2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* auxin_growth.xml: Changed export_fn_prefix to 'cell.'

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.

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

	one_acc_point_van3_growth2.xml

	tissue.xml

<?xml version="1.0" encoding="UTF-8"?>

<!-- 

  $Rev$:  Revision of last commit

  $Author$:  Author of last commit

  $Source$:  Source file

  $Date$:  Date of last commit

  This file is part of the Virtual Leaf.

  The Virtual Leaf 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.

  The Virtual Leaf 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.

-->

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

  <parameter>

    <par name="export_interval" val="1000"/>

    <par name="export_fn_prefix" val="cell."/>

    <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"/>

    <par name="target_length" val="60"/>

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

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

    <par name="auxin_dependent_growth" val="true"/>

    <par name="ode_accuracy" val="0.0001"/>

    <par name="mc_stepsize" val="0.4"/>

    <par name="mc_cell_stepsize" val="0.2"/>

    <par name="energy_threshold" val="1000"/>

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

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

    <par name="rel_cell_div_threshold" val="2"/>

    <par name="rel_perimeter_stiffness" val="2"/>

    <par name="collapse_node_threshold" val="0.05"/>

    <par name="morphogen_div_threshold" val="0.2"/>

    <par name="morphogen_expansion_threshold" val="0.01"/>

    <par name="copy_wall" val="true"/>

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

    <par name="D">

      <valarray>

        <val v="1e-06"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="initval">

      <valarray>

        <val v="0"/>

        <val v="1"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="k1" val="1"/>

    <par name="k2" val="0.3"/>

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

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

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

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

    <par name="transport" val="0.36"/>

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

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

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

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

    <par name="pin_breakdown_internal" val="0.001"/>

    <par name="aux1prod" val="0.001"/>

    <par name="aux1prodmeso" val="0"/>

    <par name="aux1decay" val="0.001"/>

    <par name="aux1decaymeso" val="0.1"/>

    <par name="aux1transport" val="0.036"/>

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

    <par name="aux_breakdown" val="0.0001"/>

    <par name="kaux1" val="1"/>

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

    <par name="leaf_tip_source" val="0.0001"/>

    <par name="sam_efflux" val="0.0001"/>

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

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

    <par name="dt" val="0.1"/>

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

    <par name="datadir" val="auxin_growth"/>

    <par name="movie" val="true"/>

    <par name="nit" val="100000"/>

    <par name="maxt" val="1e+06"/>

    <par name="xml_storage_stride" val="500"/>

    <par name="rseed" val="-1"/>

    <par name="constituous_expansion_limit" val="16"/>

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

    <par name="vessel_expansion_rate" val="0.25"/>

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

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

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

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

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

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

    <par name="rho0" val="0"/>

    <par name="rho1" val="0"/>

    <par name="c0" val="0"/>

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

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

  </parameter>

  <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;

#include <sstream>

#include <cstring>

#include <functional> 

#include <getopt.h>

#include <cerrno>

#include "mesh.h"

#include "parameter.h"

#include "random.h"

#include "pi.h"

#include "cellitem.h"

#include "canvas.h"

#include "cell.h"

#include "output.h"

#include <qwidget.h>

#include <q3process.h>

#include <qapplication.h>

#include <QDesktopWidget>

#include <QGraphicsScene>

#include <QMessageBox>

//Added by qt3to4:

#include <QMouseEvent>

#include <unistd.h>

#include <q3textstream.h> 

#ifdef HAVE_QWT

#include "data_plot.h"

#endif

#include <QPalette>

#include <QBrush>

#include <QToolTip>

#include "simplugin.h"

#include "testplugin.h"

/* #define _xstr_(s) _str_(s)

#define _str_(s) #s

#include _xstr_(REACTIONS_HEADER)

*/

extern Parameter par;

MainBase *main_window = 0;

double auxin_account = 0.;

TestPlugin *plugin = new TestPlugin();

#ifdef XFIGGRAPHICS

#define TIMESTEP double Graphics::TimeStep(void)

#endif

class PrintNode {

public:

  void operator() (const Node &n) const 

  {

    cerr << n.Index() << ": " << n <<  endl;

  }

};

class EdgeSource {

public:

  void operator() (Cell &c) {

    if (c.AtBoundaryP()) {

      cerr << "Cell " << c.Index() << " is a source cell.\n";

      c.SetSource(0,par.source);

    } else {

      cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";

    }

  }

};

class CellInfo {

public:

  void operator() (Cell &c,std::ostream &os) const {

    os << "Cell " << c.index << " says: " << endl;

    os << "c.nodes.size() = " << c.nodes.size() << endl;

    for (list<Node *>::iterator i=c.nodes.begin();

	 i!=c.nodes.end();

	 i++) {

      cerr << (*i)->Index() << " ";

    }

    cerr << endl;

  }

};

double PINSum(Cell &c) {

	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );

}

class DrawCell {

public:

  void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {

    if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {

      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) 

	if (m.ShowToolTipsP()) {

	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());

	  info_string += "\n" + c.printednodelist();

	  c.Draw(&canvas, info_string);

	} else {

	  c.Draw(&canvas);

	}

      if (m.ShowCentersP())

	c.DrawCenter(&canvas);

    if (m.ShowFluxesP())

	c.DrawFluxes(&canvas, par.arrowsize);

       }

  }

};

Mesh mesh;

bool batch=false;

void MainBase::Plot(int resize_stride) {

  clear();

  static int count=0;

  if (resize_stride) {

    if ( !((++count)%resize_stride) ) {

      FitLeafToCanvas();

    }

  }

  mesh.LoopCells(DrawCell(),canvas,*this);

  if (ShowNodeNumbersP()) 

    mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;

  if (ShowCellNumbersP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;

  if (ShowCellAxesP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );

  if (ShowCellStrainP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );

  if (ShowWallsP())

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );

	if (ShowApoplastsP()) 

		mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );

	if (ShowMeshP()) 

    mesh.DrawNodes(&canvas);

  if (ShowBoundaryOnlyP()) 

    mesh.DrawBoundary(&canvas);

	if ( ( batch || MovieFramesP() )) {

		static int frame = 0;

		// frame numbers are sequential for the most frequently written file type.

		// for the less frequently written file type they match the other type

		if (!(count%par.storage_stride) )  {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			/* 

			 fname << frame << ".pdf";

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

			// Write high-res JPG snapshot every plot step

			Save(fname.str().c_str(), "PDF");

			*/

			fname << frame << ".jpg";

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

			// Write high-res JPG snapshot every plot step

			Save(fname.str().c_str(), "JPEG",1024,768);

		}

		if (!(count%par.xml_storage_stride)) {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			fname << frame << ".xml";

			if (par.xml_storage_stride < par.storage_stride) {

				frame++;

			}

			// Write XML file every ten plot steps

			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());

		}

	}

}

void Cell::Flux(double *flux, double *D)  {

  // loop over cell edges

  for (int c=0;c<Cell::nchem;c++) flux[c]=0.;

  for (list<Wall *>::iterator i=walls.begin();

       i!=walls.end();

       i++) {

    // leaf cannot take up chemicals from environment ("no flux boundary")

    if ((*i)->c2->BoundaryPolP()) continue;

    // flux depends on edge length and concentration difference

    for (int c=0;c<Cell::nchem;c++) {

      double phi = (*i)->length * ( D[c] ) * ( (*i)->c2->chem[c] - chem[c] );

      if ((*i)->c1!=this) {

	cerr << "Warning, bad cells boundary: " << (*i)->c1->index << ", " << index << endl;

      }

      flux[c] += phi;

    }    

  }

}

INIT {

	if (leaffile) { 

    xmlNode *settings;

    mesh.XMLRead(leaffile, &settings);

    main_window->XMLReadSettings(settings);

    xmlFree(settings);

    main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));

  } else {

	  Cell &circle=mesh.CircularCell(0,0,10,10);

    circle.SetTargetArea(circle.CalcArea());

	  mesh.SetBaseArea();

	// clean up chemicals 

	  for (int c=0; c<Cell::NChem(); c++) {

		  circle.SetChemical(c, 0.);

      }

  }

}

TIMESTEP {

  static int i=0;

  static int t=0;

  static int ncells;

  if (!batch) {

    UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);

  }

  ncells=mesh.NCells();

  double dh;

  if(DynamicCellsP()) {

    dh = mesh.DisplaceNodes();

    // Only allow for node insertion, cell division and cell growth

    // if the system has equillibrized

    // i.e. cell wall tension equillibrization is much faster

    // than biological processes, including division, cell wall yielding

    // and cell expansion

    mesh.InsertNodes(); // (this amounts to cell wall yielding)

    if ( (-dh) < par.energy_threshold) {

      mesh.IncreaseCellCapacityIfNecessary();

		mesh.LoopCurrentCells(&TestPlugin::CellHouseKeeping); // this includes cell division

      // Reaction diffusion	

		/*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;

      CellReaction *cellreaction_f = new plugin->CellDynamics();

      WallReaction *wall_f = new WallDynamics();*/

      mesh.ReactDiffuse(plugin, par.rd_dt);

      t++;

      Plot(par.resize_stride);

		/*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();

		QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));

		ofstream af(afname.toStdString().c_str());

		*/

		/*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();

			 v!=angles.end();

			 v++) {

			af << v->first << " " << v->second << endl;

			}

			*/

			}

			} else {

  /*  TransportFunction *transport_f = new CelltoCellTransport();

    CellReaction *cellreaction_f = new CellDynamics();

    WallReaction *wall_f = new WallDynamics();

    mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/

				mesh.ReactDiffuse(plugin, par.rd_dt);

    Plot(par.resize_stride);

  }

  i++;

  return mesh.getTime();

}

/* Called if a cell is clicked */

void Cell::OnClick(QMouseEvent *e) {

}

void Wall::OnWallInsert(void) {

}

int main(int argc,char **argv) {

  try {

    int c;

    char *leaffile=0;

    while (1) {

      //int this_option_optind = optind ? optind : 1;

      int option_index = 0;

      static struct option long_options[] = {

	{"batch", 0, 0, 0},

	{"leaffile", 2, 0, 0}

      };

      // short option 'p' creates trouble for non-commandline usage on MacOSX. Option -p changed to -P (capital)

      static char *short_options = "bl";

      c = getopt_long (argc, argv, "bl:",

		       long_options, &option_index);

      if (c == -1)

	break;

      if (c==0) {

	printf ("option %s", long_options[option_index].name);

	if (optarg)

	  printf (" with arg %s", optarg);

	printf ("\n");

	c = short_options[option_index];

      }

      switch (c) {

      case 'b':

	cerr << "Running in batch mode\n";

	batch=true;

	break;

      case 'l':

	leaffile=strdup(optarg);

	if (!leaffile) {

	  throw("Out of memory");

	}

	printf("Reading leaf state file '%s'\n", leaffile);

	break;

      case '?':

	break;

      default:

	printf ("?? getopt returned character code 0%o ??\n", c);

      }

    }

    if (optind < argc) {

      printf ("non-option ARGV-elements: ");

      while (optind < argc)

	printf ("%s ", argv[optind++]);

      printf ("\n");

    }

	  MakeDir("Angles");

    bool useGUI = !batch;

    QApplication app(argc,argv,useGUI);

    QPalette tooltippalette = QToolTip::palette();

    QColor transparentcolor = QColor(tooltippalette.brush(QPalette::Window).color());

    tooltippalette.setBrush (QPalette::Window, QBrush (transparentcolor) );

    QToolTip::setPalette( tooltippalette );

    QGraphicsScene canvas(0,0,8000,6000);

    if (useGUI) {

         main_window=new Main(canvas, mesh);

      if ( QApplication::desktop()->width() > ((Main *)main_window)->width() + 10

	   && QApplication::desktop()->height() > ((Main *)main_window)->height() +30 ) {

	((Main *)main_window)->show();

	((Main *)main_window)->resize( ((Main *)main_window)->sizeHint());

    } else {

        ((Main *)main_window)->showMaximized();

    }

  } else {

        main_window=new MainBase(canvas, mesh);

 }

    canvas.setSceneRect(QRectF());

    if (!batch) {

      QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );

    }

    main_window->Init(leaffile);

    Cell::SetMagnification(10);

    Cell::setOffset(0,0);

    main_window->FitLeafToCanvas();

    main_window->Plot();

    if (batch) {

      double t=0.;

      do {

	t = main_window->TimeStep();

      } while (t < par.maxt);

    } else

      return app.exec();

  } catch (const char *message) {

    if (batch) { 

      cerr << "Exception caught:" << endl;

      cerr << message << endl;

      abort();

    } else {

      QString qmess=QString("Exception caught: %1").arg(message);

      QMessageBox::critical(0, "Critical Error", qmess);

      abort();

    }

  } catch (ios_base::failure) {

    stringstream error_message;

    error_message << "I/O failure: " << strerror(errno);

    if (batch) {

      cerr << error_message.str() <<endl;

      abort();

    } else {

      QString qmess(error_message.str().c_str());

      QMessageBox::critical(0, "I/O Error", qmess );

      abort();

    }

  }

}

</code>

  <code name="reactions_pce_growth.h">

// Executed after the cellular mechanics steps have equillibrized

class CellHouseKeeping {

public:

	void operator() (Cell &c) const {

		c.EnlargeTargetArea(par.cell_expansion_rate);

		if (c.Area() > par.rel_cell_div_threshold * c.BaseArea() ) {

			c.Divide();

		}

	}

};

// The number of chemical species in the cels

const int Cell::nchem = 0;

// Differential equations describing transport of chemicals from cell to cell

class CelltoCellTransport : public TransportFunction {

 public:

	virtual void operator()(Wall *w, double *dchem_c1, double *dchem_c2) {}

 };

// Differential equations describing chemical reactions taking place at or near the cell walls

// (e.g. PIN accumulation)

class WallDynamics : public WallReaction {

 public:

	virtual void operator()(Wall *w, double *dw1, double *dw2) {}; 

};

// Differential equations describing chemical reactions inside the cells

class CellDynamics : public CellReaction {

 public:

	virtual void operator()(Cell *c, double *dchem) {

	};

};

// Rules for cell coloring

void Cell::SetColor(QColor &color) { }

// To be executed after cell division

void Cell::OnDivide(ParentInfo &parent_info, Cell &daughter) {}

</code>

  <nodes n="22" target_length="3.09017">

    <node x="22.9634" y="-2.37264" fixed="false" boundary="true" sam="false"/>

    <node x="14.6882" y="17.9118" fixed="false" boundary="true" sam="false"/>

    <node x="1.57936" y="25.1246" fixed="false" boundary="true" sam="false"/>

    <node x="-9.0893" y="22.8165" fixed="false" boundary="true" sam="false"/>

    <node x="-19.7055" y="16.962" fixed="false" boundary="true" sam="false"/>

    <node x="-22.6839" y="5.00143" fixed="false" boundary="true" sam="false"/>

    <node x="-14.7271" y="-15.2131" fixed="false" boundary="true" sam="false"/>

    <node x="-6.78413" y="-23.4002" fixed="false" boundary="true" sam="false"/>

    <node x="3.60766" y="-25.1355" fixed="false" boundary="true" sam="false"/>

    <node x="21.3032" y="-13.6899" fixed="false" boundary="true" sam="false"/>

    <node x="17.4704" y="7.41573" fixed="false" boundary="true" sam="false"/>

    <node x="-17.5799" y="-5.20265" fixed="false" boundary="true" sam="false"/>

    <node x="9.86837" y="4.69636" fixed="false" boundary="false" sam="false"/>

    <node x="-9.28449" y="-3.92969" fixed="false" boundary="false" sam="false"/>

    <node x="12.5597" y="-20.5161" fixed="false" boundary="true" sam="false"/>

    <node x="-1.62187" y="-3.10623" fixed="false" boundary="false" sam="false"/>

    <node x="7.55765" y="-14.4922" fixed="false" boundary="false" sam="false"/>

    <node x="2.97596" y="-8.80653" fixed="false" boundary="false" sam="false"/>

    <node x="1.95125" y="3.2756" fixed="false" boundary="false" sam="false"/>

    <node x="-6.54614" y="15.4702" fixed="false" boundary="false" sam="false"/>

    <node x="-2.72983" y="8.96705" fixed="false" boundary="false" sam="false"/>

    <node x="9.33552" y="23.0046" fixed="false" boundary="true" sam="false"/>

  </nodes>

  <cells n="4" offsetx="0" offsety="0" magnification="10" base_area="293.893" nchem="2">

    <cell index="0" area="405.845" target_area="548.609" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">

      <node n="13"/>

      <node n="11"/>

      <node n="6"/>

      <node n="7"/>

      <node n="8"/>

      <node n="14"/>

      <node n="16"/>

      <node n="17"/>

      <node n="15"/>

      <wall w="6"/>

      <wall w="0"/>

      <wall w="1"/>

      <chem n="2">

        <val v="0.251808"/>

        <val v="0.481961"/>

      </chem>

    </cell>

    <cell index="1" area="385.557" target_area="547.081" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">

      <node n="12"/>

      <node n="10"/>

      <node n="1"/>

      <node n="21"/>

      <node n="2"/>

      <node n="3"/>

      <node n="19"/>

      <node n="20"/>

      <node n="18"/>

      <wall w="3"/>

      <wall w="4"/>

      <wall w="5"/>

      <chem n="2">

        <val v="0.250735"/>

        <val v="0.481961"/>

      </chem>

    </cell>

    <cell index="2" area="422.94" target_area="565.987" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">

      <node n="9"/>

      <node n="0"/>

      <node n="10"/>

      <node n="12"/>

      <node n="18"/>

      <node n="15"/>

      <node n="17"/>

      <node n="16"/>

      <node n="14"/>

      <wall w="1"/>

      <wall w="2"/>

      <wall w="8"/>

      <wall w="4"/>

      <chem n="2">

        <val v="0.307348"/>

        <val v="0.481245"/>

      </chem>

    </cell>