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

	* 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.

	* 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.

  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)");

  fd->setDir(par.datadir);

  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)");

  fd->setDir(par.datadir);

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

  fd->setDir(par.datadir);

  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 = "xml";

      fileName += ".";

      fileName += extension;

    }

    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());

      QString status_message;

      status_message = QString("Wrote LeafML to %1").arg(fileName);

      cerr << status_message.toStdString() << endl;

      statusBar()->showMessage(status_message);

    }

  }

}

void Main::snapshot()

{

#ifdef QDEBUG

  qDebug() << "Supported Image Formats: " << QImageWriter::supportedImageFormats() << endl;

#endif

  stopSimulation();

  Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );

  fd->setDir(par.datadir);

  fd->setMode( Q3FileDialog::AnyFile );

  QString supported_file_formats = " .pdf";

  foreach (QString format, QImageWriter::supportedImageFormats()){

  }

  fd->setFilter("Image files (" + supported_file_formats + " )");

  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 = "png";

      fileName += ".";

      fileName += extension;

    }

    if ( QFile::exists( fileName ) &&

	 QMessageBox::question(

			       this,

			       tr("Overwrite file? -- Cell data export"),

			       tr("A file called %1 already exists."

				  " Do you want to overwrite it?").arg( fileName ),

			       QMessageBox::Yes, QMessageBox::No 

			       ) == QMessageBox::No

	 ) {

      return snapshot();

    } else {

      // Save bitmaps at 1024x768

      QString status_message;

      if (Save((const char *)fileName, extension, 1024, 768)==0) {

	status_message = QString("Wrote snapshot to %1").arg(fileName);

      } else {

	status_message = QString("Error writing 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 );