EI/VirtualLeaf Changeset - 2accd83924da · Centrum Wiskunde & Informatica (CWI)

Changeset - 2accd83924da

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Roeland Merks - 15 years ago 2010-11-25 14:57:33
roeland.merks@cwi.nl

Some last fine-tuning
- File dialogs start from appropriate data directories
- XML files contain right values for datadir
- Reordered parameter dialog
- Added new "make perl" heading to the makefile
- Corrected segfault for batch mode

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed data/leaves/tutorial1_init.xml
changed data/leaves/tutorial2_init.xml
changed data/leaves/tutorial3_init.xml
changed data/leaves/tutorial4_init.xml
changed data/leaves/tutorial5_init.xml
changed src/Makefile
changed src/VirtualLeaf.cpp
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h

18 files changed:

data/leaves/auxin_growth.xml

bin+mod

data/leaves/meinhardt_init.xml

bin+mod

data/leaves/tutorial1_init.xml

bin+mod

data/leaves/tutorial2_init.xml

bin+mod

data/leaves/tutorial3_init.xml

bin+mod

data/leaves/tutorial4_init.xml

bin+mod

data/leaves/tutorial5_init.xml

bin+mod

src/Makefile

src/VirtualLeaf.cpp

src/VirtualLeafpar.tmpl

src/canvas.cpp

src/canvas.h

src/mesh.cpp

src/mesh.h

src/modelcatalogue.cpp

src/modelcatalogue.h

src/parameter.cpp

src/parameter.h

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data/leaves/auxin_growth.xml

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data/leaves/meinhardt_init.xml

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data/leaves/tutorial1_init.xml

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data/leaves/tutorial2_init.xml

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data/leaves/tutorial4_init.xml

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data/leaves/tutorial5_init.xml

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src/Makefile

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@@ @@ -13,38 +13,41 @@ ifeq ($(QMAKE),) @@
 	QMAKE=qmake
 endif
 all: VirtualLeaf libplugin plugins tutorials
 VirtualLeaf: Makefile.VirtualLeaf
 	$(MAKE) -f Makefile.VirtualLeaf
 Makefile.VirtualLeaf: VirtualLeaf.pro
 	$(QMAKE) -o $@ $<
 libplugin: Makefile.libplugin
 	$(MAKE) -f Makefile.libplugin
 Makefile.libplugin: libplugin.pro
 	$(QMAKE) -o $@ $<
 plugins:
 	$(MAKE) -C build_models -f Makefile
 tutorials:
 	$(MAKE) -C build_models -f Makefile
 	$(MAKE) -C TutorialCode -f Makefile
 perl: Makefile.perl
 	$(MAKE) -f Makefile.perl
 clean:
 	$(MAKE) -f Makefile.libplugin clean
 	$(MAKE) -f Makefile.VirtualLeaf clean
 	$(MAKE) -C build_models -f Makefile clean
 	$(MAKE) -C TutorialCode -f Makefile clean
 ifeq ($(MAKE),make)
 	touch VirtualLeaf.pro
 	touch libplugin.pro
 else
 	copy /b VirtualLeaf.pro +,,
 	copy /b libplugin.pro +,,
 endif
 #finis

src/VirtualLeaf.cpp

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@@ @@ -186,55 +186,60 @@ void MainBase::Plot(int resize_stride) @@
       fname.fill('0');
       fname.width(6);
       fname << count << ".png";
       // Write high-res PNG snapshot every plot step
       Save(fname.str().c_str(), "PNG", 1024, 768);
+    }
     if (!(count%par.xml_storage_stride)) {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << count << ".xml";
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+    }
+  }
+}
 INIT {
   //mesh.SetSimPlugin(plugin);
   if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &settings);
     main_window->XMLReadSettings(settings);
     xmlFree(settings);
     main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
     if (qApp->type()==QApplication::Tty) {
       xmlNode *settings;
       mesh.XMLRead(leaffile, &settings);
       main_window->XMLReadSettings(settings);
       xmlFree(settings);
       main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
     } else {
       ((Main *)main_window)->readStateXML(leaffile);
+    }
   } else {
     mesh.StandardInit();
+  }
   Cell::SetMagnification(1);
   Cell::setOffset(0,0);
   FitLeafToCanvas();
   Plot();
+}
 TIMESTEP {
   static int i=0;
   static int t=0;
   static int ncells;
   if (!batch) {
     UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);
+  }
   ncells=mesh.NCells();
@@ @@ -392,49 +397,49 @@ int main(int argc,char **argv) { @@
       main_window=new Main(canvas, mesh);
       if ( QApplication::desktop()->width() > ((Main *)main_window)->width() + 10
 	   && QApplication::desktop()->height() > ((Main *)main_window)->height() +30 ) {
 	((Main *)main_window)->show();
 	((Main *)main_window)->resize( ((Main *)main_window)->sizeHint());
       } else {
         ((Main *)main_window)->showMaximized();
+      }
       // show "About" window at start up
       ((Main *)main_window)->about();
     } else {
       main_window=new MainBase(canvas, mesh);
+    }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
     //    main_window->Init(leaffile);
     // Install model or read catalogue of models
-    ModelCatalogue model_catalogue(&mesh, useGUI?(Main *)main_window:0,modelfile);
     ModelCatalogue model_catalogue(&mesh, main_window,modelfile);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
     /*    Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     main_window->FitLeafToCanvas();
     main_window->Plot();
     */
     if (batch) {
       double t=0.;
       do {
 	t = main_window->TimeStep();
       } while (t < par.maxt);
     } else
       return app.exec();
   } catch (const char *message) {

src/VirtualLeafpar.tmpl

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 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 = 0 / int
 label = / label
 label = <b>Data Export</b> / label
 export_interval = 0 / int
 export_fn_prefix = cell. / string
 storage_stride = 10 / int
 xml_storage_stride = 500 / int
 datadir = . / directory
 label = / label
 label = <b>Cell mechanics</b> / label
 T = 1.0 / double
 lambda_length = 100. / double
 yielding_threshold = 4. / 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
@@ @@ -59,71 +66,66 @@ 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
 gamma = 0. / double
 eps = 0. / double
 label = / label
 label = <b>User-defined parameters</b> / label
 k = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 i1 = 0 / int
 i2 = 0 / int
 i3 = 0 / int
 i4 = 0 / int
 i5 = 0 / int
 s1 =  / string
 s2 =  / string
 s3 =  / string
 b1 = false / bool
 b2 = false / bool
 b3 = false / bool
 b4 = false / bool
 dir1 = . / directory
 dir2 = . / directory
 export_interval = 0 / int
 export_fn_prefix = cell. / string

src/canvas.cpp

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@@ @@ -624,116 +624,120 @@ void Main::newView() @@
   m->show();
   qApp->setMainWidget(0);
+}
 void Main::EditParameters()
+{
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
   // Make sure the values in the parameter dialog are updated after a file is read
   // each method changing the parameters (reading XML or PAR files) should
   // emit this signal
   QObject::connect(   this, SIGNAL( ParsChanged() ), pardial, SLOT( Reset() ) );
+}
 void Main::savePars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Parameter files (*.par)");
   fd->setDir(par.datadir);
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     ofstream parfile((const char *)fileName);
     par.Write(parfile);
+  }
   startSimulation();
+}
 void Main::readPars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::ExistingFile );
   fd->setFilter( "Parameter files (*.par)");
   fd->setDir(par.datadir);
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
+}
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "LeafML files (*.xml)");
   fd->setDir(par.datadir);
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return saveStateXML();
     } else {
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
+    }
+  }
+}
 void Main::snapshot()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setDir(par.datadir);
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Image files (*.pdf *.png *.jpg *.tif *.bpm)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "jpg";
       fileName += ".";
       fileName += extension;
+    }
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite file? -- Cell data export"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?").arg( fileName ),
@@ @@ -889,62 +893,101 @@ void Main::readLastStateXML() @@
+  }
+}
 void Main::readFirstStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.front();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 QDir Main::GetLeafDir(void) {
   QDir LeafDir(QApplication::applicationDirPath());
   QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"
 #if defined(Q_OS_WIN)
   if (LeafDir.dirName().toLower() =="debug"
       ||LeafDir.dirName().toLower() =="release")
     LeafDir.cdUp();
   //plugin_filters << "*.dll";
 #elif defined(Q_OS_MAC)
   if (LeafDir.dirName() =="MacOS"){
     LeafDir.cdUp();
     LeafDir.cdUp();
     LeafDir.cdUp();
+  }
 #endif
   // for all OS-es. Move from "bin" directory to root application folder.
   if (LeafDir.dirName() == "bin") {
     LeafDir.cdUp();
+  }
   LeafDir.cd("data/leaves");
   /* if (!LeafDir.cd("data/leaves")) {
     QString status_message = QString("No directory data/leaves");
     statusBar()->showMessage(status_message);
     return LeafDir;
+  }
   */
   return LeafDir;
+}
 void Main::readStateXML()
+{
   //  extern Mesh mesh;
   stopSimulation();
 #ifdef QDEBUG
   qDebug() << "Trying to open an OptionFileDialog" << endl;
 #endif
   OptionFileDialog *fd = new OptionFileDialog( this, "read dialog", TRUE );
   fd->setMode( OptionFileDialog::ExistingFile );
   fd->setFilter( "LeafML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
   } else {
     fd->setDir(par.datadir);
+  }
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if (working_dir) {
       delete working_dir;
+    }
     working_dir = fd->dir();
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::about()
+{
   static QMessageBox* about = new QMessageBox
@@ @@ -1374,70 +1417,69 @@ xmlNode *Main::XMLSettingsTree(void) @@
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
   showbordercellp =  view->isItemChecked(border_id);
   shownodenumbersp =  view->isItemChecked(node_number_id);
   showcellnumbersp =  view->isItemChecked(cell_number_id);
   showcellsaxesp = view->isItemChecked( cell_axes_id );
   showcellstrainp = view->isItemChecked( cell_strain_id );
   movieframesp = view->isItemChecked(movie_frames_id);;
   showboundaryonlyp =  view->isItemChecked(only_boundary_id);
   showfluxesp = view->isItemChecked(fluxes_id);
   dynamicscellsp = options->isItemChecked(dyn_cells_id);
   showwallsp = view->isItemChecked( cell_walls_id);
   //showapoplastsp = view->isItemChecked( apoplasts_id);
   hidecellsp = view->isItemChecked( hide_cells_id);
   xmlNode *settings = MainBase::XMLSettingsTree();
   QTransform viewport(editor->transform());
   xmlAddChild(settings, XMLViewportTree(viewport));
   return settings;
+}
 #define QDEBUG
 void Main::exportCellData(QString fileName) {
 #ifdef QDEBUG
   qDebug() << "exportCellData fileName: " << fileName << endl;
 #endif
   QFile file(fileName);
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportWallData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
+  }
+}
 void Main::exportCellData() {
   QString fileName;
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
+  fd->setDir(par.datadir);
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "csv";
       fileName += ".";
       fileName += extension;
+    }
     if (extension!="csv" && extension!="CSV") {
       if (
 	  QMessageBox::question(
 				 this,
 				 tr("Change extension? -- Cell data export"),
 				 tr("VirtualLeaf can only export data to CSV format (Excel-compatible)."
 				    "Do you want to change the file extension to \".csv\"?"),
 				 QMessageBox::Yes, QMessageBox::No ) == QMessageBox::No

src/canvas.h

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@@ @@ -9,48 +9,49 @@ @@
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  VirtualLeaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _CANVAS_H_
 #define _CANVAS_H_
 #include <q3popupmenu.h>
 #include <q3mainwindow.h>
 #include <q3intdict.h>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <QList>
 #include <QDir>
 #include <string>
 #include <sstream>
 //Added by qt3to4:
 #include <QMouseEvent>
 #include <vector>
 #include "simitembase.h"
 #include "mainbase.h"
 #include "cellitem.h"
 #include "infobar.h"
 #include "nodeitem.h"
 #include "cell.h"
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include <libxml/xpath.h>
 #include <libxml/xmlreader.h>
 #if defined(Q_OS_MAC)
 #define PREFIX "cmd"
@@ @@ -141,87 +142,88 @@ class Main : public Q3MainWindow, public @@
   void about();
   void gpl();
   void TimeStepWrap();
   void togglePaused();
   void setFluxArrowSize(int size);
   void RestartSim(void);
   void toggleShowCellCenters(void);
   void toggleShowNodes(void);
   void toggleShowBorderCells(void);
   void toggleShowFluxes(void);
   void toggleNodeNumbers(void);
   void toggleCellNumbers(void);
   void toggleCellAxes(void);
   void toggleCellStrain(void);
   void toggleShowWalls(void);
   void toggleShowApoplasts(void);
   void toggleDynCells(void);
   void toggleMovieFrames(void);
   void toggleLeafBoundary(void);
   void toggleHideCells(void);
   void print();
   void startSimulation(void);
   void stopSimulation(void);
   void RefreshInfoBar(void);
   int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);
   void EnterRotationMode(void)
+  {
     UserMessage("Rotation mode. Click mouse to exit.");
     if (editor) {
       editor->rot_angle = 0. ;
       // Exit rotation mode if mouse is clicked
       connect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));
       editor->setMouseTracking(true);
+    }
+  }
   void ExitRotationMode(void)
+  {
     UserMessage("Exited rotation mode.",2000);
     options->setItemChecked(rotation_mode_id, false);
     if (editor)
       disconnect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));
     editor->setMouseTracking(false);
+  }
   virtual void UserMessage(QString message, int timeout=0);
   void Refresh(void) { Plot(); }
   void PauseIfRunning(void);
   void ContIfRunning(void);
   virtual void XMLReadSettings(xmlNode *settings);
   private slots:
   void aboutQt();
   void newView();
   void EditParameters();
   QDir GetLeafDir(void);
   void readStateXML();
   int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);
   void readNextStateXML();
   void readPrevStateXML();
   void readFirstStateXML();
   void readLastStateXML();
   void exportCellData();
   void exportCellData(QString);
   void saveStateXML();
   void snapshot();
   void savePars();
   void readPars();
   void clear();
   void init();
   virtual void CutSAM() { MainBase::CutSAM(); Refresh();}
   void enlarge();
   void shrink();
   void zoomIn();
   void zoomOut();
   void CleanMesh();
   void CleanMeshChemicals(void);
   void CleanMeshTransporters(void);
   void RandomizeMesh();

src/mesh.cpp

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@@ @@ -2044,38 +2044,74 @@ double Mesh::Compactness(double *res_com @@
 // DataExport
 void Mesh::CSVExportCellData(QTextStream &csv_stream) const {
   csv_stream << "\"Cell Index\",\"Center of mass (x)\",\"Center of mass (y)\",\"Cell area\",\"Cell length\"";
   for (int c=0;c<Cell::NChem(); c++) {
     csv_stream << ",\"Chemical " << c << "\"";
+  }
   csv_stream << endl;
   for (vector<Cell *>::const_iterator i=cells.begin();
        i!=cells.end();
        i++) {
     Vector centroid = (*i)->Centroid();
     csv_stream << (*i)->Index() << ", "
 	       << centroid.x << ", "
 	       << centroid.y << ", "
 	       <<  (*i)->Area() << ", "
 	       <<(*i)->Length();
     for (int c=0;c<Cell::NChem(); c++) {
       csv_stream << ", " << (*i)->Chemical(c);
+    }
     csv_stream << endl;
+  }
+}
 // DataExport
 void Mesh::CSVExportWallData(QTextStream &csv_stream) const {
   csv_stream << "\"Wall Index\",\"Cell A\",\"Cell B\",\"Length\"";
   for (int c=0;c<Cell::NChem(); c++) {
     csv_stream << ",\"Transporter A:" << c << "\"";
+  }
   for (int c=0;c<Cell::NChem(); c++) {
     csv_stream << ",\"Transporter B:" << c << "\"";
+  }
   csv_stream << endl;
   for (list<Wall *>::const_iterator i=walls.begin();
        i!=walls.end();
        i++) {
     csv_stream << (*i)->Index() << ","
 	       << (*i)->C1()->Index() << ","
 	       << (*i)->C2()->Index() << ","
 	       << (*i)->Length();
     for (int c=0;c<Cell::NChem(); c++) {
       csv_stream << "," << (*i)->Transporters1(c);
+    }
     for (int c=0;c<Cell::NChem(); c++) {
       csv_stream << "," << (*i)->Transporters2(c);
+    }
     csv_stream << endl;
+  }
+}
 void Mesh::CSVExportMeshData(QTextStream &csv_stream) {
   csv_stream << "\"Morph area\",\"Number of cells\",\"Number of nodes\",\"Compactness\",\"Hull area\",\"Morph circumference\",\"Hull circumference\"" << endl;
   double res_compactness, res_area, res_cell_area, hull_circumference;
   Compactness(&res_compactness, &res_area, &res_cell_area, &hull_circumference);
   double morph_circumference = boundary_polygon->ExactCircumference();
   csv_stream << Area() << ", " << NCells() << ", " << NNodes() << ", " << res_compactness << ", " << res_area << ", " << morph_circumference << ", " << hull_circumference << endl;
+}
 /* finis */

src/mesh.h

➞

Show inline comments

@@ @@ -367,48 +367,49 @@ class Mesh { @@
   void DeleteLooseWalls(void);
   void FitLeafToCanvas(double width, double height);
   void AddNodeSet(NodeSet *node_set) {
     node_sets.push_back(node_set);
+  }
   void CleanChemicals(const vector<double> &clean_chem);
   void CleanTransporters(const vector<double> &clean_transporters);
   void RandomizeChemicals(const vector<double> &max_chem, const vector<double> &max_transporters);
   inline double getTime(void) const { return time; }
   string getTimeHours(void) const;
   inline void setTime(double t) { time = t; }
   double CalcProtCellsWalls(int ch) const;
   void SettoInitVals(void);
   QVector<qreal> VertexAngles(void);
   QVector< QPair<qreal,int> > VertexAnglesValues(void);
   void SetSimPlugin(SimPluginInterface *new_plugin) {
     plugin=new_plugin;
+  }
   QString ModelID(void) { return plugin?plugin->ModelID():QString("undefined"); }
   void StandardInit(void);
   double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0, double *hull_circumference=0);
   void CSVExportCellData(QTextStream &csv_stream) const;
   void CSVExportWallData(QTextStream &csv_stream) const;
   void CSVExportMeshData(QTextStream &csv_stream);
   Node* findNextBoundaryNode(Node*);
  private:
   // Data members
   vector<Cell *> cells;
   vector<Node *> nodes;
   list<Wall *> walls; // we need to erase elements from this container frequently, hence a list.
  public:
   vector<NodeSet *> node_sets;
  private:
   vector<Node *> shuffled_nodes;
   vector<Cell *> shuffled_cells;
   unique_queue<Edge> node_insertion_queue;
   BoundaryPolygon *boundary_polygon;
   double time;
   SimPluginInterface *plugin;
   // Private member functions
   void AddNodeToCell(Cell *c, Node *n, Node *nb1 , Node *nb2);
   void AddNodeToCellAtIndex(Cell *c, Node *n, Node *nb1 , Node *nb2, list<Node *>::iterator ins_pos);
   void InsertNode(Edge &e);

src/modelcatalogue.cpp

➞

Show inline comments

@@ @@ -4,49 +4,49 @@ @@
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include "modelcatalogue.h"
 #include <QVariant>
 static const std::string _module_id("$Id$");
-ModelCatalogue::ModelCatalogue(Mesh *_mesh, Main *_mainwin, const char *model=0) {
+ModelCatalogue::ModelCatalogue(Mesh *_mesh, MainBase *_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();
@@ @@ -105,80 +105,83 @@ void ModelCatalogue::LoadPlugin(const ch @@
+  }
   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);
+    QAction *modelaction = new QAction(model->ModelID(), (Main *)mainwin);
     QVariant data;
     data.setValue(model);
     modelaction->setData(data);
     mainwin->modelmenu->addAction(modelaction);
+    ((Main *)mainwin)->modelmenu->addAction(modelaction);
+  }
   connect(mainwin->modelmenu, SIGNAL(triggered(QAction *)), this, SLOT(InstallModel(QAction *)) );
+  connect(((Main *)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...)
   mesh->Clean();
   plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
   mesh->SetSimPlugin(plugin);
   Cell::SetNChem(plugin->NChem());
   plugin->SetParameters(&par);
   if (mainwin) {
     mainwin->RefreshInfoBar();
     if (!qApp->type()==QApplication::Tty)  // only do this if we are running a GUI
       ((Main *)mainwin)->RefreshInfoBar();
     if (plugin->DefaultLeafML().isEmpty()) {
       mainwin->Init(0);
     } else {
       // locate LeafML file
       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();
+      }
 #endif
       // for all OS-es. Move from "bin" directory to root application folder.
       if (pluginDir.dirName() == "bin") {

src/modelcatalogue.h

➞

Show inline comments

@@ @@ -20,43 +20,43 @@ @@
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _MODELCATALOGUE_H_
 #define _MODELCATALOGUE_H_
 #include "warning.h"
 #include "cell.h"
 #include "mesh.h"
 #include "simplugin.h"
 #include "canvas.h"
 #include <QPluginLoader>
 #include <Q3PopupMenu>
 #include <QAction>
 #include <QDir>
 #include <QApplication>
 #include <QObject>
 #include <QAction>
 #include <QMenu>
 class ModelCatalogue : public QObject {
   Q_OBJECT
     public:
-  ModelCatalogue(Mesh *mesh, Main *mainwin, const char *model);
+  ModelCatalogue(Mesh *mesh, MainBase *mainwin, const char *model);
   void LoadPlugins();
   void LoadPlugin(const char *model);
   void InstallFirstModel();
   void PopulateModelMenu();
   public slots:
   void InstallModel(SimPluginInterface *model);
   void InstallModel(QAction *modelaction);
  private:
   QVector<SimPluginInterface *> models;
   Mesh *mesh;
-  Main *mainwin;
+  MainBase *mainwin;
 };
 #endif
 /* finis */

src/parameter.cpp

➞

Show inline comments

@@ @@ -30,48 +30,54 @@ @@
 #include <iostream>
 #include <sstream>
 #include "output.h"
 #include "parse.h"
 #include "xmlwrite.h"
 #include "warning.h"
 #include <QLocale>
 #include <QDir>
 #include <QStringList>
 using namespace std;
 static const std::string _module_id("$Id$");
 Parameter::Parameter() {
   arrowcolor = strdup("white");
   arrowsize = 100;
   textcolor = strdup("red");
   cellnumsize = 1;
   nodenumsize = 1;
   node_mag = 1.0;
   outlinewidth = 1.0;
   cell_outline_color = strdup("forestgreen");
   resize_stride = 0;
   export_interval = 0;
   export_fn_prefix = strdup("cell.");
   storage_stride = 10;
   xml_storage_stride = 500;
   datadir = strdup(".");
   datadir = AppendHomeDirIfPathRelative(datadir);
   T = 1.0;
   lambda_length = 100.;
   yielding_threshold = 4.;
   lambda_celllength = 0.;
   target_length = 60.;
   cell_expansion_rate = 1.;
   cell_div_expansion_rate = 0.;
   auxin_dependent_growth = true;
   ode_accuracy = 1e-4;
   mc_stepsize = 0.4;
   mc_cell_stepsize = 0.2;
   energy_threshold = 1000.;
   bend_lambda = 0.;
   alignment_lambda = 0.;
   rel_cell_div_threshold = 2.;
   rel_perimeter_stiffness = 2;
   collapse_node_threshold = 0.05;
   morphogen_div_threshold = 0.2;
   morphogen_expansion_threshold = 0.01;
   copy_wall = true;
   source = 0.;
   D = new double[15];
   D[0] = 0.;
   D[1] = 0.0;
@@ @@ -114,165 +120,167 @@ Parameter::Parameter() { @@
   ka = 1;
   pin_prod = 0.001;
   pin_prod_in_epidermis = 0.1;
   pin_breakdown = 0.001;
   pin_breakdown_internal = 0.001;
   aux1prod = 0.001;
   aux1prodmeso = 0.;
   aux1decay = 0.001;
   aux1decaymeso = 0.1;
   aux1transport = 0.036;
   aux_cons = 0.;
   aux_breakdown = 0.;
   kaux1 = 1;
   kap = 1;
   leaf_tip_source = 0.001;
   sam_efflux = 0.0001;
   sam_auxin = 10.;
   sam_auxin_breakdown = 0;
   van3prod = 0.002;
   van3autokat = 0.1;
   van3sat = 10;
   k2van3 = 0.3;
   dt = 0.1;
   rd_dt = 1.0;
   datadir = strdup(".");
   datadir = AppendHomeDirIfPathRelative(datadir);
   movie = false;
   nit = 100000;
   maxt = 1000.;
   storage_stride = 10;
   xml_storage_stride = 500;
   rseed = -1;
   constituous_expansion_limit = 16;
   vessel_inh_level = 1;
   vessel_expansion_rate = 0.25;
   d = 0.;
   e = 0.;
   f = 0.;
   c = 0.;
   mu = 0.;
   nu = 0.;
   rho0 = 0.;
   rho1 = 0.;
   c0 = 0.;
   gamma = 0.;
   eps = 0.;
   k = new double[15];
   k[0] = 0.;
   k[1] = 0.0;
   k[2] = 0.0;
   k[3] = 0.;
   k[4] = 0.;
   k[5] = 0.;
   k[6] = 0.;
   k[7] = 0.;
   k[8] = 0.;
   k[9] = 0.;
   k[10] = 0.;
   k[11] = 0.;
   k[12] = 0.;
   k[13] = 0.;
   k[14] = 0.;
   i1 = 0;
   i2 = 0;
   i3 = 0;
   i4 = 0;
   i5 = 0;
   s1 = strdup("");
   s2 = strdup("");
   s3 = strdup("");
   b1 = false;
   b2 = false;
   b3 = false;
   b4 = false;
   dir1 = strdup(".");
   dir2 = strdup(".");
   export_interval = 0;
   export_fn_prefix = strdup("cell.");
+}
 Parameter::~Parameter() {
 // destruct parameter object
 // free string parameter
 CleanUp();
+}
 void Parameter::CleanUp(void) {
   if (arrowcolor)
      free(arrowcolor);
   if (textcolor)
      free(textcolor);
   if (cell_outline_color)
      free(cell_outline_color);
   if (export_fn_prefix)
      free(export_fn_prefix);
   if (datadir)
      free(datadir);
   if (D)
      free(D);
   if (initval)
      free(initval);
   if (datadir)
      free(datadir);
   if (k)
      free(k);
   if (s1)
      free(s1);
   if (s2)
      free(s2);
   if (s3)
      free(s3);
   if (dir1)
      free(dir1);
   if (dir2)
      free(dir2);
   if (export_fn_prefix)
      free(export_fn_prefix);
+}
 void Parameter::Read(const char *filename) {
   static bool ReadP=false;
   if (ReadP) {
     //throw "Run Time Error in parameter.cpp: Please Read parameter file only once!!";
     CleanUp();
   } else
     ReadP=true;
   FILE *fp=OpenReadFile(filename);
   arrowcolor = sgetpar(fp, "arrowcolor", "white", true);
   arrowsize = fgetpar(fp, "arrowsize", 100, true);
   textcolor = sgetpar(fp, "textcolor", "red", true);
   cellnumsize = igetpar(fp, "cellnumsize", 1, true);
   nodenumsize = igetpar(fp, "nodenumsize", 1, true);
   node_mag = fgetpar(fp, "node_mag", 1.0, true);
   outlinewidth = fgetpar(fp, "outlinewidth", 1.0, true);
   cell_outline_color = sgetpar(fp, "cell_outline_color", "forestgreen", true);
   resize_stride = igetpar(fp, "resize_stride", 0, true);
   export_interval = igetpar(fp, "export_interval", 0, true);
   export_fn_prefix = sgetpar(fp, "export_fn_prefix", "cell.", true);
   storage_stride = igetpar(fp, "storage_stride", 10, true);
   xml_storage_stride = igetpar(fp, "xml_storage_stride", 500, true);
   datadir = sgetpar(fp, "datadir", ".", true);
   datadir = AppendHomeDirIfPathRelative(datadir);
   if (strcmp(datadir, "."))
     MakeDir(datadir);
   T = fgetpar(fp, "T", 1.0, true);
   lambda_length = fgetpar(fp, "lambda_length", 100., true);
   yielding_threshold = fgetpar(fp, "yielding_threshold", 4., true);
   lambda_celllength = fgetpar(fp, "lambda_celllength", 0., true);
   target_length = fgetpar(fp, "target_length", 60., true);
   cell_expansion_rate = fgetpar(fp, "cell_expansion_rate", 1., true);
   cell_div_expansion_rate = fgetpar(fp, "cell_div_expansion_rate", 0., true);
   auxin_dependent_growth = bgetpar(fp, "auxin_dependent_growth", true, true);
   ode_accuracy = fgetpar(fp, "ode_accuracy", 1e-4, true);
   mc_stepsize = fgetpar(fp, "mc_stepsize", 0.4, true);
   mc_cell_stepsize = fgetpar(fp, "mc_cell_stepsize", 0.2, true);
   energy_threshold = fgetpar(fp, "energy_threshold", 1000., true);
   bend_lambda = fgetpar(fp, "bend_lambda", 0., true);
   alignment_lambda = fgetpar(fp, "alignment_lambda", 0., true);
   rel_cell_div_threshold = fgetpar(fp, "rel_cell_div_threshold", 2., true);
   rel_perimeter_stiffness = fgetpar(fp, "rel_perimeter_stiffness", 2, true);
   collapse_node_threshold = fgetpar(fp, "collapse_node_threshold", 0.05, true);
   morphogen_div_threshold = fgetpar(fp, "morphogen_div_threshold", 0.2, true);
   morphogen_expansion_threshold = fgetpar(fp, "morphogen_expansion_threshold", 0.01, true);
   copy_wall = bgetpar(fp, "copy_wall", true, true);
   source = fgetpar(fp, "source", 0., true);
   D = dgetparlist(fp, "D", 15, true);
   initval = dgetparlist(fp, "initval", 15, true);
   k1 = fgetpar(fp, "k1", 1., true);
@@ @@ -285,122 +293,127 @@ void Parameter::Read(const char *filenam @@
   ka = fgetpar(fp, "ka", 1, true);
   pin_prod = fgetpar(fp, "pin_prod", 0.001, true);
   pin_prod_in_epidermis = fgetpar(fp, "pin_prod_in_epidermis", 0.1, true);
   pin_breakdown = fgetpar(fp, "pin_breakdown", 0.001, true);
   pin_breakdown_internal = fgetpar(fp, "pin_breakdown_internal", 0.001, true);
   aux1prod = fgetpar(fp, "aux1prod", 0.001, true);
   aux1prodmeso = fgetpar(fp, "aux1prodmeso", 0., true);
   aux1decay = fgetpar(fp, "aux1decay", 0.001, true);
   aux1decaymeso = fgetpar(fp, "aux1decaymeso", 0.1, true);
   aux1transport = fgetpar(fp, "aux1transport", 0.036, true);
   aux_cons = fgetpar(fp, "aux_cons", 0., true);
   aux_breakdown = fgetpar(fp, "aux_breakdown", 0., true);
   kaux1 = fgetpar(fp, "kaux1", 1, true);
   kap = fgetpar(fp, "kap", 1, true);
   leaf_tip_source = fgetpar(fp, "leaf_tip_source", 0.001, true);
   sam_efflux = fgetpar(fp, "sam_efflux", 0.0001, true);
   sam_auxin = fgetpar(fp, "sam_auxin", 10., true);
   sam_auxin_breakdown = fgetpar(fp, "sam_auxin_breakdown", 0, true);
   van3prod = fgetpar(fp, "van3prod", 0.002, true);
   van3autokat = fgetpar(fp, "van3autokat", 0.1, true);
   van3sat = fgetpar(fp, "van3sat", 10, true);
   k2van3 = fgetpar(fp, "k2van3", 0.3, true);
   dt = fgetpar(fp, "dt", 0.1, true);
   rd_dt = fgetpar(fp, "rd_dt", 1.0, true);
   datadir = sgetpar(fp, "datadir", ".", true);
   datadir = AppendHomeDirIfPathRelative(datadir);
   if (strcmp(datadir, "."))
     MakeDir(datadir);
   movie = bgetpar(fp, "movie", false, true);
   nit = igetpar(fp, "nit", 100000, true);
   maxt = fgetpar(fp, "maxt", 1000., true);
   storage_stride = igetpar(fp, "storage_stride", 10, true);
   xml_storage_stride = igetpar(fp, "xml_storage_stride", 500, true);
   rseed = igetpar(fp, "rseed", -1, true);
   constituous_expansion_limit = igetpar(fp, "constituous_expansion_limit", 16, true);
   vessel_inh_level = fgetpar(fp, "vessel_inh_level", 1, true);
   vessel_expansion_rate = fgetpar(fp, "vessel_expansion_rate", 0.25, true);
   d = fgetpar(fp, "d", 0., true);
   e = fgetpar(fp, "e", 0., true);
   f = fgetpar(fp, "f", 0., true);
   c = fgetpar(fp, "c", 0., true);
   mu = fgetpar(fp, "mu", 0., true);
   nu = fgetpar(fp, "nu", 0., true);
   rho0 = fgetpar(fp, "rho0", 0., true);
   rho1 = fgetpar(fp, "rho1", 0., true);
   c0 = fgetpar(fp, "c0", 0., true);
   gamma = fgetpar(fp, "gamma", 0., true);
   eps = fgetpar(fp, "eps", 0., true);
   k = dgetparlist(fp, "k", 15, true);
   i1 = igetpar(fp, "i1", 0, true);
   i2 = igetpar(fp, "i2", 0, true);
   i3 = igetpar(fp, "i3", 0, true);
   i4 = igetpar(fp, "i4", 0, true);
   i5 = igetpar(fp, "i5", 0, true);
   s1 = sgetpar(fp, "s1", "", true);
   s2 = sgetpar(fp, "s2", "", true);
   s3 = sgetpar(fp, "s3", "", true);
   b1 = bgetpar(fp, "b1", false, true);
   b2 = bgetpar(fp, "b2", false, true);
   b3 = bgetpar(fp, "b3", false, true);
   b4 = bgetpar(fp, "b4", false, true);
   dir1 = sgetpar(fp, "dir1", ".", true);
   if (strcmp(dir1, "."))
     MakeDir(dir1);
   dir2 = sgetpar(fp, "dir2", ".", true);
   if (strcmp(dir2, "."))
     MakeDir(dir2);
   export_interval = igetpar(fp, "export_interval", 0, true);
   export_fn_prefix = sgetpar(fp, "export_fn_prefix", "cell.", true);
+}
 const char *sbool(const bool &p) {
   const char *true_str="true";
   const char *false_str="false";
   if (p)
     return true_str;
   else
     return false_str;
+}
 void Parameter::Write(ostream &os) const {
   if (arrowcolor)
   os << " arrowcolor = " << arrowcolor << endl;
   os << " arrowsize = " << arrowsize << endl;
   if (textcolor)
   os << " textcolor = " << textcolor << endl;
   os << " cellnumsize = " << cellnumsize << endl;
   os << " nodenumsize = " << nodenumsize << endl;
   os << " node_mag = " << node_mag << endl;
   os << " outlinewidth = " << outlinewidth << endl;
   if (cell_outline_color)
   os << " cell_outline_color = " << cell_outline_color << endl;
   os << " resize_stride = " << resize_stride << endl;
   os << " export_interval = " << export_interval << endl;
   if (export_fn_prefix)
   os << " export_fn_prefix = " << export_fn_prefix << endl;
   os << " storage_stride = " << storage_stride << endl;
   os << " xml_storage_stride = " << xml_storage_stride << endl;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      os << " datadir = " << dataDir.dirName().toStdString() << endl;
+                                 }
                                  else {
                                      os << "datadir = ." << endl;
+                                 }
   os << " T = " << T << endl;
   os << " lambda_length = " << lambda_length << endl;
   os << " yielding_threshold = " << yielding_threshold << endl;
   os << " lambda_celllength = " << lambda_celllength << endl;
   os << " target_length = " << target_length << endl;
   os << " cell_expansion_rate = " << cell_expansion_rate << endl;
   os << " cell_div_expansion_rate = " << cell_div_expansion_rate << endl;
   os << " auxin_dependent_growth = " << sbool(auxin_dependent_growth) << endl;
   os << " ode_accuracy = " << ode_accuracy << endl;
   os << " mc_stepsize = " << mc_stepsize << endl;
   os << " mc_cell_stepsize = " << mc_cell_stepsize << endl;
   os << " energy_threshold = " << energy_threshold << endl;
   os << " bend_lambda = " << bend_lambda << endl;
   os << " alignment_lambda = " << alignment_lambda << endl;
   os << " rel_cell_div_threshold = " << rel_cell_div_threshold << endl;
   os << " rel_perimeter_stiffness = " << rel_perimeter_stiffness << endl;
   os << " collapse_node_threshold = " << collapse_node_threshold << endl;
   os << " morphogen_div_threshold = " << morphogen_div_threshold << endl;
   os << " morphogen_expansion_threshold = " << morphogen_expansion_threshold << endl;
   os << " copy_wall = " << sbool(copy_wall) << endl;
   os << " source = " << source << endl;
   os << " D = "<< D[0] << ", " << D[1] << ", " << D[2] << ", " << D[3] << ", " << D[4] << ", " << D[5] << ", " << D[6] << ", " << D[7] << ", " << D[8] << ", " << D[9] << ", " << D[10] << ", " << D[11] << ", " << D[12] << ", " << D[13] << ", " << D[14] << endl;
   os << " initval = "<< initval[0] << ", " << initval[1] << ", " << initval[2] << ", " << initval[3] << ", " << initval[4] << ", " << initval[5] << ", " << initval[6] << ", " << initval[7] << ", " << initval[8] << ", " << initval[9] << ", " << initval[10] << ", " << initval[11] << ", " << initval[12] << ", " << initval[13] << ", " << initval[14] << endl;
   os << " k1 = " << k1 << endl;
@@ @@ -413,104 +426,91 @@ void Parameter::Write(ostream &os) const @@
   os << " ka = " << ka << endl;
   os << " pin_prod = " << pin_prod << endl;
   os << " pin_prod_in_epidermis = " << pin_prod_in_epidermis << endl;
   os << " pin_breakdown = " << pin_breakdown << endl;
   os << " pin_breakdown_internal = " << pin_breakdown_internal << endl;
   os << " aux1prod = " << aux1prod << endl;
   os << " aux1prodmeso = " << aux1prodmeso << endl;
   os << " aux1decay = " << aux1decay << endl;
   os << " aux1decaymeso = " << aux1decaymeso << endl;
   os << " aux1transport = " << aux1transport << endl;
   os << " aux_cons = " << aux_cons << endl;
   os << " aux_breakdown = " << aux_breakdown << endl;
   os << " kaux1 = " << kaux1 << endl;
   os << " kap = " << kap << endl;
   os << " leaf_tip_source = " << leaf_tip_source << endl;
   os << " sam_efflux = " << sam_efflux << endl;
   os << " sam_auxin = " << sam_auxin << endl;
   os << " sam_auxin_breakdown = " << sam_auxin_breakdown << endl;
   os << " van3prod = " << van3prod << endl;
   os << " van3autokat = " << van3autokat << endl;
   os << " van3sat = " << van3sat << endl;
   os << " k2van3 = " << k2van3 << endl;
   os << " dt = " << dt << endl;
   os << " rd_dt = " << rd_dt << endl;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      os << " datadir = " << dataDir.dirName().toStdString() << endl;
+                                 }
                                  else {
                                      os << "datadir = ." << endl;
+                                 }
   os << " movie = " << sbool(movie) << endl;
   os << " nit = " << nit << endl;
   os << " maxt = " << maxt << endl;
   os << " storage_stride = " << storage_stride << endl;
   os << " xml_storage_stride = " << xml_storage_stride << endl;
   os << " rseed = " << rseed << endl;
   os << " constituous_expansion_limit = " << constituous_expansion_limit << endl;
   os << " vessel_inh_level = " << vessel_inh_level << endl;
   os << " vessel_expansion_rate = " << vessel_expansion_rate << endl;
   os << " d = " << d << endl;
   os << " e = " << e << endl;
   os << " f = " << f << endl;
   os << " c = " << c << endl;
   os << " mu = " << mu << endl;
   os << " nu = " << nu << endl;
   os << " rho0 = " << rho0 << endl;
   os << " rho1 = " << rho1 << endl;
   os << " c0 = " << c0 << endl;
   os << " gamma = " << gamma << endl;
   os << " eps = " << eps << endl;
   os << " k = "<< k[0] << ", " << k[1] << ", " << k[2] << ", " << k[3] << ", " << k[4] << ", " << k[5] << ", " << k[6] << ", " << k[7] << ", " << k[8] << ", " << k[9] << ", " << k[10] << ", " << k[11] << ", " << k[12] << ", " << k[13] << ", " << k[14] << endl;
   os << " i1 = " << i1 << endl;
   os << " i2 = " << i2 << endl;
   os << " i3 = " << i3 << endl;
   os << " i4 = " << i4 << endl;
   os << " i5 = " << i5 << endl;
   if (s1)
   os << " s1 = " << s1 << endl;
   if (s2)
   os << " s2 = " << s2 << endl;
   if (s3)
   os << " s3 = " << s3 << endl;
   os << " b1 = " << sbool(b1) << endl;
   os << " b2 = " << sbool(b2) << endl;
   os << " b3 = " << sbool(b3) << endl;
   os << " b4 = " << sbool(b4) << endl;
   if (dir1)
   os << " dir1 = " << dir1 << endl;
   if (dir2)
   os << " dir2 = " << dir2 << endl;
   os << " export_interval = " << export_interval << endl;
   if (export_fn_prefix)
   os << " export_fn_prefix = " << export_fn_prefix << endl;
+}
 void Parameter::XMLAdd(xmlNode *root) const {
     xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL);
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowcolor" );
   ostringstream text;
   if (arrowcolor)
     text << arrowcolor;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowsize" );
   ostringstream text;
     text << arrowsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "textcolor" );
   ostringstream text;
@@ @@ -544,48 +544,89 @@ xmlNewProp(xmlpar, BAD_CAST "val", BAD_C @@
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "outlinewidth" );
   ostringstream text;
     text << outlinewidth;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_outline_color" );
   ostringstream text;
   if (cell_outline_color)
     text << cell_outline_color;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "resize_stride" );
   ostringstream text;
     text << resize_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_interval" );
   ostringstream text;
     text << export_interval;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_fn_prefix" );
   ostringstream text;
   if (export_fn_prefix)
     text << export_fn_prefix;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "storage_stride" );
   ostringstream text;
     text << storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "xml_storage_stride" );
   ostringstream text;
     text << xml_storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "datadir" );
   ostringstream text;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      text << dataDir.dirName().toStdString();
+                                   }
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "T" );
   ostringstream text;
     text << T;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_length" );
   ostringstream text;
     text << lambda_length;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "yielding_threshold" );
   ostringstream text;
     text << yielding_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_celllength" );
   ostringstream text;
     text << lambda_celllength;
@@ @@ -1098,94 +1139,69 @@ xmlNewProp(xmlpar, BAD_CAST "val", BAD_C @@
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k2van3" );
   ostringstream text;
     text << k2van3;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dt" );
   ostringstream text;
     text << dt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rd_dt" );
   ostringstream text;
     text << rd_dt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "datadir" );
   ostringstream text;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      text << dataDir.dirName().toStdString();
+                                   }
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "movie" );
   ostringstream text;
 text << sbool(movie);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nit" );
   ostringstream text;
     text << nit;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "maxt" );
   ostringstream text;
     text << maxt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "storage_stride" );
   ostringstream text;
     text << storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "xml_storage_stride" );
   ostringstream text;
     text << xml_storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rseed" );
   ostringstream text;
     text << rseed;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "constituous_expansion_limit" );
   ostringstream text;
     text << constituous_expansion_limit;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_inh_level" );
   ostringstream text;
     text << vessel_inh_level;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_expansion_rate" );
   ostringstream text;
     text << vessel_expansion_rate;
@@ @@ -1450,104 +1466,109 @@ xmlNewProp(xmlpar, BAD_CAST "val", BAD_C @@
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b4" );
   ostringstream text;
 text << sbool(b4);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir1" );
   ostringstream text;
   if (dir1)
     text << dir1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir2" );
   ostringstream text;
   if (dir2)
     text << dir2;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_interval" );
   ostringstream text;
     text << export_interval;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_fn_prefix" );
   ostringstream text;
   if (export_fn_prefix)
     text << export_fn_prefix;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+}
 void Parameter::AssignValToPar(const char *namec, const char *valc) {
   QLocale standardlocale(QLocale::C);
   bool ok;
 if (!strcmp(namec, "arrowcolor")) {
   if (arrowcolor) { free(arrowcolor); }
   arrowcolor=strdup(valc);
+}
 if (!strcmp(namec, "arrowsize")) {
   arrowsize = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'arrowsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "textcolor")) {
   if (textcolor) { free(textcolor); }
   textcolor=strdup(valc);
+}
 if (!strcmp(namec, "cellnumsize")) {
   cellnumsize = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'cellnumsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "nodenumsize")) {
   nodenumsize = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nodenumsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "node_mag")) {
   node_mag = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'node_mag' from XML file.",valc); }
+}
 if (!strcmp(namec, "outlinewidth")) {
   outlinewidth = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'outlinewidth' from XML file.",valc); }
+}
 if (!strcmp(namec, "cell_outline_color")) {
   if (cell_outline_color) { free(cell_outline_color); }
   cell_outline_color=strdup(valc);
+}
 if (!strcmp(namec, "resize_stride")) {
   resize_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'resize_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "export_interval")) {
   export_interval = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'export_interval' from XML file.",valc); }
+}
 if (!strcmp(namec, "export_fn_prefix")) {
   if (export_fn_prefix) { free(export_fn_prefix); }
   export_fn_prefix=strdup(valc);
+}
 if (!strcmp(namec, "storage_stride")) {
   storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "xml_storage_stride")) {
   xml_storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'xml_storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "datadir")) {
   if (datadir) { free(datadir); }
   datadir=strdup(valc);
   datadir = AppendHomeDirIfPathRelative(datadir);
+}
 if (!strcmp(namec, "T")) {
   T = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'T' from XML file.",valc); }
+}
 if (!strcmp(namec, "lambda_length")) {
   lambda_length = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_length' from XML file.",valc); }
+}
 if (!strcmp(namec, "yielding_threshold")) {
   yielding_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'yielding_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "lambda_celllength")) {
   lambda_celllength = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_celllength' from XML file.",valc); }
+}
 if (!strcmp(namec, "target_length")) {
   target_length = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'target_length' from XML file.",valc); }
+}
 if (!strcmp(namec, "cell_expansion_rate")) {
   cell_expansion_rate = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'cell_expansion_rate' from XML file.",valc); }
+}
@@ @@ -1712,72 +1733,59 @@ if (!strcmp(namec, "sam_auxin_breakdown" @@
 if (!strcmp(namec, "van3prod")) {
   van3prod = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3prod' from XML file.",valc); }
+}
 if (!strcmp(namec, "van3autokat")) {
   van3autokat = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3autokat' from XML file.",valc); }
+}
 if (!strcmp(namec, "van3sat")) {
   van3sat = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3sat' from XML file.",valc); }
+}
 if (!strcmp(namec, "k2van3")) {
   k2van3 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k2van3' from XML file.",valc); }
+}
 if (!strcmp(namec, "dt")) {
   dt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'dt' from XML file.",valc); }
+}
 if (!strcmp(namec, "rd_dt")) {
   rd_dt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rd_dt' from XML file.",valc); }
+}
 if (!strcmp(namec, "datadir")) {
   if (datadir) { free(datadir); }
   datadir=strdup(valc);
   datadir = AppendHomeDirIfPathRelative(datadir);
+}
 if (!strcmp(namec, "movie")) {
 movie = strtobool(valc);
+}
 if (!strcmp(namec, "nit")) {
   nit = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nit' from XML file.",valc); }
+}
 if (!strcmp(namec, "maxt")) {
   maxt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'maxt' from XML file.",valc); }
+}
 if (!strcmp(namec, "storage_stride")) {
   storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "xml_storage_stride")) {
   xml_storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'xml_storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "rseed")) {
   rseed = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'rseed' from XML file.",valc); }
+}
 if (!strcmp(namec, "constituous_expansion_limit")) {
   constituous_expansion_limit = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'constituous_expansion_limit' from XML file.",valc); }
+}
 if (!strcmp(namec, "vessel_inh_level")) {
   vessel_inh_level = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_inh_level' from XML file.",valc); }
+}
 if (!strcmp(namec, "vessel_expansion_rate")) {
   vessel_expansion_rate = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_expansion_rate' from XML file.",valc); }
+}
 if (!strcmp(namec, "d")) {
   d = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'd' from XML file.",valc); }
+}
 if (!strcmp(namec, "e")) {
   e = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'e' from XML file.",valc); }
+}
@@ @@ -1848,56 +1856,48 @@ if (!strcmp(namec, "s2")) { @@
 if (!strcmp(namec, "s3")) {
   if (s3) { free(s3); }
   s3=strdup(valc);
+}
 if (!strcmp(namec, "b1")) {
 b1 = strtobool(valc);
+}
 if (!strcmp(namec, "b2")) {
 b2 = strtobool(valc);
+}
 if (!strcmp(namec, "b3")) {
 b3 = strtobool(valc);
+}
 if (!strcmp(namec, "b4")) {
 b4 = strtobool(valc);
+}
 if (!strcmp(namec, "dir1")) {
   if (dir1) { free(dir1); }
   dir1=strdup(valc);
+}
 if (!strcmp(namec, "dir2")) {
   if (dir2) { free(dir2); }
   dir2=strdup(valc);
+}
 if (!strcmp(namec, "export_interval")) {
   export_interval = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'export_interval' from XML file.",valc); }
+}
 if (!strcmp(namec, "export_fn_prefix")) {
   if (export_fn_prefix) { free(export_fn_prefix); }
   export_fn_prefix=strdup(valc);
+}
+}
 void Parameter::AssignValArrayToPar(const char *namec, vector<double> valarray) {
 if (!strcmp(namec, "D")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      D[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "initval")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      initval[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "k")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      k[i++]=*(v++);
+  }
+}
+}

src/parameter.h

➞

Show inline comments

@@ @@ -32,48 +32,53 @@ @@
 #include <libxml/parser.h>
 #include <libxml/tree.h>
  class Parameter {
  public:
    Parameter();
    ~Parameter();
    void CleanUp(void);
    void Read(const char *filename);
    void Write(ostream &os) const;
    void XMLAdd(xmlNode *root) const;
    void XMLRead(xmlNode *root);
    void AssignValToPar(const char *namec, const char *valc);
    void AssignValArrayToPar(const char *namec, vector<double> valarray);
   char * arrowcolor;
   double arrowsize;
   char * textcolor;
   int cellnumsize;
   int nodenumsize;
   double node_mag;
   double outlinewidth;
   char * cell_outline_color;
   int resize_stride;
   int export_interval;
   char * export_fn_prefix;
   int storage_stride;
   int xml_storage_stride;
   char * datadir;
   double T;
   double lambda_length;
   double yielding_threshold;
   double lambda_celllength;
   double target_length;
   double cell_expansion_rate;
   double cell_div_expansion_rate;
   bool auxin_dependent_growth;
   double ode_accuracy;
   double mc_stepsize;
   double mc_cell_stepsize;
   double energy_threshold;
   double bend_lambda;
   double alignment_lambda;
   double rel_cell_div_threshold;
   double rel_perimeter_stiffness;
   double collapse_node_threshold;
   double morphogen_div_threshold;
   double morphogen_expansion_threshold;
   bool copy_wall;
   double source;
   double * D;
   double * initval;
   double k1;
@@ @@ -86,70 +91,65 @@ @@
   double ka;
   double pin_prod;
   double pin_prod_in_epidermis;
   double pin_breakdown;
   double pin_breakdown_internal;
   double aux1prod;
   double aux1prodmeso;
   double aux1decay;
   double aux1decaymeso;
   double aux1transport;
   double aux_cons;
   double aux_breakdown;
   double kaux1;
   double kap;
   double leaf_tip_source;
   double sam_efflux;
   double sam_auxin;
   double sam_auxin_breakdown;
   double van3prod;
   double van3autokat;
   double van3sat;
   double k2van3;
   double dt;
   double rd_dt;
   char * datadir;
   bool movie;
   int nit;
   double maxt;
   int storage_stride;
   int xml_storage_stride;
   int rseed;
   int constituous_expansion_limit;
   double vessel_inh_level;
   double vessel_expansion_rate;
   double d;
   double e;
   double f;
   double c;
   double mu;
   double nu;
   double rho0;
   double rho1;
   double c0;
   double gamma;
   double eps;
   double * k;
   int i1;
   int i2;
   int i3;
   int i4;
   int i5;
   char * s1;
   char * s2;
   char * s3;
   bool b1;
   bool b2;
   bool b3;
   bool b4;
   char * dir1;
   char * dir2;
   int export_interval;
   char * export_fn_prefix;
  private:
  };
  ostream &operator<<(ostream &os, Parameter &p);
  const char *sbool(const bool &p);
 #endif

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