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Michael Guravage
Export Cell Data at interval specified in the leafML file or explicitly via the file menu.
Added new parameters to VirtualLeafpar.tmpl
Added GPL boilerplate to make_{parameter,pardialog}_source.pl files.
Added new parameters to auxin_growth.xml. See respective ChangeLog files for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed src/ChangeLog
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
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<div class="header">
###Title###
<hr class="header"/>
</div>
<div class="document" id="the-virtual-leaf">
<h1 class="title">The Virtual Leaf</h1>

<div class="section" id="friday-11-june-2010">
<h1>Friday 11 June 2010</h1>
<p>Issues:</p>
<blockquote>
<ol class="arabic">
<li><p class="first">Every class that has an association or composition eventually will
need its own custom view page template, e.g. sed_view. For the moment
I have set the default view for these classes to dev_view ( a copy of
base_view ).</p>
</li>
<li><p class="first">An association in UML is cast as a ReferenceField in the resulting
class schema. Open the association and add the widget:label tag to
the class that is being associated.</p>
</li>
<li><p class="first">The default description text for a class should be a informative
description of the class, not the instance, derived from the
SED-ML manual.</p>
</li>
<li><p class="first">Apply 'searchable' tags to the appropriate class attributes.</p>
</li>
<li><p class="first">I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
this work?</p>
</li>
<li><p class="first">What should be added to our implementation of SED-ML to make it
more than merely a mirror image of the SED-ML XML format?</p>
<blockquote>
<ol class="loweralpha simple">
<li>The ability to attach files at various points, e.g. parameter files.</li>
<li>Additional output types, e.g. animations.</li>
<li>Custom page templates</li>
<li>Custom search form</li>
<li>Custom catalog indexes</li>
<li>Custom portlet(s)</li>
<li>Custom viewlet(s)</li>
</ol>
</blockquote>
</li>
</ol>
</blockquote>
</div>
<div class="section" id="friday-24-september-2010">
<h1>Friday 24 September 2010</h1>
<dl class="docutils">
<dt>To Do:</dt>
<dd><ol class="first last arabic simple">
<li>Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.</li>
<li>Create a vleaf mailing list (Henk).</li>
</ol>
</dd>
</dl>
<p>Found an article on SBRML - a markup language for associating systems
biology data with models. At a glance the schema seems bigger than
SED-ML's, but SBRML appears to be SBML specific.</p>
</div>
<div class="section" id="monday-27-september-2010">
<h1>Monday 27 September 2010</h1>
<p>Spoke with Chris about publishing the Mercurial repositories and
deploying Plone. Both can be accomplished in their own project space
on a server in the DMZ. Chris said he would supply me with login
credentials for both accounts. I will install Plone and Chris (or
Maarten) will help me configure Apache/nginx and Varnish. Chris will
install the required Mercurial packages; after which I can clone the
repositories to their new home.</p>
</div>
<div class="section" id="tuesday-5-october-20010">
<h1>Tuesday 5 October 20010</h1>
<div class="section" id="tutorial0-pro">
<h2>tutorial0.pro</h2>
<p>Added simplugin.h to list of header files. NB: this is the only
tutorial in which simplugin.h appears.</p>
</div>
<div class="section" id="auxingrowthplugin-h">
<h2>auxingrowthplugin.h</h2>
<p>Declared, and defined, a virtual function named <tt class="docutils literal">DefaultLeafML()</tt>
which merely returns a QString naming a LeafML filename sans path.</p>
</div>
<div class="section" id="virtualleaf-cpp">
<h2>VirtualLeaf.cpp</h2>
<p>Moved <tt class="docutils literal"><span class="pre">Cell::SetMagnification()</span></tt> and <tt class="docutils literal"><span class="pre">Cell::SetOffset()</span></tt> from
<tt class="docutils literal">main()</tt> to <tt class="docutils literal"><span class="pre">MainBase::Init()</span></tt>.</p>
</div>
<div class="section" id="canvas-h">
<h2>canvas.h</h2>
<p>Declare <tt class="docutils literal">exportCellData()</tt>.</p>
</div>
<div class="section" id="canvas-cpp">
<h2>canvas.cpp</h2>
<p>Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - <tt class="docutils literal"><span class="pre">Main::exportCellData()</span></tt>:</p>
<pre class="literal-block">
void Main::exportCellData(void) {
  QFile file(&quot;areas.csv&quot;);
  if ( file.open( IO_WriteOnly ) ) {
    QTextStream stream( &amp;file );
    mesh.CSVExportCellData(stream);
    mesh.CSVExportMeshData(stream);
    file.close();
  }
}
</pre>
</div>
<div class="section" id="mesh-h">
<h2>mesh.h</h2>
<p>Include <tt class="docutils literal">&lt;QTextStream&gt;</tt></p>
<p>Set the boundary_poloygon pointer to zero in the class constructor,
and delete it, if it exists, in the class destructor.</p>
<p>Declare <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>:</p>
<pre class="literal-block">
double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);
void CSVExportCellData(QTextStream &amp;csv_stream) const;
void CSVExportMeshData(QTextStream &amp;csv_stream);
</pre>
</div>
<div class="section" id="mesh-cpp">
<h2>mesh.cpp</h2>
<p>In <tt class="docutils literal"><span class="pre">mesh::clear()</span></tt>, delete the boundary_polygon only if the pointer hasn't been assigned:</p>
<pre class="literal-block">
if (boundary_polygon) {
   delete boundary_polygon;
   boundary_polygon=0;
 }
</pre>
<p>Ditto for <tt class="docutils literal"><span class="pre">mesh::clean()</span></tt>.</p>
<p>Define the code for <tt class="docutils literal">Compactness()</tt>, <tt class="docutils literal">CSVExportCellData()</tt> and <tt class="docutils literal">CSVExportMeshData()</tt>.</p>
</div>
<div class="section" id="modelcatalogue-cpp">
<h2>modelcatalogue.cpp</h2>
<p>In <tt class="docutils literal">InstallModel()</tt>, find and load the default LeafML file.</p>
</div>
<div class="section" id="simplugin-h">
<h2>simplugin.h</h2>
<p>Declare <tt class="docutils literal">DefaultLeafML()</tt>:</p>
<pre class="literal-block">
// Default LeafML-file to be read after model startup
virtual QString DefaultLeafML(void);
</pre>
</div>
<div class="section" id="simplugin-cpp">
<h2>simplugin.cpp</h2>
<p>Define <tt class="docutils literal">DefaultLeafML()</tt>. Returns an empty <tt class="docutils literal">QString</tt>:</p>
<pre class="literal-block">
QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
</pre>
</div>
<div class="section" id="xmlwrite-cpp">
<h2>xmlwrite.cpp</h2>
<p>In <tt class="docutils literal"><span class="pre">Mesh::XMLReadCells()</span></tt> - Delete the boundary_ploygon only if its
pointer has been assigned.</p>
</div>
</div>
</div>
<div class="footer">
<hr class="footer" />
###Page###
</div>
</body>
</html>