EI/VirtualLeaf Changeset - ec439fed4af8 · Centrum Wiskunde & Informatica (CWI)

Changeset - ec439fed4af8

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Michael Guravage - 15 years ago 2010-10-15 19:27:29
michael.guravage@cwi.nl

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

9 files changed with 915 insertions and 239 deletions:

doc/v1.html

doc/v1.pdf

717

223

doc/v1.rst

src/ChangeLog

src/VirtualLeaf.cpp

src/canvas.cpp

src/canvas.h

src/mainbase.h

src/mesh.h

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doc/v1.html

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@@ @@ -547,25 +547,25 @@ LanguageError: IOError: [Errno 2] No tra @@
 <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</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>
@@ @@ -585,19 +585,93 @@ work. e.g. graphical logs and diff highl @@
 <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>
 </div>
 <div class="footer">
 <hr class="footer" />
 ###Page###
 </div>
 </body>
 </html>

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doc/v1.rst

➞

Show inline comments

@@ @@ -283,37 +283,37 @@ All goes tolerably until you tick in the @@
 RE-INSTALL
 ++++++++++
 . easy_install mercurial
 . mkdir src
 . cd src
 . hg clone http://www.riverbankcomputing.com/hg/sip
 . cd sip
 . python build.py prepare
 . python configure.py
 . make
 . make install
-. cd ..
+. cd \.\.
 . wget http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
 . tar xzf PyQt-x11-gpl-4.7.7
+. tar xzf PyQt-x11-gpl-4.7.7.tar.gz
 . cd PyQt-x11-gpl-4.7.7
 . python configure.py
 . make
 . make install
-. cd ..
+. cd \.\.
 . hg clone https://litsol@bitbucket.org/bfrog/cutehg
 . cd cutehg
 . python setup.py build
 . python setup.py install
-. cd ..
+. cd \.\.
 . easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
 This procedure fails as before.
 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 ``easy_install rhodecode`` 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.
@@ @@ -341,12 +341,90 @@ introduce the new schema changes. @@
 Wednesday 13 October 2010
 -------------------------
 Tweaked ``.bashrc`` and ``virtualenvwrapper.sh`` to facilitate
 virtualenv and virtualenvwrapper - many unbound variables!
 Pushed recent changes to repository from where Roeland can retrieve
 and test them.
 OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.
 Friday 15 October 2010
 ----------------------
 Rhodecode
 +++++++++
 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:
 . Python
 . Bison (for sip)
 . Flex (for sip)
 . m4 (for Bison)
 . Qt (for PyQt)
 . GLIBCXX_3.4.9 (for Qt) - I draw the line at (re)installing GCC!
 OK. Forget sip bison, flex, m4, Qt and the rest. Let's install just
 the minimum.
 First, install sqlite; we'll see in a minute that Python requires
 it. The sources are available at: http://www.sqlite.org/download.html.
 Second, install Python. My initial attempt complained it was missing
 the following bits and pieces::
  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.
 So install sqlite first. And, since Python's configure script doesn't
 have an option for it, I had to tweak ``setup.py`` to enumerate the
 path where it would find sqlite;
 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::
  clone https://litsol@bitbucket.org/marcinkuzminski/rhodecode
 Replacing the egg installed by easy_install by this code does display
 the branch/merge graphics.
 Fourth, setup and serve rhodecode. Following the instructions posted
 online at: http://packages.python.org/RhodeCode/setup.html#setup works as advertised::
  paster make-config RhodeCode production.ini
  paster setup-app production.ini
  paster serve production.ini
 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.
 The Virtual Leaf
 ++++++++++++++++
 Added ``incrementIterations()``, ``getIterations()`` and ``int
 iterations`` to mesh.h. ``incrementIterations()`` is called in TIMESTEP in
 VirtualLeaf.cpp. The actual counter, ``iterations`` is initalized to
 zero in the Mesh class constructor.
 The iterations are inquired in two places: for the frame count in
 ``MainBase::Plot`` in ``VirtualLeaf.cpp` and for the export cell data
 interval in ``Main::TimeStepWrap`` in ``canvas.cpp``.
 The questions remain: Should we use this count, and if yes, where
 should it be incremented? The previous count was incremented in
 ``Main::TimeStepWrap``. Or should we simply use
 ``(int)mesh.getTime()``? Since this is not an ordinal count, the
 results look strange.

src/ChangeLog

➞

Show inline comments

 -10-15    <guravage@caterpie.sen.cwi.nl>
 	* mesh.h (Mesh): Added iterations. incrementIterations() and
 	getIterations().
 	* VirtualLeaf.cpp (Plot): Replaced local frame counter with
 	mesh.incrementIterations().
 	* canvas.cpp (TimeStepWrap): Replaced local counter with
 	mesh.incrementIterations().
 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Turned debug off to make all profiles must be
 	consistant.
 	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX
 	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the
 	uninstaller all go in the bin directory. And leaves directory
 	placed under data directory.
 	* canvas.cpp (exportCellData): Added a check to inquire before
 	overwritting an existing file.
 -10-14    <merks@cwi.nl>
 	* mesh.cpp: In response to referees' comments, added new parameter "yield_threshold" instead of fixed parameter '4' for yield threshold.
 	* mesh.cpp: In response to referees' comments, added new parameter
 	"yield_threshold" instead of fixed parameter '4' for yield
 	threshold.
 	* wallitem.cpp: when clicking a wall, both the wall type was cycled and the transporterdialog popped up. Corrected this - for wall type cycling, hold the Control button while left clicking. TransporterDialog only pops up for left click. Also made sure the wall is redrawn after changing the transporter values.
 	* wallitem.cpp: when clicking a wall, both the wall type was
 	cycled and the transporterdialog popped up. Corrected this - for
 	wall type cycling, hold the Control button while left
 	clicking. TransporterDialog only pops up for left click. Also made
 	sure the wall is redrawn after changing the transporter values.
 	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference
 	* hull.h: added an operator< to sort Points
 	* hull.cpp: added an operator< to sort Points
 	* cellbase.cpp (ExactCircumference): I added a new function
 	ExactCircumference, yielding the circumference of the cell along
 	its wall_elements
 	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

src/VirtualLeaf.cpp

➞

Show inline comments

@@ @@ -171,52 +171,54 @@ void MainBase::Plot(int resize_stride) @@
 /*  if (ShowApoplastsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
 */
   if (ShowMeshP())
     mesh.DrawNodes(&canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&canvas);
   if ( ( batch || MovieFramesP() )) {
     static int frame = 0;
+     static int frame = 0;
     // frame numbers are sequential for the most frequently written file type.
     // for the less frequently written file type they match the other type
     if (!(count%par.storage_stride) )  {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame++;
 	//frame = (int)mesh.getTime();
 	frame = mesh.getIterations();
+      }
       // Write high-res JPG snapshot every plot step
       Save(fname.str().c_str(), "JPEG",1024,768);
+    }
     if (!(count%par.xml_storage_stride)) {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << frame << ".xml";
       if (par.xml_storage_stride < par.storage_stride) {
 	frame++;
 	//frame = (int)mesh.getTime();
 	frame = mesh.getIterations();
+      }
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+    }
+  }
  count++;
+}
 INIT {
@@ @@ -273,24 +275,25 @@ TIMESTEP { @@
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       // Reaction diffusion
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
+    }
   } else {
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   mesh.incrementIterations(); // WHERE SHOULD THIS GO?!
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e){}
 /* Custom message handler - Default appends a newline character to the end of each line. */
 void vlMessageOutput(QtMsgType type, const char *msg)
+{

src/canvas.cpp

➞

Show inline comments

@@ @@ -575,24 +575,25 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   // Start timer which repetitively invokes
   // a simulation time step
   timer = new QTimer( this );
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
@@ @@ -1156,40 +1157,43 @@ void Main::print() @@
     if (cw>ch) {
       pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));
     } else {
       pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));
+    }
     canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));
+  }
+}
 void Main::TimeStepWrap(void)
+{
-  static int t=0;
   static int t;
   stringstream fname;
   TimeStep();
   t++;
   if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){
   //mesh.incrementIterations();
   t = mesh.getIterations();
   //t = (int)mesh.getTime();
   if ((par.export_interval > 0) && !(t%par.export_interval)){
     fname << par.datadir << "/" << par.export_fn_prefix;
     fname.fill('0');
     fname.width(6);
     fname << t << ".csv";
     this->exportCellData(QString(fname.str().c_str()));
+  }
   // check number of timesteps
   if (t==par.nit) {
+  if (t == par.nit) {
     emit SimulationDone();
+  }
+}
 void Main::RestartSim(void)
+{
   stopSimulation();
   if ( QMessageBox::question(
 			     this,
 			     tr("Restart simulation?"),

src/canvas.h

➞

Show inline comments

@@ @@ -127,25 +127,24 @@ class Main : public Q3MainWindow, public @@
   virtual bool InsertModeP(void) { return options->isItemChecked(insert_mode_id); }
   virtual bool ShowToolTipsP(void) { return helpmenu->isItemChecked(tooltips_id); }
   virtual bool HideCellsP(void) { return view->isItemChecked(hide_cells_id); }
   void scale(double factor);
   virtual double getFluxArrowsize(void)
+  {
     return flux_arrow_size;
+  }
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   void about();
   void gpl();
   void TimeStepWrap();
   void togglePaused();
   void setFluxArrowSize(int size);
   void RestartSim(void);
   void toggleShowCellCenters(void);
   void toggleShowNodes(void);
   void toggleShowBorderCells(void);
   void toggleShowFluxes(void);

src/mainbase.h

➞

Show inline comments

@@ @@ -99,28 +99,31 @@ class MainBase { @@
   void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
   void CutSAM(void);
   void Plot(int resize_stride=10);
   virtual void UserMessage(QString message, int timeout = 0) {
     cerr << message.toAscii().constData() << endl;
+  }
   Mesh &mesh;
   QTransform viewport;
  protected:
   QGraphicsScene &canvas;
   virtual xmlNode *XMLSettingsTree(void) const;
   virtual xmlNode *XMLViewportTree(QTransform &transform) const;
  protected:
   bool showcentersp;
   bool showmeshp;
   bool showbordercellp;
   bool shownodenumbersp;
   bool showcellnumbersp;
   bool showcellsaxesp;
   bool showcellstrainp;
   bool movieframesp;
   bool showboundaryonlyp;
   bool showwallsp;

src/mesh.h

➞

Show inline comments

@@ @@ -74,24 +74,25 @@ class Mesh { @@
     // Make sure the reserved value is large enough if a cell is added
     // in "Divide" when the capacity is insufficient, "cells" might be
     // relocated including the current Cell (i.e. the value of *this)
     // calling "Mesh::IncreaseCapacityIfNecessary" (from another
     // object than Cell, e.g. Mesh) before entering Divide will solve
     // this issue (solved now).
     cells.reserve(2);
     nodes.reserve(500);
     time = 0.;
     plugin = 0;
     boundary_polygon=0;
     iterations = 0;
   };
   ~Mesh(void) {
     if (boundary_polygon) {
       delete boundary_polygon;
       boundary_polygon=0;
+    }
   };
   void Clean(void);
   Cell &EllipticCell(double xc, double yc, double ra, double rb, int nnodes=10, double rotation=0);
   Cell &CircularCell(double xc, double yc, double r, int nnodes=10) {
     return EllipticCell(xc, yc, r, r, nnodes, 0);
@@ @@ -382,24 +383,28 @@ class Mesh { @@
   QVector< QPair<qreal,int> > VertexAnglesValues(void);
   void SetSimPlugin(SimPluginInterface *new_plugin) {
     plugin=new_plugin;
+  }
   QString ModelID(void) { return plugin?plugin->ModelID():QString("undefined"); }
   void StandardInit(void);
   double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0, double *hull_circumference=0);
   void CSVExportCellData(QTextStream &csv_stream) const;
   void CSVExportMeshData(QTextStream &csv_stream);
   Node* findNextBoundaryNode(Node*);
   int iterations;
   int getIterations(){return this->iterations;}
   void incrementIterations(){this->iterations++;}
  private:
   // Data members
   vector<Cell *> cells;
   vector<Node *> nodes;
   list<Wall *> walls; // we need to erase elements from this container frequently, hence a list.
  public:
   vector<NodeSet *> node_sets;
  private:
   vector<Node *> shuffled_nodes;
   vector<Cell *> shuffled_cells;
   unique_queue<Edge> node_insertion_queue;

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