EI/VirtualLeaf Changeset - d4a19fde7f8d · Centrum Wiskunde & Informatica (CWI)

Changeset - d4a19fde7f8d

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0 7 0

Michael Guravage - 15 years ago 2010-06-23 09:32:29
michael.guravage@cwi.nl

Corrected several small problems with qDebug. See ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed doc/installation.pdf
changed doc/installation.rst
changed src/ChangeLog
changed src/canvas.cpp
changed src/mesh.cpp
changed src/random.cpp
changed src/wall.cpp

7 files changed with 44 insertions and 35 deletions:

doc/installation.pdf

doc/installation.rst

src/ChangeLog

src/canvas.cpp

src/mesh.cpp

src/random.cpp

src/wall.cpp

0 comments (0 inline, 0 general)

doc/installation.pdf

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doc/installation.rst

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 .. $Id$
 .. |date| date::
 .. |time| date:: %H:%M
 .. header::
   ###Title###  -  |date|
 .. footer::
   ###Page###
 Installation Instructions
 =========================
 Requirements
 ------------
 The Virtual Leaf is written with the QT Cross platform application and
 UI framework, and can run on Linux, Apple Macintosh and Windows
 machines. To compile the Virtual Leaf you will need to install the QT
 software development kit which you can download from the `QT download
+software development kit (SDK) which you can download from the `QT download
 site <http://qt.nokia.com/downloads/downloads#lgpl/>`_. Whether
 installed globally by a system administrator our locally in your own
 user space, make sure the QT bin directory containing qmake is in your
 execution path.
 All Platforms
 -------------
 Compilation is effected with make, either the native ``make`` on UNIX
 and MAC systems or the ``mingw32-make`` distributed with the windows
 version of QT. In the Virtual Leaf ``src`` directory you will find a
 ``Makefile``, the root of a hierarchy of makefiles, that will guide
 the compilation and installation of the VirtualLeaf executable, its
 default plugins and the tutorial examples.  To facilitate cross
 platform compatibility, the makefiles expect an environment variable
 named ``MAKE`` to name the make utility to use. The fallback default
 is 'make.' Platform specific instructions follow.
 Linux
 -----
 Prepend the QT bin directory to your path, for example::
  > PATH=/opt/QT/qt/bin:$PATH
 If you wish to use some other make utility than make, instantiate an
 environment variable named ``MAKE``, for example::
  > export MAKE=gmake.
 Go to the ``src`` directory and invoke make, for example::
  > cd /home/michael/VirtualLeaf/v1.0/src
  > make
 When complete, you will find the ``VirtualLeaf`` binary in
 ``v1.0/bin`` and the plugins in ``v1.0/bin/models``.
 Windows
 -------
 For convenience sake the libiconv, libxml2 and libz header files and
 libraries are distributed with the Virtual Leaf code, and Virtual Leaf
 will compile correctly with them. If, however, you wish to compile
 with other versions of these libraries, you will need to reassign the
 ``LIBZML2DIR``, ``LIBICONVDIR`` and ``LIBZDIR`` variables in all the
 project files.
 After installing QT you should be able to invoke a QT command window
 from the start menu. This shell automatically includes the necessary
 QT folder in your execution PATH. Within this command window, go to the
 Virtual Leaf's src directory,
 In the start menu, right click on My Computer and choose properties
 from the drop down list. In the advanced tab click on environment
 variables. Append the QT
 MacOS
 -----

src/ChangeLog

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Show inline comments

 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* mesh.cpp (Clear): Added parentheses to qDebug statments.
 	(TestIllegalWalls): Replaced qDebug().
 	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.
 	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (tutorials): Add tutorials target.
 -06-21    <guravage@caterpie.sen.cwi.nl>
 	* parameter.cpp: Added particular reassignment of datadir.
 	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.
 -06-18    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (gpl): Added gpl slot to display GPL license.
 	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
 	* libplugin.pro: Ditto.
 	* Makefile (clean): add if stmt not to `touch` on windows.
 -06-17    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed perl references.
 	* libplugin.pro: Ditto.
 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.
 	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.
 	* xmlwrite.h (XMLIO): Ditto!
 	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;
 	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
 	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
 	(XMLReadCells): Removed unused count variable.
 	(XMLReadSimtime): Removed unused cur variable.
 	(XMLRead): Removed unused v_str variable.
 	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
 	(SimItemBase) Ditto.
 	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.
 	* output.cpp (OpenWriteFile): Removed unused par variable.
 	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.
 	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.
 	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.
 	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
 	(mousePressEvent): Removed unused item variable.
 	* apoplastitem.cpp
 	(ApoplastItem): Removed unused par variable.
 	(OnClick): Use NULL assignment merely to obviate compilation warning.
 	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.
 	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* 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>
 	* pardialog.h: Added default versions of this automatically generated file.
 	* pardialog.cpp: ditto.
 	* parameter.h: ditto.
 	* parameter.cpp: ditto.
 	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
  	* libplugin.pro: dito.
 	* Makefile: Added top-level Makefile
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

src/canvas.cpp

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Show inline comments

@@ @@ -180,385 +180,385 @@ void FigureEditor::mousePressEvent(QMous @@
     intersection_line->setLine( QLineF(p,p) );
     intersection_line->setZValue( 100 );
     intersection_line->show();
+  }
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
 #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
 #endif
     if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
       stringstream data_strstream;
       data_strstream << (dynamic_cast<NodeItem*>(*it))->getNode();
       dynamic_cast<Main *>(parent())->UserMessage(QString(data_strstream.str().c_str()));
       (dynamic_cast<NodeItem*>(*it))->OnClick(e->button());
+    }
     else
       if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
 	Cell &c=((dynamic_cast<CellItem *>(*it))->getCell());
 	// OnClick to be defined in end-user code
 	c.OnClick(e);
       } else {
 	if ( !strcmp(typeid(**it).name(),"8WallItem") ) {
 	  (dynamic_cast<WallItem *>(*it))->OnClick(e);
+	}
+      }
+  }
   FullRedraw();
   moving = 0;
+}
 void FigureEditor::mouseMoveEvent(QMouseEvent* e)
+{
   // User chooses "rotation mode" and we can rotate the object around its center of mass
   if (dynamic_cast<Main *>(parent())->RotationModeP()) {
     QPointF p = mapToScene(e->pos());
     p.setX(p.x() / Cell::Magnification());
     p.setY(p.y() / Cell::Magnification());
     // get object's center of mass
     QPointF rotation_midpoint = mesh.Centroid()*Cell::Factor() - Cell::Offset();
     // calculate rotation angle
     double dy = (rotation_midpoint.y() - p.y());
     double dx = (rotation_midpoint.x() - p.x());
     double new_rot_angle = atan2(dx, dy);
     double d_alpha = new_rot_angle - rot_angle;
     rot_angle = new_rot_angle;
     mesh.Rotate(d_alpha, ( Vector(rotation_midpoint) + Cell::Offset() ) / Cell::Factor() );
     dynamic_cast<Main *>(parent())->Plot(0);
     FullRedraw();
     return;
+  }
   if ( moving ) {
     QPointF p = mapToScene(e->pos());
     moving->userMove(p.x() - moving_start.x(),
 		     p.y() - moving_start.y());
     moving_start = p;
     scene()->update();
+  }
   //cerr << "event";
   // keep track of intersection line to interactively cut a growing leaf
   if ( intersection_line ) {
     QPointF sp = intersection_line -> line().p1(); // startpoint
     QPointF ep = mapToScene(e->pos()); // endpoint
     intersection_line -> setLine( QLineF(sp, ep) );
     scene()->update();
     // Need this for Mac
     FullRedraw();
+  }
+}
 //void FigureEditor::contentsMouseReleaseEvent(QMouseEvent* e)
 void FigureEditor::mouseReleaseEvent(QMouseEvent* e)
+{
   emit MouseReleased();
   // intersection line for leaf was finished now.
   if (e->button()==Qt::LeftButton) {
     if (intersection_line ) {
 #ifdef QDEBUG
       qDebug() << "Trying to cut leaf" << endl;
 #endif
       QPointF sp = intersection_line -> line().p1(); // startpoint
       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) {
 #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();
       NodeSet *node_set = new NodeSet;
       for (vector<CellItem *>::iterator it = intersected_cells.begin(); it != intersected_cells.end(); it++) {
 	(*it)->setBrush(QBrush("purple"));
 	Cell &c=(*it)->getCell();
 	// sometimes the cell hasn't properly divided yet before the
 	// 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();
 #ifdef QDEBUG
 	qDebug() << "Dividing Cell " << c.Index() << endl;
 #endif
 	c.DivideOverGivenLine( startpoint, endpoint, true, node_set);
+      }
       node_set->CleanUp();
       mesh.AddNodeSet(node_set);
 #ifdef QDEBUG
       qDebug() << "Done DivideOverGivenLine" << endl;
 #endif
       mesh.TestIllegalWalls();
       // Do the actual cutting and removing
       if (intersected_cells.size()) {
 	mesh.CutAwayBelowLine( startpoint, endpoint );
 	// Correct flags of nodeset
 	for (NodeSet::iterator i = node_set->begin(); i != node_set->end(); i++) {
 	  (*i)->SetSAM();
 	  (*i)->SetBoundary();
+	}
 	// Make cells attached to nodeset part of the boundary
 	// This is a temporary solution for the following:
 	//   If a cell attached to a NodeSet divides (with a division plane intersecting the node set),
 	//   we must insert a new node into the node set.
 	// For now, we add a layer of "virtual cells" inbetween.
 	list<Cell *> cells_attached_to_nodeset = node_set->getCells();
 	for ( list<Cell *>::iterator c = cells_attached_to_nodeset.begin(); c != cells_attached_to_nodeset.end(); c++) {
 	  (*c)->SetBoundary(Cell::SAM);
+	}
 #ifdef QDEBUG
 	qDebug() << "Done CutAwayBelowLine" << endl;
 #endif
 	mesh.TestIllegalWalls();
 	mesh.RepairBoundaryPolygon();
 #ifdef QDEBUG
 	qDebug() << "Done RepairBoundaryPolygon" << endl;
 #endif
 	mesh.TestIllegalWalls();
 	mesh.CleanUpWalls();
 #ifdef QDEBUG
 	qDebug() << "Done CleanUpWalls" << endl;
 #endif
 	mesh.TestIllegalWalls();
+      }
       dynamic_cast<Main *>(parent())->Plot();
 #ifdef QDEBUG
-      qDebug() << "NodeSet of cutting line: " << *node_set << endl;
+      cerr << "NodeSet of cutting line: " << *node_set << endl;
 #endif
+    }
   } else
     if (e->button()==Qt::RightButton) {
       if (intersection_line /* && !angle_line*/) {
 	QPointF p = mapToScene(e->pos());
 	QPointF sp = intersection_line->line().p1();
 	viewport()->setMouseTracking( TRUE );
+      }
+    }
+}
 // returns a vector of pointer to cells colliding with intersection line
 vector <CellItem *> FigureEditor::getIntersectedCells(void)
+{
   vector <CellItem *> colliding_cells;
   QList<QGraphicsItem *> l = intersection_line->collidingItems( );
 #ifdef QDEBUG
   qDebug() <<  "l.size() = " << l.size() << endl;
 #endif
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
 #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
 #endif
     if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
       colliding_cells.push_back(dynamic_cast<CellItem *>(*it));
+    }
+  }
   delete intersection_line;
   intersection_line = 0;
   return colliding_cells;
+}
 void FigureEditor::FullRedraw(void)
+{
   QList<QRectF> rl;
   rl << sceneRect();
   updateScene(rl);
+}
 NodeItem *FigureEditor::selectedNodeItem(QList<QGraphicsItem *> graphicItems) const
+{
   NodeItem *nodeItem = 0;
   // graphicItems is a list of the QgraphicItems under the mouse click event
   QList<QGraphicsItem *>::Iterator it = graphicItems.begin();
   for (; it != graphicItems.end(); ++it) {
     if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
       // the object under the mouse click is a Nodeitem
       nodeItem = dynamic_cast<NodeItem *>(*it);
       // indicate we've selected it
       nodeItem->setBrush(dark_red);
       break;
+    }
+  }
   return nodeItem;
+}
 void FigureEditor::insertNode(QPointF p)
+{
   Node *node = new Node(p.x(), p.y(), 0);
   mesh.AddNode(node);
   scene()->clearSelection();
   dynamic_cast<Main *>(parent())->Plot();
   FullRedraw();
 #ifdef QDEBUG
   qDebug() << "Node: " << p << endl;
 #endif
+}
 static uint mainCount = 0;
 Main::Main(QGraphicsScene& c, Mesh &m, QWidget* parent, const char* name, Qt::WindowFlags f) :
   Q3MainWindow(parent,name,f),
   MainBase(c,m),
   mesh(m)
+{
   editor = new FigureEditor(canvas,mesh, this);
 #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 );
   file->insertItem("&Read leaf", this, SLOT(readStateXML()));
   file->insertItem("&Save leaf", this, SLOT(saveStateXML()));
   file->insertItem("Snapshot", this, SLOT(snapshot()), Qt::CTRL+Qt::SHIFT+Qt::Key_S);
   file->insertSeparator();
   file->insertItem("Read next leaf", this, SLOT(readNextStateXML()), Qt::Key_PageDown);
   file->insertItem("Read previous leaf", this, SLOT(readPrevStateXML()), Qt::Key_PageUp);
   file->insertItem("Read last leaf", this, SLOT(readLastStateXML()), Qt::Key_End);
   file->insertItem("Read first leaf", this, SLOT(readFirstStateXML()), Qt::Key_Home);
   file->insertSeparator();
   file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);
   file->insertSeparator();
   file->insertItem("E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q);
   menu->insertItem("&File", file);
   Q3PopupMenu* edit = new Q3PopupMenu( menu );
   edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );
   edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );
   edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );
   edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );
   edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));
   menu->insertItem("&Edit", edit);
   run = new Q3PopupMenu( menu );
   running = false;
   paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
   menu->insertItem("&Run", run);
   view = new Q3PopupMenu( menu );
   view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);
   view->insertItem("Zoom &out", this, SLOT(zoomOut()), Qt::CTRL+Qt::Key_Minus);
   view->insertSeparator();
   com_id = view->insertItem("Show cell &centers", this, SLOT(toggleShowCellCenters()));
   view->setItemChecked(com_id, FALSE);
   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, FALSE);
   cell_number_id = view->insertItem("Show cell numbers", this, SLOT(toggleCellNumbers()));
   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()));
   view->setItemChecked(cell_axes_id, FALSE);
   fluxes_id = view->insertItem("Show &fluxes", this, SLOT(toggleShowFluxes()));
   view->setItemChecked(fluxes_id, FALSE);
   cell_walls_id = view->insertItem("Show transporters", this, SLOT(toggleShowWalls()));
   view->setItemChecked(cell_walls_id, FALSE);
   apoplasts_id = view->insertItem("Show apoplasts", this, SLOT(toggleShowApoplasts()));
   view->setItemChecked(apoplasts_id, FALSE);
   view->insertSeparator();
   only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));
   view->insertSeparator();
   movie_frames_id = view->insertItem("Start saving movie &frames", this, SLOT(toggleMovieFrames()));
   view->setItemChecked(movie_frames_id, par.movie);
   view->setItemChecked(only_boundary_id, FALSE);
   menu->insertItem("&View", view);
   options = new Q3PopupMenu( menu );
   dyn_cells_id = options->insertItem("Cell growth", this, SLOT(toggleDynCells()));
   options->setItemChecked(dyn_cells_id, true);
   options->insertItem("Edit &parameters", this, SLOT(EditParameters()), Qt::CTRL+Qt::Key_E);
   rotation_mode_id = options->insertItem("Rotate leaf", this, SLOT(EnterRotationMode()), Qt::CTRL + Qt::SHIFT + Qt::Key_R);
   options->setItemChecked(rotation_mode_id, false);
   menu->insertItem("&Options",options);
   // Menu of models
   modelmenu = new QMenu( menu );
   menu->insertItem("&Models", modelmenu);
   menu->insertSeparator();
   helpmenu = new Q3PopupMenu( menu );
   tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));
   helpmenu->setItemChecked(tooltips_id, true);
   helpmenu->insertSeparator();
   helpmenu->insertItem("&About", this, SLOT(about()) ); //, Key_F1);
   helpmenu->insertSeparator();

src/mesh.cpp

➞

Show inline comments

@@ @@ -306,386 +306,386 @@ Cell &Mesh::LeafPrimordium(int nnodes, d @@
   Node *n1 = *it_n1;
   Node *n2 = *it_n2;
   Node *n3=AddNode( new Node ( *n2 + Vector( 0, pet_length, 0) ) );
   Node *n4=AddNode( new Node ( *n1 + Vector( 0, pet_length, 0) ) );
   n3->boundary=true;
   n4->boundary=true;
   AddNodeToCell(petiole, *it_n1,
 		n4,
 		nodes[(*it_n2)->Index()
 		      + (( (*it_n1)->Index() - (*it_n2)->Index() )-1+nnodes)%nnodes]);
   list<Node *>::reverse_iterator i=it_n1; i++;
   for (; i!=it_n2; ++i) {
     AddNodeToCell(petiole, *i,
 		  nodes[(*it_n2)->Index() + (((*i)->Index()-(*it_n2)->Index()) + 1)%nnodes],
 		  nodes[(*it_n2)->Index() + (((*i)->Index()-(*it_n2)->Index())-1+nnodes)%nnodes]);
+  }
   AddNodeToCell(petiole, *it_n2, *it_n2 + 1, n3);
   (*it_n2)->boundary=true;
   AddNodeToCell(petiole, n3, n2, n4);
   AddNodeToCell(petiole, n4, n3, n1);
 #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;
   for (int i=0;i<nnodes;i++) {
     if (nodes[(first_node + i)]->owners.size()==1) {
       AddNodeToCell(boundary_polygon,
 		    nodes[first_node +i],
 		    nodes[first_node+ (nnodes+i-1)%nnodes],
 		    nodes[first_node+ (i + 1)%nnodes]);
       nodes[first_node+i]->boundary=true;
+    }
+  }
   AddNodeToCell(boundary_polygon, *it_n2, nodes[(nnodes+(*it_n2)->Index() - 1)%nnodes], n3);
   AddNodeToCell(boundary_polygon, n3, n2, n4);
   AddNodeToCell(boundary_polygon, n4, n3, n1);
   // make petiole solid
   for (list<Node *>::iterator i=petiole->nodes.begin(); i!=petiole->nodes.end(); i++) {
     (*i)->Fix();
+  }
   petiole->Fix();
   petiole->area=petiole->CalcArea();
   petiole->target_area=petiole->area;
   petiole->ConstructNeighborList();
   circle->ConstructNeighborList();
   boundary_polygon->ConstructConnections();
   boundary_polygon->ConstructNeighborList();
   circle->setCellVec(Vector(0,1,0));
   return *circle;
+}
 /*Cell &Mesh::Box() {
   }*/
 // return bounding box of mesh
 void Mesh::BoundingBox(Vector &LowerLeft, Vector &UpperRight) {
   LowerLeft = **nodes.begin();
   UpperRight = **nodes.begin();
   for (vector<Node *>::iterator c=nodes.begin(); c!=nodes.end(); c++) {
     if ((*c)->x < LowerLeft.x)
       LowerLeft.x = (*c)->x;
     if ((*c)->y < LowerLeft.y)
       LowerLeft.y = (*c)->y;
     if ((*c)->z < LowerLeft.z)
       LowerLeft.z = (*c)->z;
     if ((*c)->x > UpperRight.x)
       UpperRight.x = (*c)->x;
     if ((*c)->y > UpperRight.y)
       UpperRight.y = (*c)->y;
     if ((*c)->z > UpperRight.z)
       UpperRight.z = (*c)->z;
+  }
+}
 double Mesh::Area(void) {
   double area=0;
   vector<Cell *>::iterator i=cells.begin();
   while (i != cells.end()) {
     area += (*(i++))->Area();
+  }
   return area;
+}
 void Mesh::SetBaseArea(void) {
   // Set base area to mean area.
   // This method is typically called during initiation, after
   // defining the first cell
   Cell::BaseArea() = Area()/cells.size();
+}
 // for optimization, we moved Displace to Mesh
 class DeltaIntgrl {
 public:
   double area;
   double ix, iy;
   double ixx,ixy,iyy;
   DeltaIntgrl(double sarea,double six,double siy,double sixx,double sixy,double siyy) {
     area=sarea;
     ix=six;
     iy=siy;
     ixx=sixx;
     ixy=sixy;
     iyy=siyy;
+  }
 };
 void Mesh::Clear(void) {
   // clear nodes
   for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     delete *i;
+  }
   nodes.clear();
   Node::nnodes=0;
   node_insertion_queue.clear();
   // Clear NodeSets
   for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
+  }
   node_sets.clear();
   time = 0;
   // clear cells
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
+  }
   cells.clear();
   Cell::NCells() = 0;
   delete boundary_polygon;
   // Clear walls
   for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
+  }
   walls.clear();
   WallBase::nwalls = 0;
   //tmp_walls->clear();
   shuffled_cells.clear();
   shuffled_nodes.clear();
   //Cell::ncells=0;
   /*    Cell::ClearNCells();
 	Node::nnodes=0;
 	cells.clear();
 	nodes.clear();
 	shuffled_cells.clear();
 	shuffled_nodes.clear();
 	node_insertion_queue.empty();
 	cerr << "Meshed cleared: cells: " << cells.size() << ", nodes: " << nodes.size() << endl;
   */
 #ifdef QDEBUG
   qDebug() << "cells.size() = " << cells.size() << endl;
   qDebug << "walls.size() = " << walls.size() << endl;
   qDebug << "nodes.size() = " << nodes.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);
   double sum_dh=0;
   list<DeltaIntgrl> delta_intgrl_list;
   for_each( node_sets.begin(), node_sets.end(), mem_fun( &NodeSet::ResetDone ) );
   for (vector<Node *>::const_iterator i=shuffled_nodes.begin(); i!=shuffled_nodes.end(); i++) {
     //int n=shuffled_nodes[*i];
     Node &node(**i);
     // Do not allow displacement if fixed
     //if (node.fixed) continue;
     if (node.DeadP()) continue;
     // Attempt to move this cell in a random direction
     double rx=par.mc_stepsize*(RANDOM()-0.5); // was 100.
     double ry=par.mc_stepsize*(RANDOM()-0.5);
     // Uniform with a circle of radius par.mc_stepsize
     /* double r = RANDOM() * par.mc_stepsize;
        double th = RANDOM()*2*Pi;
        double rx = r * cos(th);
        double ry = r * sin(th);
     */
     Vector new_p(node.x+rx,node.y+ry,0);
     Vector old_p(node.x,node.y,0);
     /* if (node.boundary  && boundary_polygon->MoveSelfIntersectsP(n,  new_p )) {
     // reject if move of boundary results in self intersection
     continue;
     }*/
     if (node.node_set) {
       // move each node set only once
       if (!node.node_set->DoneP())
 	node.node_set->AttemptMove(rx,ry);
     } else {
       // for all cells to which this node belongs:
       //   calculate energy difference
       double area_dh=0.;
       double length_dh=0.;
       double bending_dh=0.;
       double cell_length_dh=0.;
       double alignment_dh=0.;
       double old_l1=0.,old_l2=0.,new_l1=0.,new_l2=0.;
       double sum_stiff=0.;
       double dh=0.;
       for (list<Neighbor>::const_iterator cit=node.owners.begin(); cit!=node.owners.end(); cit++) {
 	//Cell &c=m->getCell(cit->cell);
 	//Cell &c=cit->cell->BoundaryPolP()?*boundary_polygon:*(cit->cell);
 	Cell &c=*((Cell *)(cit->cell));
 	//Cell &c=cells[cit->cell];
 	if (c.MoveSelfIntersectsP(&node,  new_p )) {
 	  // reject if move results in self intersection
 	  //
 	  // I know: using goto's is bad practice... except when jumping out
 	  // of deeply nested loops :-)
 	  //cerr << "Rejecting due to self-intersection\n";
 	  goto next_node;
+	}
 	// summing stiffnesses of cells. Move has to overcome this minimum required energy.
 	sum_stiff += c.stiffness;
 	// area - (area after displacement): see notes for derivation
 	//Vector i_min_1 = m->getNode(cit->nb1);
 	Vector i_min_1 = *(cit->nb1);
 	//Vector i_plus_1 = m->getNode(cit->nb2);
 	Vector i_plus_1 = *(cit->nb2);
 	// We must double the weights for the perimeter (otherwise they start bulging...)
 	double w1, w2;
 	if (node.boundary && cit->nb1->boundary)
 #ifdef FLEMING
 	  w1 = par.rel_perimeter_stiffness;
 #else
 	w1=2;
 #endif
 	else
 	  w1 = 1;
 	if (node.boundary && cit->nb2->boundary)
 #ifdef FLEMING
 	  w2 = par.rel_perimeter_stiffness;
 #else
 	w2 = 2;
 #endif
 	else
 	  w2 = 1;
 	//if (cit->cell>=0) {
 	if (!cit->cell->BoundaryPolP()) {
 	  double delta_A = 0.5 * ( ( new_p.x - old_p.x ) * (i_min_1.y - i_plus_1.y) +
 				   ( new_p.y - old_p.y ) * ( i_plus_1.x - i_min_1.x ) );
 	  area_dh +=  delta_A * (2 * c.target_area - 2 * c.area + delta_A);
 	  // cell length constraint
 	  // expensive and not always needed
 	  // so we check the value of lambda_celllength
 	  if (/* par.lambda_celllength */  cit->cell->lambda_celllength) {
 	    double delta_ix =
 	      (i_min_1.x + new_p.x)
 	      * (new_p.x * i_min_1.y- i_min_1.x * new_p.y) +
 	      (new_p.x + i_plus_1.x)
 	      * (i_plus_1.x * new_p.y- new_p.x * i_plus_1.y) -
 	      (i_min_1.x + old_p.x)
 	      * (old_p.x * i_min_1.y- i_min_1.x * old_p.y) -
 	      (old_p.x + i_plus_1.x)
 	      * (i_plus_1.x * old_p.y - old_p.x * i_plus_1.y);
 	    double delta_iy =
 	      (i_min_1.y + new_p.y)
 	      * (new_p.x * i_min_1.y- i_min_1.x * new_p.y) +
 	      (new_p.y + i_plus_1.y)
 	      * (i_plus_1.x * new_p.y- new_p.x * i_plus_1.y) -
 	      (i_min_1.y + old_p.y)
 	      * (old_p.x * i_min_1.y- i_min_1.x * old_p.y) -
 	      (old_p.y + i_plus_1.y)
 	      * (i_plus_1.x * old_p.y - old_p.x * i_plus_1.y);
 	    double delta_ixx =
 	      (new_p.x*new_p.x+
 	       i_min_1.x*new_p.x+
 	       i_min_1.x*i_min_1.x ) *
 	      (new_p.x*i_min_1.y - i_min_1.x*new_p.y) +
 	      (i_plus_1.x*i_plus_1.x+
 	       new_p.x*i_plus_1.x+
 	       new_p.x*new_p.x ) *
 	      (i_plus_1.x*new_p.y - new_p.x*i_plus_1.y) -
 	      (old_p.x*old_p.x+
 	       i_min_1.x*old_p.x+
 	       i_min_1.x*i_min_1.x ) *
 	      (old_p.x*i_min_1.y - i_min_1.x*old_p.y) -
 	      (i_plus_1.x*i_plus_1.x+
 	       old_p.x*i_plus_1.x+
 	       old_p.x*old_p.x ) *
 	      (i_plus_1.x*old_p.y - old_p.x*i_plus_1.y);
 	    double delta_ixy =
 	      (i_min_1.x*new_p.y-
 	       new_p.x*i_min_1.y)*
 	      (new_p.x*(2*new_p.y+i_min_1.y)+
 	       i_min_1.x*(new_p.y+2*i_min_1.y)) +
 	      (new_p.x*i_plus_1.y-
 	       i_plus_1.x*new_p.y)*
 	      (i_plus_1.x*(2*i_plus_1.y+new_p.y)+
 	       new_p.x*(i_plus_1.y+2*new_p.y)) -
 	      (i_min_1.x*old_p.y-
 	       old_p.x*i_min_1.y)*
 	      (old_p.x*(2*old_p.y+i_min_1.y)+
 	       i_min_1.x*(old_p.y+2*i_min_1.y)) -
 	      (old_p.x*i_plus_1.y-
 	       i_plus_1.x*old_p.y)*
 	      (i_plus_1.x*(2*i_plus_1.y+old_p.y)+
 	       old_p.x*(i_plus_1.y+2*old_p.y));
@@ @@ -1136,385 +1136,385 @@ void Mesh::CircumCircle(double x1,double @@
   rsqr = dx*dx + dy*dy;
   *r = sqrt(rsqr);
   return;
   // Suggested
   // return((drsqr <= rsqr + EPSILON) ? TRUE : FALSE);
+}
 //
 // return the total amount of chemical "ch" in the leaf
 double Mesh::SumChemical(int ch) {
   double sum=0.;
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     sum+=(*i)->chem[ch];
+  }
   return sum;
+}
 void Mesh::CleanUpCellNodeLists(void) {
   typedef vector <vector<Cell *>::iterator> CellItVect;
   CellItVect cellstoberemoved;
   vector<int> cellind;
   // Start of by removing all stale walls.
   //DeleteLooseWalls();
   // collect all dead cells that need to be removed from the simulation
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     if ((*i)->DeadP()) {
       // collect the iterators
       cellstoberemoved.push_back(i);
       // collect the indices
       cellind.push_back((*i)->index);
     } else {
       // Remove pointers to dead Walls
       for (list<Wall *>::iterator w=(*i)->walls.begin(); w!=(*i)->walls.end(); w++) {
 	if ((*w)->DeadP()) {
 	  (*w)=0;
+	}
+      }
       (*i)->walls.remove(0);
+    }
+  }
   // Remove pointers to dead Walls from BoundaryPolygon
   for (list<Wall *>::iterator w=boundary_polygon->walls.begin(); w!=boundary_polygon->walls.end(); w++) {
     if ((*w)->DeadP()) {
       (*w)=0;
+    }
+  }
   boundary_polygon->walls.remove(0);
   // Renumber cells; this is most efficient if the list of dead cell indices is sorted
   sort(cellind.begin(),cellind.end());
   // Reindexing of Cells
   for (vector<int>::reverse_iterator j=cellind.rbegin(); j!=cellind.rend(); j++) {
     for (vector<Cell *>::reverse_iterator i=cells.rbegin(); i!=cells.rend(); i++) {
       if (*j < (*i)->index) (*i)->index--;
+    }
+  }
   // Actual deleting of Cells
   // We must delete in reverse order, otherwise the iterators become redefined
   for ( CellItVect::reverse_iterator i=cellstoberemoved.rbegin(); i!=cellstoberemoved.rend(); i++) {
     Cell::NCells()--;
     cells.erase(*i);
+  }
   // same for nodes
   typedef vector <vector<Node *>::iterator> NodeItVect;
   NodeItVect nodestoberemoved;
   vector<int> nodeindlist;
   // collect iterators and indices of dead nodes
   for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     if ((*i)->DeadP()) {
       nodestoberemoved.push_back( i );
       nodeindlist.push_back((*i)->index);
+    }
+  }
   // sort the list of dead nodes for renumbering
   sort(nodeindlist.begin(),nodeindlist.end());
   // Reindicing of Nodes
   for (vector<int>::reverse_iterator j=nodeindlist.rbegin(); j!=nodeindlist.rend(); j++) {
     for (vector<Node *>::reverse_iterator i=nodes.rbegin(); i!=nodes.rend(); i++) {
       if (*j < (*i)->index) {
 	(*i)->index--;
+      }
+    }
+  }
   // Actual deleting of nodes
   // We must delete in reverse order, otherwise the iterators become redefined
   for ( NodeItVect::reverse_iterator i=nodestoberemoved.rbegin(); i!=nodestoberemoved.rend(); i++) {
     Node::nnodes--;
     nodes.erase(*i);
+  }
   for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     if ((*w)->DeadP()) {
       Wall::nwalls--;
       delete *w;
       *w = 0;
+    }
+  }
   walls.remove( 0 );
   // Clean up all intercellular connections and redo everything
   for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     (*i)->owners.clear();
+  }
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     (*i)->ConstructConnections();
+  }
   boundary_polygon->ConstructConnections();
   // remake shuffled_nodes and shuffled cells
   shuffled_nodes.clear();
   shuffled_nodes = nodes;
   shuffled_cells.clear();
   shuffled_cells = cells;
+}
 void Mesh::CutAwayBelowLine( Vector startpoint, Vector endpoint) {
   // Kills all cells below the line startpoint -> endpoint
   Vector perp = (endpoint-startpoint).Perp2D().Normalised();
 #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
     Vector cellvec = ((*i)->Centroid()-startpoint);
     if ( InnerProduct(perp, cellvec) < 0 ) {
       // remove those cells
       (*i)->Apoptose();
+    }
+  }
 #ifdef QDEBUG
   qDebug() << "Before CleanUpCellNodeLists" << endl;
 #endif
   TestIllegalWalls();
   CleanUpCellNodeLists();
+}
 void Mesh::CutAwaySAM(void) {
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     if( (*i)->Boundary() == Cell::SAM ) {
       (*i)->Apoptose();
+    }
+  }
   TestIllegalWalls();
   CleanUpCellNodeLists();
+}
 void Mesh::TestIllegalWalls(void) {
   for (list<Wall *>::iterator w = walls.begin(); w!=walls.end(); w++) {
     if ((*w)->IllegalP() ) {
 #ifdef QDEBUG
-      qDebug() << "Wall " << **w << " is illegal." << endl;
+      cerr << "Wall " << **w << " is illegal." << endl;
 #endif
+    }
+  }
+}
 class node_owners_eq : public unary_function<Node, bool> {
   int no;
 public:
   explicit node_owners_eq(int nn) { no=nn; }
   bool operator() (const Node &n) const {
     if (n.CellsSize()==1)
       return true;
     else
       return false;
+  }
 };
 void Mesh::RepairBoundaryPolygon(void) {
   // After serious manipulations (e.g. after cutting part off the
   // leaf) repair the boundary polygon. It assumes the cut line has
   // already been marked "boundary" and the original boundary marks
   // were not removed.
   //
   // So, this function just puts boundary nodes into the boundary
   // polygon in the right order; it cannot detect boundaries from
   // scratch.
   Node *boundary_node=0, *next_boundary_node=0, *internal_node;
   set<int> original_boundary_nodes, repaired_boundary_nodes;
   vector<int> difference; // set difference result
   // Step 0: print out current boundary polygon
 #ifdef QDEBUG
   qDebug() << endl << "Original Boundary Polygon node indices: ";
   foreach (Node* node, boundary_polygon->nodes) {
     qDebug() << node->Index() << " " ;
+  }
   qDebug() << endl << endl;
 #endif
   // Step 1a: Create a set containing the current boundary polygon nodes' Indices.
   foreach (Node* node, boundary_polygon->nodes) {
     original_boundary_nodes.insert(node->Index());
+  }
   // Step 1b: remove all nodes from boundary polygon
   boundary_polygon->nodes.clear();
   // Step 2: Remove all references to the boundary polygon from the Mesh's current list of nodes
   foreach (Node* node, nodes) {
     node->Unmark(); // remove marks, we need them to determine if we have closed the circle
     list<Neighbor>::iterator boundary_ref_pos;
     if ((boundary_ref_pos = find_if (node->owners.begin(), node->owners.end(),
 				     bind2nd(mem_fun_ref(&Neighbor::CellEquals), -1))) != node->owners.end()) {
       // i.e. if one of the node's owners is the boundary polygon
       node->owners.erase(boundary_ref_pos); // remove the reference
+    }
+  }
   // Step 3: Search for the first boundary node.  We reconstruct the
   // boundary polygon by moving along the boundary nodes until we've
   // encircled the polygon. Since manually adding nodes may have
   // turned nodes previously along the boundary into internal nodes,
   // we search through all the node until we find first boundary node
   // and proceed from there. If findNextBoundaryNode() returns a node
   // other than the one passed to it, the original node is the first
   // boundary node.
   foreach (Node* node, nodes) {
     if ((findNextBoundaryNode(node))->index != node->index){
       next_boundary_node = node;
       break;
+    }
+  }
   // We have a problem if we arrive here without having found a boundary node.
   if (!next_boundary_node) throw("Cannot find a boundary node!.");
   // Reconstruct the list of boundary polygon nodes.
   do {
     boundary_node = next_boundary_node;
     boundary_node->Mark();
     boundary_polygon->nodes.push_back(boundary_node);
     next_boundary_node = findNextBoundaryNode(boundary_node);
   } while ( !next_boundary_node->Marked() );
   // Create a set containing the reconstructed boundary polygon nodes' Indices.
   for (list<Node *>::iterator it = boundary_polygon->nodes.begin(); it!=boundary_polygon->nodes.end(); ++it) {
     repaired_boundary_nodes.insert((*it)->Index());
+  }
   // Calculate the difference between the original and repaired sets of boundary nodes
   // yielding the set of nodes that are no longer part of the boundary polygon.
   set_difference(original_boundary_nodes.begin(), original_boundary_nodes.end(),
                  repaired_boundary_nodes.begin(), repaired_boundary_nodes.end(), back_inserter(difference));
   // Tell each node in the difference that it's no longer part of the boundary polygon
   vector<Node *>::iterator internal_node_it;
   foreach (int i, difference){
     internal_node_it = find_if (nodes.begin(), nodes.end(), bind2nd(mem_fun(&Node::IndexEquals), i));
     internal_node = *internal_node_it; // dereference the itterator to get to the node pointer
     if (!internal_node) throw("Found a null Node pointer.");
     internal_node->UnsetBoundary();
+  }
   boundary_polygon->ConstructConnections();
   for (list<Wall *>::iterator w=boundary_polygon->walls.begin(); w!=boundary_polygon->walls.end(); w++) {
     if ((*w)->DeadP()) {
       (*w)=0;
+    }
+  }
   boundary_polygon->walls.remove(0);
   boundary_polygon->ConstructNeighborList();
 #ifdef QDEBUG
   qDebug() << "Repaired Boundary Polygon node indices: ";
   foreach (Node* node, boundary_polygon->nodes){
     qDebug() << node->Index() << " " ;
+  }
   qDebug() << endl ;
 #ifdef _undefined_
   qDebug() << "NODES:" << endl;
   foreach(Node* node, nodes) {
     qDebug() << *node;
+  }
   qDebug() << endl;
   qDebug() << "WALLS:" << endl;
   foreach(Wall* wall, walls) {
     qDebug() << *wall;
+  }
   qDebug() << endl;
   qDebug() << "CELLS:" << endl;
   foreach(Cell* cell, cells) {
     qDebug() << *cell;
+  }
   qDebug() << endl;
 #endif
 #endif
+}
 Node* Mesh::findNextBoundaryNode(Node* boundary_node) {
   bool found_next_boundary_node = false;
   Node *next_boundary_node = NULL;
   set<int> boundary_node_owners; // This is a list of the current boundary node's owners' Ids
   vector<int> neighborIds; // A list of the current boundary node's owners' 2nd neighbor Ids
   vector<set<int> *>  nodeOwners; // A vector of set pointers where each set contains the owner Ids of the nodes in the neighborIds list.
   vector<int> intersection; // set intersection result
   // The next boundary node is that which has only one owner in common with the current boundary node
   for (list<Neighbor>::iterator it=boundary_node->owners.begin(); it!=boundary_node->owners.end(); ++it) {
     if (it->cell->Index() != -1) boundary_node_owners.insert(it->cell->Index()); // Save each of the current boundary node's owners' Ids - except the boundary polygon
     set<int> *owners = new set<int>; // create a set to hold a 2nd neighbor's owners' Ids
     nodeOwners.push_back(owners);
     neighborIds.push_back(it->nb2->Index());
     foreach(Neighbor neighbor, it->nb2->owners){
       if (neighbor.cell->Index() != -1) owners->insert(neighbor.cell->Index()); // Save second neighbors' owners' Ids - except the boundary polygon
+    }
+  }
   vector<int>::iterator itt = neighborIds.begin();
   vector<set<int> *>::iterator it = nodeOwners.begin();
 #ifdef QDEBUG
   qDebug() << "Boundary node: " <<  boundary_node->Index() << " is owned by the following cells: ";
   foreach (int i, boundary_node_owners){
     qDebug() << i << "  ";
+  }
   qDebug() << endl;
 #endif
   for (; it < nodeOwners.end(); it++, itt++) {
     intersection.clear();
     set_intersection(boundary_node_owners.begin(), boundary_node_owners.end(), (*it)->begin(), (*it)->end(), back_inserter(intersection));
 #ifdef QDEBUG
     qDebug() << "The intersection of the boundary node(" << boundary_node->Index() << ") owners and its 2nd neighbor(" <<  *itt << ") owners is: ";
     foreach (int i, intersection){
       qDebug() << i << "  ";
+    }
     qDebug() << endl;
 #endif
     if (intersection.size() == 1){

src/random.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  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"
 static const std::string _module_id("$Id$");
 static int idum = -1;
 using namespace std;
 static int counter=0;
 /*! \return A random double between 0 and 1
 **/
 double RANDOM(void)
 /* Knuth's substrative method, see Numerical Recipes */
+{
   static int inext,inextp;
   static long ma[56];
   static int iff=0;
   counter++;
   long mj,mk;
   int i,ii,k;
   if (idum < 0 || iff == 0) {
     iff=1;
     mj=MSEED-(idum < 0 ? -idum : idum);
     mj %= MBIG;
     ma[55]=mj;
     mk=1;
     i=1;
     do {
       ii=(21*i) % 55;
       ma[ii]=mk;
       mk=mj-mk;
       if (mk < MZ) mk += MBIG;
       mj=ma[ii];
     } while ( ++i <= 54 );
     k=1;
     do {
       i=1;
       do {
         ma[i] -= ma[1+(i+30) % 55];
         if (ma[i] < MZ) ma[i] += MBIG;
       } while ( ++i <= 55 );
     } while ( ++k <= 4 );
     inext=0;
     inextp=31;
     idum=1;
+  }
   if (++inext == 56) inext=1;
   if (++inextp == 56) inextp=1;
   mj=ma[inext]-ma[inextp];
   if (mj < MZ) mj += MBIG;
   ma[inext]=mj;
   return mj*FAC;
+}
 /*! \param An integer random seed
   \return the random seed
 **/
 int Seed(int seed)
+{
   if (seed < 0) {
     int rseed=Randomize();
 #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();
     return seed;
+  }
+}
 /*! Returns a random integer value between 1 and 'max'
   \param The maximum value (long)
   \return A random integer (long)
 **/
 long RandomNumber(long max)
+{
   return((long)(RANDOM()*max+1));
+}
 /*! Interactively ask for the seed
   \param void
   \return void
 **/
 void AskSeed(void)
+{
   int seed;
   printf("Please enter a random seed: ");
   scanf("%d",&seed);
   printf("\n");
   Seed(seed);
+}
 int RandomCounter(void) {
   return counter;
+}
 /*! Make a random seed based on the local time
   \param void
   \return void
 **/
 int Randomize(void) {
   // Set the seed according to the local time
   struct timeb t;
   int seed;
   ftime(&t);
   seed=abs((int)((t.time*t.millitm)%655337));
   Seed(seed);
 #ifdef QDEBUG
-  qdebug() << "Random seed is " << seed << endl;
+  qDebug() << "Random seed is " << seed << endl;
 #endif
   return seed;
+}
 /* finis */

src/wall.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include "wall.h"
 #include "cell.h"
 #include "wallitem.h"
 #include "node.h"
 #include "apoplastitem.h"
 #include <algorithm>
 #include <QGraphicsScene>
 static const std::string _module_id("$Id$");
 /*! Check if this Wall still belongs to Cell a, otherwise gives it to Cell b.
   \return true: Wall was corrected
   \return false: Wall was still correct
 */
 bool Wall::CorrectWall( void ) {
   // collect all cells to which my nodes are connected on one list
   list<CellBase *> owners;
   transform(n1->owners.begin(),n1->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
   transform(n2->owners.begin(),n2->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
   // get the list of duplicates
   list<CellBase *> wall_owners;
   owners.sort();
   //transform(owners.begin(), owners.end(), ostream_iterator<int>(cerr, ", "), mem_fun(&Cell::Index));
   duplicates_copy( owners.begin(), owners.end(), back_inserter(wall_owners) );
   // duplicates are the cells to which the Wall belongs
   // 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 */) {
 #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 )
 					       );
     if (bpit!=wall_owners.end()) {
       // add a Wall with the boundary_polygon to each cell
       Wall *bp_wall1 = new Wall( n2, n1, c1, (*bpit) );
       bp_wall1->CopyWallContents(*this);
       ((Cell *)c1)->AddWall( bp_wall1);
       ((Cell *)(*bpit))->AddWall(bp_wall1);
       Wall *bp_wall2 = new Wall( n1, n2, c2, (*bpit) );
       bp_wall2->CopyWallContents(*this);
       ((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;
+      cerr << "Wall: " << *this << endl;
       qDebug() << "Owners are: ";
-      transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(qDebug(), "  "), mem_fun (&CellBase::Index) );
+      transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(cerr, "  "), 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() << ": ";
       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) {
     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) ) {
     return false;
+  }
   if ( c1 == cell1 ) {
     //cerr << "Block 1\n";
     ((Cell *)c2) -> RemoveWall(this);
     c2 = cell2;
     ((Cell *)c2) -> AddWall(this);
   } else {
     if ( c1 == cell2 ) {
       //	cerr << "Block 2\n";
       ((Cell *)c2) -> RemoveWall(this);
       c2 = cell1;
       ((Cell *)c2) -> AddWall(this);
     } else {
       if ( c2 == cell1) {
 	((Cell *)c1)->RemoveWall(this);
 	c1 = cell2;
 	((Cell *)c1) -> AddWall(this);
 	//  cerr << "Block 3\n";
       } else {
 	if ( c2 == cell2) {
 	  ((Cell *)c1)->RemoveWall(this);
 	  c1 = cell1;
 	  ((Cell *)c1)->AddWall(this);
 	  //	  cerr << "Block 3\n";
 	} else {
 #ifdef QDEBUG
 	  qDebug() << "Warning, cell wall was not corrected." << endl;
 #endif
 	  return false;
+	}
+      }
+    }
+  }
   return true;
+}
 void Wall::Draw(QGraphicsScene *c) {
   WallItem *wi1 = new WallItem(this, 1, c);
   WallItem *wi2 = new WallItem(this, 2, c);
   wi1->show();
   wi2->show();
+}
 void Wall::DrawApoplast(QGraphicsScene *c) {
   ApoplastItem *apo = new ApoplastItem(this, c);
   apo->show();
+}
 void Wall::ShowStructure(QGraphicsScene *c) {
   Vector offset = Cell::Offset();
   double factor = Cell::Factor();
   Vector startpoint ( ((offset.x+n1->x)*factor),((offset.y+n1->y)*factor)),
     endpoint (((offset.x+n2->x)*factor),((offset.y+n2->y)*factor));
   Vector linevec = endpoint - startpoint;
   Vector midline = startpoint + linevec/2.;
   Vector perpvec = linevec.Normalised().Perp2D();
   Vector textpos1 = midline + 100 * perpvec;
   Vector textpos2 = midline - 100 * perpvec;
   QGraphicsLineItem *line = new QGraphicsLineItem(0,c);
   line->setPen( QPen(QColor(par.arrowcolor),2) );
   line->setLine(startpoint.x, startpoint.y, endpoint.x, endpoint.y );
   line->setZValue(10);
   line->show();
   QGraphicsSimpleTextItem *text1 = new QGraphicsSimpleTextItem( QString("%1").arg(c2->Index()),0,c);
   QGraphicsSimpleTextItem *text2 = new QGraphicsSimpleTextItem( QString("%1").arg(c1->Index()),0,c);
   text1 -> setPos( textpos1.x, textpos1.y );
   text2 -> setPos( textpos2.x, textpos2.y );
   text1->setZValue(20); text2->setZValue(20);
   text1->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
   text2->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
   text1->setPen ( QColor(par.textcolor) );
   text2->setPen ( text1->pen() );
   text1->show(); text2->show();
+}
 string Wall::WallTypetoStr(const WallType &wt) const {
   if (wt == Normal) {
     return string("normal");
+  }
   if (wt == AuxSource) {
     return string("aux_source");
+  }
   if (wt == AuxSink) {
     return string("aux_sink");
+  }
   return string("");
+}
 /* finis */

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