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Michael Guravage
Synchronise leaf movie frame and cell export data timestep references.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.h
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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 class="section" id="wednesday-6-october-2010">
<h1>Wednesday 6 October 2010</h1>
<p>Wrote Simon van Mourik about his missing libiconv-2.dll.</p>
</div>
<div class="section" id="thursday-7-october-2010">
<h1>Thursday 7 October 2010</h1>
<p>Added a Q3FileDialog in <tt class="docutils literal"><span class="pre">canvas.cpp:Main::exportCellData(void)</span></tt> to
choose where to write the exported cell data.</p>
</div>
<div class="section" id="friday-8-october-2010">
<h1>Friday 8 October 2010</h1>
<p>Added new parameters to control perodic cell exprt data.</p>
<p>Added code to relize perodic cell export.</p>
</div>
<div class="section" id="monday-11-october-2010">
<h1>Monday 11 October 2010</h1>
<div class="section" id="mercurial-hooks">
<h2>Mercurial hooks</h2>
<p>Tried several alternatives for Mercurial's <tt class="docutils literal">pretxnchangegroup.forbid_2heads</tt> hook.</p>
<ol class="arabic simple">
<li><a class="reference external" href="http://bitbucket.org/dgc/headcount">http://bitbucket.org/dgc/headcount</a>: <strong>Headcount</strong> <tt class="docutils literal">ui</tt> complains of a missing data member</li>
<li><a class="reference external" href="http://stackoverflow.com/questions/1705921/useful-mercurial-hooks">http://stackoverflow.com/questions/1705921/useful-mercurial-hooks</a>: <strong>forbid2_heads.py</strong> doesn't load</li>
<li><a class="reference external" href="http://davidherron.com/node/961">http://davidherron.com/node/961</a>: <strong>forbid2_heads.sh</strong> works as advertised</li>
</ol>
</div>
<div class="section" id="mercurial-repositories">
<h2>Mercurial Repositories</h2>
<p>Tried to install Rhode Code from: <a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>.</p>
<ol class="arabic simple">
<li><a class="reference external" href="http://bitbucket.org/marcinkuzminski/rhodecode">http://bitbucket.org/marcinkuzminski/rhodecode</a></li>
<li><a class="reference external" href="http://packages.python.org/RhodeCode">http://packages.python.org/RhodeCode</a>, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc3">http://pypi.python.org/pypi/RhodeCode/1.0.0rc3</a></li>
<li><a class="reference external" href="http://hg.python-works.com">http://hg.python-works.com</a> (demo,demo)</li>
<li><a class="reference external" href="http://bitbucket.org/bfrog/cutehg">http://bitbucket.org/bfrog/cutehg</a></li>
<li><a class="reference external" href="http://pypi.python.org/pypi/SIP">http://pypi.python.org/pypi/SIP</a>, <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>
<li><a class="reference external" href="http://pypi.python.org/pypi/PyQt">http://pypi.python.org/pypi/PyQt</a></li>
<li><a class="reference external" href="http://ask.github.com/celery">http://ask.github.com/celery</a></li>
</ol>
<p>All goes tolerably until you tick in the url; at which point RhodeCode complains that:</p>
<pre class="literal-block">
Exception happened during processing of request from ('127.0.0.1', 35803)
Traceback (most recent call last):
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 1068, in process_request_in_thread
   self.finish_request(request, client_address)
 File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py&quot;, line 320, in finish_request
   self.RequestHandlerClass(request, client_address, self)
 File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py&quot;, line 615, in __init__
   self.handle()
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 442, in handle
   BaseHTTPRequestHandler.handle(self)
 File &quot;/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py&quot;, line 329, in handle
   self.handle_one_request()
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 437, in handle_one_request
   self.wsgi_execute()
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py&quot;, line 287, in wsgi_execute
   self.wsgi_start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py&quot;, line 130, in __call__
   return self.apps[-1](environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py&quot;, line 379, in __call__
   app_iter = self.application(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py&quot;, line 33, in __call__
   return self.application(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py&quot;, line 163, in __call__
   self.app, new_environ, catch_exc_info=True)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py&quot;, line 48, in call_wsgi_application
   app_iter = application(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py&quot;, line 156, in __call__
   return self.application(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py&quot;, line 55, in __call__
   return self.application(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py&quot;, line 152, in __call__
   return self.wrap_app(environ, session_start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py&quot;, line 131, in __call__
   response = self.app(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 98, in __call__
   self.setup_app_env(environ, start_response)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 203, in setup_app_env
   pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
 File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py&quot;, line 165, in _get_translator
   raise LanguageError('IOError: %s' % ioe)
LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
</pre>
</div>
<div class="section" id="re-install">
<h2>RE-INSTALL</h2>
<ol class="arabic simple">
<li>easy_install mercurial</li>
<li>mkdir src</li>
<li>cd src</li>
<li>hg clone <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>
<li>cd sip</li>
<li>python build.py prepare</li>
<li>python configure.py</li>
<li>make</li>
<li>make install</li>
<li>cd ..</li>
<li>wget <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
<li>tar xzf PyQt-x11-gpl-4.7.7.tar.gz</li>
<li>cd PyQt-x11-gpl-4.7.7</li>
<li>python configure.py</li>
<li>make</li>
<li>make install</li>
<li>cd ..</li>
<li>hg clone <a class="reference external" href="https://litsol&#64;bitbucket.org/bfrog/cutehg">https://litsol&#64;bitbucket.org/bfrog/cutehg</a></li>
<li>cd cutehg</li>
<li>python setup.py build</li>
<li>python setup.py install</li>
<li>cd ..</li>
<li>easy_install rhodecode, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc2">http://pypi.python.org/pypi/RhodeCode/1.0.0rc2</a></li>
</ol>
<p>This procedure fails as before.</p>
<p>However, upon inspection I saw that the i18n directory was missing
from my build but present in the rhodecode clone from bitbucket. While
I think that the <tt class="docutils literal">easy_install rhodecode</tt> invocation is necessary to
install the various subsidiary packages, moving the cloned rhodecode
into the site-packages directory seems to have made most functionality
work. e.g. graphical logs and diff highlighting.</p>
</div>
</div>
<div class="section" id="tuesday-12-october-2010">
<h1>Tuesday 12 October 2010</h1>
<div class="section" id="rhodecode">
<h2>RhodeCode</h2>
<p>I think that if Chris can install RhodeCode, I can serve individual
instance from my home directory.</p>
</div>
<div class="section" id="sed-ml-l1v1rc1">
<h2>SED-ML L1V1RC1</h2>
<p>Walking through the new SED-ML schema I see that they've dropped the
generic simulation class and added AddXML and RemoveXML model change
classes. Adding several more SED-ML examples for the symposium might
still be justified - though they become obsolete the moment I
introduce the new schema changes.</p>
</div>
</div>
<div class="section" id="wednesday-13-october-2010">
<h1>Wednesday 13 October 2010</h1>
<p>Tweaked <tt class="docutils literal">.bashrc</tt> and <tt class="docutils literal">virtualenvwrapper.sh</tt> to facilitate
virtualenv and virtualenvwrapper - many unbound variables!</p>
<p>Pushed recent changes to repository from where Roeland can retrieve
and test them.</p>
<p>OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.</p>
</div>
<div class="section" id="friday-15-october-2010">
<h1>Friday 15 October 2010</h1>
<div class="section" id="id1">
<h2>Rhodecode</h2>
<p>Installing RhodeCode locally on the nhypnos is a real pain. In
addition to the previous list of dependencies, for the caterpie, add
these for the nhypnos:</p>
<ol class="arabic simple">
<li>Python</li>
<li>Bison (for sip)</li>
<li>Flex (for sip)</li>
<li>m4 (for Bison)</li>
<li>Qt (for PyQt)</li>
<li>GLIBCXX_3.4.9 (for Qt) - I draw the line at (re)installing GCC!</li>
</ol>
<p>OK. Forget sip bison, flex, m4, Qt and the rest. Let's install just
the minimum.</p>
<p>First, install sqlite; we'll see in a minute that Python requires
it. The sources are available at: <a class="reference external" href="http://www.sqlite.org/download.html">http://www.sqlite.org/download.html</a>.</p>
<p>Second, install Python. My initial attempt complained it was missing
the following bits and pieces:</p>
<pre class="literal-block">
Python build finished, but the necessary bits to build these modules were not found:
_bsddb             _sqlite3           _ssl
_tkinter           bsddb185           dl
imageop            readline           sunaudiodev
To find the necessary bits, look in setup.py in detect_modules() for the module's name.
</pre>
<p>So install sqlite first. And, since Python's configure script doesn't
have an option for it, I had to tweak <tt class="docutils literal">setup.py</tt> to enumerate the
path where it would find sqlite;</p>
<p>Third, install RhodeCode. I first installed it using easy_install, but
while the result worked, the changelog view did not display the
branch/merge graphics. I then cloned the code from its bitbucket repository:</p>
<pre class="literal-block">
clone https://litsol&#64;bitbucket.org/marcinkuzminski/rhodecode
</pre>
<p>Replacing the egg installed by easy_install by this code does display
the branch/merge graphics.</p>
<p>Fourth, setup and serve rhodecode. Following the instructions posted
online at: <a class="reference external" href="http://packages.python.org/RhodeCode/setup.html#setup">http://packages.python.org/RhodeCode/setup.html#setup</a> works as advertised:</p>
<pre class="literal-block">
paster make-config RhodeCode production.ini
paster setup-app production.ini
paster serve production.ini
</pre>
<p>All that's left is an apache rewrite rule directing
virtualleaf.project.cwi.nl/repository to port 5000, or whaterver we
change it to, on the nhypnos.</p>
</div>
<div class="section" id="id2">
<h2>The Virtual Leaf</h2>
<p>Added <tt class="docutils literal">incrementIterations()</tt>, <tt class="docutils literal">getIterations()</tt> and <tt class="docutils literal">int
iterations</tt> to mesh.h. <tt class="docutils literal">incrementIterations()</tt> is called in TIMESTEP in
VirtualLeaf.cpp. The actual counter, <tt class="docutils literal">iterations</tt> is initalized to
zero in the Mesh class constructor.</p>
<p>The iterations are inquired in two places: for the frame count in
<tt class="docutils literal"><span class="pre">MainBase::Plot</span></tt> in <tt class="docutils literal">VirtualLeaf.cpp` and for the export cell data
interval in <span class="pre">``Main::TimeStepWrap</span></tt> in <tt class="docutils literal">canvas.cpp</tt>.</p>
<p>The questions remain: Should we use this count, and if yes, where
should it be incremented? The previous count was incremented in
<tt class="docutils literal"><span class="pre">Main::TimeStepWrap</span></tt>. Or should we simply use
<tt class="docutils literal">(int)mesh.getTime()</tt>? Since this is not an ordinal count, the
results look strange.</p>
</div>
</div>
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