EI/VirtualLeaf Changeset - 18e4f7f50259 · Centrum Wiskunde & Informatica (CWI)

Changeset - 18e4f7f50259

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Michael Guravage - 15 years ago 2010-06-15 11:06:33
michael.guravage@cwi.nl

Wrapped diagnostic messages in QDEBUG blocks. Information messages still go to stderr.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/forwardeuler.cpp
changed src/mesh.cpp
changed src/mesh.h
changed src/random.cpp
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallitem.cpp

14 files changed with 368 insertions and 277 deletions:

src/ChangeLog

src/VirtualLeaf.cpp

119

142

src/build_models/Makefile

src/canvas.cpp

src/cell.cpp

src/cellbase.h

src/data_plot.cpp

src/forwardeuler.cpp

src/mesh.cpp

src/mesh.h

src/random.cpp

src/wall.cpp

src/wallbase.cpp

src/wallitem.cpp

0 comments (0 inline, 0 general)

src/ChangeLog

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 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* cellbase.h
 	* data_plot.cpp ditto.
 	* forwardeuler.cpp ditto.
 	* mesh.cpp ditto.
 	* mesh.h
 	* random.cpp ditto.
 	* wall.cpp ditto.
 	* wallbase.cpp ditto.
 	* wallitem.cpp ditto.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -06-03    <guravage@caterpie.sen.cwi.nl>

src/VirtualLeaf.cpp

➞

Show inline comments

@@ @@ -55,25 +55,24 @@ @@
 #include "simplugin.h"
 #include <QPluginLoader>
 #include <QDir>
 #include "modelcatalogue.h"
 /* #define _xstr_(s) _str_(s)
 #define _str_(s) #s
 #include _xstr_(REACTIONS_HEADER)
    #define _str_(s) #s
    #include _xstr_(REACTIONS_HEADER)
 */
 static const std::string _module_id("$Id$");
 extern Parameter par;
 MainBase *main_window = 0;
 //double auxin_account = 0.;
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
@@ @@ -93,13 +92,12 @@ public: @@
       cerr << "Cell " << c.Index() << " is a source cell.\n";
       c.SetSource(0,par.source);
     } else {
       cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";
+    }
+  }
 };
 class CellInfo {
 public:
@@ @@ -113,51 +111,43 @@ public: @@
+    }
     cerr << endl;
+  }
 };
 double PINSum(Cell &c) {
 	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
   return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() && !m.HideCellsP())
 	if (m.ShowToolTipsP()) {
 	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\n" + c.printednodelist();
 	  c.Draw(&canvas, info_string);
 	} else {
 	  c.Draw(&canvas);
+	}
       if (m.ShowCentersP())
 	c.DrawCenter(&canvas);
     if (m.ShowFluxesP())
+      if (m.ShowFluxesP())
 	c.DrawFluxes(&canvas, par.arrowsize);
+       }
+    }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride) {
   clear();
   static int count=0;
   if (resize_stride) {
     if ( !((++count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
@@ @@ -173,89 +163,85 @@ void MainBase::Plot(int resize_stride) { @@
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );
 	if (ShowApoplastsP())
 		mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
   if (ShowApoplastsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
-	if (ShowMeshP())
+  if (ShowMeshP())
     mesh.DrawNodes(&canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&canvas);
 	if ( ( batch || MovieFramesP() )) {
   if ( ( batch || MovieFramesP() )) {
 		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) )  {
     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);
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
 			/*
 			 fname << frame << ".pdf";
 			if (par.storage_stride <= par.xml_storage_stride) {
 				frame++;
+			}
       /*
 	 fname << frame << ".pdf";
 	 if (par.storage_stride <= par.xml_storage_stride) {
 	 frame++;
+	 }
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "PDF");
 			*/
 	 // Write high-res JPG snapshot every plot step
 	 Save(fname.str().c_str(), "PDF");
       */
 			fname << frame << ".jpg";
 			if (par.storage_stride <= par.xml_storage_stride) {
 				frame++;
+			}
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame++;
+      }
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "JPEG",1024,768);
+		}
       // 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 (!(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++;
+			}
 			// Write XML file every ten plot steps
 			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+		}
+	}
       if (par.xml_storage_stride < par.storage_stride) {
 	frame++;
+      }
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+    }
+  }
+}
 INIT {
 	//mesh.SetSimPlugin(plugin);
 	if (leaffile) {
 		xmlNode *settings;
 		mesh.XMLRead(leaffile, &settings);
   //mesh.SetSimPlugin(plugin);
   if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &settings);
     main_window->XMLReadSettings(settings);
     xmlFree(settings);
     main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
   } else {
-	  mesh.StandardInit();
+    mesh.StandardInit();
+  }
+}
 TIMESTEP {
   static int i=0;
@@ @@ -280,104 +266,99 @@ TIMESTEP { @@
     // than biological processes, including division, cell wall yielding
     // and cell expansion
     mesh.InsertNodes(); // (this amounts to cell wall yielding)
     if ( (-dh) < par.energy_threshold) {
 		mesh.IncreaseCellCapacityIfNecessary();
 		mesh.DoCellHouseKeeping();
 		//mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       mesh.IncreaseCellCapacityIfNecessary();
       mesh.DoCellHouseKeeping();
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       // Reaction diffusion
 		/*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
       CellReaction *cellreaction_f = new plugin->CellDynamics();
       WallReaction *wall_f = new WallDynamics();*/
       /*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
 	CellReaction *cellreaction_f = new plugin->CellDynamics();
 	WallReaction *wall_f = new WallDynamics();*/
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
 		/*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
 		QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 		ofstream af(afname.toStdString().c_str());
 		*/
       /*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
 	QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 	ofstream af(afname.toStdString().c_str());
       */
 		/*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
 			 v!=angles.end();
 			 v++) {
 			af << v->first << " " << v->second << endl;
+			}
 			*/
+			}
       /*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
 	v!=angles.end();
 	v++) {
 	af << v->first << " " << v->second << endl;
+	}
       */
+    }
-			} else {
+  } else {
   /*  TransportFunction *transport_f = new CelltoCellTransport();
     CellReaction *cellreaction_f = new CellDynamics();
     WallReaction *wall_f = new WallDynamics();
     /*  TransportFunction *transport_f = new CelltoCellTransport();
 	CellReaction *cellreaction_f = new CellDynamics();
 	WallReaction *wall_f = new WallDynamics();
     mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
 				mesh.ReactDiffuse(par.rd_dt);
 	mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
   /* #ifdef HAVE_QWT
 	// Launch DataPlot window
 	QStringList curvenames;
     for (int i=0;i<NChem();i++) {
 		curvenames += QString("Chem #%1").arg(i);
+	}
     PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
     QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
                      plot, SLOT(AddValue(double,double *)));
 #endif
 	*/
 	//getMesh().plugin->OnClick(*this);
   // Launch DataPlot window
   QStringList curvenames;
   for (int i=0;i<NChem();i++) {
   curvenames += QString("Chem #%1").arg(i);
+  }
   PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
   QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
   plot, SLOT(AddValue(double,double *)));
   #endif
   */
   //getMesh().plugin->OnClick(*this);
+}
 /* Custom message handler - Default appends a newline character to the end of each line. */
  void vlMessageOutput(QtMsgType type, const char *msg)
+ {
      switch (type) {
      case QtDebugMsg:
        //fprintf(stderr, "Debug: %s\n", msg);
        cerr << msg << flush;
        break;
      case QtWarningMsg:
        //fprintf(stderr, "Warning: %s\n", msg);
        cerr << "Warning: " << msg << flush;
        break;
      case QtCriticalMsg:
        fprintf(stderr, "Critical: %s\n", msg);
        cerr << "Critical: " << msg << flush;
        break;
      case QtFatalMsg:
        //fprintf(stderr, "Fatal: %s\n", msg);
        cerr << "Fatal: " << msg << flush;
        abort();
+     }
+ }
 void vlMessageOutput(QtMsgType type, const char *msg)
+{
   switch (type) {
   case QtDebugMsg:
     //fprintf(stderr, "Debug: %s\n", msg);
     cerr << msg << flush;
     break;
   case QtWarningMsg:
     //fprintf(stderr, "Warning: %s\n", msg);
     cerr << "Warning: " << msg << flush;
     break;
   case QtCriticalMsg:
     fprintf(stderr, "Critical: %s\n", msg);
     cerr << "Critical: " << msg << flush;
     break;
   case QtFatalMsg:
     //fprintf(stderr, "Fatal: %s\n", msg);
     cerr << "Fatal: " << msg << flush;
     abort();
+  }
+}
 Parameter par;
 int main(int argc,char **argv) {
@@ @@ -467,42 +448,42 @@ int main(int argc,char **argv) { @@
     QToolTip::setPalette( tooltippalette );
     QGraphicsScene canvas(0,0,8000,6000);
     if (useGUI) {
-         main_window=new Main(canvas, mesh);
       main_window=new Main(canvas, mesh);
       if ( QApplication::desktop()->width() > ((Main *)main_window)->width() + 10
 	   && QApplication::desktop()->height() > ((Main *)main_window)->height() +30 ) {
 	((Main *)main_window)->show();
 	((Main *)main_window)->resize( ((Main *)main_window)->sizeHint());
       } else {
         ((Main *)main_window)->showMaximized();
+      }
     } else {
         ((Main *)main_window)->showMaximized();
       main_window=new MainBase(canvas, mesh);
+    }
   } else {
         main_window=new MainBase(canvas, mesh);
+ }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
 	  // Load plugins
 	  /*QVector<SimPluginInterface *> plugins = LoadPlugins();
 	  InstallPlugin(plugins[0], main_window);
     // Load plugins
     /*QVector<SimPluginInterface *> plugins = LoadPlugins();
       InstallPlugin(plugins[0], main_window);
 	  cerr << "List of models:" << endl;
 	  foreach (SimPluginInterface *p, plugins) {
 		  cerr << p->ModelID().toStdString() << endl;
+	  }
 	  */
       cerr << "List of models:" << endl;
       foreach (SimPluginInterface *p, plugins) {
       cerr << p->ModelID().toStdString() << endl;
+      }
     */
     // Install model or read catalogue of models
     ModelCatalogue model_catalogue(&mesh, useGUI?(Main *)main_window:0,modelfile);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
@@ @@ -514,17 +495,14 @@ int main(int argc,char **argv) { @@
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     main_window->FitLeafToCanvas();
     main_window->Plot();
     if (batch) {
       double t=0.;
       do {
 	t = main_window->TimeStep();
       } while (t < par.maxt);
@@ @@ -551,8 +529,7 @@ int main(int argc,char **argv) { @@
     } else {
       QString qmess(error_message.str().c_str());
       QMessageBox::critical(0, "I/O Error", qmess );
       abort();
+    }
+  }
+}

src/build_models/Makefile

➞

Show inline comments

 # $Id$
 QMAKE = qmake
-all: plugin_auxingrowth plugin_leaf plugin_meinhardt plugin_test
 all: plugin_auxingrowth plugin_meinhardt plugin_test
 plugin_auxingrowth: Makefile.plugin_auxingrowth
 	make -f Makefile.plugin_auxingrowth
 Makefile.plugin_auxingrowth: plugin_auxingrowth.pro
 	$(QMAKE) -makefile -o $@ $<
 plugin_leaf: Makefile.plugin_leaf
 	make -f Makefile.plugin_leaf
 Makefile.plugin_leaf: plugin_leaf.pro
 	$(QMAKE) -makefile -o $@ $<
 plugin_meinhardt: Makefile.plugin_meinhardt
 	make -f Makefile.plugin_meinhardt
 Makefile.plugin_meinhardt: plugin_meinhardt.pro
 	$(QMAKE) -makefile -o $@ $<
@@ @@ -27,15 +21,13 @@ plugin_test: Makefile.plugin_test @@
 Makefile.plugin_test: plugin_test.pro
 	$(QMAKE) -makefile -o $@ $<
 clean:
 	make -f Makefile.plugin_auxingrowth clean
 	make -f Makefile.plugin_leaf clean
 	make -f Makefile.plugin_meinhardt clean
 	make -f Makefile.plugin_test clean
 	touch plugin_auxingrowth.pro
 	touch plugin_leaf.pro
 	touch plugin_meinhardt.pro
 	touch plugin_test.pro
 #finis

src/canvas.cpp

➞

Show inline comments

@@ @@ -40,12 +40,13 @@ @@
 #include <qpixmap.h>
 #include <qfile.h>
 #include <qdir.h>
 #include <q3filedialog.h>
 #include <QGraphicsItem>
 #include <QList>
 #include <QDebug>
 #include <set>
 //Added by qt3to4:
 #include <Q3ValueList>
 #include <Q3PopupMenu>
@@ @@ -225,14 +226,16 @@ void FigureEditor::mousePressEvent(QMous @@
     for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
       /*if ( (*it)->rtti() == imageRTTI ) {
 	ImageItem *item= (ImageItem*)(*it);
 	if ( !item->hit( p ) )
 	continue;
 	}*/
       cerr << typeid(**it).name() << endl;
       #ifdef QDEBUG
       qDebug() << typeid(**it).name() << endl;
       #endif QDEBUG
       if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
 	//moving = dynamic_cast<NodeItem*>(*it);
 	//moving = *it;
 	//moving_start = p;
 	stringstream data_strstream;
@@ @@ -345,26 +348,29 @@ void FigureEditor::mouseReleaseEvent(QMo @@
   emit MouseReleased();
   // intersection line for leaf was finished now.
   if (e->button()==Qt::LeftButton) {
     if (intersection_line ) {
       cerr << "Trying to cut leaf\n";
       #ifdef QDEBUG
       qDebug() << "Trying to cut leaf" << endl;
       #endif
       QPointF sp = intersection_line -> line().p1(); // startpoint
       //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
       QPointF ep = mapToScene(e->pos());
       intersection_line -> setLine( QLineF(sp, ep) );
       intersection_line -> show();
       vector <CellItem *> intersected_cells = getIntersectedCells();
       // no cells selected, do nothing
       if (intersected_cells.size()==0) {
 	cerr << "No cells detected :-( \n";
         #ifdef QDEBUG
 	qDebug() << "No cells detected :-(" << endl;
 	#endif
 	return;
+      }
       Vector startpoint = Vector(sp.x(), sp.y()) / Cell::Factor() - Cell::Offset();
       Vector endpoint = Vector(ep.x(), ep.y()) / Cell::Factor() - Cell::Offset();
@@ @@ -385,20 +391,26 @@ void FigureEditor::mouseReleaseEvent(QMo @@
 	// next division is called?  so check for it?  let's find a way
 	// to do this later. Note that this functionality currently
 	// might result in a segmentation fault for users who are
 	// quickly dragging and releasing division lines...
 	scene()->update();
 	cerr << "Dividing Cell " << c.Index() << endl;
 	#ifdef QDEBUG
 	qDebug() << "Dividing Cell " << c.Index() << endl;
 	#endif
 	c.DivideOverGivenLine( startpoint, endpoint, true, node_set);
+      }
       node_set->CleanUp();
       mesh.AddNodeSet(node_set);
       cerr << "Done DivideOverGivenLine\n";
       #ifdef QDEBUG
       qDebug() << "Done DivideOverGivenLine" << endl;
       #endif
       mesh.TestIllegalWalls();
       // Do the actual cutting and removing
       if (intersected_cells.size()) {
 	//      Mesh &m(intersected_cells.front()->getCell().getMesh());
 	mesh.CutAwayBelowLine( startpoint, endpoint );
@@ @@ -422,26 +434,33 @@ void FigureEditor::mouseReleaseEvent(QMo @@
 	      c++) {
 	  (*c)->SetBoundary(Cell::SAM);
+	}
 	cerr << "Done CutAwayBelowLine\n";
 	#ifdef QDEBUG
 	qDebug() << "Done CutAwayBelowLine" << endl;
 	#endif
 	mesh.TestIllegalWalls();
 	mesh.RepairBoundaryPolygon();
 	cerr << "Done RepairBoundaryPolygon\n";
 	#ifdef QDEBUG
 	qDebug() << "Done RepairBoundaryPolygon" << endl;
 	#endif
 	mesh.TestIllegalWalls();
 	mesh.CleanUpWalls();
 	cerr << "Done CleanUpWalls\n";
 	#ifdef QDEBUG
 	qDebug() << "Done CleanUpWalls" << endl;
 	#endif
 	mesh.TestIllegalWalls();
+      }
       dynamic_cast<Main *>(parent())->Plot();
       cerr << "NodeSet of cutting line: " << *node_set << endl;
         #ifdef QDEBUG
 	qDebug() << "NodeSet of cutting line: " << *node_set << endl;
 	#endif
+    }
   } else
     if (e->button()==Qt::RightButton) {
       if (intersection_line /* && !angle_line*/) {
@@ @@ -466,16 +485,21 @@ void FigureEditor::mouseReleaseEvent(QMo @@
 vector <CellItem *> FigureEditor::getIntersectedCells(void) {
   vector <CellItem *> colliding_cells;
   QList<QGraphicsItem *> l = intersection_line->collidingItems( );
   cerr << "l.size() = " << l.size() << endl;
   #ifdef QDEBUG
   qDebug() <<  "l.size() = " << l.size() << endl;
   #endif
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
     cerr << typeid(**it).name() << endl;
     #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
     #endif
     if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
       colliding_cells.push_back(dynamic_cast<CellItem *>(*it));
+    }
@@ @@ -531,13 +555,17 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   MainBase(c,m),
   mesh(m)
 	  //canvas(c)
+{
   editor = new FigureEditor(canvas,mesh, this);
   cerr << "Interactive = " << editor->isEnabled();
   #ifdef QDEBUG
   qDebug() << "Interactive = " << editor->isEnabled();
   #endif
   working_dir = 0;
   QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));
   QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));
   QMenuBar* menu = menuBar();
   Q3PopupMenu* file = new Q3PopupMenu( menu );
@@ @@ -588,15 +616,15 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
 	com_id = view->insertItem("Show cell &centers", this, SLOT(toggleShowCellCenters()));
   view->setItemChecked(com_id, FALSE);
   //view->insertItem("Cell monitor", this, SLOT(cellmonitor()));
   mesh_id = view->insertItem("Show &nodes", this, SLOT(toggleShowNodes()), Qt::CTRL+Qt::SHIFT+Qt::Key_N);
   view->setItemChecked(mesh_id, TRUE);
   node_number_id = view->insertItem("Show node numbers", this, SLOT(toggleNodeNumbers()), Qt::CTRL+Qt::SHIFT+Qt::Key_M);
-  view->setItemChecked(node_number_id, TRUE);
+  view->setItemChecked(node_number_id, FALSE);
   cell_number_id = view->insertItem("Show cell numbers", this, SLOT(toggleCellNumbers()));
-  view->setItemChecked(cell_number_id, TRUE);
+  view->setItemChecked(cell_number_id, FALSE);
   hide_cells_id = view->insertItem("Hide cells", this, SLOT(toggleHideCells()));
   view->setItemChecked(hide_cells_id, FALSE);
   border_id = view->insertItem("Show &border cells", this, SLOT(toggleShowBorderCells()));
   view->setItemChecked(border_id, FALSE);
   cell_axes_id = view->insertItem("Show cell &axes", this, SLOT(toggleCellAxes()));
   cell_strain_id = view->insertItem("Show cell &strain", this, SLOT(toggleCellStrain()));
@@ @@ -908,13 +936,15 @@ void Main::readPrevStateXML() { @@
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime) {
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 	cerr << "Reading done.\n";
     #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
     #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
@@ @@ -924,13 +954,15 @@ int Main::readStateXML(const char *filen @@
     Plot();
     QString status_message = QString("Succesfully read leaf from file %1. Time is %2 h.\n").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
 	setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
 	cerr << "Done. Returning 0.\n";
     #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
     #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
 		    QMessageBox::Ok | QMessageBox::Default,
@@ @@ -1025,13 +1057,15 @@ void Main::readFirstStateXML() { @@
 void Main::readStateXML() {
   //  extern Mesh mesh;
   stopSimulation();
   cerr << "Trying to open an OptionFileDialog\n";
   #ifdef QDEBUG
   qDebug() << "Trying to open an OptionFileDialog" << endl;
   #endif
   OptionFileDialog *fd = new OptionFileDialog( this, "read dialog", TRUE );
   fd->setMode( OptionFileDialog::ExistingFile );
   fd->setFilter( "XML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
+  }
@@ @@ -1201,25 +1235,25 @@ void Main::toggleHideCells(void) { @@
     running = true;
+  }
   void Main::stopSimulation(void) {
     //run->setItemChecked(paused_id, true);
     timer->stop();
-    cerr << "Stopping simulation\n";
+    cerr << "Stopping simulation" << endl;
     statusBar()->message("Simulation paused");
     running = false;
+  }
   void Main::togglePaused()
+  {
     bool s = run->isItemChecked(paused_id);
     if (s) {
-      cerr << "Calling start simulation\n";
+      cerr << "Calling start simulation" << endl;
       startSimulation();
     } else {
-      cerr << "Calling stop simulation\n";
+      cerr << "Calling stop simulation" << endl;
       stopSimulation();
+    }
+  }
   void Main::setFluxArrowSize(int size) {
@@ @@ -1270,20 +1304,24 @@ void Main::toggleHideCells(void) { @@
     if ( printer->setup(this) ) {
       //    extern Mesh mesh;
       Vector bbll,bbur;
       mesh.BoundingBox(bbll,bbur);
       cerr << "bbll = " << bbll << endl;
       cerr << "bbur = " << bbur << endl;
       #ifdef QDEBUG
       qDebug() << "bbll = " << bbll << endl;
       qDebug() << "bbur = " << bbur << endl;
       #endif
       double cw = (bbur.x - bbll.x);
       double ch = (bbur.y - bbll.y);
       QPainter pp(printer);
       QRect vp=pp.viewport();
       cerr << "Paper width = " << vp.width() << " x " << vp.height() << endl;
       #ifdef QDEBUG
       qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;
       #endif
       // Note that Cell is also translated...
       pp.translate(-bbur.x,-bbur.y);
       if (cw>ch) {
 	pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));
       } else {
@@ @@ -1313,13 +1351,13 @@ void Main::toggleHideCells(void) { @@
 			       this,
 			       tr("Restart simulation?"),
 			       tr("Restart simulation.\n"
 				  "Are you sure?"),
 							   QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
-		cerr << "Restarting simulation\n";
+      cerr << "Restarting simulation" << endl;
       //    extern Mesh mesh;
       mesh.Clear();
       Init();
 		Plot();
 		editor->FullRedraw();
+    }
@@ @@ -1394,19 +1432,21 @@ void Main::toggleHideCells(void) { @@
 void Main::FitCanvasToWindow(void) {
   double scale_factor_x = (double)editor->width()/(double)canvas.width();
   double scale_factor_y = (double)editor->height()/(double)canvas.height();
   double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;
   QMatrix m = editor->matrix();
   cerr << "editor->width() = " << editor->width() << endl;
   cerr << "editor->height() = " << editor->height() << endl;
   #ifdef QDEBUG
   qDebug() << "editor->width() = " << editor->width() << endl;
   qDebug() << "editor->height() = " << editor->height() << endl;
   cerr << "scale_factor = " << scale_factor << endl;
   cerr << "scale_factor_x = " << scale_factor_x << endl;
   cerr << "scale_factor_y = " << scale_factor_y << endl;
   qDebug() << "scale_factor = " << scale_factor << endl;
   qDebug() << "scale_factor_x = " << scale_factor_x << endl;
   qDebug() << "scale_factor_y = " << scale_factor_y << endl;
   #endif
   m.scale( scale_factor, scale_factor );
   editor->setMatrix( m );
   editor->show();
+}
   void Main::PauseIfRunning(void) {

src/cell.cpp

➞

Show inline comments

@@ @@ -16,24 +16,25 @@ @@
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QDebug>
 #include <string>
 #include "cell.h"
 #include "node.h"
 #include "mesh.h"
 #include "tiny.h"
 #include "nodeset.h"
 #include "cellitem.h"
 #include "nodeitem.h"
 #include "qcanvasarrow.h"
 #include "parameter.h"
 #include <QDebug>
 static const std::string _module_id("$Id$");
 extern Parameter par;
 double Cell::factor=1.;
@@ @@ -108,19 +109,21 @@ double Cell::MeanArea(void) { @@
+}
 void Cell::Apoptose(void) {
 	// First kill walls
 	cerr << "This is cell " << Index() << "\n";
 	cerr << "Number of walls: " << walls.size() << endl;
 	for (list<Wall *>::iterator w=walls.begin();
 		 w!=walls.end();
 		 w++) {
 		cerr << "Before apoptosis, wall " << (*w)->Index() << " says: c1 = " << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
         #ifdef QDEBUG
         qDebug() << "This is cell " << Index() << endl;
 	qDebug() << "Number of walls: " << walls.size() << endl;
 	#endif
 	for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
              #ifdef QDEBUG
 	     qDebug() << "Before apoptosis, wall " << (*w)->Index() << " says: c1 = "
 		      << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
              #endif
+	}
 	for (list<Wall *>::iterator w=walls.begin();
 		 w!=walls.end();
 		 w++) {
 		bool illegal_flag = false;
@@ @@ -137,31 +140,41 @@ void Cell::Apoptose(void) { @@
 			(*w)->n2 = n1;
 		} else {
 			(*w)->c2 = m->boundary_polygon;
+		}
 		#ifdef QDEBUG
 		if (illegal_flag && (*w)->c1==(*w)->c2) {
-			cerr << "I created an illegal wall.\n";
+		  qDebug() << "I created an illegal wall." << endl;
+		}
 		#endif
 		if ( ((*w)->N1()->DeadP() || (*w)->N2()->DeadP()) ||
 			((*w)->C1() == (*w)->C2() ) ){
 			// kill wall
 			cerr << "Killing wall.\n";
 		        #ifdef QDEBUG
 		        qDebug() << "Killing wall." << endl;
 			#endif
 			(*w)->Kill();
 			#ifdef QDEBUG
 			if ((*w)) {
 				cerr << "Wall " << (*w)->Index() << " says: c1 = " << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
 			  qDebug() << "Wall " << (*w)->Index() << " says: c1 = "
 				   << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
+			}
 			#endif
 			(*w)=0;
 		} else {
 			cerr << "Not killing wall.\n";
 			cerr << "Wall " << (*w)->Index() << " says: c1 = " << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
 		        #ifdef QDEBUG
 		        qDebug() << "Not killing wall." << endl;
 			qDebug() << "Wall " << (*w)->Index() << " says: c1 = "
 				 << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
                         #endif
+		}
+	}
 	walls.remove(0);
 	// Unregister me from my nodes, and delete the node if it no longer belongs to any cells
 	list<Node *> superfluous_nodes;
 	for (list<Node *>::iterator n=nodes.begin();
@@ @@ -325,13 +338,15 @@ bool Cell::DivideOverGivenLine(const Vec @@
 	// check each edge for intersection with the line
 	ItList new_node_locations;
 	cerr << "Cell " << Index() << " is doing DivideOverGivenLine \n";
 	#ifdef QDEBUG
 	qDebug() << "Cell " << Index() << " is doing DivideOverGivenLine" << endl;
 	#endif
 	for (list<Node *>::iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
 		Vector v3 = *(*i);
 		list<Node *>::iterator nb=i;
@@ @@ -358,35 +373,37 @@ bool Cell::DivideOverGivenLine(const Vec @@
 			// yes, intersection detected. Push the location to the list of iterators
 			new_node_locations.push_back(nb);
+		}
+	}
         #ifdef QDEBUG
 	if (new_node_locations.size()<2) {
 		cerr << "Line does not intersect with two edges of Cell " << Index() << endl;
 		cerr << "new_node_locations.size() = " << new_node_locations.size() << endl;
 		return false;
 	  qDebug() << "Line does not intersect with two edges of Cell " << Index() << endl;
 	  qDebug() << "new_node_locations.size() = " << new_node_locations.size() << endl;
 	  return false;
+	}
 	ItList::iterator i = new_node_locations.begin();
 	list< Node *>::iterator j;
 	cerr << "-------------------------------\n";
 	cerr << "Location of new nodes: " << (**i)->Index() << " and ";
 	qDebug() << "-------------------------------" << endl;
 	qDebug() << "Location of new nodes: " << (**i)->Index() << " and ";
 	++i;
 	j = *i;
 	if (j==nodes.begin()) j=nodes.end(); j--;
 	cerr << (*j)->Index() << endl;
 	cerr << "-------------------------------\n";
 	qDebug() << (*j)->Index() << endl;
 	qDebug() << "-------------------------------" << endl;
 	if ( **new_node_locations.begin() == *j ) {
-		cerr << "Rejecting proposed division (cutting off zero area).\n";
+	  qDebug() << "Rejecting proposed division (cutting off zero area)." << endl;
 		return false;
+	}
 	#endif
 	DivideWalls(new_node_locations, v1, v2, fix_cellwall, node_set);
 	return true;
+}
@@ @@ -448,15 +465,18 @@ void Cell::DivideWalls(ItList new_node_l @@
 		// again. We can do this here because it is the last cell added.
 		// Never, ever try to fully erase a cell elsewhere, because we
 		// make heavy use of cell indices in this project; if you erase a
 		// Cell somewhere in the middle of Mesh::Cells the indices will
 		// get totally messed up...! (e.g. the indices used in Nodes::cells)
 		cerr << "new_node_locations.size() = " << new_node_locations.size() <<endl;
 		cerr << "daughter->index = " << daughter->index << endl;
 		cerr << "cells.size() = " << m->cells.size() << endl;
 		#ifdef QDEBUG
 		qDebug() << "new_node_locations.size() = " << new_node_locations.size() <<endl;
 		qDebug() << "daughter->index = " << daughter->index << endl;
 		qDebug() << "cells.size() = " << m->cells.size() << endl;
 		#endif
 		m->cells.pop_back();
 		Cell::NCells()--;
 		m->shuffled_cells.pop_back();
 		return;
+	}
@@ @@ -526,13 +546,13 @@ void Cell::DivideWalls(ItList new_node_l @@
 		double elem_length = ( (*(**i)) - (*(*nb)) ).Norm();
 		if ( ( *(**i) - *n ).Norm() < collapse_node_threshold  * elem_length ) {
 			new_node_flag[nnc]=1;
 			new_node[nnc] = *(**i);
 			new_node_ind[nnc] = **i;
-			//cerr << **i << "\n" ;
+			//cerr << **i << endl ;
 		} else
 			if ( (*(*nb) - *n).Norm() < collapse_node_threshold * elem_length ) {
 				new_node_flag[nnc]=2;
 				new_node[nnc] = *(*nb);
 				new_node_ind[nnc] = *nb;
 			} else {
@@ @@ -782,16 +802,17 @@ void Cell::DivideWalls(ItList new_node_l @@
 				// Find wall between this cell and neighbor cell
 				w = find_if( start_search, walls.end(), bind2nd (mem_fun( &Wall::is_wall_of_cell_p ), neighbor_cell ) );
 				start_search = w; start_search++; // continue searching at next element
 			} while ( w!=walls.end() && !(*w)->IntersectsWithDivisionPlaneP( from, to ) ); // go on until we find the right one.
 			if (w == walls.end()) {
 				cerr << "Whoops, wall element not found...!\n";
 				cerr << "Cell ID: " << neighbor_cell->Index() << endl;
 				cerr << "My cell ID: " << Index() << endl;
 			        #ifdef QDEBUG
 			  qDebug() << "Whoops, wall element not found...!" << endl;
 			        qDebug() << "Cell ID: " << neighbor_cell->Index() << endl;
 				qDebug() << "My cell ID: " << Index() << endl;
                                 #endif
 			} else {
 				// 2. Split it up, if we should (sometimes, the new node coincides with an existing node so
 				// we should not split up the Wall)
 				if (new_node_ind[i]!=(*w)->n1 && new_node_ind[i]!=(*w)->n2) {
@@ @@ -892,13 +913,15 @@ void Cell::DivideWalls(ItList new_node_l @@
 			// and remove them)
 			list<Neighbor>::iterator neighb_with_this_cell=
 			find_if((*i)->owners.begin(),
 					(*i)->owners.end(),
 				bind2nd(mem_fun_ref( &Neighbor::CellEquals ),this->Index() )  );
 			if (neighb_with_this_cell==(*i)->owners.end()) {
 				cerr << "not found\n";
 			        #ifdef QDEBUG
 			  qDebug() << "not found" << endl;
                                 #endif
 				abort();
+			}
 			(*i)->owners.erase(neighb_with_this_cell);
 			daughter->nodes.push_back( *i );
@@ @@ -1616,15 +1639,17 @@ void Cell::Flux(double *flux, double *D) @@
 		// flux depends on edge length and concentration difference
 		for (int c=0;c<NChem();c++) {
 			double phi = (*i)->length * ( D[c] ) * ( ((Cell *)(*i)->c2)->chem[c] - chem[c] );
 			#ifdef QDEBUG
 			if ((*i)->c1!=this) {
-				cerr << "Warning, bad cells boundary: " << (*i)->c1->Index() << ", " << index << endl;
+			  qDebug() << "Warning, bad cells boundary: " << (*i)->c1->Index() << ", " << index << endl;
+			}
 			#endif
 			flux[c] += phi;
+		}
+	}
+}
@@ @@ -1637,13 +1662,15 @@ void Cell::Flux(double *flux, double *D) @@
 void Cell::Draw(QGraphicsScene *c, QString tooltip) {
 	// Draw the cell on a QCanvas object
 	if (DeadP()) {
 		cerr << "Cell " << index << " not drawn, because dead.\n";
 	        #ifdef QDEBUG
 	  qDebug() << "Cell " << index << " not drawn, because dead." << endl;
 		#endif
 		return;
+	}
 	CellItem* p = new CellItem(this, c);
 	QPolygonF pa(nodes.size());
@@ @@ -1937,17 +1964,18 @@ void Cell::SetWallLengths(void) { @@
 //! Add Wall w to the list of Walls
 void Cell::AddWall( Wall *w ) {
 	// if necessary, we could try later inserting it at the correct position
         #ifdef QDEBUG
 	if (w->c1 == w->c2 ){
 		cerr << "Wall between identical cells: " << w->c1->Index()<< endl;
 	  qDebug() << "Wall between identical cells: " << w->c1->Index()<< endl;
+	}
 	#endif
 	// Add Wall to Cell's list
 	walls.push_back( w );
 	// Add wall to Mesh's list if it isn't there yet
 	if (find (

src/cellbase.h

➞

Show inline comments

@@ @@ -62,16 +62,20 @@ class CellsStaticDatamembers { @@
 public:
 	CellsStaticDatamembers(void) {
 		ncells = 0;
 		nchem = 0;
 		base_area = 0.;
 		cerr << "Constructor of CellsStaticDatamembers\n";
                 #ifdef QDEBUG
 		qDebug() << "Constructor of CellsStaticDatamembers" << endl;
 		#endif
+	}
 	~CellsStaticDatamembers() {
 		cerr << "Oops! Desctructor of CellsStaticDatamembers called\n";
                 #ifdef QDEBUG
 	        qDebug() << "Oops! Desctructor of CellsStaticDatamembers called" << endl;
                 #endif
+	}
 	int ncells;
 	int nchem;
 	double base_area;

src/data_plot.cpp

➞

Show inline comments

@@ @@ -29,17 +29,19 @@ @@
 #include <qwt_legend.h>
 #include <qwt_scale_draw.h>
 #include <qwt_math.h>
 #include <QDialog>
 #include <QString>
 #include <QStringList>
 #include <QDebug>
 #include <iostream>
 #include "data_plot.h"
 static const std::string _module_id("$Id$");
 using namespace std;
 static const string _module_id("$Id$");
 //
 //  Initialize main window
 //
 DataPlot::DataPlot(QWidget *parent, const QString title, const QStringList curvenames ):
   QwtPlot(parent),
@@ @@ -87,13 +89,17 @@ DataPlot::DataPlot(QWidget *parent, cons @@
   for (int i=0;i<ncurves;i++) {
     curves[i].setTitle(curvenames[i]);
     curves[i].attach(this);
     curves[i].setPen(QPen(curvecolors[i]));
     QString col(curvecolors[i]);
     std::cerr << "Curvecolor " << col.toStdString() << std::endl;
     #ifdef QDEBUG
     qDebug() << "Curvecolor " << col.toStdString() << endl;
     #endif
     curves[i].setRawData(d_t, d_x[i], PLOT_SIZE);
+  }
   // Axis
   setAxisTitle(QwtPlot::xBottom, "Time");

src/forwardeuler.cpp

➞

Show inline comments

@@ @@ -23,13 +23,15 @@ @@
 #include <iostream>
 #include "forwardeuler.h"
 #include "warning.h"
 #include "maxmin.h"
 #include <string>
 static const std::string _module_id("$Id$");
 using namespace std;
 static const string _module_id("$Id$");
 // The value Errcon equals (5/Safety) raised to the power (1/PGrow), see use below.
 /* static float maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?	\
    (maxarg1) : (maxarg2))
@@ @@ -63,13 +65,13 @@ void ForwardEuler::odeint(double *ystart @@
   ystart is replaced byv alues at the end of the integration interval. derivs is the user-supplied
   routine for calculating the right-hand side derivative, while rkqs is the name of the stepper
   routine to be used. */
+{
   static bool warning_issued = false;
   if (!warning_issued) {
-    std::cerr << "Using inaccurate method ForwardEuler\n";
     cerr << "Using inaccurate method ForwardEuler\n";
     warning_issued=true;
     //MyWarning::warning("Using inaccurate method ForwardEuler");
+  }
   // N.B. Not for serious use and not fully usage compatible with RungeKutta
   // simply for testing API of integrator.

src/mesh.cpp

➞

Show inline comments

@@ @@ -391,15 +391,16 @@ Cell &Mesh::LeafPrimordium(int nnodes, d @@
   AddNodeToCell(petiole,
 		n4,
 		n3,
 		n1);
   cerr << circle << endl;
   cerr << petiole << endl;
   #ifdef QDEBUG
   qDebug() << circle << endl;
   qDebug() << petiole << endl;
   #endif
   AddNodeToCell(boundary_polygon, *it_n1,
 		n4,
 		*it_n2 + ((*it_n1-*it_n2)+1)%nnodes); // is this gonna work?
   (*it_n1)->boundary=true;
@@ @@ -575,16 +576,18 @@ void Mesh::Clear(void) { @@
 	 shuffled_cells.clear();
 	 shuffled_nodes.clear();
 	 node_insertion_queue.empty();
 	 cerr << "Meshed cleared: cells: " << cells.size() << ", nodes: " << nodes.size() << endl;
 	 */
 	cerr << "cells.size() = " << cells.size() << endl;
 	cerr << "walls.size() = " << walls.size() << endl;
 	cerr << "nodes.size() = " << nodes.size() << endl;
 	#ifdef QDEBUG
 	qDebug() << "cells.size() = " << cells.size() << endl;
 	qDebug << "walls.size() = " << walls.size() << endl;
 	qDebug << "nodes.size() = " << nodes.size() << endl;
         #endif
+}
 double Mesh::DisplaceNodes(void) {
   MyUrand r(shuffled_nodes.size());
   random_shuffle(shuffled_nodes.begin(),shuffled_nodes.end(),r);
@@ @@ -1442,14 +1445,16 @@ void Mesh::CleanUpCellNodeLists(void) { @@
 void Mesh::CutAwayBelowLine( Vector startpoint, Vector endpoint) {
   // Kills all cells below the line startpoint -> endpoint
   Vector perp = (endpoint-startpoint).Perp2D().Normalised();
   cerr << "Before Apoptose\n";
   #ifdef QDEBUG
   qDebug() << "Before Apoptose" << endl;
   #endif
   TestIllegalWalls();
   for (vector<Cell *>::iterator i=cells.begin();
        i!=cells.end();
        i++) {
     // do some vector geometry to check whether the cell is below the cutting line
@@ @@ -1458,13 +1463,15 @@ void Mesh::CutAwayBelowLine( Vector star @@
     if ( InnerProduct(perp, cellvec) < 0 ) {
       // remove those cells
       (*i)->Apoptose();
+    }
+  }
   cerr << "Before CleanUpCellNodeLists\n";
   #ifdef QDEBUG
   qDebug() << "Before CleanUpCellNodeLists" << endl;
   #endif
   TestIllegalWalls();
   CleanUpCellNodeLists();
+}
@@ @@ -1489,13 +1496,15 @@ void Mesh::CutAwaySAM(void) { @@
 void Mesh::TestIllegalWalls(void) {
   for (list<Wall *>::iterator w = walls.begin();
        w!=walls.end();
        w++) {
     if ((*w)->IllegalP() ) {
       cerr << "Wall " << **w << " is illegal.\n";
       #ifdef QDEBUG
       qDebug() << "Wall " << **w << " is illegal." << endl;
       #endif
+    }
+  }
+}
@@ @@ -1614,13 +1623,13 @@ void Mesh::RepairBoundaryPolygon(void) { @@
+    }
+  }
   boundary_polygon->walls.remove(0);
   boundary_polygon->ConstructNeighborList();
 #ifdef QDEBUG
-  cerr << "Repaired Boundary Polygon node indices: ";
+  qDebug() << "Repaired Boundary Polygon node indices: ";
   foreach (Node* node, boundary_polygon->nodes){
     qDebug() << node->Index() << " " ;
+  }
   qDebug() << endl ;
   #ifdef _undefined_

src/mesh.h

➞

Show inline comments

@@ @@ -37,12 +37,13 @@ @@
 #endif
 #include "cell.h"
 #include "node.h"
 #include "simplugin.h"
 #include <QVector>
 #include <QPair>
 #include <QDebug>
 using namespace std;
 // new queue which rejects duplicate elements
 template<class T, class C = deque<T> > class unique_queue : public queue<T,C> {
 public:
@@ @@ -107,14 +108,16 @@ public: @@
 	//void RandPoints(int npoints);
 	inline Cell &getCell(int i) {
 		if ((unsigned)i<cells.size())
 			return *cells[i];
 		else {
 			cerr << i << endl;
 			cerr << "size is " << cells.size() << endl;
                         #ifdef QDEBUG
                         qDebug() << i << endl;
                         qDebug() << "size is " << cells.size() << endl;
                         #endif
 			abort();
 			//	throw("Index out of range in Mesh::getCell");
+		}
+	}
 	inline Node &getNode(int i) {

src/random.cpp

➞

Show inline comments

@@ @@ -16,12 +16,13 @@ @@
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QDebug>
 #include <string>
 #include <stdio.h>
 #include <stdlib.h>
 #include <sys/timeb.h>
 #include <iostream>
 #include "random.h"
@@ @@ -81,15 +82,16 @@ double RANDOM(void) @@
 /*! \param An integer random seed
   \return the random seed
 **/
 int Seed(int seed)
+{
   if (seed < 0) {
     cerr << "Randomizing random generator, seed is ";
     int rseed=Randomize();
     cerr << rseed << "\n";
     #ifdef QDEBUG
     qDebug() << "Randomizing random generator, seed is " << rseed << endl;
     #endif
     return rseed;
   } else {
     int i;
     idum = -seed;
     for (i=0; i <100; i++)
       RANDOM();

src/wall.cpp

➞

Show inline comments

@@ @@ -58,13 +58,15 @@ bool Wall::CorrectWall( void ) { @@
 	// For the first division, wall finds three "owners", including the boundary_polygon.
 	// Remove that one from the list.
 	//cerr << "wall_owners.size() = " << wall_owners.size() << endl;
 	if (wall_owners.size() == 3 && nwalls==1 /* bug-fix 22/10/2007; confine this condition to first division only */) {
 		cerr << "nwalls = " << nwalls << endl;
 	        #ifdef QDEBUG
 	        qDebug() << "nwalls = " << nwalls << endl;
 		#endif
 		// special case for first cleavage
 		// find boundary polygon in the wall owners list
 		list<CellBase *>::iterator bpit = find_if (
 												   wall_owners.begin(), wall_owners.end(),
 												   mem_fun( &CellBase::BoundaryPolP )
@@ @@ -83,41 +85,41 @@ bool Wall::CorrectWall( void ) { @@
 			((Cell *)c2)->AddWall( bp_wall2);
 			((Cell *)(*bpit))->AddWall(bp_wall2);
 			wall_owners.erase(bpit);
 		}else {
 		  #ifdef QDEBUG
 		  qDebug() << "Wall::CorrectWall says: Wall has three owners, but none of them is the BoundaryPolygon. I have no clue what to do with this case... Sorry!" << endl;
 		  qDebug() << "Wall: " << *this << endl;
 		  qDebug() << "Owners are: ";
 		  transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(qDebug(), "  "), mem_fun (&CellBase::Index) );
 		  qDebug() << endl;
 		  qDebug() << "Owners node " << n1->Index() << ": ";
 		  for (list<Neighbor>::iterator i = n1->owners.begin(); i!=n1->owners.end(); i++) {
 		    qDebug() << i->getCell()->Index() << " ";
+		  }
 		  qDebug() << endl;
 		  qDebug() << "Owners node " << n2->Index() << ": ";
 			cerr << "Wall::CorrectWall says: Wall has three owners, but none of them is the BoundaryPolygon. I have no clue what to do with this case... Sorry!\n";
 			cerr << "Wall: " << *this << endl;
 			cerr << "Owners are: ";
 			transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(cerr, "  "), mem_fun (&CellBase::Index) );
 			cerr << endl;
 			cerr << "Owners node " << n1->Index() << ": ";
 			for (list<Neighbor>::iterator i = n1->owners.begin();
 				 i!=n1->owners.end();
 				 i++) {
 				cerr << i->getCell()->Index() << " ";
+			}
 			cerr << endl;
 			cerr << "Owners node " << n2->Index() << ": ";
 			for (list<Neighbor>::iterator i = n2->owners.begin();
 				 i!=n2->owners.end();
 				 i++) {
 				cerr << i->getCell()->Index() << " ";
+			}
 			cerr << endl;
 			std::exit(1);
 		  for (list<Neighbor>::iterator i = n2->owners.begin(); i!=n2->owners.end(); i++) {
 		    qDebug() << i->getCell()->Index() << " ";
+		  }
 		  qDebug() << endl;
                   #endif
 		  std::exit(1);
+		}
+	}
 	#ifdef QDEBUG
 	if (wall_owners.size() == 1) {
-		cerr << "Corner point. Special case.\n";
+	  qDebug() << "Corner point. Special case." << endl;
+	}
 	#endif
 	CellBase *cell1 = wall_owners.front();
 	CellBase *cell2 = wall_owners.back();
 	if ( (c1 == cell1 && c2==cell2) || (c1 == cell2 && c2 == cell1) ) {
@@ @@ -145,13 +147,15 @@ bool Wall::CorrectWall( void ) { @@
 				if ( c2 == cell2) {
 					((Cell *)c1)->RemoveWall(this);
 					c1 = cell1;
 					((Cell *)c1)->AddWall(this);
 					//	  cerr << "Block 3\n";
 				} else {
 					cerr << "Warning, cell wall was not corrected.\n";
 				        #ifdef QDEBUG
 				        qDebug() << "Warning, cell wall was not corrected." << endl;
 					#endif
 					return false;
+				}
+			}
+		}
+	}

src/wallbase.cpp

➞

Show inline comments

@@ @@ -16,12 +16,14 @@ @@
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QDebug>
 #include "wall.h"
 #include "wallbase.h"
 #include "node.h"
 #include "mesh.h"
 #include "parameter.h"
 #include <sstream>
@@ @@ -50,15 +52,17 @@ ostream &operator<<(ostream &os, const W @@
 	return os;
+}
 WallBase::WallBase(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2) {
         #ifdef QDEBUG
 	if (sc1==sc2) {
-		cerr << "Attempting to build a wall between identical cells: " << sc1->Index() << endl;
+	  qDebug() << "Attempting to build a wall between identical cells: " << sc1->Index() << endl;
+	}
 	#endif
 	c1 = sc1;
 	c2 = sc2;
 	n1 = sn1;
 	n2 = sn2;

src/wallitem.cpp

➞

Show inline comments

@@ @@ -16,12 +16,13 @@ @@
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QDebug>
 #include <string>
 #include <QGraphicsScene>
 #include <QVector>
 #include "canvas.h"
 #include "wallitem.h"
 #include "parameter.h"
@@ @@ -122,16 +123,18 @@ void WallItem::setColor(void) { @@
+}
 void WallItem::OnClick(QMouseEvent *e) {
 	Wall *w=&getWall();
 	cerr << "Wall ID = " << w->Index() << ", this = " << w << "\n";
 	cerr << "Wall item = " << this << "\n";
 	cerr << "C1 = " << w->C1()->Index() << ", C2 = " << w->C2()->Index() << endl;
 	cerr << "N1 = " << w->N1()->Index() << ", N2 = " << w->N2()->Index() << endl;
 	#ifdef QDEBUG
 	qDebug() << "Wall ID = " << w->Index() << ", this = " << w << endl;
 	qDebug() << "Wall item = " << this << endl;
 	qDebug() << "C1 = " << w->C1()->Index() << ", C2 = " << w->C2()->Index() << endl;
 	qDebug() << "N1 = " << w->N1()->Index() << ", N2 = " << w->N2()->Index() << endl;
 	#endif
 	//double tr = wn==1?w->Transporters1(1):w->Transporters2(1);
 	CellBase *c = wn==1?w->C1():w->C2();
 	TransporterDialog dialog(w, c, wn);
 	dialog.exec();

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