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.

	* 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.

  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 );

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

    supported_file_formats += (" *." + format);

  }

  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);