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Renamed tutorial examples and added makefile, etc.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added doc/gpl3.txt
added doc/installation.pdf
added doc/installation.rst
added src/TutorialCode/Makefile
added src/TutorialCode/Tutorial0/Makefile
added src/TutorialCode/Tutorial0/tutorial0.cpp
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--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added doc/gpl3.txt
added doc/installation.pdf
added doc/installation.rst
added src/TutorialCode/Makefile
added src/TutorialCode/Tutorial0/Makefile
added src/TutorialCode/Tutorial0/tutorial0.cpp
added src/TutorialCode/Tutorial0/tutorial0.h
added src/TutorialCode/Tutorial0/tutorial0.pro
added src/TutorialCode/Tutorial1A/Makefile
added src/TutorialCode/Tutorial1A/tutorial1A.cpp
added src/TutorialCode/Tutorial1A/tutorial1A.h
added src/TutorialCode/Tutorial1A/tutorial1A.pro
added src/TutorialCode/Tutorial1B/Makefile
added src/TutorialCode/Tutorial1B/tutorial1B.cpp
added src/TutorialCode/Tutorial1B/tutorial1B.h
added src/TutorialCode/Tutorial1B/tutorial1B.pro
added src/TutorialCode/Tutorial1C/Makefile
added src/TutorialCode/Tutorial1C/tutorial1C.cpp
added src/TutorialCode/Tutorial1C/tutorial1C.h
added src/TutorialCode/Tutorial1C/tutorial1C.pro
added src/TutorialCode/Tutorial1D/Makefile
added src/TutorialCode/Tutorial1D/tutorial1D.cpp
added src/TutorialCode/Tutorial1D/tutorial1D.h
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added src/TutorialCode/Tutorial2/Makefile
added src/TutorialCode/Tutorial2/tutorial2.cpp
added src/TutorialCode/Tutorial2/tutorial2.h
added src/TutorialCode/Tutorial2/tutorial2.pro
added src/TutorialCode/Tutorial3/Makefile
added src/TutorialCode/Tutorial3/tutorial3.cpp
added src/TutorialCode/Tutorial3/tutorial3.h
added src/TutorialCode/Tutorial3/tutorial3.pro
added src/TutorialCode/Tutorial4/Makefile
added src/TutorialCode/Tutorial4/tutorial4.cpp
added src/TutorialCode/Tutorial4/tutorial4.h
added src/TutorialCode/Tutorial4/tutorial4.pro
added src/TutorialCode/Tutorial5/Makefile
added src/TutorialCode/Tutorial5/tutorial5.cpp
added src/TutorialCode/Tutorial5/tutorial5.h
added src/TutorialCode/Tutorial5/tutorial5.pro
added src/perl/ChangeLog
changed src/ChangeLog
changed src/Makefile
changed src/build_models/ChangeLog
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
changed src/perl/make_xmlwritecode.pl
changed src/vleafmodel.h
removed doc/GPL
removed src/TutorialCode/Tutorial0/mymodel.cpp
removed src/TutorialCode/Tutorial0/mymodel.h
removed src/TutorialCode/Tutorial0/mymodel.pro
removed src/TutorialCode/Tutorial1/mymodel.cpp
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removed src/TutorialCode/Tutorial4/mymodel
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removed src/TutorialCode/Tutorial4/mymodel.h
removed src/TutorialCode/Tutorial4/mymodel.pro
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*
* 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.
*
*/
#include <QObject>
#include <QtGui>
#include "simplugin.h"
#include "parameter.h"
#include "wallbase.h"
#include "cellbase.h"
#include "tutorial2.h"
static const std::string _module_id("$Id$");
QString Tutorial2::ModelID(void) {
// specify the name of your model here
return QString( "2: Growth hormones" );
}
// return the number of chemicals your model uses
int Tutorial2::NChem(void) { return 1; }
// To be executed after cell division
void Tutorial2::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
// rules to be executed after cell division go here
// (e.g., cell differentiation rules)
// set one cell to source after first division
if (CellBase::NCells()==2) {
daughter1->SetCellType(1);
daughter2->SetCellType(0);
}
// if a source cells has divided, one of the daughters becomes the new source
if (daughter1->CellType()==1) {
// if both cells are at the tissue perimeter, choose at random
if (daughter1->AtBoundaryP() && daughter2->AtBoundaryP()) {
if (qrand()%2){
daughter1->SetCellType(1);
daughter2->SetCellType(0);
} else {
daughter1->SetCellType(0);
daughter2->SetCellType(1);
}
} else {
// otherwise choose the one that is still at the perimeter
if (daughter1->AtBoundaryP()) {
daughter1->SetCellType(1);
daughter2->SetCellType(0);
} else {
daughter1->SetCellType(0);
daughter2->SetCellType(1);
}
}
}
}
void Tutorial2::SetCellColor(CellBase *c, QColor *color) {
// add cell coloring rules here
// white: high concentration of growth hormone, black low concentration
double val = 1.-c->Chemical(0)/(1.+c->Chemical(0));
color->setRgbF(val, val, val);
}
void Tutorial2::CellHouseKeeping(CellBase *c) {
// add cell behavioral rules here
if (CellBase::NCells()==1)
// first cell expands unconditionally
c->EnlargeTargetArea(par->cell_expansion_rate);
else
c->EnlargeTargetArea(c->Chemical(0)*par->cell_expansion_rate);
if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
c->Divide();
}
}
void Tutorial2::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
// add biochemical transport rules here
double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) );
dchem_c1[0]+=phi;
dchem_c2[0]-=phi;
}
void Tutorial2::WallDynamics(Wall *w, double *dw1, double *dw2) {
// add biochemical networks for reactions occuring at walls here
}
void Tutorial2::CellDynamics(CellBase *c, double *dchem) {
// add biochemical networks for intracellular reactions here
if (c->CellType()==1) {
dchem[0] = par->leaf_tip_source;
}
}
Q_EXPORT_PLUGIN2(tutorial2, Tutorial2)
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