что GRASS корректно установлена и запускается из командной строки без ошибок.

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.


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:

  • nix Usually OTB applications folder points to /usr/lib/otb/applications and OTB command line tools folder is /usr/bin.
  • win 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.


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


Please visit the TauDEM homepage for installation instructions and precompiled binaries for 32-bit and 64-bit systems. IMPORTANT: You need TauDEM 5.0.6 executables. Version 5.2 is currently not supported.


There are no packages for most Linux distributions, so you should compile TauDEM by yourself. As TauDEM uses MPICH2, first install it using your favorite package manager. Alternatively, TauDEM works fine with Open MPI, so you can use it instead of MPICH2.

Download TauDEM 5.0.6 source code and extract the files in some folder.

Open the linearpart.h file, and after line

#include "mpi.h"

add a new line with

#include <stdint.h>

Т.е. у вас будет

#include "mpi.h"
#include <stdint.h>

Save the changes and close the file. Now open tiffIO.h, find line #include "stdint.h" and replace quotes ("") with <>, so you’ll get

#include <stdint.h>

Save the changes and close the file. Create a build directory and cd into it

mkdir build
cd build

Configure your build with the command

CXX=mpicxx cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..

и запустите компиляцию


Finally, to install TauDEM into /usr/local/bin, run

sudo make install