EI/VirtualLeaf Changeset - c6ad8e34e8eb · Centrum Wiskunde & Informatica (CWI)

Changeset - c6ad8e34e8eb

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Roeland Merks - 15 years ago 2010-11-25 12:02:40
roeland.merks@cwi.nl

In response to referee's comment:

"I am also afraid that

the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very
well in my hands, could the program be changed so that the correct file
extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically."

I corrected the "export cell data" dialog (it did not actually write the file in the submitted version). Also we now assume default file extensions (.jpg for snapshot and .csv for data export) if none is given.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/canvas.cpp
removed src/miscq.cpp
removed src/miscq.h

4 files changed with 64 insertions and 97 deletions:

src/VirtualLeaf.pro

src/canvas.cpp

src/miscq.cpp

src/miscq.h

0 comments (0 inline, 0 general)

src/VirtualLeaf.pro

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+#
 #  $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS += -Wall
 QMAKE_CXXFLAGS += -Wno-write-strings
 QMAKE_CXXFLAGS += -Wno-unused-parameter
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 #REACTIONS = reactions_auxin_growth.h
 #REACTIONS = reactions_meinhardt.h
 #REACTIONS = reactions_pce_growth.h
 DEFINES += QTGRAPHICS
 DEFINES += REACTIONS_HEADER=$${REACTIONS}
 DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"
 DEFINES += FLEMING
 BINDIR = ../bin
 LIBDIR = ../lib
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 TEMPLATE = app
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG -= console
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
  LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 # Input
 HEADERS += \
 # apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
        hull.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
  modelcatalogue.h \
  Neighbor.h \
  node.h \
  nodeitem.h \
  nodeset.h \
  OptionFileDialog.h \
  output.h \
  parameter.h \
  pardialog.h \
  parse.h \
  pi.h \
  qcanvasarrow.h \
  random.h \
  rungekutta.h \
  simitembase.h \
  simplugin.h \
  sqr.h \
  tiny.h \
  transporterdialog.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  wall.h \
  wallitem.h \
  warning.h \
  xmlwrite.h \
  $${PARTMPL}
 SOURCES += \
 # apoplastitem.cpp \
  canvas.cpp \
  cellbase.cpp \
  cell.cpp \
  cellitem.cpp \
  forwardeuler.cpp \
  hull.cpp \
  mainbase.cpp \
  matrix.cpp \
  mesh.cpp \
  miscq.cpp \
  modelcatalogue.cpp \
  Neighbor.cpp \
  node.cpp \
  nodeitem.cpp \
  nodeset.cpp \
  OptionFileDialog.cpp \
  output.cpp \
  parameter.cpp \
  pardialog.cpp \
  parse.cpp \
  random.cpp \
  rungekutta.cpp \
  simitembase.cpp \
  transporterdialog.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  wall.cpp \
  wallitem.cpp \
  warning.cpp \
  xmlwrite.cpp \
  $$MAINSRC
 contains( TARGET, leaf_fleming ) {
  DEFINES += FLEMING
+}
 contains(GRAPHICS, qwt) {
  #macx:LIBS += -L$$QWTDIR/lib -lqwt
  #win32:LIBS += -L$$QWTDIR/lib -lqwt5
  #LIBS += -L$$QWTDIR/lib -lqwt
  INCLUDEPATH += $$QWTDIR/include
  DEFINES += HAVE_QWT
  HEADERS += data_plot.h
  SOURCES += data_plot.cpp
+}
 contains( GRAPHICS, qt ) {
  message( "Building Qt executable" )
  QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
+}
 contains( GRAPHICS, xfig ) {
  message("Building Xfig executable (background runnable).")
  QMAKE_CXXFLAGS += -DXFIGGRAPHICS
+}
 contains( GRAPHICS, x11 ) {
  !unix {
   error("X11 graphics only available on Unix systems.")
+ }
  message("Building X11 executable")
  SOURCES += x11graph.cpp
  HEADERS += x11graph.h
  QMAKE_CXXFLAGS += -DX11GRAPHICS
  CONFIG -= qt
  CONFIG += x11
  unix:LIBS += -lpng
+}
 #contains( GRAPHICS, qwt ) {
 # 	QMAKE_POST_LINK = "install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
 #}
 # MACOSX packaging
 macx {
 ICON = leaficon.icns
 QMAKE_POST_LINK = "\
 	#install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	cp leaficon.icns $${DESTDIR}/$${TARGET}.app; \
 	cp ../doc/gpl3.txt $${DESTDIR}/$${TARGET}.app/Contents/MacOS/.                                    ; \
 	mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/QtCore.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/QtGui.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	cp -R /Library/Frameworks/Qt3Support.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	#cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
 	#install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
 	install_name_tool -change /usr/local/qwt/lib/libqwt.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
 	install_name_tool -id @executable_path/../Frameworks/QtCore.framework/Versions/Current/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtCore.framework/Versions/4.0/QtCore; \
 	install_name_tool -id @executable_path/../Frameworks/QtGui.framework/Versions/Current/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui; \
 	install_name_tool -id @executable_path/../Frameworks/Qt3Support.framework/Versions/Current/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/Qt3Support.framework/Versions/Current/Qt3Support @executable_path/../Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
 	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; "
+}
 # finis

src/canvas.cpp

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 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf 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 <time.h>
 #include <string>
 #include <fstream>
 #include <streambuf>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <qdatetime.h>
 #include <q3mainwindow.h>
 #include <qstatusbar.h>
 #include <qmessagebox.h>
 #include <qmenubar.h>
 #include <qapplication.h>
 #include <qpainter.h>
 #include <qprinter.h>
 #include <qlabel.h>
 #include <qimage.h>
 #include <q3progressdialog.h>
 #include <qtimer.h>
 #include <qslider.h>
 #include <qpixmap.h>
 #include <qfile.h>
 #include <qdir.h>
 #include <q3filedialog.h>
 #include <QGraphicsItem>
 #include <QList>
 #include <QDir>
+#include <QFileInfo>
 #include <QDebug>
 #include <set>
 //Added by qt3to4:
 #include <Q3ValueList>
 #include <Q3PopupMenu>
 #include <QMouseEvent>
 #include <typeinfo>
 #include <cstring>
 #include <q3process.h>
 #include <qlayout.h>
 #include <qspinbox.h>
 #include <fstream>
 #include <sstream>
 #include "pardialog.h"
 #include "parameter.h"
 #include "canvas.h"
 #include "node.h"
 #include "nodeset.h"
 #include "nodeitem.h"
 #include "cellitem.h"
 #include "wallitem.h"
 #include "mesh.h"
 #include "xmlwrite.h"
 #include "miscq.h"
 #include "OptionFileDialog.h"
 #include <cstdlib>
 #include <cstdio>
 #include "modelcatalogue.h"
 #include <algorithm>
 // Include VIB and PSB logos
 #include "psb.xpm"
 #include "cwi.xpm"
 static const std::string _module_id("$Id$");
 using namespace std;
 // We use a global variable to save memory - all the brushes and pens in
 // the mesh are shared.
 #define FNAMESIZE 100
 #define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)
 #define QUOTE_ME_2NDLEV(s) #s
 static QColor dark_red("darkRed");
 static const int imageRTTI = 984376;
 extern Parameter par;
 const QString Main::caption("Virtual leaf");
 const QString Main::caption_with_file("Virtual leaf: %1");
 FigureEditor::FigureEditor(
 			   QGraphicsScene& c, Mesh &m, QWidget* parent,
 			   const char* name, Qt::WindowFlags f) :
   QGraphicsView(&c,parent), mesh(m)
+{
   intersection_line = 0;
   //angle_line = 0;
   setInteractive(true);
   moving = 0;
   rotation_mode = false;
+}
 void FigureEditor::clear()
+{
   QList<QGraphicsItem *> list = scene()->items();
   QList<QGraphicsItem *>::Iterator it = list.begin();
   for (; it != list.end(); ++it) {
     delete *it;
+  }
+}
 void FigureEditor::wheelEvent(QWheelEvent *event)
+{
   scaleView(pow((double)2, -event->delta() / 240.0));
+}
 void FigureEditor::scaleView (qreal scaleFactor)
+{
   qreal factor = matrix().scale(scaleFactor, scaleFactor).mapRect(QRectF(0, 0, 1, 1)). width();
   if (factor < 0.07 || factor > 100) return;
   scale (scaleFactor, scaleFactor);
+}
 void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey)
+{
   QImage *image = new QImage(sizex, sizey, QImage::Format_RGB32);
   image->fill(QColor(Qt::white).rgb());
   QPainter *painter=new QPainter(image);
   render(painter);
   image->save(QString(fname),format);
   delete painter;
   delete image;
+}
 void FigureEditor::mousePressEvent(QMouseEvent* e)
+{
   static QList<Node*> selected;
   emit MousePressed();
   //QPointF p = matrix().inverted().map(e->pos());
   QPointF p = mapToScene(e->pos());
 #ifdef QDEBUG
   qDebug() << endl << "MousePressEvent location: (" << p.x() << "," << p.y() << ")." << endl;
   qDebug() << "Magnification:  " << Cell::Magnification() << endl;
   qDebug() << "Offsets:  " << Cell::Offset() << endl;
 #endif
   QList<QGraphicsItem *> l=scene()->items(p);
 #ifdef QDEBUG
   qDebug() << "MousePressEvents, items: " << l.size() << endl;
   qDebug() << "Mouse button modifier: " << e->modifiers() << endl;
 #endif
   if (e->button()==Qt::RightButton || l.size()==0) {
     //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;
     intersection_line = new QGraphicsLineItem( 0, scene() );
     intersection_line->setPen( QPen( QColor("red"), 3, Qt::DashLine ) );
     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
       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->insertItem("Export cell data", this, SLOT(exportCellData()));
   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->insertSeparator();
   helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );
   helpmenu->insertItem("About", this, SLOT(about()) ); //, Key_F1);
 	menu->insertItem("&Help",helpmenu);
   statusBar();
   setCentralWidget(editor);
   printer = 0;
   init();
   // Start timer which repetitively invokes
   // a simulation time step
   timer = new QTimer( this );
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
 void Main::init()
+{
   clear();
   static int r=24;
   srand(++r);
   mainCount++;
+}
 Main::~Main()
+{
   delete printer;
   if ( !--mainCount ) {
+  }
   //EndGifAnim();
+}
 void Main::newView()
+{
   // Open a new view... have it delete when closed.
   Main *m = new Main(canvas, mesh, 0, 0, Qt::WDestructiveClose);
   qApp->setMainWidget(m);
   m->show();
   qApp->setMainWidget(0);
+}
 void Main::EditParameters()
+{
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
   // Make sure the values in the parameter dialog are updated after a file is read
   // each method changing the parameters (reading XML or PAR files) should
   // emit this signal
   QObject::connect(   this, SIGNAL( ParsChanged() ), pardial, SLOT( Reset() ) );
+}
 void Main::savePars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     ofstream parfile((const char *)fileName);
     par.Write(parfile);
+  }
   startSimulation();
+}
 void Main::readPars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::ExistingFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
+}
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
-  fd->setFilter( "XML (*.xml)");
+  fd->setFilter( "LeafML files (*.xml)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return saveStateXML();
     } else {
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
+    }
+  }
+}
 void Main::snapshot()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
+  fd->setFilter( "Image files (*.pdf *.png *.jpg *.tif *.bpm)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "jpg";
       fileName += ".";
       fileName += extension;
+    }
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
-			       tr("Overwrite File? -- Leaf Growth"),
+			       tr("Overwrite file? -- Cell data export"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
 				  " Do you want to overwrite it?").arg( fileName ),
 			       QMessageBox::Yes, QMessageBox::No
 			       ) == QMessageBox::No
 	 ) {
       return snapshot();
     } else {
       // extract extension from filename
       QString extension = getExtension(fileName);
       // Save bitmaps at 1024x768
       Save((const char *)fileName, extension, 1024, 768);
       QString status_message = QString("Wrote snapshot to %1").arg(fileName);
       cerr << status_message.toStdString() << endl;
       statusBar()->showMessage(status_message);
+    }
+  }
+}
 void Main::readPrevStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     if (f==xml_files.begin()) {
       QMessageBox mb( "Read previous leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
 #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
     Plot();
     QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
     setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
 #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,
 		    Qt::NoButton,
 		    Qt::NoButton);
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     ++f;
     if (f==xml_files.end()) {
       QMessageBox mb( "Read next leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *f;
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readLastStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.back();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readFirstStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.front();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readStateXML()
+{
   //  extern Mesh mesh;
   stopSimulation();
 #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)");
+  fd->setFilter( "LeafML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
+  }
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if (working_dir) {
       delete working_dir;
+    }
     working_dir = fd->dir();
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::about()
+{
   static QMessageBox* about = new QMessageBox
     ( "VirtualLeaf V1.0",
       "<h3>VirtualLeaf V1.0</h3>"
       "<p>"
       "An Open Source framework for cell-based modeling of plant tissue growth and development <br>"
       "(c) 2005-2008, Roeland Merks <i>et al.</i><br>"
       "    <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>, "
       "Ghent, Belgium <br>"
       "(c) 2008-2010, <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a> <br>"
       "    <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica</a> and <a href=\"http://www.ncsb.nl\">Netherlands Consortium for Systems Biology</a>, Amsterdam, Netherlands <br>"
 "<br>VirtualLeaf 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.<br>"
       "<br>If you use this code for your projects, please cite our paper:"
 "<br>Merks, Guravage, Inze, and Beemster. An Open Source framework for cell-based modeling of plant tissue growth and development. <i>Plant Physiology,</i> submitted.<br> . <br>"
       "<br>Please share your model plugins and extensions at <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
 void Main::gpl()
+{
   static QMessageBox* gpl = new QMessageBox ( "GPL License", "",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   QDir docDir(QApplication::applicationDirPath());
   docDir.cd("../doc"); // Where Linux expects gpl3.txt
   QString path = docDir.filePath("gpl3.txt");
   if (!docDir.exists("gpl3.txt")){
     docDir = QApplication::applicationDirPath();
     docDir.cd("doc"); // Where Windows expects gpl3.txt
     path = docDir.filePath("gpl3.txt");
+  }
   // At this point path points either to the linux variant, which
   // exists, or the windows variant, which may exist. Testing the
   // ifstream object will determine whether we've found gpl3.txt.
   std::ifstream file(path.toStdString().c_str());
   std::string str;
   if (file) {
     file.seekg(0, std::ios::end);
     str.reserve(file.tellg());
     file.seekg(0, std::ios::beg);
     str.assign((std::istreambuf_iterator<char>(file)),
 	       std::istreambuf_iterator<char>());
     gpl->setDetailedText(QString(str.c_str()));
+  }
   gpl->setText(QString( "<h3>GNU GENERAL PUBLIC LICENSE</h3>"
 			"<p>Version 3, 29 June 2007</p>"
 			"<p>Copyright &copy; 2007 Free Software Foundation, Inc. "
 			"&lt;<a href=\"http://fsf.org/\">http://fsf.org/</a>&gt;</p><p>"
 			"Everyone is permitted to copy and distribute verbatim copies "
 			"of this license document, but changing it is not allowed.</p>"
 			"<h2>GNU GENERAL PUBLIC LICENSE</h2>"));
   gpl->setButtonText( 1, "Dismiss" );
   gpl->show();
+}
 void Main::aboutQt(){
   QMessageBox::aboutQt( this, "Virtual Leaf" );
+}
 void Main::toggleShowCellCenters()
+{
   Plot();
+}
 void Main::toggleShowWalls()
+{
   Plot();
+}
 void Main::toggleShowApoplasts()
+{
   Plot();
+}
 void Main::toggleShowNodes()
+{
   Plot();
+}
 void Main::toggleNodeNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellAxes(void)
+{
   Plot();
+}
 void Main::toggleCellStrain(void)
+{
   Plot();
+}
 void Main::toggleShowFluxes(void)
+{
   Plot();
+}
 void Main::toggleShowBorderCells()
+{
   Plot();
+}
 void Main::toggleHideCells(void)
+{
   Plot();
   editor->FullRedraw();
+}
 void Main::toggleMovieFrames(){}
 void Main::toggleLeafBoundary(){}
 void Main::toggleDynCells() {}
 void Main::startSimulation(void)
+{
   timer->start( 0 );
   statusBar()->message("Simulation started");
   running = true;
+}
 void Main::stopSimulation(void)
+{
   timer->stop();
   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" << endl;
     startSimulation();
   } else {
     cerr << "Calling stop simulation" << endl;
     stopSimulation();
+  }
+}
 void Main::setFluxArrowSize(int size)
+{
   flux_arrow_size = size/100.;
+}
 void Main::enlarge()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*4./3., canvas.height()*4./3.) );
+}
 void Main::shrink()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*3/4, canvas.height()*3/4) );
+}
 void Main::scale(double factor)
+{
   QMatrix m = editor->matrix();
   m.scale(factor, factor);
   editor->setMatrix( m );
+}
 void Main::zoomIn()
+{
   QMatrix m = editor->matrix();
   m.scale( 1.1, 1.1 );
   editor->setMatrix( m );
+}
 void Main::zoomOut()
+{
   QMatrix m = editor->matrix();
   m.scale( 0.9, 0.9 );
   editor->setMatrix( m );
+}
 void Main::print()
+{
   if ( !printer ) printer = new QPrinter;
   if ( printer->setup(this) ) {
     //    extern Mesh mesh;
     Vector bbll,bbur;
     mesh.BoundingBox(bbll,bbur);
 #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();
 #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 {
       pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));
+    }
     canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));
+  }
+}
 void Main::TimeStepWrap(void)
+{
   static int t;
   stringstream fname;
   TimeStep();
   t = (int)mesh.getTime();
   if ((par.export_interval > 0) && !(t%par.export_interval)){
     fname << par.datadir << "/" << par.export_fn_prefix;
     fname.fill('0');
     fname.width(6);
     fname << t << ".csv";
     this->exportCellData(QString(fname.str().c_str()));
+  }
   // check number of timesteps
   if (t == par.nit) {
     emit SimulationDone();
+  }
+}
 void Main::RestartSim(void)
+{
   stopSimulation();
   if ( QMessageBox::question(
 			     this,
 			     tr("Restart simulation?"),
 			     tr("Restart simulation.\n"
 				"Are you sure?"),
 			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
     cerr << "Restarting simulation" << endl;
     //    extern Mesh mesh;
     mesh.Clear();
     Init();
     Plot();
     editor->FullRedraw();
+  }
   //startSimulation();
+}
 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();
 #ifdef QDEBUG
   qDebug() << "editor->width() = " << editor->width() << endl;
   qDebug() << "editor->height() = " << editor->height() << 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)
+{
   if (running) {
     timer->stop();
+  }
+}
 void Main::ContIfRunning(void)
+{
   if (running) {
     timer->start( 0 );
+  }
+}
 void Main::FitLeafToCanvas(void)
+{
   Vector ll,ur;
   mesh.BoundingBox(ll, ur);
   ll*=Cell::Magnification(); ur*=Cell::Magnification();
   // give the leaf some space
   Vector border = ((ur-ll)/5.);
   QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );
   // cerr << ur << ", " << ll << endl;
   // editor->fitInView(bb, Qt::KeepAspectRatio);
   editor->ensureVisible(bb);
   //editor->setTransform(viewport);
+}
 void Main::CleanMesh(void)
+{
   vector<double> clean_chem(Cell::NChem());
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
     clean_transporters[i]=0.;
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshChemicals(void)
+{
   vector<double> clean_chem(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshTransporters(void)
+{
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_transporters[i]=0.;
+  }
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::RandomizeMesh(void)
+{
   vector<double> max_chem(Cell::NChem());
   vector<double> max_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     max_transporters[i]=0.;
     max_chem[i]=par.initval[i];
+  }
   // Amount of PIN1 at walls
   max_transporters[1] = 0.01;
   mesh.RandomizeChemicals(max_chem, max_transporters);
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
   view->setItemChecked(com_id, showcentersp);
   view->setItemChecked(mesh_id, showmeshp);
   view->setItemChecked(border_id, showbordercellp);
   view->setItemChecked(node_number_id, shownodenumbersp);
   view->setItemChecked(cell_number_id, showcellnumbersp);
   view->setItemChecked(cell_axes_id, showcellsaxesp);
   view->setItemChecked(cell_strain_id, showcellstrainp);
   view->setItemChecked(movie_frames_id, movieframesp);
   view->setItemChecked(only_boundary_id, showboundaryonlyp);
   view->setItemChecked(fluxes_id, showfluxesp);
   view->setItemChecked(hide_cells_id, hidecellsp);
   options->setItemChecked(dyn_cells_id, dynamicscellsp);
   view->setItemChecked( cell_walls_id, showwallsp);
  // view->setItemChecked( apoplasts_id, showapoplastsp);
   editor->setTransform(viewport);
+}
 xmlNode *Main::XMLSettingsTree(void)
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
   showbordercellp =  view->isItemChecked(border_id);
   shownodenumbersp =  view->isItemChecked(node_number_id);
   showcellnumbersp =  view->isItemChecked(cell_number_id);
   showcellsaxesp = view->isItemChecked( cell_axes_id );
   showcellstrainp = view->isItemChecked( cell_strain_id );
   movieframesp = view->isItemChecked(movie_frames_id);;
   showboundaryonlyp =  view->isItemChecked(only_boundary_id);
   showfluxesp = view->isItemChecked(fluxes_id);
   dynamicscellsp = options->isItemChecked(dyn_cells_id);
   showwallsp = view->isItemChecked( cell_walls_id);
   //showapoplastsp = view->isItemChecked( apoplasts_id);
   hidecellsp = view->isItemChecked( hide_cells_id);
   xmlNode *settings = MainBase::XMLSettingsTree();
   QTransform viewport(editor->transform());
   xmlAddChild(settings, XMLViewportTree(viewport));
   return settings;
+}
 #define QDEBUG
 void Main::exportCellData(QString fileName) {
 #ifdef QDEBUG
   qDebug() << "exportCellData fileName: " << fileName << endl;
 #endif
   QFile file(fileName);
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
+  }
+}
 void Main::exportCellData() {
   QString fileName;
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "csv";
       fileName += ".";
       fileName += extension;
+    }
     if (extension!="csv" && extension!="CSV") {
       if (
 	  QMessageBox::question(
 				 this,
 				 tr("Change extension? -- Cell data export"),
 				 tr("VirtualLeaf can only export data to CSV format (Excel-compatible)."
 				    "Do you want to change the file extension to \".csv\"?"),
 				 QMessageBox::Yes, QMessageBox::No ) == QMessageBox::No
 	  ) {
 	return exportCellData();
       } else {
 	fileName.replace(extension,"csv");
 	extension="csv";
+      }
+    }
     if ( QFile::exists( fileName ) &&
-	 !QMessageBox::question(
 	 QMessageBox::question(
 			       this,
-			       tr("Overwrite File? -- Cell Data"),
+			       tr("Overwrite file? -- Cell data export"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
 				  " Do you want to overwrite it?").arg( fileName ),
 			       QMessageBox::Yes, QMessageBox::No
 			       ) == QMessageBox::No
 	 ) {
       return exportCellData();
     } else {
       exportCellData(fileName);
       QString status_message = QString("Wrote data file to %1").arg(fileName);
       statusBar()->showMessage(status_message);
+    }
+  }
+}
 /* finis */
+  /* finis */

src/miscq.cpp

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