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The snapshot feature stopped working on Windows. The problem was in MainBase::Save, where the "format" argument was added to "image->save". On Windows the file format must be given in Capitals and in specific formats (e.g. TIFF works, TIF not).
It is much safer to leave the 'format' argument out and let the system guess the format from the file extension.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/canvas.cpp
changed src/mainbase.cpp
changed src/mainbase.h
It is much safer to leave the 'format' argument out and let the system guess the format from the file extension.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/canvas.cpp
changed src/mainbase.cpp
changed src/mainbase.h
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</head>
<body>
<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("areas.csv");
if ( file.open( IO_WriteOnly ) ) {
QTextStream stream( &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"><QTextStream></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 &csv_stream) const;
void CSVExportMeshData(QTextStream &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 "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 615, in __init__
self.handle()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle
BaseHTTPRequestHandler.handle(self)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request
self.wsgi_execute()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py", line 130, in __call__
return self.apps[-1](environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py", line 379, in __call__
app_iter = self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py", line 33, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py", line 163, in __call__
self.app, new_environ, catch_exc_info=True)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py", line 48, in call_wsgi_application
app_iter = application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py", line 156, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py", line 55, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py", line 152, in __call__
return self.wrap_app(environ, session_start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py", line 131, in __call__
response = self.app(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 98, in __call__
self.setup_app_env(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 203, in setup_app_env
pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py", 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@bitbucket.org/bfrog/cutehg">https://litsol@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@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>
</div>
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