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

	* transporterdialog.cpp (TransporterDialog): Use wn to discern

	which cell a wallitem belongs to.

	* wallitem.cpp (WallItem): Add a comment explaining how

	wallnumber(wn) can be used to tell which cell a wallitem belongs

	to.

	* VirtualLeaf-install-windows.nsi: Remove previous change that added icon directory.

	* canvas.cpp: Instead of using a separate icon directory, compile

	leaficon_small.xpm directly into canvas.cpp.

	* 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.

  } 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);

  }

}

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\

         tissue growth and development.\

       </p>\

       <p>(c) 2005-2008, Roeland Merks <i>et al.</i>\

         <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>,\

         Ghent, Belgium.\

       </p>\

       <p>(c) 2008-2010,\

         <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a>\

         <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica (CWI)</a> and\

         <a href=\"http://www.ncsb.nl\"> Netherlands Consortium for Systems Biology (NCSB)</a>,\

         Amsterdam, the Netherlands.\

       </p>\

       <p>\

         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.\

       </p>\

       <p>\

         If you use this code for your projects, please cite our paper in\

         <a href=\"http://www.plantphysiol.org\">Plant Physiology</a>, &lsquo;\

         VirtualLeaf: an Open Source framework for cell-based modeling of plant tissue growth and development</a>,<br>\

       </p>\

       <p>\

         Please share your model plugins and extensions at\

         <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.\

       </p>",

      QMessageBox::Information, 1, 0, 0, this, 0, FALSE );

  about->setButtonText( 1, "Dismiss" );

  about->setIconPixmap(QPixmap( leaficon_small ));

  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;