2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* Added: tutorial3_init.xml

	tutorial4_init.xml

	tutorial5_init.xml

	* Removed: bend.xml

	circ.xml

	explant.xml

	init.xml

	one_acc_point_van3.xml

	one_acc_point_van3_growth.xml

  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.

-->

<leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">

  <parameter>

    <par name="arrowcolor" val="white"/>

    <par name="arrowsize" val="10"/>

    <par name="textcolor" val="red"/>

    <par name="cellnumsize" val="1"/>

    <par name="nodenumsize" val="1"/>

    <par name="node_mag" val="1"/>

    <par name="outlinewidth" val="1"/>

    <par name="cell_outline_color" val="forestgreen"/>

    <par name="resize_stride" val="10"/>

    <par name="T" val="1"/>

    <par name="lambda_length" val="100"/>

    <par name="lambda_celllength" val="0"/>

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

i3 = 0 / int

i4 = 0 / int

i5 = 0 / int

s1 =  / string

s2 =  / string

s3 =  / string

b1 = false / bool

b2 = false / bool

b3 = false / bool

b4 = false / bool

dir1 = . / directory

dir2 = . / directory

 *  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 <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>

      pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));

    }

    canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));

  }

}

void Main::TimeStepWrap(void)

{

  static int t=0;

  TimeStep();

  t++;

  // check number of timesteps

  if (t==par.nit) {

    emit SimulationDone();

  }

}

void Main::RestartSim(void)

{

  stopSimulation();

  if ( QMessageBox::question(

			     this,

			     tr("Restart simulation?"),

			     tr("Restart simulation.\n"

				"Are you sure?"),

			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {

    cerr << "Restarting simulation" << endl;

  showfluxesp = view->isItemChecked(fluxes_id);

  dynamicscellsp = options->isItemChecked(dyn_cells_id);

  showwallsp = view->isItemChecked( cell_walls_id);

  //showapoplastsp = view->isItemChecked( apoplasts_id);

  hidecellsp = view->isItemChecked( hide_cells_id);

  xmlNode *settings = MainBase::XMLSettingsTree();

  QTransform viewport(editor->transform());

  xmlAddChild(settings, XMLViewportTree(viewport));

  return settings;

}

#ifdef QDEBUG  

#endif

    QFile file(fileName);

    if ( file.open( IO_WriteOnly ) ) {

      QTextStream stream( &file );

      mesh.CSVExportCellData(stream);

      mesh.CSVExportMeshData(stream);

      file.close();

    }

  }

}

/* finis */

  private slots:

  void aboutQt();

  void newView();

  void EditParameters();

  void readStateXML();

  int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);

  void readNextStateXML();

  void readPrevStateXML();

  void readFirstStateXML();

  void readLastStateXML();

  void exportCellData();

  void saveStateXML();

  void snapshot();

  void savePars();

  void readPars();

  void clear();

  void init();

  virtual void CutSAM() { MainBase::CutSAM(); Refresh();}

  void enlarge();

  void shrink();

  void zoomIn();

  void zoomOut();

  void CleanMesh();

  void CleanMeshChemicals(void);

  void CleanMeshTransporters(void);

  void RandomizeMesh();

 signals:

  void SimulationDone(void);

  void ParsChanged(void);

 protected:

  Mesh &mesh;

 private:

  NodeSet *node_set;

  FigureEditor *editor;

  Q3PopupMenu* options;

  Q3PopupMenu *view;

 *  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 "parameter.h"

#include <cstdio>

#include <cstring>

#include <cstdlib>

#include <cerrno>

#include <iostream>

#include <sstream>

#include "output.h"

#include "parse.h"

#include "xmlwrite.h"

#include "warning.h"

#include <QLocale>

  i3 = 0;

  i4 = 0;

  i5 = 0;

  s1 = strdup("");

  s2 = strdup("");

  s3 = strdup("");

  b1 = false;

  b2 = false;

  b3 = false;

  b4 = false;

  dir1 = strdup(".");

  dir2 = strdup(".");

}

Parameter::~Parameter() {

  // destruct parameter object

  // free string parameter

  CleanUp();

}

void Parameter::CleanUp(void) {

  if (arrowcolor) 

    free(arrowcolor);

  if (k) 

    free(k);

  if (s1) 

    free(s1);

  if (s2) 

    free(s2);

  if (s3) 

    free(s3);

  if (dir1) 

    free(dir1);

  if (dir2) 

    free(dir2);

}

void Parameter::Read(const char *filename) {

  static bool ReadP=false;

  if (ReadP) {

    //throw "Run Time Error in parameter.cpp: Please Read parameter file only once!!";

    CleanUp();

  s2 = sgetpar(fp, "s2", "", true);

  s3 = sgetpar(fp, "s3", "", true);

  b1 = bgetpar(fp, "b1", false, true);

  b2 = bgetpar(fp, "b2", false, true);

  b3 = bgetpar(fp, "b3", false, true);

  b4 = bgetpar(fp, "b4", false, true);

  dir1 = sgetpar(fp, "dir1", ".", true);

  if (strcmp(dir1, "."))

    MakeDir(dir1);

  dir2 = sgetpar(fp, "dir2", ".", true);

  if (strcmp(dir2, "."))

    MakeDir(dir2);

}

const char *sbool(const bool &p) {

  const char *true_str="true";

  const char *false_str="false";

  if (p)

    return true_str;

  else

    return false_str;

}

  if (s3) 

    os << " s3 = " << s3 << endl;

  os << " b1 = " << sbool(b1) << endl;

  os << " b2 = " << sbool(b2) << endl;

  os << " b3 = " << sbool(b3) << endl;

  os << " b4 = " << sbool(b4) << endl;

  if (dir1) 

    os << " dir1 = " << dir1 << endl;

  if (dir2) 

    os << " dir2 = " << dir2 << endl;

}

void Parameter::XMLAdd(xmlNode *root) const {

  xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL);

  {

    xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);

    xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowcolor" );

    ostringstream text;

    if (arrowcolor) 

      text << arrowcolor;

    xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());

      text << dir1;

    xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);

    xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir2" );

    ostringstream text;

    if (dir2) 

      text << dir2;

    xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

}

void Parameter::AssignValToPar(const char *namec, const char *valc) {

  QLocale standardlocale(QLocale::C);

  bool ok;

  if (!strcmp(namec, "arrowcolor")) {

    if (arrowcolor) { free(arrowcolor); }

    arrowcolor=strdup(valc);

  }

  if (!strcmp(namec, "arrowsize")) {

    arrowsize = standardlocale.toDouble(valc, &ok);

    if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'arrowsize' from XML file.",valc); }

  }

  }

  if (!strcmp(namec, "b4")) {

    b4 = strtobool(valc);

  }

  if (!strcmp(namec, "dir1")) {

    if (dir1) { free(dir1); }

    dir1=strdup(valc);

  }

  if (!strcmp(namec, "dir2")) {

    if (dir2) { free(dir2); }

    dir2=strdup(valc);

  }

}

void Parameter::AssignValArrayToPar(const char *namec, vector<double> valarray) {

  if (!strcmp(namec, "D")) {

    int i=0;

    vector<double>::const_iterator v=valarray.begin();

    while (v!=valarray.end() && i <= 14 ) {

      D[i++]=*(v++);

    }

  }

  if (!strcmp(namec, "initval")) {

    int i=0;

    vector<double>::const_iterator v=valarray.begin();

 *  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.

 *

 */

#ifndef _PARAMETER_H_

#define _PARAMETER_H_

#include "vector.h"

#include <vector>

#include <libxml/parser.h>

#include <libxml/tree.h>

 class Parameter {

 public: 

   Parameter();

  int i3;

  int i4;

  int i5;

  char * s1;

  char * s2;

  char * s3;

  bool b1;

  bool b2;

  bool b3;

  bool b4;

  char * dir1;

  char * dir2;

 private:

 };

 ostream &operator<<(ostream &os, Parameter &p);

 const char *sbool(const bool &p);

#endif

 *  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 "pardialog.h"

#include "parameter.h"

#include <cstring>

#include <qdialog.h>

#include <qlabel.h>

#include <qlineedit.h>

#include <qmessagebox.h>

static const std::string _module_id("$Id$");

ParameterDialog::ParameterDialog(QWidget *parent, const char *name, Qt::WindowFlags f) : QDialog(parent,name,false,f) {

  extern Parameter par;

  i3_edit = new QLineEdit( QString("%1").arg(par.i3), this, "i3_edit" );

  i4_edit = new QLineEdit( QString("%1").arg(par.i4), this, "i4_edit" );

  i5_edit = new QLineEdit( QString("%1").arg(par.i5), this, "i5_edit" );

  s1_edit = new QLineEdit( QString("%1").arg(par.s1), this, "s1_edit" );

  s2_edit = new QLineEdit( QString("%1").arg(par.s2), this, "s2_edit" );

  s3_edit = new QLineEdit( QString("%1").arg(par.s3), this, "s3_edit" );

  b1_edit = new QLineEdit( QString("%1").arg(sbool(par.b1)), this, "b1_edit" );

  b2_edit = new QLineEdit( QString("%1").arg(sbool(par.b2)), this, "b2_edit" );

  b3_edit = new QLineEdit( QString("%1").arg(sbool(par.b3)), this, "b3_edit" );

  b4_edit = new QLineEdit( QString("%1").arg(sbool(par.b4)), this, "b4_edit" );

  dir1_edit = new QLineEdit( QString("%1").arg(par.dir1), this, "dir1_edit" );

  dir2_edit = new QLineEdit( QString("%1").arg(par.dir2), this, "dir2_edit" );

  // make a 1x1 grid; it will auto-expand

  QGridLayout *grid = new QGridLayout( this, 1, 1 );

  // add the first four widgets with (row, column) addressing

  grid->addWidget( new QLabel( "", this), 0+1, 0, 1, -1);

  grid->addWidget( new QLabel( " <b>Visualization</b>", this), 3, 0, 1, 2 );

  grid->addWidget( new QLabel( "arrowcolor", this ),4, 0 );

  grid->addWidget( arrowcolor_edit, 4, 0+1  );

  grid->addWidget( new QLabel( "arrowsize", this ),5, 0 );

  grid->addWidget( arrowsize_edit, 5, 0+1  );

  grid->addWidget( new QLabel( "textcolor", this ),6, 0 );

  grid->addWidget( textcolor_edit, 6, 0+1  );

  grid->addWidget( new QLabel( "cellnumsize", this ),7, 0 );

  grid->addWidget( cellnumsize_edit, 7, 0+1  );

  grid->addWidget( new QLabel( "nodenumsize", this ),8, 0 );

  grid->addWidget( nodenumsize_edit, 8, 0+1  );

  grid->addWidget( new QLabel( "b1", this ),25, 6 );

  grid->addWidget( b1_edit, 25, 6+1  );

  grid->addWidget( new QLabel( "b2", this ),26, 6 );

  grid->addWidget( b2_edit, 26, 6+1  );

  grid->addWidget( new QLabel( "b3", this ),27, 6 );

  grid->addWidget( b3_edit, 27, 6+1  );

  grid->addWidget( new QLabel( "b4", this ),28, 6 );

  grid->addWidget( b4_edit, 28, 6+1  );

  grid->addWidget( new QLabel( "dir1", this ),29, 6 );

  grid->addWidget( dir1_edit, 29, 6+1  );

  grid->addWidget( new QLabel( "dir2", this ),3, 8 );

  grid->addWidget( dir2_edit, 3, 8+1  );

  QPushButton *pb = new QPushButton( "&Write", this );

  grid->addWidget(pb, 31, 6 );

  connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) );

  QPushButton *pb2 = new QPushButton( "&Close", this );

  grid->addWidget(pb2,31, 6+1 );

  connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) );

  QPushButton *pb3 = new QPushButton( "&Reset", this );

  grid->addWidget(pb3, 31, 6+2 );

  connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) );

  show();

};

  delete i3_edit;

  delete i4_edit;

  delete i5_edit;

  delete s1_edit;

  delete s2_edit;

  delete s3_edit;

  delete b1_edit;

  delete b2_edit;

  delete b3_edit;

  delete b4_edit;

  delete dir1_edit;

  delete dir2_edit;

}

void ParameterDialog::write(void) {

  extern Parameter par;

  QString tmpval;

  par.arrowcolor = strdup((const char *)arrowcolor_edit->text());

  par.arrowsize = arrowsize_edit->text().toDouble();

  par.textcolor = strdup((const char *)textcolor_edit->text());

  par.cellnumsize = cellnumsize_edit->text().toInt();

  par.nodenumsize = nodenumsize_edit->text().toInt();

  par.node_mag = node_mag_edit->text().toDouble();

    if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b3"),"True","False", QString::null, 0, 1)==0) par.b3=true;

    else par.b3=false;

  }

  tmpval = b4_edit->text().stripWhiteSpace();

  if (tmpval == "true" || tmpval == "yes" ) par.b4 = true;

  else if (tmpval == "false" || tmpval == "no") par.b4 = false;

  else {

    if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b4"),"True","False", QString::null, 0, 1)==0) par.b4=true;

    else par.b4=false;

  }

  par.dir1 = strdup((const char *)dir1_edit->text());

  par.dir2 = strdup((const char *)dir2_edit->text());

  Reset();

}

void ParameterDialog::Reset(void) {

  extern Parameter par;

  arrowcolor_edit->setText( QString("%1").arg(par.arrowcolor) );

  arrowsize_edit->setText( QString("%1").arg(par.arrowsize) );

  textcolor_edit->setText( QString("%1").arg(par.textcolor) );

  cellnumsize_edit->setText( QString("%1").arg(par.cellnumsize) );

  nodenumsize_edit->setText( QString("%1").arg(par.nodenumsize) );

  node_mag_edit->setText( QString("%1").arg(par.node_mag) );

  outlinewidth_edit->setText( QString("%1").arg(par.outlinewidth) );

  i3_edit->setText( QString("%1").arg(par.i3) );

  i4_edit->setText( QString("%1").arg(par.i4) );

  i5_edit->setText( QString("%1").arg(par.i5) );

  s1_edit->setText( QString("%1").arg(par.s1) );

  s2_edit->setText( QString("%1").arg(par.s2) );

  s3_edit->setText( QString("%1").arg(par.s3) );

  b1_edit->setText( QString("%1").arg(sbool(par.b1)));

  b2_edit->setText( QString("%1").arg(sbool(par.b2)));

  b3_edit->setText( QString("%1").arg(sbool(par.b3)));

  b4_edit->setText( QString("%1").arg(sbool(par.b4)));

  dir1_edit->setText( QString("%1").arg(par.dir1) );

  dir2_edit->setText( QString("%1").arg(par.dir2) );

}

/* finis */

#ifndef PARAMETER_DIALOG_H

#define PARAMETER_DIALOG_H

#include <qdialog.h>

#include <qspinbox.h>

#include <qlineedit.h>

#include <qlayout.h>

#include <qpushbutton.h>

#include <iostream>

class ParameterDialog : public QDialog {

    Q_OBJECT

  QLineEdit *i3_edit;

  QLineEdit *i4_edit;

  QLineEdit *i5_edit;

  QLineEdit *s1_edit;

  QLineEdit *s2_edit;

  QLineEdit *s3_edit;

  QLineEdit *b1_edit;

  QLineEdit *b2_edit;

  QLineEdit *b3_edit;

  QLineEdit *b4_edit;

  QLineEdit *dir1_edit;

  QLineEdit *dir2_edit;

};

#endif

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* make_parameter_source.pl: Added datadir changes.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* make_pardialog_source.pl: Reformatted. If datadir is relative append it to the user's home directory.

	* make_parameter_source.pl: Ditto.

	* make_xmlwritecode.pl: Ditto.

    if ($convtype[$i] eq "char *") {

	$value[$i] = "\"$value[$i]\"";

    }

    #print cppfile "param = $param, value = $value, type = $type\n";

    $i++;

}

$lines=$i;

print cppfile <<END_HEADER;

// WARNING: This file is automatically generated by make_parameter_source.pl.

// Do not edit. All edits will be discarded.

#include "parameter.h"

#include <cstdio>

#include <cstring>

#include <cstdlib>

#include <cerrno>

#include <iostream>

#include <sstream>

#include "output.h"

#include "parse.h"

#include "xmlwrite.h"

#include "warning.h"

#include <QLocale>

#include <QDir>

#include <QStringList>

using namespace std;

Parameter::Parameter() {

END_HEADER