EI/VirtualLeaf Changeset - b3943d0b8126 · Centrum Wiskunde & Informatica (CWI)

Changeset - b3943d0b8126

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0 2 6

Michael Guravage - 15 years ago 2010-10-07 17:16:03
michael.guravage@cwi.nl

Added a Q3FileDialog in canvas.cpp:Main::exportCellData() inquire
where to write the exportCellData.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added doc/Makefile
added doc/stylesheet.json
added doc/v1.html
added doc/v1.pdf
added doc/v1.rst
added src/leaficon.png
changed src/ChangeLog
changed src/canvas.cpp

8 files changed with 2499 insertions and 6 deletions:

doc/Makefile

doc/stylesheet.json

557

doc/v1.html

469

doc/v1.pdf

1229

doc/v1.rst

200

src/ChangeLog

src/canvas.cpp

src/leaficon.png

bin+new file

0 comments (0 inline, 0 general)

doc/Makefile

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Show inline comments

@@ new file 100644 @@
 .SUFFIXES : .rst .html .pdf
 .rst.pdf :
 	rst2pdf -s stylesheet.json $< -o $@
 .rst.html :
 	rst2html.py $< $@
 all: v1.pdf v1.html
 v1.pdf : v1.rst
 v1.html : v1.rst
 clean:
 	/bin/rm -f v1.pdf v1.html
 #finis
@@ \ No newline at end of file @@

doc/stylesheet.json

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Show inline comments

@@ new file 100644 @@
+{
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   "pageSetup" : {
     "size": "A4",
     "width": null,
     "height": null,
     "margin-top": "2cm",
     "margin-bottom": "2cm",
     "margin-left": "2cm",
     "margin-right": "2cm",
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     "firstTemplate": "oneColumn"
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     },
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             ["0cm", "0cm", "100%", "100%"]
         ],
         "showHeader" : true,
         "showFooter" : true
     },
     "twoColumn": {
         "frames": [
             ["0cm", "0cm", "49%", "100%"],
             ["51%", "0cm", "49%", "100%"]
         ],
         "showHeader" : true,
         "showFooter" : true
     },
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         "frames": [
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         ],
         "showHeader" : true,
         "showFooter" : true
     },
     "cutePage": {
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         ],
         "showHeader" : true,
         "showFooter" : true,
         "defaultFooter" : "###Page###",
         "defaultHeader" : "###Section###"
+    }
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   "fontsAlias" : {
     "stdFont": "Helvetica",
     "stdBold": "Helvetica-Bold",
     "stdItalic": "Helvetica-Oblique",
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     "stdSerif": "Times-Roman"
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     ["heading5" , {
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     ["topic-title" , {
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     ["sidebar-subtitle" , {
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     ["sidebar" , {
       "float": "none",
       "width": "100%",
       "parent": "normal",
       "backColor": "beige",
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       "backColor": "beige",
       "borderColor": "darkgray",
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       "commands":[
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+      ]
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+      ]
     }],
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       "alignment" : "TA_CENTER"
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     ["table-heading" , {
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         ],
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     }]
+  ]
+}

doc/v1.html

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@@ new file 100644 @@
 <?xml version="1.0" encoding="utf-8" ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
 <title>The Virtual Leaf</title>
 <style type="text/css">
 /*
 :Author: David Goodger (goodger@python.org)
 :Id: $Id: html4css1.css 5951 2009-05-18 18:03:10Z milde $
 :Copyright: This stylesheet has been placed in the public domain.
 Default cascading style sheet for the HTML output of Docutils.
 See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
 customize this style sheet.
 */
 /* used to remove borders from tables and images */
 .borderless, table.borderless td, table.borderless th {
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 ###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>
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 ###Page###
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doc/v1.rst

➞

Show inline comments

@@ new file 100644 @@
 .. header::
    ###Title###
 .. footer::
    ###Page###
 ================
 The Virtual Leaf
 ================
 Friday 11 June 2010
 -------------------
 Issues:
 . 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 ).
 . 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.
 . The default description text for a class should be a informative
     description of the class, not the instance, derived from the
     SED-ML manual.
 . Apply 'searchable' tags to the appropriate class attributes.
 . I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
     this work?
 . 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?
      a. The ability to attach files at various points, e.g. parameter files.
      b. Additional output types, e.g. animations.
      c. Custom page templates
      d. Custom search form
      e. Custom catalog indexes
      f. Custom portlet(s)
      g. Custom viewlet(s)
 Friday 24 September 2010
 ------------------------
 To Do:
 . Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.
 . Create a vleaf mailing list (Henk).
 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.
 Monday 27 September 2010
 ------------------------
 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.
 Tuesday 5 October 20010
 -----------------------
 tutorial0.pro
 +++++++++++++
 Added simplugin.h to list of header files. NB: this is the only
 tutorial in which simplugin.h appears.
 auxingrowthplugin.h
 +++++++++++++++++++
 Declared, and defined, a virtual function named ``DefaultLeafML()``
 which merely returns a QString naming a LeafML filename sans path.
 VirtualLeaf.cpp
 +++++++++++++++
 Moved ``Cell::SetMagnification()`` and ``Cell::SetOffset()`` from
 ``main()`` to ``MainBase::Init()``.
 canvas.h
 ++++++++
 Declare ``exportCellData()``.
 canvas.cpp
 ++++++++++
 Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - ``Main::exportCellData()``::
   void Main::exportCellData(void) {
     QFile file("areas.csv");
     if ( file.open( IO_WriteOnly ) ) {
       QTextStream stream( &file );
       mesh.CSVExportCellData(stream);
       mesh.CSVExportMeshData(stream);
       file.close();
+    }
+  }
 mesh.h
 ++++++
 Include ``<QTextStream>``
 Set the boundary_poloygon pointer to zero in the class constructor,
 and delete it, if it exists, in the class destructor.
 Declare ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``::
   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);
 mesh.cpp
 ++++++++
 In ``mesh::clear()``, delete the boundary_polygon only if the pointer hasn't been assigned::
  if (boundary_polygon) {
     delete boundary_polygon;
     boundary_polygon=0;
+  }
 Ditto for ``mesh::clean()``.
 Define the code for ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``.
 modelcatalogue.cpp
 ++++++++++++++++++
 In ``InstallModel()``, find and load the default LeafML file.
 simplugin.h
 +++++++++++
 Declare ``DefaultLeafML()``::
   // Default LeafML-file to be read after model startup
   virtual QString DefaultLeafML(void);
 simplugin.cpp
 +++++++++++++
 Define ``DefaultLeafML()``. Returns an empty ``QString``::
  QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
 xmlwrite.cpp
 ++++++++++++
 In ``Mesh::XMLReadCells()`` - Delete the boundary_ploygon only if its
 pointer has been assigned.
 Wednesday 6 October 2010
 ------------------------
 Wrote Simon van Mourik about his missing libiconv-2.dll.
 Thursday 7 October 2010
 -----------------------
 Added a Q3FileDialog in ``canvas.cpp:Main::exportCellData(void)`` to
 choose where to write the exported cell data.

src/ChangeLog

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 -10-07    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire
 	where to write the exportCellData.
 -06-28    <guravage@caterpie.sen.cwi.nl>

src/canvas.cpp

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@@ @@ -1367,17 +1367,32 @@ xmlNode *Main::XMLSettingsTree(void) @@
+}
 void Main::exportCellData(void) {
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   QString fileName;
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
 #ifdef QDEBUG
     qDebug() << "exportCellData filename: " << fileName << endl;
 #endif
   // perhaps make this more general: a popup window were user selects data he wants to export
   // can go to "settings" section of XML file as well so this can also be measured off-line
   // mesh.CSVExport would take an QMap or so to record all options
   // first line gives legenda
   QFile file("areas.csv");
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
     QFile file(fileName);
     if ( file.open( IO_WriteOnly ) ) {
       QTextStream stream( &file );
       mesh.CSVExportCellData(stream);
       mesh.CSVExportMeshData(stream);
       file.close();
+    }
+  }
+}
 /* finis */

src/leaficon.png

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