EI/VirtualLeaf Changeset - 5564fc0d72bc · Centrum Wiskunde & Informatica (CWI)

Changeset - 5564fc0d72bc

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Roeland Merks - 15 years ago 2010-06-04 15:55:15
roeland.merks@cwi.nl

Updated the Makefiles and updated testplugin to new plugin interface.

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/Makefile
added src/build_models/Makefile
changed src/VirtualLeaf.pro
changed src/build_models/leafplugin.cpp
changed src/build_models/leafplugin.h
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
removed src/build_models/simplugin.h

8 files changed with 117 insertions and 133 deletions:

src/Makefile

src/VirtualLeaf.pro

src/build_models/Makefile

src/build_models/leafplugin.cpp

src/build_models/leafplugin.h

src/build_models/simplugin.h

src/build_models/testplugin.cpp

src/build_models/testplugin.h

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src/Makefile

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@@ new file 100644 @@
 # $Id: Makefile,v 3f0977faba37 2010/06/03 15:54:37 michael $
 QMAKE = qmake
 all: VirtualLeaf libplugin plugins
 VirtualLeaf: Makefile.VirtualLeaf
 	make -f Makefile.VirtualLeaf
 Makefile.VirtualLeaf: VirtualLeaf.pro
 	$(QMAKE) -makefile -o $@ $<
 libplugin: Makefile.libplugin
 	make -f Makefile.libplugin
 Makefile.libplugin: libplugin.pro
 	$(QMAKE) -makefile -o $@ $<
 plugins:
 	make -C build_models
 clean:
 	make -f Makefile.libplugin clean
 	make -f Makefile.VirtualLeaf clean
 	make -C build_models clean
 #finis

src/VirtualLeaf.pro

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@@ @@ -110,13 +110,13 @@ system(perl $$PERLDIR/make_pardialog_sou @@
 HEADERS += \
  apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
+# forwardeuler.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
@@ @@ -151,13 +151,13 @@ HEADERS += \ @@
 SOURCES += \
  apoplastitem.cpp \
  canvas.cpp \
  cellbase.cpp \
  cell.cpp \
  cellitem.cpp \
  forwardeuler.cpp \
+# forwardeuler.cpp \
  mainbase.cpp \
  matrix.cpp \
  mesh.cpp \
  miscq.cpp \
  modelcatalogue.cpp \
  Neighbor.cpp \

src/build_models/Makefile

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@@ new file 100644 @@
 # $Id: Makefile,v 3f0977faba37 2010/06/03 15:54:37 michael $
 QMAKE = qmake
 all: plugin_auxingrowth plugin_leaf plugin_meinhardt plugin_test
 plugin_auxingrowth: Makefile.plugin_auxingrowth
 	make -f Makefile.plugin_auxingrowth
 Makefile.plugin_auxingrowth: plugin_auxingrowth.pro
 	$(QMAKE) -makefile -o $@ $<
 plugin_leaf: Makefile.plugin_leaf
 	make -f Makefile.plugin_leaf
 Makefile.plugin_leaf: plugin_leaf.pro
 	$(QMAKE) -makefile -o $@ $<
 plugin_meinhardt: Makefile.plugin_meinhardt
 	make -f Makefile.plugin_meinhardt
 Makefile.plugin_meinhardt: plugin_meinhardt.pro
 	$(QMAKE) -makefile -o $@ $<
 plugin_test: Makefile.plugin_test
 	make -f Makefile.plugin_test
 Makefile.plugin_test: plugin_test.pro
 	$(QMAKE) -makefile -o $@ $<
 clean:
 	make -f Makefile.plugin_auxingrowth clean
 	make -f Makefile.plugin_leaf clean
 	make -f Makefile.plugin_meinhardt clean
 	make -f Makefile.plugin_test clean
 #finis

src/build_models/leafplugin.cpp

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@@ @@ -34,15 +34,15 @@ @@
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
-void LeafPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+void LeafPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
 		// PIN1 distributes between parent and daughter according to area
-  double area = daughter1.Area(), daughter_area = daughter2.Area();
+  double area = daughter1->Area(), daughter_area = daughter2->Area();
   double tot_area = area + daughter_area;
   //chem[1]*=(area/tot_area);
   //daughter.chem[1]*=(daughter_area/tot_area);
   // For lack of detailed data, or a better rule, we assume that cells remain polarized
@@ @@ -51,54 +51,54 @@ void LeafPlugin::OnDivide(ParentInfo &pa @@
   // So the PIN1 is redistributed according to the original polarization over the walls
   // parent_info contains info about the parent
   // redistribute the PIN in the endosome according to area
 	// "Fudge" rule: if one of the cells is at the boundary, remove all AUX1 in the other cell
   if (daughter1.AtBoundaryP() && !daughter2.AtBoundaryP()) {
     //daughter2.new_chem[2]=daughter2.chem[2]=0.;
 		daughter2.SetNewChem(2,0);
 		daughter2.SetChemical(2,0);
   if (daughter1->AtBoundaryP() && !daughter2->AtBoundaryP()) {
     //daughter2->new_chem[2]=daughter2->chem[2]=0.;
 		daughter2->SetNewChem(2,0);
 		daughter2->SetChemical(2,0);
 		//daughter.new_chem[0]=daughter.chem[0]=0.;
 		//cerr << "Clearing daughter\n";
 		//for (list<Wall *>::const_iterator w=daughter.walls.begin();
 		//	 w!=daughter.walls.end();
 		//	 w++) {
 		//	(*w)->setTransporter(&daughter, 1, 0.);
 		//}
 		//new_chem[2]=chem[2]=parent_info.PINendosome;
 		daughter1.SetNewChem(2,parent_info.PINendosome);
 		daughter1.SetChemical(2,parent_info.PINendosome);
 		//new_chem[2]=chem[2]=parent_info->PINendosome;
 		daughter1->SetNewChem(2,parent_info->PINendosome);
 		daughter1->SetChemical(2,parent_info->PINendosome);
 	} else {
-		if (daughter2.AtBoundaryP() && !daughter1.AtBoundaryP()) {
+		if (daughter2->AtBoundaryP() && !daughter1->AtBoundaryP()) {
 		  //new_chem[2]=chem[2]=0.;
 		  daughter1.SetNewChem(2,0);
 		  daughter1.SetChemical(2,0);
 		  daughter1->SetNewChem(2,0);
 		  daughter1->SetChemical(2,0);
 			/*new_chem[0]=chem[0]=0.;
 			for (list<Wall *>::const_iterator w=walls.begin();
 				 w!=walls.end();
 				 w++) {
 				(*w)->setTransporter(this, 1, 0.);
 			}*/
 		  //daughter2.chem[2]=parent_info.PINendosome;
 		  daughter2.SetChemical(2,parent_info.PINendosome);
 		  //daughter2->chem[2]=parent_info->PINendosome;
 		  daughter2->SetChemical(2,parent_info->PINendosome);
 		  //cerr << "Clearing parent\n";
 		} else {
 		  //daughter1.new_chem[2]=daughter1.chem[2] = parent_info.PINendosome*(area/tot_area);
 		  daughter1.SetNewChem(2,parent_info.PINendosome*(area/tot_area));
 		  daughter1.SetChemical(2, parent_info.PINendosome*(area/tot_area));
 		  //daughter2.new_chem[2]=daughter2.chem[2] = parent_info.PINendosome*(daughter_area/tot_area);
 		  daughter2.SetNewChem(2,parent_info.PINendosome*(daughter_area/tot_area));
 		  daughter2.SetChemical(2,parent_info.PINendosome*(daughter_area/tot_area));
 		  //daughter1->new_chem[2]=daughter1->chem[2] = parent_info->PINendosome*(area/tot_area);
 		  daughter1->SetNewChem(2,parent_info->PINendosome*(area/tot_area));
 		  daughter1->SetChemical(2, parent_info->PINendosome*(area/tot_area));
 		  //daughter2->new_chem[2]=daughter2->chem[2] = parent_info->PINendosome*(daughter_area/tot_area);
 		  daughter2->SetNewChem(2,parent_info->PINendosome*(daughter_area/tot_area));
 		  daughter2->SetChemical(2,parent_info->PINendosome*(daughter_area/tot_area));
+		}
+	}
 	/*
 	  // NB: Code commented out; not yet adapted to plugin format... RM 18/12/2009
@@ @@ -109,18 +109,18 @@ void LeafPlugin::OnDivide(ParentInfo &pa @@
 	// distribute wallPINs according to the circumference of the parent and daughter
 	double circ = Circumference( );
 	double daughter_circ = daughter.Circumference();
 	double tot_circ = circ + daughter_circ;
 	double wallPINs = (circ / tot_circ) * parent_info.PINmembrane;
 	double daughter_wallPINs = (daughter_circ / tot_circ) * parent_info.PINmembrane;
 	double wallPINs = (circ / tot_circ) * parent_info->PINmembrane;
 	double daughter_wallPINs = (daughter_circ / tot_circ) * parent_info->PINmembrane;
-     	//cerr << "wallPINs = " << wallPINs <<  ", daughter_wallPINs =  " << daughter_wallPINs << "sum = " << wallPINs + daughter_wallPINs << ", PINmembrane = " << parent_info.PINmembrane << endl;
+     	//cerr << "wallPINs = " << wallPINs <<  ", daughter_wallPINs =  " << daughter_wallPINs << "sum = " << wallPINs + daughter_wallPINs << ", PINmembrane = " << parent_info->PINmembrane << endl;
 	// distrubute it according to the overall polarity
-	Vector polarization = parent_info.polarization.Normalised().Perp2D();
+	Vector polarization = parent_info->polarization.Normalised().Perp2D();
 	double sum=0.;
 	for (list<Wall *>::const_iterator w=walls.begin();
 		 w!=walls.end();
 		 w++) {
@@ @@ -140,36 +140,36 @@ void LeafPlugin::OnDivide(ParentInfo &pa @@
 	//SetNewChem(1, Chemical(1));
 	//cerr << "[ "  << sum_wall_Pi + Chemical(1) << "]";
 	*/
+}
-void LeafPlugin::SetCellColor(CellBase &c, QColor &color) {
+void LeafPlugin::SetCellColor(CellBase *c, QColor *color) {
 	// Red: AUX1
 	// Green: Auxin
 	// Blue: van-3
   //  color.setRgb(chem[2]/(1+chem[2]) * 255.,(chem[0]/(1+chem[0]) * 255.),(chem[3]/(1+chem[3]) *255.) );
   color.setRgb(c.Chemical(2)/(1+c.Chemical(2)) * 255.,(c.Chemical(0)/(1+c.Chemical(0)) * 255.),(c.Chemical(3)/(1+c.Chemical(3)) *255.) );
   //  color->setRgb(chem[2]/(1+chem[2]) * 255.,(chem[0]/(1+chem[0]) * 255.),(chem[3]/(1+chem[3]) *255.) );
   color->setRgb(c->Chemical(2)/(1+c->Chemical(2)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
+}
-void LeafPlugin::CellHouseKeeping(CellBase &c) {
+void LeafPlugin::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();
+    }
     // expand if this is not a provascular cell
     if (c.Chemical(3) < 0.7 ) {
       c.EnlargeTargetArea(par->cell_expansion_rate);
     if (c->Chemical(3) < 0.7 ) {
       c->EnlargeTargetArea(par->cell_expansion_rate);
+    }
+  }
+}
 void LeafPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
@@ @@ -356,21 +356,21 @@ void LeafPlugin::WallDynamics(Wall *w, d @@
   dw1[1] = dPijdt1;
   dw2[1] = dPijdt2;
+}
-double LeafPlugin::complex_PijAj(CellBase &here, CellBase &nb, Wall &w) {
+double LeafPlugin::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 LeafPlugin::CellDynamics(CellBase *c, double *dchem) {

src/build_models/leafplugin.h

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@@ @@ -34,31 +34,31 @@ class LeafPlugin : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void) { return QString( "Traveling wave model with influx carriers - Merks and Beemster, 2006-2008" ); }
 	// 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; }
  private:
-	double complex_PijAj(CellBase &here, CellBase &nb, Wall &w);
+	double complex_PijAj(CellBase *here, CellBase *nb, Wall *w);
 };
 #endif

src/build_models/simplugin.h

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deleted file

src/build_models/testplugin.cpp

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@@ @@ -32,32 +32,32 @@ @@
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
-void TestPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+void TestPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
+}
-void TestPlugin::SetCellColor(CellBase &c, QColor &color) {
+void TestPlugin::SetCellColor(CellBase *c, QColor *color) {
 	static QStringList colors;
 	if (colors.size()==0) {
 		colors << "red" << "green" << "blue";
+	}
-	color = colors[c.Index()%colors.size()];
+	color->setNamedColor(colors[c->Index()%colors.size()]);
+}
-void TestPlugin::CellHouseKeeping(CellBase &c) {
+void TestPlugin::CellHouseKeeping(CellBase *c) {
 	c.EnlargeTargetArea(par->cell_expansion_rate);
 	if (c.Area() > par->rel_cell_div_threshold * c.BaseArea() ) {
 		c.Divide();
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 		c->Divide();
+	}
+}
 void TestPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {}
 void TestPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {}
 void TestPlugin::CellDynamics(CellBase *c, double *dchem) { }

src/build_models/testplugin.h

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@@ @@ -32,28 +32,28 @@ class TestPlugin : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void) { return QString( "Test model" ); }
 	// 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 0; }
 };

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