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updated help

git-svn-id: http://sextante.googlecode.com/svn/trunk/soft/bindings/qgis-plugin@216 881b9c09-3ef8-f3c2-ec3d-21d735c97f4d
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volayaf
volayaf committed Jun 4, 2012
1 parent b47ca35 commit 496d0ae50e088b571eabaa6908ffa271ad76de9f
@@ -101,7 +101,7 @@ <h3>A note on vector layer selections<a class="headerlink" href="#a-note-on-vect
<p>By default, when an external algorithm takes a vector layer, it will use
all its features, even if a selection exist in QGIS. You can make an
external algorithm aware of that selection by checking the <em>Use selected
features in eternal applications</em> item in the <em>General</em> settings group.
features in external applications</em> item in the <em>General</em> settings group.
When you do so, each time you execute an external algorithm that uses a
vector layer, the selected features of that layer will be exported to a
new layer, and the algorithm will work with that new layer instead.</p>
@@ -135,7 +135,7 @@ <h2>SAGA<a class="headerlink" href="#saga" title="Permalink to this headline">¶
the algorithm descriptions (needed to create the parameters dialog and
give SEXTANTE the information it needs about the algorithm) are not
included with SAGA, but with SEXTANTE instead. That is, they are part of
SEXTANTE, so you have them in yur installation even if you have not
SEXTANTE, so you have them in your installation even if you have not
installed SEXTANTE. Running the algorithm, however, needs SAGA binaries
installed in your system.</p>
<div class="section" id="about-saga-grid-system-limitations">
@@ -144,7 +144,7 @@ <h3>About SAGA grid system limitations<a class="headerlink" href="#about-saga-gr
require them to have the same grid system. That is, to cover the same
geographic area and have the same cellsize, so their corresponding grids
match. When calling SAGA algorithms from SEXTANTE, you can use any
layer, regarless of its cellsize and extent. When multiple raster layers
layer, regardless of its cellsize and extent. When multiple raster layers
are used as input for a SAGA algorithm, SEXTANTE 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).</p>
@@ -248,7 +248,7 @@ <h2>R. Creating R scripts<a class="headerlink" href="#r-creating-r-scripts" titl
</pre></div>
</div>
<p>The variable <tt class="docutils literal"><span class="pre">polygon</span></tt> already contains a <tt class="docutils literal"><span class="pre">SpatialPolygonsDataFrame</span></tt>
object, so it can be usedto call the <tt class="docutils literal"><span class="pre">spsample</span></tt> method, just like the
object, so it can be used to call the <tt class="docutils literal"><span class="pre">spsample</span></tt> method, just like the
<tt class="docutils literal"><span class="pre">numpoints</span></tt> one, which indicates the number of points to add to the
created sample grid.</p>
<p>Since we have declared an output of type vector named <tt class="docutils literal"><span class="pre">out</span></tt>, we have
@@ -277,7 +277,7 @@ <h2>R. Creating R scripts<a class="headerlink" href="#r-creating-r-scripts" titl
&gt;lillie.test(layer[[field]])</pre>
</div>
<p>The output ot the last line is printed, but the output of the first is
not (and neither are the otputs from other command lines added
not (and neither are the outputs from other command lines added
automatically by SEXTANTE).</p>
<p>If your algorithm creates any kind of graphics (using the <tt class="docutils literal"><span class="pre">plot()</span></tt>
method), add the following line:</p>
Binary file not shown.
Binary file not shown.
Binary file not shown.
@@ -3,7 +3,7 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.

Welcome to SEXTANTE for QGIS's documentation!
SEXTANTE for QGIS's documentation
=============================================

Contents:
@@ -62,7 +62,7 @@ the modeler window:
- Boolean value

Double-clicking on any of them, a dialog is shown to define its
characteristics. Depending on the parameter itself, the dialog will
caracteristics. Depending on the parameter itself, the dialog will
contain just one basic element (the description, which is what the user
will see when executing the model) or more of them. For instance, when
adding a numerical value, as it can be seen in the next figure, apart
@@ -97,7 +97,7 @@ To add an algorithm, double-click on its name. An execution dialog will
appear, with a content similar to the one found in the execution panel
that SEXTANTE shows when executing the algorithm from the toolbox. the
one shown next correspond to the SAGA convergence index algorithm, the
same one we saw in the section dedicated to the SEXTANTE toolbox.
same one we saw in the section dedicated to the SEXTANTe toolbox.

.. figure:: models_parameters4.png
:align: center
@@ -114,7 +114,7 @@ you supply will be the description for the output, which will be the one
the user will see when executing the model.

Selecting the value of each parameter is also a bit different, since
there are important differences between the context of the modeler and
there are importante differences between the context of the modeler and
the toolbox one. Let's see how to introduce the values for each type of
parameter.

@@ -154,8 +154,7 @@ Elements can be dragged to a different position within the canvas, to
change the way the module structure is displayed and make it more clear
and intuitive. Links between elements are update automatically.

You can run your algorithm anytime clicking on the *Run* button. However,
in order to use it from the toolbox, it has to be saved and the modeler dialog closed, to allow the toolbox to refresh its contents.
You can run your algorithm anytime clicking on the *Run* button. However, in order to use it from the toolbox, it has to be saved and the modeler dialog closed, to allow the toolbox to refresh its contents.

Saving and loading models
-------------------------
@@ -193,6 +192,41 @@ renders all the algorithms in that provider unusable by the modeler,
which might cause problems when loading models. Keep that in mind when
you have trouble loading or executing models.

Editing a model
---------------

You can edit the model you are currently creating, redefining the workflow and the relationships between the algorithms and inputs that define the model itself.

If you right-click on an algorithm in the canvas representing the model, you will see a context menu like the one shown next:

.. figure:: modeler_right_click.png
:align: center


Selecting the *Remove* option will cause the selected algorithm to be removed. An algorithm can be removed only if there are no other algorithms dependind on it. That is, if no output from the algorithm is used in a different one as input. If you try to remove an algorithm that has others depending on it, SEXTANTE will show you a warning message like the one you can see below:

.. figure:: cannot_delete_alg.png
:align: center

Selecting the *Edit* option or simply double-clicking on the algorithm icon will show the parameters dialog of the algorithm, so you can change the inputs and parameter values. Not all input elements available in the model will appear in this case as available inputs. Layers or values generated at a more advanced step in the workflow defined by the model will not be available if they cause circular dependencies.

Select the new values and then click on the *OK* button as usual. The connections between the model elements will change accordingly in the modeler canvas.

Activating and deactivating algorithms
--------------------------------------

Algorithms can be deactivated in the modeler, so they will not be executed once the model is run. This can be used to test just a given part of the model, or when you do not need all the outputs it generates.

To deactivate an algorithm, right--click on its icon in the model canvas and select the *Deactivate* option. You will see that the algorithm is represented now with a red label under its name indicating that is not active.

.. figure:: deactivated.png
:align: center

All algorithms depending (directly or undirectly) on that algorithm will also appear as inactive, since they cannot be executed now.

To activate an algorithm, just right--click on its icon and select the *Activate* option.


Editing model help files and meta-information
---------------------------------------------

@@ -218,7 +252,7 @@ if the number of output layers cannot be know in advance), then it is
not possible to use it within a model, and thus does not appear in the
list of them that you can find in the modeler dialog.

Additionally, you will see some algorithms in the modeler that are not
Additionaly, you will see some algorithms in the modeler that are not
found in the toolbox. This algorithms are meant to be used exclusively
as part of a model, and they are of no interest in a different context.
The *Calculator* algorithm is an example of that. It is just a simple
@@ -230,6 +264,8 @@ make too much sense.
SEXTANTE models as Python code
------------------------------

*[This feature is temporarily unavailable]*

Along with the tab that contains the graphical design of the model, you
will find another one containing a Python script which performs the same
task as the model itself. Using that code, you can create a console
@@ -157,7 +157,7 @@ <h2>Calling SEXTANTE from the Python console<a class="headerlink" href="#calling
<div class="highlight-python"><pre>&gt; runalg{name_of_the_algorithm, param1, param2, ..., paramN,
Output1, Output2, ..., OutputN)</pre>
</div>
<p>The list of parameters and ouputs to add depends on the algorithm you
<p>The list of parameters and outputs to add depends on the algorithm you
want to run, and is exactly the list that the <tt class="docutils literal"><span class="pre">describealg</span></tt> method
gives you, in the same order as shown.</p>
<p>Depending on the type of parameter, values are introduced differently.
@@ -214,7 +214,7 @@ <h2>Calling SEXTANTE from the Python console<a class="headerlink" href="#calling
as it is done from the toolbox. If you want to save the result to a
temporary file, use <tt class="docutils literal"><span class="pre">None</span></tt>. The extension of the file determines the
file format. If you enter a file extension not included in the ones
supportede by the algorithm, the default file format for that output
supported by the algorithm, the default file format for that output
type will be used, and its corresponding extension appended to the given
filepath.</p>
<p>Unlike when an algorithm is executed from the toolbox, outputs are not
@@ -292,7 +292,7 @@ <h2>Creating scripts and running them from the toolbox<a class="headerlink" href
</ul>
<p>The parameter name is the name that will be shown to the user when
executing the algorithm, and also the variable name to use in the script
code. The value entered by the user for that parameter will be asigned
code. The value entered by the user for that parameter will be assigned
to a variable with that name.</p>
<p>Layers and tables values are strings containing the filepath of the
corresponding object. To turn them into a QGIS object, you can use the
@@ -307,15 +307,15 @@ <h2>Creating scripts and running them from the toolbox<a class="headerlink" href
<li><tt class="docutils literal"><span class="pre">output</span> <span class="pre">html</span></tt></li>
<li><tt class="docutils literal"><span class="pre">output</span> <span class="pre">file</span></tt></li>
</ul>
<p>The value asigned to the output variables is always a string with a
<p>The value assigned to the output variables is always a string with a
filepath. It will correspond to a temporary filepath in case the user
has not entered any output filename.</p>
<p>When you declare an output, SEXTANTE will try to add it to QGIS once the
algorithm is finished. That is the reason why, although the <tt class="docutils literal"><span class="pre">runalg()</span></tt>
method does not load the layers it produces, the final TWI layer will be
loaded, since it is saved to the file entered by the user, which is the
value of the corresponding output.</p>
<p>Do not use the <tt class="docutils literal"><span class="pre">load()</span></tt> method in your scripta algorithms, but just
<p>Do not use the <tt class="docutils literal"><span class="pre">load()</span></tt> method in your script algorithms, but just
when working with the console line. If a layer is created as output of
an algorithm, it should be declared as such. Otherwise, you will not be
able to properly use the algorithm in the modeler, since its syntax (as
@@ -8,7 +8,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

<title>Welcome to SEXTANTE for QGIS’s documentation! &mdash; SEXTANTE for QGIS 1.0 documentation</title>
<title>SEXTANTE for QGIS’s documentation &mdash; SEXTANTE for QGIS 1.0 documentation</title>

<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -47,8 +47,8 @@ <h3>Navigation</h3>
<div class="bodywrapper">
<div class="body">

<div class="section" id="welcome-to-sextante-for-qgis-s-documentation">
<h1>Welcome to SEXTANTE for QGIS&#8217;s documentation!<a class="headerlink" href="#welcome-to-sextante-for-qgis-s-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="sextante-for-qgis-s-documentation">
<h1>SEXTANTE for QGIS&#8217;s documentation<a class="headerlink" href="#sextante-for-qgis-s-documentation" title="Permalink to this headline"></a></h1>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
@@ -71,6 +71,8 @@ <h1>Welcome to SEXTANTE for QGIS&#8217;s documentation!<a class="headerlink" hre
<li class="toctree-l2"><a class="reference internal" href="modeler.html#definition-of-inputs">Definition of inputs</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#definition-of-the-workflow">Definition of the workflow</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#saving-and-loading-models">Saving and loading models</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#editing-a-model">Editing a model</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#activating-and-deactivating-algorithms">Activating and deactivating algorithms</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#editing-model-help-files-and-meta-information">Editing model help files and meta-information</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#about-available-algorithms">About available algorithms</a></li>
<li class="toctree-l2"><a class="reference internal" href="modeler.html#sextante-models-as-python-code">SEXTANTE models as Python code</a></li>
@@ -126,7 +128,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
<div class="sphinxsidebarwrapper">
<h3><a href="#">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Welcome to SEXTANTE for QGIS&#8217;s documentation!</a><ul>
<li><a class="reference internal" href="#">SEXTANTE for QGIS&#8217;s documentation</a><ul>
</ul>
</li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
@@ -27,7 +27,7 @@
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="SEXTANTE for QGIS 1.0 documentation" href="index.html" />
<link rel="next" title="The SEXTANTE toolbox" href="toolbox.html" />
<link rel="prev" title="Welcome to SEXTANTE for QGIS’s documentation!" href="index.html" />
<link rel="prev" title="SEXTANTE for QGIS’s documentation" href="index.html" />
</head>
<body>
<div class="related">
@@ -40,7 +40,7 @@ <h3>Navigation</h3>
<a href="toolbox.html" title="The SEXTANTE toolbox"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="index.html" title="Welcome to SEXTANTE for QGIS’s documentation!"
<a href="index.html" title="SEXTANTE for QGIS’s documentation"
accesskey="P">previous</a> |</li>
<li><a href="index.html">SEXTANTE for QGIS 1.0 documentation</a> &raquo;</li>
</ul>
@@ -62,11 +62,11 @@ <h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to t
<div class="section" id="basic-elements-of-the-sextante-gui">
<h2>Basic elements of the SEXTANTE GUI<a class="headerlink" href="#basic-elements-of-the-sextante-gui" title="Permalink to this headline"></a></h2>
<p>There are four basic elements in the SEXTANTE GUI, which are used to run
SEXTANTE algorithms for different purposes. Chosing one tool or another
SEXTANTE algorithms for different purposes. Choosing one tool or another
will depend on the kind of analysis that is to be performed and the
particular characteristics of each user and project. All of them (except
for the batch processing interface, which is called from the toolbox, as
we will see) can be accesed from the <em>SEXTANTE</em> menu item (you will see
we will see) can be accessed from the <em>SEXTANTE</em> menu item (you will see
more than four entries. The remaining ones are not used to execute
algorithms and will be explained later in this chapter).</p>
<ul>
@@ -120,7 +120,7 @@ <h3><a href="index.html">Table Of Contents</a></h3>

<h4>Previous topic</h4>
<p class="topless"><a href="index.html"
title="previous chapter">Welcome to SEXTANTE for QGIS&#8217;s documentation!</a></p>
title="previous chapter">SEXTANTE for QGIS&#8217;s documentation</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="toolbox.html"
title="next chapter">The SEXTANTE toolbox</a></p>
@@ -156,7 +156,7 @@ <h3>Navigation</h3>
<a href="toolbox.html" title="The SEXTANTE toolbox"
>next</a> |</li>
<li class="right" >
<a href="index.html" title="Welcome to SEXTANTE for QGIS’s documentation!"
<a href="index.html" title="SEXTANTE for QGIS’s documentation"
>previous</a> |</li>
<li><a href="index.html">SEXTANTE for QGIS 1.0 documentation</a> &raquo;</li>
</ul>

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