EI/VirtualLeaf Changeset - 413a4067bfff · Centrum Wiskunde & Informatica (CWI)

Changeset - 413a4067bfff

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0 17 19

Roeland Merks - 15 years ago 2010-06-03 18:40:26
roeland.merks@cwi.nl

Changed interface for model plugins to make usage of pointers and references consistent.
Added codes for tutorial belonging to VLeaf manuscript.
Something changed in modelcatalogue. I'm not sure what...

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial0/mymodel.cpp
added src/TutorialCode/Tutorial0/mymodel.h
added src/TutorialCode/Tutorial0/mymodel.pro
added src/TutorialCode/Tutorial1/mymodel.cpp
added src/TutorialCode/Tutorial1/mymodel.h
added src/TutorialCode/Tutorial1/mymodel.pro
added src/TutorialCode/Tutorial2/mymodel.cpp
added src/TutorialCode/Tutorial2/mymodel.h
added src/TutorialCode/Tutorial2/mymodel.pro
added src/TutorialCode/Tutorial3/mymodel.cpp
added src/TutorialCode/Tutorial3/mymodel.h
added src/TutorialCode/Tutorial3/mymodel.pro
added src/TutorialCode/Tutorial4/mymodel.cpp
added src/TutorialCode/Tutorial4/mymodel.h
added src/TutorialCode/Tutorial4/mymodel.pro
added src/TutorialCode/Tutorial5/mymodel.cpp
added src/TutorialCode/Tutorial5/mymodel.h
added src/TutorialCode/Tutorial5/mymodel.pro
added src/build_models/translate_plugin.pl
changed src/VirtualLeafpar.tmpl
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h

36 files changed with 1394 insertions and 72 deletions:

src/TutorialCode/Tutorial0/mymodel.cpp

src/TutorialCode/Tutorial0/mymodel.h

src/TutorialCode/Tutorial0/mymodel.pro

src/TutorialCode/Tutorial1/mymodel.cpp

src/TutorialCode/Tutorial1/mymodel.h

src/TutorialCode/Tutorial1/mymodel.pro

src/TutorialCode/Tutorial2/mymodel.cpp

src/TutorialCode/Tutorial2/mymodel.h

src/TutorialCode/Tutorial2/mymodel.pro

src/TutorialCode/Tutorial3/mymodel.cpp

src/TutorialCode/Tutorial3/mymodel.h

src/TutorialCode/Tutorial3/mymodel.pro

src/TutorialCode/Tutorial4/mymodel.cpp

src/TutorialCode/Tutorial4/mymodel.h

src/TutorialCode/Tutorial4/mymodel.pro

src/TutorialCode/Tutorial5/mymodel.cpp

120

src/TutorialCode/Tutorial5/mymodel.h

src/TutorialCode/Tutorial5/mymodel.pro

src/VirtualLeafpar.tmpl

src/build_models/auxingrowthplugin.cpp

src/build_models/auxingrowthplugin.h

src/build_models/meinhardtplugin.cpp

src/build_models/meinhardtplugin.h

src/build_models/plugin_auxingrowth.pro

src/build_models/plugin_leaf.pro

src/build_models/plugin_meinhardt.pro

src/build_models/plugin_test.pro

src/build_models/translate_plugin.pl

src/cell.cpp

src/cellbase.cpp

src/cellbase.h

src/libplugin.pro

src/mesh.cpp

src/mesh.h

src/modelcatalogue.cpp

src/simplugin.h

0 comments (0 inline, 0 general)

src/TutorialCode/Tutorial0/mymodel.cpp

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Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "My first model in VirtualLeaf" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial0/mymodel.h

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Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial0/mymodel.pro

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Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial1/mymodel.pro

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Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial2/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial2/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial2/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial3/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->DivideOverAxis(Vector(1,0,0));
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial3/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial3/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial4/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Growth, division, coloring" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	if (c->Area()/c->BaseArea()>1.8) { color->setNamedColor("blue"); }
 	else { color->setNamedColor("green"); }
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial4/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial4/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial5/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Growth hormones" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 1; }
 // To be executed after cell division
 void MyModel::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 MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	// white: high concentration of growth hormone, black low concentration
 	double val = c->Chemical(0)/(1.+c->Chemical(0));
 	color->setRgbF(val, val, val);
+}
 void MyModel::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 MyModel::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 MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::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(mymodel, MyModel)

src/TutorialCode/Tutorial5/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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 <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial5/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/VirtualLeafpar.tmpl

➞

Show inline comments

 title = Parameter values for The Virtual Leaf / title
 label = <b>Visualization</b> / label
 arrowcolor = white / string
 arrowsize = 100 / double
 textcolor = red / string
 cellnumsize = 1 / int
 nodenumsize = 1 / int
 node_mag = 1.0 / double
 outlinewidth = 1.0 / double
 cell_outline_color = forestgreen / string
-resize_stride = 10 / int
+resize_stride = 0 / int
 label = / label
 label = <b>Cell mechanics</b> / label
 T = 1.0 / double
 lambda_length = 100. / double
 lambda_celllength = 0. / double
 target_length = 60. / double
 cell_expansion_rate = 1. / double
 cell_div_expansion_rate = 0. / double
 auxin_dependent_growth = true / bool
 ode_accuracy = 1e-4 / double
 mc_stepsize = 0.4 / double
 mc_cell_stepsize = 0.2 / double
 energy_threshold = 1000. / double
 bend_lambda = 0. / double
 alignment_lambda = 0. / double
 rel_cell_div_threshold = 2. / double
 rel_perimeter_stiffness = 2 / double
 collapse_node_threshold = 0.05 / double
 morphogen_div_threshold = 0.2 / double
 morphogen_expansion_threshold = 0.01 / double
 copy_wall = true / bool
 label = / label
 label = <b>Auxin transport and PIN1 dynamics</b> / label
 source = 0. / double
 D = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 initval = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 k1 = 1. / double
 k2 = 0.3 / double
 r = 1. / double
 kr = 1. / double
 #k3 = 1 / double
 #k4 = 0.3 / double
 km = 1. / double
 Pi_tot = 1. / double
 transport = 0.036 / double
 ka = 1 / double
 # d = 1e-06 / double
 # e = 0.01 / double
 # f = 10 / double
 pin_prod = 0.001 / double
 pin_prod_in_epidermis = 0.1 / double
 pin_breakdown = 0.001 / double
 pin_breakdown_internal = 0.001 / double
 aux1prod = 0.001 / double
 aux1prodmeso = 0. / double
 aux1decay = 0.001 / double
 aux1decaymeso = 0.1 / double
 aux1transport = 0.036 / double
 aux_cons = 0. / double
 aux_breakdown = 0. / double
 kaux1 = 1 / double
 kap = 1 / double
 leaf_tip_source = 0.001 / double
 sam_efflux = 0.0001 / double
 sam_auxin = 10. / double
 # gf_prod = 1e-3 / double
 # gf_decay = 1e-3 / double
 sam_auxin_breakdown = 0 / double
 #label = / label
 #label = <b>miscellaneous</b> / label
 van3prod = 0.002 / double
 van3autokat = 0.1 / double
 van3sat = 10 / double
 k2van3 = 0.3 / double
 #glvprod = 0.0 / double
 #glvbreakdown = 0. / double
 label = / label
 label = <b>Integration parameters</b> / label
 dt = 0.1 / double
 rd_dt = 1.0 / double
 datadir = . / directory
 movie = false / bool
 nit = 100000 / int
 maxt = 1000. / double
 storage_stride = 10 / int
 xml_storage_stride = 500 / int
 rseed = -1 / int
 #label = / label
 #label = <b>Parameters for new chemical</b> / label
 #glvproduction = 0. / double
 #glvdecay = 0. / double
 #glvdiffthreshold = 0. / double
 label = / label
 label = <b>Meinhardt leaf venation model</b> / label
 constituous_expansion_limit = 16 / int
 vessel_inh_level = 1 / double
 vessel_expansion_rate = 0.25 / double
 d = 0. / double
 e = 0. / double
 f = 0. / double
 c = 0. / double
 mu = 0. / double
 nu = 0. / double
 rho0 = 0. / double
 rho1 = 0. / double
 c0 = 0. / double

src/build_models/auxingrowthplugin.cpp

➞

Show inline comments

 /*
+ *
  *  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 "auxingrowthplugin.h"
 #include "far_mem_5.h"
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
-void AuxinGrowthPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+void AuxinGrowthPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
 	// Auxin distributes between parent and daughter according to area
-	double area1 = daughter1.Area(), area2 = daughter2.Area();
+	double area1 = daughter1->Area(), area2 = daughter2->Area();
 	double tot_area = area1 + area2;
 	daughter1.SetChemical(0,daughter1.Chemical(0)*(area1/tot_area));
 	daughter2.SetChemical(0,daughter2.Chemical(0)*(area2/tot_area));
 	daughter1->SetChemical(0,daughter1->Chemical(0)*(area1/tot_area));
 	daughter2->SetChemical(0,daughter2->Chemical(0)*(area2/tot_area));
 	// After divisions, parent and daughter cells get a standard stock of PINs.
 	daughter1.SetChemical(1, par->initval[1]);
 	daughter2.SetChemical(1, par->initval[1]);
 	daughter1->SetChemical(1, par->initval[1]);
 	daughter2->SetChemical(1, par->initval[1]);
 	// Reset transporter values of parent and daughter
 	QList<WallBase *> walls;
 	foreach(WallBase *w, walls) {
-		w->setTransporter(&daughter1, 1, 0.);
 		w->setTransporter(daughter1, 1, 0.);
+	}
 	//daughter1.LoopWalls(Wall::setTransporter(&daughter1, 1, 0.));
 	/* for (list<Wall *>::const_iterator w=daughter2.walls.begin();
 		 w!=daughter2.walls.end();
 		 w++) {
 		// reset transporter value
 		(*w)->setTransporter(&daughter2, 1, 0.);
+	}
 	*/
+}
-void AuxinGrowthPlugin::SetCellColor(CellBase &c, QColor &color) {
+void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color) {
 	// Red: PIN1
 	// Green: Auxin
 	if (c.CellType()==1) color = QColor("Blue");
 	else color.setRgb(c.Chemical(1)/(1+c.Chemical(1)) * 255.,(c.Chemical(0)/(1+c.Chemical(0)) * 255.),/* (chem[2]/(1+chem[2]) *255.) */ 0);
 	if (c->CellType()==1) color->setNamedColor("Blue");
 	else color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),/* (chem[2]/(1+chem[2]) *255.) */ 0);
+}
-void AuxinGrowthPlugin::CellHouseKeeping(CellBase &c) {
+void AuxinGrowthPlugin::CellHouseKeeping(CellBase *c) {
 	if (c.Boundary()==CellBase::None) {
 		if (c.Area() > par->rel_cell_div_threshold * c.BaseArea() ) {
 			c.SetChemical(0,0);
 			c.Divide();
 	if (c->Boundary()==CellBase::None) {
 		if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 			c->SetChemical(0,0);
 			c->Divide();
+        }
 		if (c.Chemical(0)>0.6) {
 			c.SetCellType(1);
 		if (c->Chemical(0)>0.6) {
 			c->SetCellType(1);
+		}
 		// expand according to auxin concentration
-   		c.EnlargeTargetArea(par->auxin_dependent_growth?(c.Chemical(0)/(1.+c.Chemical(0)))*par->cell_expansion_rate:par->cell_expansion_rate);
+   		c->EnlargeTargetArea(par->auxin_dependent_growth?(c->Chemical(0)/(1.+c->Chemical(0)))*par->cell_expansion_rate:par->cell_expansion_rate);
+	}
+}
 void AuxinGrowthPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
 	// leaf edge is const source of auxin
     // (Neumann boundary condition: we specify the influx)
     if (w->C2()->BoundaryPolP()) {
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c1[0]+= aux_flux;
 			// dchem_c2 is undefined..!
 			return;
 		} else {
 			return;
+		}
+	}
 	if (w->C1()->BoundaryPolP()) {
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c2[0] += aux_flux;
 			// dchem_c1 is undefined...!
 			return;
 		} else {
 			if (w->AuxinSink()) {
 				// efflux into Shoot Apical meristem
 				// we assume all PINs are directed towards shoot apical meristem
 				dchem_c2[0] -= par->sam_efflux * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0));
 				return;
 			} else
 				return;
+		}
+    }
 	// Passive fluxes (Fick's law)
     // only auxin flux now
     // flux depends on edge length and concentration difference
     int c=0;
     double phi = w->Length() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );
     dchem_c1[c] += phi;
     dchem_c2[c] -= phi;
     // Active fluxes (PIN1 mediated transport)
     // (Transporters measured in moles, here)
     // efflux from cell 1 to cell 2
     double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) );
     // efflux from cell 2 to cell 1
     double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) );
     dchem_c1[0] += trans21 - trans12;
     dchem_c2[0] += trans12 - trans21;
+}
 void AuxinGrowthPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
     // Cells polarize available PIN1 to Shoot Apical Meristem
     if (w->C2()->BoundaryPolP()) {
 		if (w->AuxinSink()) {
 			dw1[0] = 0.; dw2[0] = 0.;
 			//dw1[2] = 0.; dw2[2] = 0.;
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated0
 			double nb_auxin = par->sam_auxin;
 			double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
 			dw1[1] = par->k1 * w->C1()->Chemical(1) * receptor_level /( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
 			dw2[1] = 0.;
 			return;
 		} else {
 			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
 			return;
+		}
+    }
     if (w->C1()->BoundaryPolP()) {
 		if (w->AuxinSink())  {
 			dw1[0] = 0.; dw2[0] = 0.;
 			//dw1[2] = 0.; dw2[2] = 0.;
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated
 			double nb_auxin = par->sam_auxin;
 			double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
 			dw2[1] = par->k1 * w->C2()->Chemical(1) * receptor_level /( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
 			dw1[1] = 0.;
 			return;
 		}  else {
 			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
 			return;
+		}
+    }
     // PIN1 localization at wall 1
     // Note: chemical 0 is Auxin (intracellular storage only)
     // Chemical 1 is PIN1 (walls and intracellular storage)
     //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
     // Note that Pij is measured in term of concentration (mol/L)
     // Pi in terms of quantity (mol)
     double dPijdt1=0., dPijdt2=0.;
     // normal cell
     double  auxin2 = w->C2()->Chemical(0);
     double receptor_level1 = auxin2 * par->r / (par->kr + auxin2);
     dPijdt1 =
 	// exocytosis regulated
     par->k1 * w->C1()->Chemical(1) * receptor_level1 / ( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
     double  auxin1 = w->C1()->Chemical(0);
     double receptor_level2 = auxin1 * par->r / (par->kr + auxin1);
     // normal cell
     dPijdt2 =
 	// exocytosis regulated
 	par->k1 * w->C2()->Chemical(1) * receptor_level2 / ( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
     /* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */
     dw1[0] = 0.; dw2[0] = 0.;
     //dw1[2] = 0.; dw2[2] = 0.;
     dw1[1] = dPijdt1;
     dw2[1] = dPijdt2;
+}
-double AuxinGrowthPlugin::complex_PijAj(CellBase &here, CellBase &nb, Wall &w) {
+double AuxinGrowthPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
 	// gives the amount of complex "auxinreceptor-Pin1"  at the wall (at QSS)
 	//return here.Chemical(1) * nb.Chemical(0) / ( par->km + here.Chemical(1));
-	double nb_aux = (nb.BoundaryPolP() && w.AuxinSink()) ? par->sam_auxin : nb.Chemical(0);
+	double nb_aux = (nb->BoundaryPolP() && w->AuxinSink()) ? par->sam_auxin : nb->Chemical(0);
 	double receptor_level = nb_aux * par->r / (par->kr + nb_aux);
-	return here.Chemical(1) * receptor_level / ( par->km + here.Chemical(1));
+	return here->Chemical(1) * receptor_level / ( par->km + here->Chemical(1));
+}
 void AuxinGrowthPlugin::CellDynamics(CellBase *c, double *dchem) {
 	// Note: Pi and Pij measured in numbers of molecules, not concentrations
 		double dPidt = 0.;
 		double sum_Pij = c->SumTransporters( 1 );
 		// exocytosis regulated:
 	dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &AuxinGrowthPlugin::complex_PijAj ) ) + par->k2 * sum_Pij;
 	/*for ( list<Wall *>::const_iterator w = c->walls.begin();
 		 w!=walls.end();
 		 w++) {
 		if ((*w)->C1() == c)
 			dPidt +=  complex_PijAj( (*w)->C1(), (*w)->C2(), *w );
 		else
 			dPidt +=  complex_PijAj( (*w)->C2(), (*w)->C1(), *w );
 	}*/
 	// production of PIN depends on auxin concentration
 	dPidt +=  (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
 	// no PIN production in SAM
 	if (c->Boundary() == CellBase::SAM) {
 			dchem[1]=0.;
 		dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);
 	} else {
 		dchem[1] = dPidt;
 		// source of auxin
 		dchem[0] = par->aux_cons - par->aux_breakdown * c->Chemical(0);
+	}
+}
 Q_EXPORT_PLUGIN2(auxingrowthplugin, AuxinGrowthPlugin)

src/build_models/auxingrowthplugin.h

➞

Show inline comments

 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #ifndef _AUXINGROWTHPLUGIN_H_
 #define _AUXINGROWTHPLUGIN_H_
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "../simplugin.h"
 class AuxinGrowthPlugin : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void) { return QString( "Auxin accumulation and growth" ); }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping (CellBase &c);
+	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2);
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color);
+	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void) { return 2; }
 private:
-	double complex_PijAj(CellBase &here, CellBase &nb, Wall &w);
+	double complex_PijAj(CellBase *here, CellBase *nb, Wall *w);
 };
 #endif

src/build_models/meinhardtplugin.cpp

➞

Show inline comments

 /*
+ *
  *  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 "../simplugin.h"
 #include "parameter.h"
 #include "warning.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "meinhardtplugin.h"
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
-void MeinhardtPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+void MeinhardtPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
+}
-void MeinhardtPlugin::SetCellColor(CellBase &c, QColor &color) {
+void MeinhardtPlugin::SetCellColor(CellBase *c, QColor *color) {
-	if (fpclassify(c.Chemical(0))==FP_NAN) {
+	if (fpclassify(c->Chemical(0))==FP_NAN) {
 		// somehow the function isnan doesn't work properly on my system... SuSE Linux
 		// 10.0 64-bits (isnan seems not be implemented using fpclassify).
 		MyWarning::warning("Whoops! Numerical instability!!");
-		color.setNamedColor("red");
+		color->setNamedColor("red");
 	} else {
 		double range_min = 0.;//, range_max = 1.;
-		if (c.Chemical(0)<range_min) {
+		if (c->Chemical(0)<range_min) {
 			MyWarning::warning("Whoops! Numerical instability!!");
-			color.setNamedColor("blue");
+			color->setNamedColor("blue");
 		} else {
-			color.setRgb(c.Chemical(1)/(1+c.Chemical(1)) * 255.,(c.Chemical(0)/(1+c.Chemical(0)) * 255.),(c.Chemical(3)/(1+c.Chemical(3)) *255.) );
+			color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
+		}
+	}
+}
-void MeinhardtPlugin::CellHouseKeeping(CellBase &c) {
+void MeinhardtPlugin::CellHouseKeeping(CellBase *c) {
 	if (c.Area() > par->rel_cell_div_threshold * c.BaseArea() ) {
 		c.Divide();
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 		c->Divide();
+	}
     // cell expansion is inhibited by substrate (chem 3)
 	if (!par->constituous_expansion_limit || c.NCells()<par->constituous_expansion_limit) {
 		c.EnlargeTargetArea(par->cell_expansion_rate );
 	if (!par->constituous_expansion_limit || c->NCells()<par->constituous_expansion_limit) {
 		c->EnlargeTargetArea(par->cell_expansion_rate );
 	} else {
-		if (c.Chemical(0)<0.5) {
+		if (c->Chemical(0)<0.5) {
 			double tmp;
-			c.EnlargeTargetArea((tmp=(1.-par->vessel_inh_level*c.Chemical(3))*par->cell_expansion_rate /* + c.Chemical(4)*/)<0?0:tmp);
+			c->EnlargeTargetArea((tmp=(1.-par->vessel_inh_level*c->Chemical(3))*par->cell_expansion_rate /* + c->Chemical(4)*/)<0?0:tmp);
 		} else {
-			c.EnlargeTargetArea(par->vessel_expansion_rate);
+			c->EnlargeTargetArea(par->vessel_expansion_rate);
+		}
+	}
+}
 void MeinhardtPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
 	// No flux boundaries for all chemicals, except activator: boundary is sink
   if (w->C1()->BoundaryPolP() || w->C2()->BoundaryPolP()) {
 		if (w->C1()->BoundaryPolP()) {
 			dchem_c2[1] -=  w->Length() * ( par->D[1] ) * ( w->C2()->Chemical(1) );
 			} else {
 			dchem_c1[1] -=  w->Length() * ( par->D[1] ) * ( w->C1()->Chemical(1) );
+			}
 		return;
+		}
     // Passive fluxes (Fick's law)
     for (int c=0;c<NChem();c++) {
 		double phi = w->Length() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );
 		dchem_c1[c] += phi;
 		dchem_c2[c] -= phi;
+	}
+}
 void MeinhardtPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
 	for (int c = 0;c<NChem();c++) {
 		dw1[c] = 0.; dw2[c] = 0.;
+    }
+}
 void MeinhardtPlugin::CellDynamics(CellBase *c, double *dchem) {
 	double Y = c->Chemical(0);
 	double A = c->Chemical(1);
 	double H = c->Chemical(2);
 	double S = c->Chemical(3);
 	//double expansin = c->Chemical(4);
     dchem[0] = ( par->d * A - par->e * Y + Y*Y/(1 + par->f * Y*Y ) );
 	dchem[1] = ( par->c * A*A*S/H - par->mu * A + par->rho0*Y );
 	dchem[2] = ( par->c * A*A*S - par->nu*H + par->rho1*Y );
 	dchem[3] = ( par->c0 - par->gamma*S - par->eps * Y * S );
 	//dchem[4] = ( -par->expansindecay * expansin );
 	//for (int i=0;i<4;i++) { cerr << "[ " << dchem[i] << " ]"; } cerr << endl;
 //	cerr << "Chemicals: "; for (int i=0;i<NChem();i++) { cerr << c->Chemical(i) << " "; } cerr << endl;
 // test:	dchem[0] = 0.01 * c->Chemical(0) * ( 1. - c->Chemical(0));
+}
 Q_EXPORT_PLUGIN2(meinhardtplugin, MeinhardtPlugin)

src/build_models/meinhardtplugin.h

➞

Show inline comments

 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #ifndef _MEINHARDTPLUGIN_H_
 #define _MEINHARDTPLUGIN_H_
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
+#include "../simplugin.h"
 class MeinhardtPlugin : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void) { return QString( "Meinhardt 1976, with growth" ); }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping (CellBase &c);
+	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2);
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color);
+	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void) { return 4; }
 };
 #endif

src/build_models/plugin_auxingrowth.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = auxingrowth
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_leaf.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = leaf
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_meinhardt.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = meinhardt
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_test.pro

➞

Show inline comments

+#
 # $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = test
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/translate_plugin.pl

➞

Show inline comments

@@ new file 100755 @@
 #!/usr/bin/perl
 $cfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $hfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $pfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $ocfname = $cfilename; $ocfname =~ s/\.cpp/_tl.cpp/g;
 $ohfname = $hfilename; $ohfname =~ s/\.h/_tl.h/g;
 $opfname = $pfilename; $opfname =~ s/\.pro/_tl.pro/g;
 print STDERR "Translating '$cfilename' to '$ocfname', '$hfilename' to '$ohfname', and '$pfilename' to '$opfname'\n";
 open cfile,"<$cfilename";
 open ocfile,">$ocfname";
 while (<cfile>) {
 	#s/$hfilename/$ohfname/g;
 	# translate function definitions
 	if (/[a-zA-Z0-9 ]*::OnDivide/) {
 		s/ParentInfo &parent_info/ParentInfo *parent_info/g;
 		s/CellBase &daughter1/CellBase *daughter1/g;
 		s/CellBase &daughter2/CellBase *daughter2/g;
+	}
 	if (/[a-zA-Z0-9 ]*::SetCellColor/) {
 		s/CellBase &c/CellBase *c/g;
 		s/QColor &color/QColor *color/g;
+	}
 	if (/[a-zA-Z0-9 ]*::CellHouseKeeping/) {
 		s/CellBase &c/CellBase *c/g;
+	}
 	# translate member function calls
 	s/\bparent_info\b\./parent_info->/g;
 	s/\bdaughter1\b\./daughter1->/g;
 	s/\bdaughter2\b\./daughter2->/g;
 	s/\bc\b\./c->/g;
 	s/\bcolor\b\./color->/g;
 	print ocfile;
+}
 open hfile,"<$hfilename";
 open ohfile,">$ohfname";
 while (<hfile>) {
 	if (/[ \t]*virtual[ \t]+void[ \t]+CellHouseKeeping/) {
 		s/CellBase &c/CellBase *c/g;
+	}
 	if (/[ \t]*virtual[ \t]+void[ \t]+OnDivide/) {
 		s/ParentInfo &parent_info/ParentInfo *parent_info/g;
 		s/CellBase &daughter1/CellBase *daughter1/g;
 		s/CellBase &daughter2/CellBase *daughter2/g;
+	}
 	if (/[ \t]*virtual[ \t]+void[ \t]+SetCellColor/) {
 		s/CellBase &c/CellBase *c/g;
 		s/QColor &color/QColor *color/g;
+	}
 	print ohfile;
+}
 open pfile,"<$pfilename";
 open opfile,">$opfname";
 while (<pfile>) {
 	s/\bplugin\b\.h/plugin_tl\.h/g;
 	s/\bplugin\b\.cpp/plugin_tl\.cpp/g;
 	print opfile;
+}
@@ \ No newline at end of file @@

src/cell.cpp

➞

Show inline comments

@@ @@ -322,192 +322,193 @@ void Cell::ConstructConnections(void) { @@
 bool Cell::DivideOverGivenLine(const Vector v1, const Vector v2, bool fix_cellwall, NodeSet *node_set ) {
 	if (dead) return false;
 	// check each edge for intersection with the line
 	ItList new_node_locations;
 	cerr << "Cell " << Index() << " is doing DivideOverGivenLine \n";
 	for (list<Node *>::iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
 		Vector v3 = *(*i);
 		list<Node *>::iterator nb=i;
 		nb++;
 		if (nb == nodes.end()) {
 			nb = nodes.begin();
+		}
 		Vector v4 = *(*nb);
 		double denominator =
 		(v4.y - v3.y)*(v2.x - v1.x) - (v4.x - v3.x)*(v2.y - v1.y);
 		double ua =
 		((v4.x - v3.x)*(v1.y - v3.y) - (v4.y - v3.y)*(v1.x -v3.x))/denominator;
 		double ub =
 		((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 		/* double intersec_x = v1.x + ua*(v2.x-v1.x);
 		 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 		//cerr << "Edge " << *i << " to " << *nb << ": ua = " << ua << ", ub = " << ub << ":  ";
 		// this construction with "TINY" should simulate open/closed interval <0,1]
 		if ( ( TINY < ua && ua < 1.+TINY ) && ( TINY < ub && ub < 1.+TINY ) ) {
 			// yes, intersection detected. Push the location to the list of iterators
 			new_node_locations.push_back(nb);
+		}
+	}
 	if (new_node_locations.size()<2) {
 		cerr << "Line does not intersect with two edges of Cell " << Index() << endl;
 		cerr << "new_node_locations.size() = " << new_node_locations.size() << endl;
 		return false;
+	}
 	ItList::iterator i = new_node_locations.begin();
 	list< Node *>::iterator j;
 	cerr << "-------------------------------\n";
 	cerr << "Location of new nodes: " << (**i)->Index() << " and ";
 	++i;
 	j = *i;
 	if (j==nodes.begin()) j=nodes.end(); j--;
 	cerr << (*j)->Index() << endl;
 	cerr << "-------------------------------\n";
 	if ( **new_node_locations.begin() == *j ) {
 		cerr << "Rejecting proposed division (cutting off zero area).\n";
 		return false;
+	}
 	DivideWalls(new_node_locations, v1, v2, fix_cellwall, node_set);
 	return true;
+}
 // Core division procedure
 void Cell::DivideWalls(ItList new_node_locations, const Vector from, const Vector to, bool fix_cellwall, NodeSet *node_set) {
 	if (dead) return;
 	bool boundary_touched_flag=false;
 	// Step 0: keep some data about the parent before dividing
 	ParentInfo parent_info;
 	parent_info.polarization = ReduceCellAndWalls<Vector>( PINdir );
 	parent_info.polarization.Normalise();
 	parent_info.PINmembrane = SumTransporters(1);
 	parent_info.PINendosome = Chemical(1);
 	//cerr << "Parent polarization before division: " << parent_info.polarization << endl;
 	// Step 1: create a daughter cell
 	Cell *daughter=m->AddCell(new Cell());
 	// Step 2: Copy the basics of parent cell to daughter
 	for (int i=0;i<NChem();i++) {
 		daughter->chem[i]=chem[i];
+	}
 	daughter->cell_type = cell_type;
 	//extern double auxin_account;
 	//auxin_account += daughter->chem[0];
 	for (int i=0;i<NChem();i++) {
 		daughter->new_chem[i]=new_chem[i];
+	}
 	daughter->boundary=boundary;
 	daughter->m=m;
 	daughter->target_area=target_area/2.;
 	target_area/=2;
 	daughter->cellvec=cellvec;
 //	daughter->BaseArea()  = base_area;
 	// Division currently only works for convex cells: i.e. if the division line
 	// intersects the cells at two points only.
 	if (new_node_locations.size()!=2) {
 		// Note: if you would add the possibility of dividing non-convex
 		// cells, remember to update the code below. There are some
 		// fixed-size arrays over there!
 		cerr << "Warning in Cell::Division: division of non-convex cells not fully implemented" << endl;
 		// Reject the daughter cell and decrement the amount of cells
 		// again. We can do this here because it is the last cell added.
 		// Never, ever try to fully erase a cell elsewhere, because we
 		// make heavy use of cell indices in this project; if you erase a
 		// Cell somewhere in the middle of Mesh::Cells the indices will
 		// get totally messed up...! (e.g. the indices used in Nodes::cells)
 		cerr << "new_node_locations.size() = " << new_node_locations.size() <<endl;
 		cerr << "daughter->index = " << daughter->index << endl;
 		cerr << "cells.size() = " << m->cells.size() << endl;
 		m->cells.pop_back();
 		Cell::NCells()--;
 		m->shuffled_cells.pop_back();
 		return;
+	}
 	// We can be sure we only need two positions here because divisions
 	// of non-convex cells are rejected above.
 	Vector new_node[2];
 	Node *new_node_ind[2];
 	int new_node_flag[2];
 	Edge div_edges[2];
 	int nnc=0;
 	Wall *div_wall[4];
 	double orig_length[2];
 	for (int i=0;i<4;i++) { div_wall[i]=0; orig_length[i/2] = 0.; }
 	// construct new Nodes at the intersection points
 	// unless they coincide with existing points
 	for ( ItList::const_iterator i=new_node_locations.begin();
 		 i!=new_node_locations.end();
 		 i++) {
 		// intersection between division axis
 		// and line from this node to its predecessor
 		// method used: http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/
 		Vector v1 = from;
 		Vector v2 = to;
 		Vector v3 = *(**i);
 		// get previous node
 		list<Node *>::iterator nb=*i;
 		if (nb == nodes.begin()) {
 			nb = nodes.end();
+		}
 		nb--;
 		Vector v4=*( *nb );
 		double denominator =
 		(v4.y - v3.y)*(v2.x - v1.x) - (v4.x - v3.x)*(v2.y - v1.y);
 		double ua =
 		((v4.x - v3.x)*(v1.y - v3.y) - (v4.y - v3.y)*(v1.x -v3.x))/denominator;
 		double intersec_x = v1.x + ua*(v2.x-v1.x);
 		double intersec_y = v1.y + ua*(v2.y-v1.y);
 		// construct a new node at intersec
 		// we construct a vector temporarily,
 		// until we are sure we are going to keep the node...
 		// Node count is damaged if we construct superfluous nodes
 		Vector *n=new Vector(intersec_x,intersec_y,0);
@@ @@ -1000,193 +1001,193 @@ void Cell::DivideWalls(ItList new_node_l @@
 	// optionally add the new node to the nodeset (passed by pointer)
 	// (in this way we can move the NodeSet as a whole; useful for a fixed cutting line)
 	if (node_set) {
 		node_set->AddNode( new_node_ind[1] );
+	}
 	// move the new nodes to the parent
 	nodes.clear();
 	copy( new_nodes_parent.begin(),
 		 new_nodes_parent.end(),
 		 back_inserter(nodes) );
 	// Repair cell lists of Nodes, and node connectivities
 	ConstructConnections();
 	daughter->ConstructConnections();
 	if (boundary_touched_flag) {
 		m->boundary_polygon->ConstructConnections();
+	}
 	// collecting neighbors of divided cell
 	list<CellBase *> broken_neighbors;
 	// this cell's old neighbors
 	copy(neighbors.begin(), neighbors.end(), back_inserter(broken_neighbors) );
 	// this cell
 	broken_neighbors.push_back(this);
 	// its daughter
 	broken_neighbors.push_back(daughter);
 	// Recalculate area of parent and daughter
 	area = CalcArea();
 	daughter->area = daughter->CalcArea();
 	SetIntegrals();
 	daughter->SetIntegrals();
 	// Add a "Cell Wall" for diffusion algorithms
 	Wall *wall = new Wall( new_node_ind[0], new_node_ind[1], this, daughter );
 	AddWall( wall );
 	daughter->AddWall( wall );
 	//cerr << "Correct walls of cell " << Index() << " and daughter " << daughter->Index() << endl;
 	// Move Walls to daughter cell
 	list <Wall *> copy_walls = walls;
 	for (list<Wall *>::iterator w = copy_walls.begin();
 		 w!=copy_walls.end();
 		 w++) {
 		//cerr << "Doing wall, before:  " << **w << endl;
 		//  checks the nodes of the wall and gives it away if appropriate
 		(*w)->CorrectWall ( );
 		//cerr << "and after: " << **w << endl;
+	}
 	// Correct tranporterconcentrations of divided walls
 	for (int i=0;i<4;i++) {
 		if (div_wall[i]) {
 			div_wall[i]->SetLength();
 			div_wall[i]->CorrectTransporters(orig_length[i/2]);
+		}
+	}
 	//neighbors.push_back( daughter );
 	//daughter->neighbors.push_back( this );
 	//cerr << "Cell " << index << " has been dividing, and gave birth to Cell " << daughter->index << endl;
 	// now reconstruct neighbor list for all "broken" neighbors
 	for (list<CellBase *>::iterator i=broken_neighbors.begin();
 		 i!=broken_neighbors.end();i++) {
 		((Cell *)(*i))->ConstructNeighborList();
+	}
 	ConstructNeighborList();
 	daughter->ConstructNeighborList();
-	m->plugin->OnDivide(parent_info,*daughter, *this);
+	m->plugin->OnDivide(&parent_info, daughter, this);
 	// wall->OnWallInsert();
 	//daughter->OnDivide();
 	daughter->div_counter=(++div_counter);
+}
 // Move the whole cell
 void Cell::Move(const Vector T) {
     for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
 		*(*i)+=T;
+    }
+}
 double Cell::Displace(double dx, double dy, double dh) {
 	// Displace whole cell, add resulting energy to dh,
 	// and accept displacement if energetically favorable
 	//
 	// Method is called if a "fixed" node is displaced
 	// Warning: length constraint not yet  CORRECTLY implemented for this function
 	// Attempt to move this cell in a random direction
 	//  Vector movement(par.mc_cell_stepsize*(RANDOM()-0.5),par.mc_cell_stepsize*(RANDOM()-0.5),0);
 	dh=0;
 	Vector movement(dx,dy,0);
 	vector< pair<Node *, Node *> > length_edges;
 	vector<double> cellareas;
 	cellareas.reserve(neighbors.size());
 	// for the length constraint, collect all edges to this cell's nodes,
 	// which are not part of the cell
 	// the length of these edges will change
 	double old_length=0.;
 	for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
 		//if ((*i)->Fixed()) return; // commented out 01/12/05
 		for (list<Neighbor>::const_iterator n=(*i)->owners.begin();
 			 n!=(*i)->owners.end();
 			 n++) {
 			if (n->getCell()!=this) {
 				//if (!(m->getNode(n->nb1).Fixed() && m->getNode(n->nb2).Fixed())) {
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb1) );
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb2) );
 				old_length +=
 				DSQR(Node::target_length-(*(*i)-*(n->nb1)).Norm())+
 				DSQR(Node::target_length-(*(*i)-*(n->nb2)).Norm());
 				//}
+			}
+		}
+	}
 	// calculate area energy difference of neighboring cells
 	// (this cells' shape remains unchanged)
 	double old_area_energy=0., old_length_energy=0.;
 	for (list<CellBase *>::const_iterator i=neighbors.begin();
 		 i!=neighbors.end();
 		 i++) {
 		old_area_energy += DSQR((*i)->Area()-(*i)->TargetArea());
 		old_length_energy += DSQR((*i)->Length()-(*i)->TargetLength());
+	}
 	Move(movement);
 	double new_area_energy=0., new_length_energy=0.;
 	for (list<CellBase *>::const_iterator i=neighbors.begin();
 		 i!=neighbors.end();
 		 i++) {
 		cellareas.push_back((*i)->CalcArea());
 		new_area_energy += DSQR(cellareas.back()-(*i)->TargetArea());
 		new_length_energy += DSQR((*i)->CalcLength()-(*i)->TargetLength());
+	}
 	double new_length=0;
 	for ( vector< pair< Node *, Node * > >::const_iterator e = length_edges.begin();
 		 e != length_edges.end();
 		 e++) {
 		new_length +=  DSQR(Node::target_length-
 							(*(e->first)-*(e->second)).Norm());
+	}
 	dh += (new_area_energy - old_area_energy) + (new_length_energy - old_length_energy) * lambda_celllength +
@@ @@ -1567,193 +1568,193 @@ void Cell::ConstructWalls(void) { @@
 void BoundaryPolygon::Draw(QGraphicsScene *c, QString tooltip) {
 	// Draw the BoundaryPolygon on a QCanvas object
 	CellItem* p = new CellItem(this, c);
 	QPolygonF pa(nodes.size());
 	int cc=0;
 	for (list<Node *>::const_iterator n=nodes.begin();
 		 n!=nodes.end();
 		 n++) {
 		Node *i=*n;
 		pa[cc++] = QPoint((int)((Offset().x+i->x)*Factor()),
 						  (int)((Offset().y+i->y)*Factor()) );
+	}
 	p->setPolygon(pa);
 	p->setPen(par.outlinewidth>=0?QPen( QColor(par.cell_outline_color),par.outlinewidth):QPen(Qt::NoPen));
 	p->setBrush( Qt::NoBrush );
 	p->setZValue(1);
 	if (!tooltip.isEmpty())
 		p->setToolTip(tooltip);
 	p->show();
+}
 void Cell::Flux(double *flux, double *D)  {
 	// loop over cell edges
 	for (int c=0;c<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<NChem();c++) {
 			double phi = (*i)->length * ( D[c] ) * ( ((Cell *)(*i)->c2)->chem[c] - chem[c] );
 			if ((*i)->c1!=this) {
 				cerr << "Warning, bad cells boundary: " << (*i)->c1->Index() << ", " << index << endl;
+			}
 			flux[c] += phi;
+		}
+	}
+}
 // graphics stuff, not compiled for batch versions
 #ifdef QTGRAPHICS
 #include "canvas.h"
 void Cell::Draw(QGraphicsScene *c, QString tooltip) {
 	// Draw the cell on a QCanvas object
 	if (DeadP()) {
 		cerr << "Cell " << index << " not drawn, because dead.\n";
 		return;
+	}
 	CellItem* p = new CellItem(this, c);
 	QPolygonF pa(nodes.size());
 	int cc=0;
 	for (list<Node *>::const_iterator n=nodes.begin();
 		 n!=nodes.end();
 		 n++) {
 		Node *i=*n;
 		pa[cc++] = QPoint((int)((offset[0]+i->x)*factor),
 						  (int)((offset[1]+i->y)*factor) );
+	}
 	QColor cell_color;
-	m->plugin->SetCellColor(*this,cell_color);
+	m->plugin->SetCellColor(this,&cell_color);
 	p->setPolygon(pa);
 	p->setPen(par.outlinewidth>=0?QPen( QColor(par.cell_outline_color),par.outlinewidth):QPen(Qt::NoPen));
 	p->setBrush( cell_color );
 	p->setZValue(1);
 	if (!tooltip.isEmpty())
 		p->setToolTip(tooltip);
 	p->show();
+}
 void Cell::DrawCenter(QGraphicsScene *c) const {
   // Maginfication derived similarly to that in nodeitem.cpp
   // Why not use Cell::Magnification()?
   const double mag = par.node_mag;
 	// construct an ellipse
   QGraphicsEllipseItem *disk = new QGraphicsEllipseItem ( -1*mag, -1*mag, 2*mag, 2*mag, 0, c );
 	disk->setBrush( QColor("forest green") );
 	disk->setZValue(5);
 	disk->show();
 	Vector centroid=Centroid();
 	disk -> setPos((offset[0]+centroid.x)*factor,(offset[1]+centroid.y)*factor);
+}
 void Cell::DrawNodes(QGraphicsScene *c) const {
 	for (list<Node *>::const_iterator n=nodes.begin();
 		 n!=nodes.end();
 		 n++) {
 		Node *i=*n;
 		//QCanvasEllipse *item = new QCanvasEllipse( 10, 10, c);
 		NodeItem *item = new NodeItem ( &(*i), c );
 		//QGraphicsRectItem *item = new QGraphicsRectItem(-50, -50, 50, 50, 0, c);
 		//disk->setBrush( QColor("IndianRed") );
 		/*if (i->sam) {
 		 item->setBrush( purple );
 		 } else {
 		 if (i->boundary) {
 		 item->setBrush( deep_sky_blue );
+		 }
 		 else {
 		 item->setBrush( indian_red );
+		 }
 		 }*/
 		item->setColor();
 		/*(if (item->getNode().DeadP()) {
 		 item->setBrush( QBrush (Qt::Dense6Pattern) );
 		 }*/
 		item->setZValue(5);
 		item->show();
 		item ->setPos(((offset[0]+i->x)*factor),
 					  ((offset[1]+i->y)*factor) );
+	}
+}
 void Cell::DrawIndex(QGraphicsScene *c) const {
 	//  stringstream text;
 	//     text << index;
 	//     Vector centroid = Centroid();
 	//     QCanvasText *number = new QCanvasText ( QString (text.str()), c );
 	//     number->setColor( QColor(par.textcolor) );
 	//     number->setZ(20);
 	//     number->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
 	//     number->show();
 	//     number -> move((int)((offset[0]+centroid.x)*factor),
 	// 		   (int)((offset[1]+centroid.y)*factor) );
 	DrawText( c, QString("%1").arg(index));
+}
 // Draw any text in the cell's center
 void Cell::DrawText(QGraphicsScene *c, const QString &text) const {
 	Vector centroid = Centroid();
 	QGraphicsSimpleTextItem *ctext = new QGraphicsSimpleTextItem ( text, 0, c );
 	ctext->setPen( QPen(QColor(par.textcolor)) );
 	ctext->setZValue(20);
 	ctext->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
 	//ctext->setTextFlags(Qt::AlignCenter);
 	ctext->show();
 	ctext ->setPos(((offset[0]+centroid.x)*factor),
 				   ((offset[1]+centroid.y)*factor) );
+}
 void Cell::DrawAxis(QGraphicsScene *c) const {

src/cellbase.cpp

➞

Show inline comments

@@ @@ -8,310 +8,313 @@ @@
  *  (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 <cmath>
 #include <string>
 #include <sstream>
 #include <vector>
 #include <algorithm>
 #include <functional>
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>
 #include <qpainter.h>
 #include <qcolor.h>
 #include <qfont.h>
 #include <qwidget.h>
 //Added by qt3to4:
 #include <Q3PointArray>
 #include <fstream>
 #include "nodeitem.h"
 #include "cellitem.h"
 #include "qcanvasarrow.h"
 #endif
 #include "nodeset.h"
 //#include "cond_operator.h"
 #include "cellbase.h"
 //#include "node.h"
 #include "wall.h"
 #include "random.h"
 #include "parameter.h"
 #include "mesh.h"
 #include "sqr.h"
 #include "tiny.h"
 static const std::string _module_id("$Id$");
 extern Parameter par;
 const char* CellBase::boundary_type_names[4] = {"None", "NoFlux", "SourceSink", "SAM"};
 // These statics have moved to class "CellsStaticDatamembers"
 //double CellBase::static_base_area = 0.;
 //int CellBase::ncells=0;
 //int CellBase::NChem()=0;
 #ifndef VLEAFPLUGIN
 CellsStaticDatamembers *CellBase::static_data_members = new CellsStaticDatamembers();
 #else
 CellsStaticDatamembers *CellBase::static_data_members = 0;
 #endif
 CellBase::CellBase(QObject *parent) :
 QObject(parent),
 Vector()
+{
 	chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		chem[i]=0.;
+	}
 	new_chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		new_chem[i]=0.;
+	}
 	boundary=None;
 	index=(NCells()++);
 	area=0.;
 	target_area=1;
 	target_length=0; //par.target_length;
 	lambda_celllength = 0; //par.lambda_celllength;
 	intgrl_xx=0.; intgrl_xy=0.; intgrl_yy=0.;
 	intgrl_x=0.; intgrl_y=0.;
 	source = false;
 	source_conc = 0.;
 	source_chem = 0;
 	at_boundary=false;
 	fixed = false;
 	pin_fixed = false;
 	stiffness = 0;
 	marked = false;
 	dead = false;
 	div_counter=0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
 CellBase::CellBase(double x,double y,double z) : QObject(), Vector(x,y,z)
+{
 #ifndef VLEAFPLUGIN
 	if (static_data_members == 0) {
 		static_data_members = new CellsStaticDatamembers();
+	}
 #endif
 	chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		chem[i]=0.;
+	}
 	new_chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		new_chem[i]=0.;
+	}
 	boundary=None;
 	area=0.;
 	target_area=1;
 	target_length=0; //par.target_length;
 	lambda_celllength=0; // par.lambda_celllength;
 	index=(NCells()++);
 	intgrl_xx=0.; intgrl_xy=0.; intgrl_yy=0.;
 	intgrl_x=0.; intgrl_y=0.;
 	source = false;
 	fixed = false;
 	at_boundary=false;
 	pin_fixed = false;
 	stiffness = 0;
 	marked=false;
 	dead  = false;
 	div_counter = 0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
 CellBase::CellBase(const CellBase &src) :  Vector(src), QObject()
+{
 	chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		chem[i]=src.chem[i];
+	}
 	new_chem=new double[NChem()];
 	for (int i=0;i<NChem();i++) {
 		new_chem[i]=src.new_chem[i];
+	}
 	boundary=src.boundary;
 	area=src.area;
 	target_length=src.target_length;
 	lambda_celllength=src.lambda_celllength;
 	intgrl_xx=src.intgrl_xx; intgrl_xy=src.intgrl_xy; intgrl_yy=src.intgrl_yy;
 	intgrl_x=src.intgrl_x; intgrl_y=src.intgrl_y;
 	target_area=src.target_area;
 	index=src.index;
 	nodes=src.nodes;
 	neighbors=src.neighbors;
 	walls=src.walls;
 	source = src.source;
 	fixed = src.fixed;
 	source_conc = src.source_conc;
 	source_chem = src.source_chem;
 	cellvec = src.cellvec;
 	at_boundary=src.at_boundary;
 	pin_fixed = src.pin_fixed;
 	stiffness = src.stiffness;
 	marked = src.marked;
 	dead = src.dead;
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
-	</i>
+	division_axis = src.division_axis;
+}
 CellBase CellBase::operator=(const CellBase &src) {
 	Vector::operator=(src);
 	//  QObject::operator=(src);
 	for (int i=0;i<NChem();i++) {
 		chem[i]=src.chem[i];
+	}
 	for (int i=0;i<NChem();i++) {
 		new_chem[i]=src.chem[i];
+	}
 	boundary=src.boundary;
 	area=src.area;
 	intgrl_xx=src.intgrl_xx; intgrl_xy=src.intgrl_xy; intgrl_yy=src.intgrl_yy;
 	intgrl_x=src.intgrl_x; intgrl_y=src.intgrl_y;
 	target_area=src.target_area;
 	target_length=src.target_length;
 	lambda_celllength=src.lambda_celllength;
 	index=src.index;
 	nodes=src.nodes;
 	neighbors=src.neighbors;
 	walls=src.walls;
 	source = src.source;
 	fixed = src.fixed;
 	source_conc = src.source_conc;
 	source_chem = src.source_chem;
 	cellvec = src.cellvec;
 	at_boundary=src.at_boundary;
 	pin_fixed = src.pin_fixed;
 	stiffness = src.stiffness;
 	marked = src.marked;
 	dead = src.dead;
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
 	division_axis = src.division_axis;
 	return *this;
+}
 void CellBase::SetChemical(int c, double conc) {
 	if (c>=NChem()) {
 		stringstream error;
 		error << "SetChemical: value c = " << c << " is out of range\n";
 		throw error.str().c_str();
+	}
 	chem[c]=conc;
+}
 ostream &CellBase::print(ostream &os) const {
 	os << "[ index = " << index << " {" << x << ", " << y << ", " << z << "}: {";
 	for (int i=0;i<NChem()-1;i++) {
 		os << chem[i] << ", ";
+	}
 	os << chem[NChem()-1] << " } ]";
 	os << endl << "Nodelist = { " << endl;
 	for (list<Node *>::const_iterator i =  nodes.begin(); i!=nodes.end(); i++) {
 		os << (*i)->Index() << "( " << *i << ") ";
+	}
 	os << " } ";
 	for (list<Wall *>::const_iterator i =  walls.begin(); i!=walls.end(); i++) {
 		(*i)->print(os);
 		os << ", ";
+	}
 	os << endl;
 	os << " [ area = " << area << " ]";
 	os << " [ walls = ";
 	for (list<Wall *>::const_iterator i= walls.begin();
 		 i!=walls.end();
 		 i++) {
 		os << (*i)->n1->Index() << " -> " << (*i)->n2->Index() << ", " <<  (*i)->c1->Index() << " | " << (*i)->c2->Index() << ", ";
+	}
 	os << " ] ";
 	os << "div_counter = " << div_counter << endl;
 	os << "cell_type = " << cell_type << endl;
 	os << endl;
 	return os;
+}
 ostream &operator<<(ostream &os, const CellBase &c) {
 	c.print(os);
 	return os;
+}
 double CellBase::CalcArea(void) const {
 	double loc_area=0.;
 	for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=(nodes.end());
 		 i++) {
 		list<Node *>::const_iterator i_plus_1=i; i_plus_1++;
 		if (i_plus_1==nodes.end())
 			i_plus_1=nodes.begin();
 		loc_area+= (*i)->x * (*i_plus_1)->y;
 		loc_area-= (*i_plus_1)->x * (*i)->y;
+	}
 	// http://technology.niagarac.on.ca/courses/ctec1335/docs/arrays2.pdf
 	//return loc_area/2.0;
 	return fabs(loc_area)/2.0;
+}
 Vector CellBase::Centroid(void) const {
 	double area=0.;
 	double integral_x_dxdy=0.,integral_y_dxdy=0.;
 	for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=(nodes.end());
 		 i++) {
 		list<Node *>::const_iterator i_plus_1=i; i_plus_1++;
 		if (i_plus_1==nodes.end())
 			i_plus_1=nodes.begin();
 		area+= (*i)->x * (*i_plus_1)->y;
 		area-= (*i_plus_1)->x * (*i)->y;
 		integral_x_dxdy+=

src/cellbase.h

➞

Show inline comments

@@ @@ -3,486 +3,495 @@ @@
  *  $Id$
+ *
  *  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.
+ *
  */
 // CellBase derives from Vector, where Vector is simply used as a Vertex
 #ifndef _CELLBASE_H_
 #define _CELLBASE_H_
 #include <list>
 #include <vector>
 #include <iostream>
 #include <QString>
 #include <QDebug>
 #include "vector.h"
 #include "parameter.h"
 #include "wall.h"
 #include "warning.h"
 #include "assert.h"
 extern Parameter par;
 using namespace std;
 class Mesh;
 class Node;
 class CellBase;
 class NodeSet;
 struct ParentInfo {
 	Vector polarization;
 	double PINmembrane;
 	double PINendosome;
 };
 // We need a little trick here, to make sure the plugin and the main application will see the same static datamembers
 // otherwise each have their own instantation.
 // My solution is as follow. I collect all original statics in a class. The main application instantiates it and
 // has a static pointer to it. After loading the plugin I set a static pointer to the same class
 class CellsStaticDatamembers {
 public:
 	CellsStaticDatamembers(void) {
 		ncells = 0;
 		nchem = 0;
 		base_area = 0.;
 		cerr << "Constructor of CellsStaticDatamembers\n";
+	}
 	~CellsStaticDatamembers() {
 		cerr << "Oops! Desctructor of CellsStaticDatamembers called\n";
+	}
 	int ncells;
 	int nchem;
 	double base_area;
 };
 class CellBase :  public QObject, public Vector
+{
 	Q_OBJECT
 	friend class Mesh;
 	friend class CellInfo;
 	friend class Node;
 	friend class WallBase;
 	friend class SimPluginInterface;
  public:
 	CellBase(QObject *parent=0);
 	CellBase(double x,double y,double z=0); // constructor
   virtual ~CellBase() {
 	  delete[] chem;
 	  delete[] new_chem;
 	  if (division_axis) delete division_axis;
 	  //cerr << "CellBase " << index << " is dying. " << endl;
+  }
 	CellBase(const CellBase &src); // copy constructor
 	virtual bool BoundaryPolP(void) const { return false; }
 	//  CellBase(const Vector &src); // not allowed (we cannot know to which mesh
 	/// the CellBase will belong...)
     CellBase operator=(const CellBase &src); // assignment operator
     CellBase operator=(const Vector &src);
     void SetChemical(int chem, double conc);
     inline void SetNewChem(int chem, double conc) {
       new_chem[chem] = conc;
+    }
     void SetSource(int chem, double conc) {
       source=true;
       source_chem = chem;
       source_conc = conc;
+	}
     void UnfixNodes(void);
     void FixNodes(void);
     void UnsetSource(void) {
       source = false;
+    }
 	inline bool Source(void) { return source; }
     enum boundary_type {None, Noflux, SourceSink, SAM};
     static const char * boundary_type_names[4];
     inline const char *BoundaryStr(void) { return boundary_type_names[boundary]; }
     ostream &print(ostream &os) const;
     inline double Chemical(int c) const { // returns the value of chemical c
     #ifdef _undefined_
       qDebug() << endl << "Entering cellbase::chemical(" << c << "), and nchem is: " << NChem() << "." << endl;
     #endif
       int nchem = NChem();
       #ifdef _undefined_
       if ((c<0) || (c>=nchem))
 	MyWarning::warning("CellBase::Chemical says: index c is: %d, but nchem is: %d. Merely return zero", c, nchem);
       #endif
       return ((c<0) || (c>=nchem)) ? 0 : chem[c];
+    }
     //void print_nblist(void) const;
     boundary_type SetBoundary(boundary_type bound) {
       if (bound!=None) {
 	//area=0.;
 	//length=0.;
+      }
       return boundary=bound;
+    }
     boundary_type ResetBoundary(void) {
       return boundary=None;
+    }
     boundary_type Boundary(void) const {
       return boundary;
+    }
     static int &NChem(void) {
       return static_data_members->nchem;
+    }
     double CalcArea(void) const;
     double RecalcArea(void) {
       return area = CalcArea();
+    }
     Vector Centroid(void) const;
     void SetIntegrals(void) const;
     double Length(Vector *long_axis = 0, double *width = 0) const;
     double CalcLength(Vector *long_axis = 0, double *width = 0) const;
     inline int Index(void) const {
       return index;
+    }
     void SetTargetArea(double tar_ar) {
       target_area=tar_ar;
+    }
     inline void SetTargetLength(double tar_l) {
       target_length=tar_l;
+    }
     inline void SetLambdaLength(double lambda_length) {
       lambda_celllength = lambda_length;
+    }
     inline double TargetArea(void) {
       return target_area;
+    }
     inline void SetStiffness(double stiff) {
       stiffness = stiff;
+    }
     inline double Stiffness(void) {
       return stiffness;
+    }
     inline double EnlargeTargetArea(double da) {
       return target_area+=da;
+    }
     inline double Area(void) const {
       return area;
+    }
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
 	inline void DivideOverAxis(const Vector &v) {
 		division_axis = new Vector(v);
 		flag_for_divide = true;
+	}
     //Vector Strain(void) const;
     inline double Circumference(void) const {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum +=  (*w)->Length();
+      }
       return sum;
+    }
 	QList<WallBase *> getWalls(void) {
 		QList<WallBase *> wall_list;
 		for (list<Wall *>::iterator i=walls.begin();
 			 i!=walls.end();
 			 i++) {
 			wall_list << *i;
+		}
 		return wall_list;
+	}
   //  void XFigPrint(std::ostream &os) const;
     void Dump(ostream &os) const;
 	QString printednodelist(void);
    // void OnDivide(ParentInfo &parent_info, CellBase &daughter);
     inline bool DeadP(void) { return dead; }
     inline void MarkDead(void) { dead  = true; }
 	static double &BaseArea(void) {
 		return static_data_members->base_area;
+	}
     void CheckForDivision(void);
     // write flux from neighboring cells into "flux"
     void Flux(double *flux, double *D);
     inline bool FixedP(void) { return fixed; }
     inline bool Fix(void) {  FixNodes(); return (fixed=true); }
     inline bool Unfix(void) { UnfixNodes(); return (fixed=false);}
     inline void setCellVec(Vector cv) { cellvec = cv; }
 	bool AtBoundaryP(void) const;
     static inline int &NCells(void) {
       return static_data_members->ncells;
+    }
     inline void Mark(void) {
       marked=true;
+    }
     inline void Unmark(void) {
       marked=false;
+    }
     inline bool Marked(void) const {
       return marked;
+    }
 	//! Returns the sum of chemical "chem" of this CellBase's neighbors
     double SumChemicalsOfNeighbors(int chem) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum +=  (*w)->Length() * ( (*w)->c1!=this ? (*w)->c1->Chemical(chem) : (*w)->c2->Chemical(chem) );
+      }
       return sum;
+    }
     //! Generalization of the previous member function
     template<class P, class Op> P ReduceNeighbors(Op f) {
       P sum=0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->c1 != this ? f( *((*w)->c1) ) : f ( *((*w)->c2) );
+      }
       return sum;
+    }
     //! The same, but now for the walls
     template<class P, class Op> P ReduceWalls(Op f, P sum) {
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += f( **w );
+      }
       return sum;
+    }
     //! The same, but now for the walls AND neighbors
     template<class P, class Op> P ReduceCellAndWalls(Op f) {
       P sum = 0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->c1 == this ?
 	  f( *((*w)->c1), *((*w)->c2), **w ) :
 	  f( *((*w)->c2), *((*w)->c1), **w );
 	sum += ((*w)->c1 == this) ?
 	  f( ((*w)->c1), ((*w)->c2), *w ) :
 	  f( ((*w)->c2), ((*w)->c1), *w );
+      }
       return sum;
+    }
 	/* template<class Op> void LoopWalls(Op f) {
 		for (list<Wall *>::const_iterator w=walls.begin();
 			 w!=walls.end();
 			 w++) {
 			( **w)->f;
+		}
 	}*/
     //! Sum transporters at this CellBase's side of the walls
     double SumTransporters(int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, ch);
+      }
       return sum;
+    }
     inline int NumberOfDivisions(void) { return div_counter; }
     //! Sum transporters at this CellBase's side of the walls
     double SumLengthTransporters(int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, ch) * (*w)->Length();
+      }
       return sum;
+    }
     double SumLengthTransportersChemical(int trch, int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, trch) * ( (*w)->c1!=this ? (*w)->c1->Chemical(ch) : (*w)->c2->Chemical(ch) );
+      }
       return sum;
+    }
 	inline int CellType(void) const { return cell_type; }
 	inline void SetCellType(int ct) { cell_type = ct; }
 	static void SetNChem(int new_nchem) {
 		if (NCells()) {
 			MyWarning::error("CellBase::SetNChem says: not permitted, call SetNChem after deleting all cells.");
 		} else {
 			NChem() = new_nchem;
+		}
+	}
 	inline double TargetLength() const { return target_length; }
 	static inline CellsStaticDatamembers *GetStaticDataMemberPointer(void) { return static_data_members; }
 protected:
 	// (define a list of Node* iterators)
 	typedef list < list<Node *>::iterator > ItList;
     int index;
 	inline void SetChemToNewchem(void) {
 		for (int c=0;c<CellBase::NChem();c++) {
 			chem[c]=new_chem[c];
+		}
+    }
     inline void SetNewChemToChem(void) {
 		for (int c=0;c<CellBase::NChem();c++) {
 			new_chem[c]=chem[c];
+		}
+    }
 	inline double NewChem(int c) const { return new_chem[c]; }
  protected:
     list<Node *> nodes;
     void ConstructNeighborList(void);
 	long wall_list_index (Wall *elem) const;
     // DATA MEMBERS
     // list of nodes, in clockwise order
     // a (non-ordered) list of neighboring cells (actually I think the
     // introduction of ConstructWalls() has made these
     // lists ordered (clockwise), but I am not yet 100% sure...).
     list<CellBase *> neighbors;
     list<Wall *> walls;
     double *chem;
     double *new_chem;
     boundary_type boundary;
     mutable double area;
     double target_area;
     double target_length;
     double lambda_celllength;
     double stiffness; // stiffness like in Hogeweg (2000)
     bool fixed;
     bool pin_fixed;
     bool at_boundary;
     bool dead;
 	bool flag_for_divide;
 	Vector *division_axis;
 	int cell_type;
     //double length;
     //Vector meanflux;
     //int valence;
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
     bool source;
     Vector cellvec;
 	// STATIC DATAMEMBERS MOVED TO CLASS
 	static CellsStaticDatamembers *static_data_members;
 	double source_conc;
     int source_chem;
     // PRIVATE MEMBER FUNCTIONS
     inline static void ClearNCells(void) {
       NCells()=0;
+    }
     bool marked;
     int div_counter;
 };
 ostream &operator<<(ostream &os, const CellBase &v);
 inline Vector PINdir(CellBase &here, CellBase &nb, Wall &w) {
 	return w.getTransporter( &here, 1)  *  w.getInfluxVector(&here);
 inline Vector PINdir(CellBase *here, CellBase *nb, Wall *w) {
 	return w->getTransporter( here, 1)  *  w->getInfluxVector(here);
+}
 #endif

src/libplugin.pro

➞

Show inline comments

+#
 #  $Id$
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += staticlib
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
-DESTDIR = build_models/lib
+DESTDIR = ../lib
 PERLDIR = ./perl
 PARTMPL = VirtualLeafpar.tmpl
 QT += qt3support
 TARGET = vleaf
 TEMPLATE = lib
 HEADERS = \
  cellbase.h \
  matrix.h \
  output.h \
  parameter.h \
  parse.h \
  random.h \
  simplugin.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  warning.h
 SOURCES = \
  cellbase.cpp \
  matrix.cpp \
  output.cpp \
  parameter.cpp \
  parse.cpp \
  random.cpp \
  simplugin.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  warning.cpp
 unix {
  system(rm -f parameter.cpp parameter.h) # this is performed here when qmake is envoked and not in the resulting makefile.
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 win32 {
  system(DEL parameter.cpp parameter.h)
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
 system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
 #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
+#

src/mesh.cpp

➞

Show inline comments

 /*
+ *
  *  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 <string>
 #include <algorithm>
 #include <vector>
 #include <sstream>
 #include <cstdlib>
 //#include <cerrno>
 #include <cstring>
 #include <numeric>
 #include <functional>
 #include <fstream>
 #include <QPair>
 #include "mesh.h"
 #include "tiny.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "parse.h"
 #include "matrix.h"
 #include "sqr.h"
 #include "nodeset.h"
 #include "nodeitem.h"
 #include "simplugin.h"
 #include <QDebug>
 #include <set>
 #include <iostream>
 #include <iterator>
 static const std::string _module_id("$Id$");
+static const std::string _module_id("$Id: mesh.cpp,v 79f94eaa3b9e 2010/04/14 07:51:02 michael $");
 extern Parameter par;
 void Mesh::AddNodeToCellAtIndex(Cell *c, Node *n, Node *nb1, Node *nb2, list<Node *>::iterator ins_pos) {
   c->nodes.insert(ins_pos, n);
   n->owners.push_back( Neighbor(c, nb1, nb2 ) );
+}
 void Mesh::AddNodeToCell(Cell *c, Node *n, Node *nb1, Node *nb2) {
   c->nodes.push_back( n );
   n->owners.push_back( Neighbor(c, nb1, nb2 ) );
+}
 void Mesh::PerturbChem(int chemnum, double range) {
   for (vector<Cell *>::iterator i=cells.begin();
        i!=cells.end();
        i++) {
     (*i)->chem[chemnum] += range*(RANDOM()-0.5);
     if ((*i)->chem[chemnum]<0.) (*i)->chem[chemnum]=0.;
+  }
+}
 void Mesh::CellFiles(const Vector ll, const Vector ur) {
   Cell *cell = RectangularCell(ll,ur,0.001);
   for (int c=0;c<Cell::NChem();c++) {
     cell->SetChemical(c,par.initval[c]);
+  }
   cell->SetTargetArea(cell->CalcArea());
   Vector axis(1,0,0);
   // divide rectangle a number of times
   for (int i=0;i<6;i++) {
     IncreaseCellCapacityIfNecessary();
     vector <Cell *> current_cells = cells;
     for (vector<Cell *>::iterator j=current_cells.begin();
 	 j!=current_cells.end();j++) {
       (*j)->DivideOverAxis(axis);
+    }
     axis=axis.Perp2D();
+  }
   IncreaseCellCapacityIfNecessary();
   axis=axis.Perp2D();
   vector <Cell *> current_cells = cells;
   for (vector<Cell *>::iterator j=current_cells.begin();
 	 j!=current_cells.end();j++) {
    (*j)->DivideOverAxis(axis);
+ }
  double sum_l=0; int n_l=0;
   for (list<Node *>::const_iterator i=cell->nodes.begin();
        i!=cell->nodes.end();
        i++) {
     list<Node *>::const_iterator nb=i; nb++;
     if (nb==cell->nodes.end())
       nb=cell->nodes.begin();
     double l = (**nb-**i).Norm();
     sum_l += l;
     n_l++;
+  }
   Node::target_length = sum_l/(double)n_l;
   // a bit more tension
   Node::target_length/=4.;
   SetBaseArea();
+}
 Cell *Mesh::RectangularCell(const Vector ll, const Vector ur, double rotation) {
   Cell *cell=AddCell(new Cell());
   cell->m=this;
   Matrix rotmat;
   rotmat.Rot2D(rotation); // rotation over 0,0
   Node *n1=AddNode(new Node(rotmat * ll));
@@ @@ -1890,194 +1890,206 @@ void Mesh::DeleteLooseWalls(void) { @@
 void Mesh::CleanChemicals(const vector<double> &clean_chem, const vector<double> &clean_transporters) {
   if (clean_chem.size()!=(unsigned)Cell::NChem() || clean_transporters.size()!=(unsigned)Cell::NChem()) {
     throw "Run time error in Mesh::CleanChemicals: size of clean_chem and clean_transporters should be equal to Cell::NChem()";
+  }
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*c)->SetChemical(i,clean_chem[i]);
+    }
     (*c)->SetNewChemToChem();
+  }
   // clean transporters
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*w)->setTransporters1(i,clean_transporters[i]); (*w)->setNewTransporters1(i,clean_transporters[i]);
       (*w)->setTransporters2(i,clean_transporters[i]); (*w)->setNewTransporters2(i,clean_transporters[i]);
+    }
+  }
+}
 void Mesh::RandomizeChemicals(const vector<double> &max_chem, const vector<double> &max_transporters) {
   if (max_chem.size()!=(unsigned)Cell::NChem() || max_transporters.size()!=(unsigned)Cell::NChem()) {
     throw "Run time error in Mesh::CleanChemicals: size of max_chem and max_transporters should be equal to Cell::NChem()";
+  }
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*c)->SetChemical(i,max_chem[i]*RANDOM());
+    }
     (*c)->SetNewChemToChem();
+  }
   // randomize transporters
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*w)->setTransporters1(i,max_transporters[i] * RANDOM()); (*w)->setNewTransporters1(i, (*w)->Transporters1(i) );
       (*w)->setTransporters2(i,max_transporters[i] * RANDOM()); (*w)->setNewTransporters2(i, (*w)->Transporters1(i) );
+    }
+  }
+}
 //!\brief Calculates a vector with derivatives of all variables, which
 // we can pass to an ODESolver.
 void Mesh::Derivatives(double *derivs) {
   int nwalls = walls.size();
   int ncells = cells.size();
   int nchems = Cell::NChem();
   // two eqs per chemical for each walls, and one eq per chemical for each cell
   // This is for generality. For a specific model you may optimize
   // this by removing superfluous (empty) equations.
   int neqs = 2 * nwalls * nchems + ncells * nchems;
   //static double *derivs = 0;
   // derivs is allocated by RungeKutta class.
   for (int i=0;i<neqs;i++) { derivs[i]=0.;}
   // Layout of derivatives: cells [ chem1 ... chem n]  walls [ [ w1(chem 1) ... w1(chem n) ] [ w2(chem 1) ... w2(chem n) ] ]
   int i=0;
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     //(*cr)(*c, &(derivs[i]));
 	  plugin->CellDynamics(*c, &(derivs[i]));
 	  i+=nchems;
+  }
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
    // (*wr)(*w, &(derivs[i]), &(derivs[i+nchems]));
 	  plugin->WallDynamics(*w,  &(derivs[i]), &(derivs[i+nchems]));
     // Transport function adds to derivatives of cell chemicals
 	  plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 								  &(derivs[(*w)->c2->Index() * nchems]));
 	  double *dchem_c1 = &(derivs[(*w)->c1->Index() * nchems]);
 	  double *dchem_c2 = &(derivs[(*w)->c2->Index() * nchems]);
 	  //plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 							//	  &(derivs[(*w)->c2->Index() * nchems]));
 	  // quick fix: dummy values to prevent end user from writing into outer space and causing a crash :-)
 	  // start here if you want to implement chemical input/output into environment over boundaries
 	  double dummy1, dummy2;
 	  if ((*w)->c1->Index()<0) { // tests if c1 is the boundary pol
 		  dchem_c1 = &dummy1;
+	  }
 	  if ((*w)->c2->Index()<0) {
 		  dchem_c2 = &dummy2;
+	  }
 	  plugin->CelltoCellTransport(*w, dchem_c1, dchem_c2);
 	  //(*tf)(*w, &(derivs[(*w)->c1->Index() * nchems]),
       //&(derivs[(*w)->c2->Index() * nchems] ) );
     i+=2*nchems;
+  }
+}
 void Mesh::setValues(double x, double *y) {
   //int nwalls = walls.size();
   //int ncells = cells.size();
   int nchems = Cell::NChem();
   // two eqs per chemical for each walls, and one eq per chemical for each cell
   // This is for generality. For a specific model you may optimize
   // this by removing superfluous (empty) equations.
   //int neqs = 2 * nwalls * nchems + ncells * nchems;
   // Layout of derivatives: cells [ chem1 ... chem n]  walls [ [ w1(chem 1) ... w1(chem n) ] [ w2(chem 1) ... w2(chem n) ] ]
   int i=0;
   static int emit_count=0;
   const int stride = 100;
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     for (int ch=0;ch<nchems;ch++) {
       (*c)->SetChemical(ch, y[i+ch]);
+    }
     if ( !(emit_count%stride)) {
       (*c)->EmitValues(x);
+    }
     i+=nchems;
+  }
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
     for (int ch=0;ch<nchems;ch++) {
       (*w)->setTransporters1(ch,y[i+ch]);
+    }
     i+=nchems;
     for (int ch=0;ch<nchems;ch++) {
       (*w)->setTransporters2(ch,y[i+ch]);
+    }
     i+=nchems;
+  }
   emit_count++;
+}
 double *Mesh::getValues(int *neqs) {
   int nwalls = walls.size();
   int ncells = cells.size();
   int nchems = Cell::NChem();
   // two eqs per chemical for each wall, and one eq per chemical for each cell
   // This is for generality. For a specific model you may optimize
   // this by removing superfluous (empty) equations.
   (*neqs) = 2 * nwalls * nchems + ncells * nchems;
   // Layout of derivatives: cells [ chem1 ... chem n]  walls [ [ w1(chem 1) ... w1(chem n) ] [ w2(chem 1) ... w2(chem n) ] ]
   static double *values = 0;
   if (values!=0) { delete[] values; }
   values = new double[*neqs];
   int i=0;
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     for (int ch=0;ch<nchems;ch++) {
       values[i+ch]=(*c)->Chemical(ch);
+    }
     i+=nchems;
+  }
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
     for (int ch=0;ch<nchems;ch++) {
       values[i+ch]=(*w)->Transporters1(ch);
+    }
     i+=nchems;
     for (int ch=0;ch<nchems;ch++) {
       values[i+ch]=(*w)->Transporters2(ch);
+    }

src/mesh.h

➞

Show inline comments

@@ @@ -145,197 +145,203 @@ public: @@
 	 Using this template requires some fiddling with function adaptors bind2nd and mem_fun_ref.
 	 Example usage for calling a member function on each cell:
 	 mesh.LoopCells( bind2nd (mem_fun_ref( &Cell::DrawDiffEdges), &canvas ) );
 	 This calls Cell's member function DrawDiffEdges, taking one
 	 argument canvas, on all Cell objects in the current Mesh.
 	 */
 	template<class Op> void LoopCells(Op f) {
 		for (vector <Cell *>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			f(**i);
+		}
 		//for_each(cells.begin(),cells.end(),f);
+	}
 	template<class Op> void LoopWalls(Op f) {
 		for (list <Wall *>::iterator i=walls.begin();
 			 i!=walls.end();
 			 i++) {
 			f(**i);
+		}
+	}
 	// if the amount of cells might increase, during looping, use this template
 	template<class Op> void LoopCurrentCells(Op f) {
 		vector<Cell *> current_cells = cells;
 		for (vector <Cell *>::iterator i=current_cells.begin();
 			 i!=current_cells.end();
 			 i++) {
 			f(**i);
+		}
 		//for_each(cells.begin(),cells.end(),f);
+	}
 	template<class Op> void LoopNodes(Op f) {
 		for (vector<Node *>::iterator i=nodes.begin();
 			 i!=nodes.end();
 			 i++) {
 			f(**i);
+		}
+	}
 	template<class Op> void RandomlyLoopNodes(Op f) {
 		MyUrand r(shuffled_nodes.size());
 		random_shuffle(shuffled_nodes.begin(),shuffled_nodes.end(),r);
 		for (vector<Node *>::const_iterator i=shuffled_nodes.begin();
 			 i!=shuffled_nodes.end();
 			 i++) {
 			f(*shuffled_nodes[*i]);
+		}
+	}
 	template<class Op> void RandomlyLoopCells(Op f) {
 		MyUrand r(shuffled_cells.size());
 		random_shuffle(shuffled_cells.begin(),shuffled_cells.end(),r);
 		for (vector<Cell *>::const_iterator i=shuffled_cells.begin();
 			 i!=shuffled_cells.end();
 			 i++) {
 			f(*shuffled_cells[*i]);
+		}
+	}
 	template<class Op1, class Op2> void LoopCells(Op1 f, Op2 &g) {
 		for (vector<Cell *>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			f(**i,g);
+		}
+	}
 	template<class Op1, class Op2, class Op3> void LoopCells(Op1 f, Op2 &g, Op3 &h) {
 		for (vector<Cell *>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			f(**i,g,h);
+		}
+	}
 	void DoCellHouseKeeping(void) {
 		vector<Cell *> current_cells = cells;
 		for (vector<Cell *>::iterator i = current_cells.begin();
 			 i != current_cells.end();
 			 i ++) {
-			plugin->CellHouseKeeping(**i);
 			plugin->CellHouseKeeping(*i);
 			// Call functions of Cell that cannot be called from CellBase, including Division
 			if ((*i)->flag_for_divide) {
 				if ((*i)->division_axis) {
 					(*i)->DivideOverAxis(*(*i)->division_axis);
 					delete (*i)->division_axis;
 					(*i)->division_axis = 0;
 				} else {
 				(*i)->Divide();
+				}
 				(*i)->flag_for_divide=false;
+			}
+		}
+	}
 /*	template<class Op1, class Cont> void ExtractFromCells(Op1 f, Cont res) {
 		for (vector<Cell>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			*(res++) = ( f(*i) );
+		}
 	}*/
 	// Apply "f" to cell i
 	// i.e. this is an adapter which allows you to call a function
 	// operating on Cell on its numeric index index
 	template<class Op> void cell_index_adapter(Op f,int i) {
 		f(cells[i]);
+	}
 	double DisplaceNodes(void);
 	void BoundingBox(Vector &LowerLeft, Vector &UpperRight);
 	int NEqs(void) {     int nwalls = walls.size();
 		int ncells =cells.size();
 		int nchems = Cell::NChem();
 		// two eqs per chemical for each walls, and one eq per chemical for each cell
 		// This is for generality. For a specific model you may optimize
 		// this by removing superfluous (empty) equations.
 		int neqs = 2 * nwalls * nchems + ncells * nchems;
 		return neqs;
+	}
 	void IncreaseCellCapacityIfNecessary(void) {
 		return;
 		// cerr << "Entering Mesh::IncreaseCellCapacityIfNecessary \n";
 		// make sure we always have enough space
 		// to have each cell divide at least once
 		//
 		// Note that we must do this, because Cell::Divide pushes a new Cell
 		// onto Mesh::cells. As a result, Mesh::cells might be relocated
 		// if we are _within_ a Cell object: i.e. pointer "this" will be changed!!
 		//
 		// An alternative solution could be to make "Mesh::cells" a list,
 		// but this won't work because we need random access for
 		// the Monte Carlo algorithm.
 		if (2*cells.size()>cells.capacity()) {
 			cerr << "Increasing capacity to "  << 2*cells.capacity() << endl;
 			cerr << "Current capacity is " << cells.capacity() << endl;
 			cells.reserve(cells.capacity()*2);
+		}
+	}
 	void ReserveMoreCells(int n) {
 		if (nodes.size()+n>nodes.capacity()) {
 			nodes.reserve(size()+n);
+		}
+	}
 	double Area(void);
 	double MeanArea(void) {
 		double sum=0.;
 		for (vector<Cell *>::const_iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			sum+=(*i)->Area();
+		}
 		return sum/(double)NCells();
+	}
 	void SetBaseArea(void);
 	int NCells(void) const {
 		return cells.size();
+	}
 	inline int NNodes(void) const {
 		return nodes.size();
+	}
 	void PrintQueue(ostream &os) {
 		while (!node_insertion_queue.empty()) {
 			os << node_insertion_queue.front() << endl;
 			node_insertion_queue.pop();
+		}
 		//copy (node_insertion_queue.begin(),node_insertion_queue.end(),ostream_iterator<Edge>(cerr, " "));
+	}
 	void InsertNodes(void) {
 		// insert the nodes in the insertion queue
 		while (!node_insertion_queue.empty()) {
 			//cerr << node_insertion_queue.front() << endl;
 			InsertNode(node_insertion_queue.front());
 			node_insertion_queue.pop();
+		}
+	}

src/modelcatalogue.cpp

➞

Show inline comments

 /*
+ *
  *  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 <string>
 #include "modelcatalogue.h"
 #include <QVariant>
 static const std::string _module_id("$Id$");
 ModelCatalogue::ModelCatalogue(Mesh *_mesh, Main *_mainwin, const char *model=0) {
 	mesh = _mesh;
 	mainwin = _mainwin;
 	if (model) {
 	  cerr << "Loading model: " << model << endl;
 		LoadPlugin(model);
 	} else {
 	  cerr << "Loading all models." << endl;
 		LoadPlugins();
+	}
+}
 void ModelCatalogue::LoadPlugins() {
 	QDir pluginDir(QApplication::applicationDirPath());
 	QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"
 #if defined(Q_OS_WIN)
 	if (pluginDir.dirName().toLower() =="debug"
 		||pluginDir.dirName().toLower() =="release")
 		pluginDir.cdUp();
 	plugin_filters << "*.dll";
 	#elif defined(Q_OS_MAC)
 	if (pluginDir.dirName() =="MacOS"){
 		pluginDir.cdUp();
 		pluginDir.cdUp();
 		pluginDir.cdUp();
+	}
 	plugin_filters << "*.dylib";
 #endif
 	pluginDir.setNameFilters(plugin_filters);
 	if (!pluginDir.cd("models")) {
 		MyWarning::error("Directory 'models' not found!");
+	}
 	//QVector<SimPluginInterface *> plugins;
 	foreach (QString fileName, pluginDir.entryList(QDir::Files)){
 		QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
 		if (SimPluginInterface *plugin =
 			qobject_cast<SimPluginInterface *>(loader.instance())) {
 			models.append(plugin);
 		} else {
 			MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
 			cerr << loader.errorString().toStdString().c_str() << endl;
 			MyWarning::warning("Could not load model %s: %s",fileName.toStdString().c_str(), loader.errorString().toStdString().c_str());
+		}
+	}
 	if (models.size()==0) {
 		MyWarning::error("No models could be loaded.");
+	}
+}
 void ModelCatalogue::LoadPlugin(const char *model) {
   QDir pluginDir(QApplication::applicationDirPath());
   QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"
 #if defined(Q_OS_WIN)
   if (pluginDir.dirName().toLower() =="debug"
       ||pluginDir.dirName().toLower() =="release")
     pluginDir.cdUp();
   //plugin_filters << "*.dll";
 #elif defined(Q_OS_MAC)
   if (pluginDir.dirName() =="MacOS"){
     pluginDir.cdUp();
     pluginDir.cdUp();
     pluginDir.cdUp();
+  }
   //plugin_filters << "*.dylib";
 #endif
   plugin_filters << model;
   pluginDir.setNameFilters(plugin_filters);
   if (!pluginDir.cd("models")) {
     MyWarning::error("Directory 'models' not found!");
+  }
   //QVector<SimPluginInterface *> plugins;
   QStringList modelnames=pluginDir.entryList(QDir::Files);
   if (modelnames.empty()) {
     MyWarning::error("Model %s not found - hint: do not include path in filename.",model);
+  }
   foreach (QString fileName, modelnames){
     QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
     if (SimPluginInterface *plugin =
 	qobject_cast<SimPluginInterface *>(loader.instance())) {
       models.append(plugin);
       //MyWarning::warning("Successfully loaded model %s",fileName.toStdString().c_str());
     } else {
       MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
+    }
+  }
+}
 void ModelCatalogue::InstallFirstModel() {
 	InstallModel(models[0]);
+}
 void ModelCatalogue::PopulateModelMenu() {
 	foreach (SimPluginInterface *model, models) {
 		QAction *modelaction = new QAction(model->ModelID(), mainwin);
 		QVariant data;
 		data.setValue(model);
 		modelaction->setData(data);
 		mainwin->modelmenu->addAction(modelaction);
+	}
 	connect(mainwin->modelmenu, SIGNAL(triggered(QAction *)), this, SLOT(InstallModel(QAction *)) );
+}
 void ModelCatalogue::InstallModel(QAction *modelaction) {
 	QVariant data = modelaction->data();
 	SimPluginInterface *model = data.value<SimPluginInterface *>();
 	cerr << "You chose model " << model->ModelID().toStdString() << "!\n";
 	mesh->Clean();
 	InstallModel(model);
+}
 void ModelCatalogue::InstallModel(SimPluginInterface *plugin) {
   // make sure both main and plugin use the same static datamembers (ncells, nchems...)
   plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
   mesh->SetSimPlugin(plugin);
   Cell::SetNChem(plugin->NChem());
   plugin->SetParameters(&par);
   if (mainwin) {
     mainwin->RefreshInfoBar();
     mainwin->Init(0);
+  }
   //	mesh->StandardInit();
+}

src/simplugin.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #ifndef _SIMPLUGIN_H_
 #define _SIMPLUGIN_H_
 #include <QtPlugin>
 #include <QMetaType>
 #include "cellbase.h"
 #include "wallbase.h"
 class Parameter;
 #include <QColor>
 #include <QString>
 class SimPluginInterface {
 public:
 	virtual QString ModelID(void) = 0;
 	virtual ~SimPluginInterface() { }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping(CellBase &c) = 0;
+	virtual void CellHouseKeeping(CellBase *c) = 0;
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *, double *dchem_c1, double *dchem_c2) = 0;
 	// Differential equations describing chemical reactions taking place at or near the cell walls
 	// (e.g. PIN accumulation)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw)  = 0;
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem) = 0;
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) = 0;
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) = 0;
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color) = 0;
+	virtual void SetCellColor(CellBase *c, QColor *color) = 0;
 	// Number of chemicals
 	virtual int NChem(void) = 0;
 	// For internal use; not to be redefined by end users
 	virtual void SetParameters(Parameter *pass_pars);// { par = pass_pars; }
 	virtual void SetCellsStaticDatamembers (CellsStaticDatamembers *cells_static_data_members_of_main);
 protected:
 	class Parameter *par;
 };
 Q_DECLARE_INTERFACE(SimPluginInterface,
-                    "nl.cwi.VirtualLeaf.SimPluginInterface/1.1")
+                    "nl.cwi.VirtualLeaf.SimPluginInterface/1.2")
 Q_DECLARE_METATYPE(SimPluginInterface *)
 #endif
@@ \ No newline at end of file @@

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