2011-02-28    <guravage@petitdru.sen.cwi.nl>

	* canvas.cpp (about): Correct citation text.

	Resolves issue #4: http://code.google.com/p/virtualleaf/issues/detail?id=4.

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().

# $Id$

# 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_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

{

  // 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

       <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;\

         Roeland M. H. Merks, Michael Guravage, Dirk Inzé, and Gerrit T.S. Beemster,\

         <a href=\"http://www.plantphysiol.org/cgi/reprint/155/2/656.pdf\">\

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

         Plant Physiology 2011: 155:656-666.\

       </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();

}