2010-10-14    <merks@cwi.nl>

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:

	(TimeStamp): New private TimeStamp() function.

	(TimeStepWrap): Added invocation of exportCellData().

	(exportCellData): Created two polymorphic functions: one with a

	single QString argument, the other with no argument. The former is

	called from TimeStepWrap() while the latter is called from the

	"Export cell areas" item in the file menu.

2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire

	where to write the exportCellData.

2010-06-28    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc

	directory (Linux) or a decedent doc directory (Windows, via the

	binary installer).

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.

	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.

	Add missing libiconv/bin, libxml2bin and libz/bin directories.

	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* libplugin.pro: Use correct library path.

	* VirtualLeaf.pro: Ditto.

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* simitembase.cpp: Removed NULL assignments to unused variables.

	* VirtualLeaf.cpp: Ditto.

	* apoplastitem.cpp: Ditto.

	* canvas.cpp: Ditto.

	* cell.cpp: Ditto.

	* cellbase.h: Ditto.

	* forwardeuler.cpp: Ditto.

	* mainbase.h: Ditto.

	* nodeitem.cpp: Ditto.

	* qcanvasarrow.h: Ditto.

	* simitembase.cpp: Ditto.

	* Makefile (clean): Add -f Makefile argument to each make invocation.

	* VirtualLeaf-install.nsi: New gpl license text.

	* VirtualLeaf.pro: Disabled console mode.

	* 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.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <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.

2010-06-18    <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.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.

	* libplugin.pro: Ditto.

2010-06-15    <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.

2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.

	* libplugin.pro: ditto.

2010-06-03    <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

  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)");

  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."

			       .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 );

  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."

			       .arg( fileName ),

			       tr("&Yes"), tr("&No"),

			       QString::null, 1, 1 ) ) {

      return snapshot();

    } else {

      // extract extension from filename

      QString extension = getExtension(fileName);

      // Save bitmaps at 1024x768

      Save((const char *)fileName, extension, 1024, 768);

    }

  }

}

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)");

  if (working_dir) {

    fd->setDir(*working_dir);

  }

  QString fileName;

  if ( fd->exec() == QDialog::Accepted ) {

    fileName = fd->selectedFile();

    if (working_dir) {

      delete working_dir;

  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;

}

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();