2011-01-13    <guravage@petitdru.sen.cwi.nl>

	* VirtualLeaf-install-windows.nsi: Add new icons directory

	* canvas.cpp (about): Added virtual leaf logo to About message box.

2011-01-12    <guravage@petitdru.sen.cwi.nl>

	* transporterdialog.cpp (TransporterDialog): Add a proper title to

	the dialog, and place the cell and wall pairs in a seperate labe.

2011-01-10    <guravage@petitdru.sen.cwi.nl>

	* transporterdialog.cpp (TransporterDialog): Start numbering Transporter fields at zero.

	Resolves issue #1: http://code.google.com/p/virtualleaf/issues/detail?id=1.

	* wallitem.cpp (OnClick): Change dialog modality to Qt::WindowModal.

	Resolves issue #2: http://code.google.com/p/virtualleaf/issues/detail?id=2.

	* canvas.cpp (about): Add link to Plant Physiology paper.

	Resolves issue #3: http://code.google.com/p/virtualleaf/issues/detail?id=3.

2010-11-30    <guravage@petitdru.sen.cwi.nl>

	* canvas.cpp (snapshot): Preface each image format extension with

	an asterisk so files with those extensions to appear in the file

	dialogue.

	(snapshot): Forgot to add asterisk before our own pdf format.

	* VirtualLeaf-install-windows.nsi: Include imageformats folder

	alongside executable.

	* canvas.cpp (snapshot): PNG is the default image format.

2010-11-29    <guravage@petitdru.sen.cwi.nl>

	* canvas.cpp (snapshot): Query and display supported snapshot file

	formats.

	* VirtualLeaf-install-windows.nsi: To facilitate debugging I added

	the debug versions of all the windows DLLs.

2010-10-19    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): Use format specified in function prototype.

	* VirtualLeaf.cpp (Plot): Render PNG instead of JPEG. Write image

	and XML files dependent only on getTime().

2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): QDir::toNativeSeparators(fname). Invoke

	save with format argument set to zero to force QImage to guess the

	format by looking at fileName's suffix.

	* VirtualLeaf-install.nsi: Put uninstaller in top directory.

	* modelcatalogue.cpp (InstallModel): For all OS-es. Move from "bin" directory to root application folder.

	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.

	* Makefile (Makefile.libplugin): Removed -makefile qmake option.

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and

	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with

	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with

	mesh.incrementIterations().

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

	* VirtualLeaf.pro: Turned debug off to make all profiles must be

	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX

	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the

	uninstaller all go in the bin directory. And leaves directory

	placed under data directory.

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

	overwritting an existing file.

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

	* mesh.cpp: In response to referees' comments, added new parameter

	"yield_threshold" instead of fixed parameter '4' for yield

	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was

	cycled and the transporterdialog popped up. Corrected this - for

	wall type cycling, hold the Control button while left

	clicking. TransporterDialog only pops up for left click. Also made

	sure the wall is redrawn after changing the transporter values.

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

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

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

	* cellbase.cpp (ExactCircumference): I added a new function

	ExactCircumference, yielding the circumference of the cell along

	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates

	need to be sorted in x,y order for the convex hull algorithm

	(thanks Margriet!). I updated CSVExportCellData so it exports the

	circumferences of hull and boundary_polygon.

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.

# $Id$

# appends \ to the path if missing

# example: !insertmacro GetCleanDir "c:\blabla"

# Pop $0 => "c:\blabla\"

!macro GetCleanDir INPUTDIR

  ; ATTENTION: USE ON YOUR OWN RISK!

  ; Please report bugs here: http://stefan.bertels.org/

  !define Index_GetCleanDir 'GetCleanDir_Line${__LINE__}'

  Push $R0

  Push $R1

  StrCpy $R0 "${INPUTDIR}"

  StrCmp $R0 "" ${Index_GetCleanDir}-finish

  StrCpy $R1 "$R0" "" -1

  StrCmp "$R1" "\" ${Index_GetCleanDir}-finish

  StrCpy $R0 "$R0\"

${Index_GetCleanDir}-finish:

  Pop $R1

  Exch $R0

  !undef Index_GetCleanDir

!macroend

# similar to "RMDIR /r DIRECTORY", but does not remove DIRECTORY itself

# example: !insertmacro RemoveFilesAndSubDirs "$INSTDIR"

!macro RemoveFilesAndSubDirs DIRECTORY

  # ATTENTION: USE ON YOUR OWN RISK!

  # Please report bugs here: http://stefan.bertels.org/

  !define Index_RemoveFilesAndSubDirs 'RemoveFilesAndSubDirs_${__LINE__}'

  Push $R0

  Push $R1

  Push $R2

  !insertmacro GetCleanDir "${DIRECTORY}"

  Pop $R2

  FindFirst $R0 $R1 "$R2*.*"

${Index_RemoveFilesAndSubDirs}-loop:

  StrCmp $R1 "" ${Index_RemoveFilesAndSubDirs}-done

  StrCmp $R1 "." ${Index_RemoveFilesAndSubDirs}-next

  StrCmp $R1 ".." ${Index_RemoveFilesAndSubDirs}-next

  IfFileExists "$R2$R1\*.*" ${Index_RemoveFilesAndSubDirs}-directory

  ; file

  Delete "$R2$R1"

  goto ${Index_RemoveFilesAndSubDirs}-next

${Index_RemoveFilesAndSubDirs}-directory:

  ; directory

  RMDir /r "$R2$R1"

${Index_RemoveFilesAndSubDirs}-next:

  FindNext $R0 $R1

  Goto ${Index_RemoveFilesAndSubDirs}-loop

${Index_RemoveFilesAndSubDirs}-done:

  FindClose $R0

  Pop $R2

  Pop $R1

  Pop $R0

  !undef Index_RemoveFilesAndSubDirs

!macroend

!define PRODUCT_NAME "The Virtual Leaf"

!define PRODUCT_VERSION "1.0"

!define PRODUCT_PUBLISHER "Center for Mathematics and Computer Science (CWI)"

!define PRODUCT_WEB_SITE "www.cwi.nl"

!define EXECUTABLE "VirtualLeaf.exe"

!define PROGICON "leaficon.ico"

!define SETUP_BITMAP "leaficon.ico"

# MUI 1.67 compatible ------

!include "MUI.nsh"

!include "EnvVarUpdate.nsh"

# MUI Settings

!define MUI_ABORTWARNING

!define MUI_ICON "leaficon.ico"

!define MUI_UNICON "leaficon.ico"

# Welcome page

!insertmacro MUI_PAGE_WELCOME

# License page

!insertmacro MUI_PAGE_LICENSE "..\doc\gpl3.txt"

# Components page

!insertmacro MUI_PAGE_COMPONENTS

# Directory page

!insertmacro MUI_PAGE_DIRECTORY

# Instfiles page

!insertmacro MUI_PAGE_INSTFILES

# Finish page

!insertmacro MUI_PAGE_FINISH

# Uninstaller pages

!insertmacro MUI_UNPAGE_CONFIRM

!insertmacro MUI_UNPAGE_INSTFILES

!insertmacro MUI_UNPAGE_FINISH

# Language files

!insertmacro MUI_LANGUAGE "English"

# MUI end ------

# set the name of the installer

outfile "VirtualLeaf-install.exe"

Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"

ShowInstDetails show

ShowUnInstDetails show

# define the directory to install to

installDir C:\VirtualLeaf

# Request application privileges

RequestExecutionLevel user

section "Virtual Leaf executable"

  #sectionIn RO

  # define the output path for the Virtual Leaf executable

  setOutPath $INSTDIR\bin

  writeUninstaller $INSTDIR\uninstaller.exe

  file ..\bin\VirtualLeaf.exe

  # Required DLLs

  setOutPath $INSTDIR\bin

  file ..\lib\libiconv\bin\libiconv-2.dll

  file ..\lib\libxml2\lib\libxml2.dll

  file ..\lib\libz\bin\zlib1.dll

  # Is the pegging of these DLLs to a specific QT version a problem?

  file C:\Qt\2010.02.1\mingw\bin\mingwm10.dll

  file C:\Qt\2010.02.1\mingw\bin\libgcc_s_dw2-1.dll

  file C:\Qt\2010.02.1\qt\bin\Qt3Support4.dll

  file C:\Qt\2010.02.1\qt\bin\QtCore4.dll

  file C:\Qt\2010.02.1\qt\bin\QtGui4.dll

  file C:\Qt\2010.02.1\qt\bin\QtNetwork4.dll

  file C:\Qt\2010.02.1\qt\bin\QtSql4.dll

  file C:\Qt\2010.02.1\qt\bin\QtXml4.dll

  # Prepend the Virtual Leaf bin directory to the installers PATH

  ${EnvVarUpdate} $0 "PATH" "P" "HKCU" "$INSTDIR\bin"  

  # create a shortcut named "VirtualLeaf" in the start menu programs directory

  # point the new shortcut at the program VirtualLeaf

  createShortCut "$SMPROGRAMS\VirtualLeaf.lnk" "$INSTDIR\bin\VirtualLeaf.exe"

sectionEnd

section "Image Formats"

  # define the output path for the Qt Image Formats

  setOutPath $INSTDIR\bin\imageformats

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qgif4.dll

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qico4.dll

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qjpeg4.dll

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qmng4.dll

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qsvg4.dll

  file C:\Qt\2010.02.1\qt\plugins\imageformats\qtiff4.dll

sectionEnd

section "Virtual Leaf plugins"

  # define the output path for the Virtual Leaf models

  setOutPath $INSTDIR\bin\models

  file ..\bin\models\*

sectionEnd

section "Virtual Leaf data"

  # define the output path for the Virtual Leaf models

  setOutPath $INSTDIR\data\leaves

  file ..\data\leaves\*

sectionEnd

section "Virtual Leaf docs"

  # define the output path for the Virtual Leaf documentation

  setOutPath $INSTDIR\doc

  file ..\doc\*

sectionEnd

# create a section to define what the uninstaller does.

# the section will always be named "Uninstall"

section "Uninstall"

  # Always delete uninstaller first

  delete $INSTDIR\uninstaller.exe

  # Now delete installed file

  !insertmacro RemoveFilesAndSubDirs "$INSTDIR"

  # Delete shortcut from start menu

  delete "$SMPROGRAMS\VirtualLeaf.lnk"

  # Last but not least - delete the path  

  ${un.EnvVarUpdate} $0 "PATH" "R" "HKCU" "$INSTDIR\bin"

sectionEnd

# finis

/*

 *

 *  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 <QImageWriter>

#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 "OptionFileDialog.h"

#include <cstdlib>

#include <cstdio>

#include "modelcatalogue.h"

#include <algorithm>

#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.

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);

  }

}

QDir Main::GetLeafDir(void) {

  QDir LeafDir(QApplication::applicationDirPath()); 

  QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"

#if defined(Q_OS_WIN) 

  if (LeafDir.dirName().toLower() =="debug" 

      ||LeafDir.dirName().toLower() =="release") 

    LeafDir.cdUp(); 

  //plugin_filters << "*.dll";

#elif defined(Q_OS_MAC) 

  if (LeafDir.dirName() =="MacOS"){ 

    LeafDir.cdUp(); 

    LeafDir.cdUp(); 

    LeafDir.cdUp(); 

  }

#endif

  // for all OS-es. Move from "bin" directory to root application folder.

  if (LeafDir.dirName() == "bin") {

    LeafDir.cdUp();

  }

  LeafDir.cd("data/leaves");

  /* if (!LeafDir.cd("data/leaves")) {

    QString status_message = QString("No directory data/leaves");

    statusBar()->showMessage(status_message);

    return LeafDir;

  } 

  */

  return LeafDir;

}

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( "LeafML files (*.xml)");

  if (working_dir) {

    fd->setDir(*working_dir);

  } else {

    fd->setDir(par.datadir);

  }

  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\