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

16 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

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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/tutorial3_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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 # $Id$
 # Set an environment varible $(MAKE) to the name of the make command
 # on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.
 # Fallback default is UNIX make.
 ifeq ($(MAKE),)
 	MAKE=make
 endif
 # Ditto for QMAKE
 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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@@ @@ -114,199 +114,204 @@ public: @@
   void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) {
 	if (m.ShowToolTipsP()) {
 	  //QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 		QString info_string=QString("Cell %1, chemicals(%2): ").arg(c.Index()).arg(Cell::NChem());
 		for (int i=0;i<Cell::NChem();i++) {
 			info_string += QString("%1 ").arg(c.Chemical(i));
+		}
 		info_string += QString("\nArea is %1\n Circumference is %2\n Boundary type is %3").arg(c.Area()).arg(c.WallCircumference()).arg(c.BoundaryStr());
 	  info_string += "\nNodes: " + c.printednodelist();
 	  c.Draw(&canvas, info_string);
 	} else {
 	  c.Draw(&canvas);
+	}
+      }
       if (m.ShowCentersP()){
 	c.DrawCenter(&canvas);
+      }
       if (m.ShowFluxesP()){
 	c.DrawFluxes(&canvas, par.arrowsize);
+      }
+    }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride)
+{
   clear();
   int count=(int)mesh.getTime();
   if (resize_stride) {
     if ( !((count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );
 /*  if (ShowApoplastsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
 */
   if (ShowMeshP())
     mesh.DrawNodes(&canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&canvas);
   if ( ( batch || MovieFramesP() )) {
     if (!(count%par.storage_stride) ) {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       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();
   double dh;
   if(DynamicCellsP()) {
     dh = mesh.DisplaceNodes();
     // Only allow for node insertion, cell division and cell growth
     // if the system has equillibrized
     // i.e. cell wall tension equillibrization is much faster
     // than biological processes, including division, cell wall yielding
     // and cell expansion
     mesh.InsertNodes(); // (this amounts to cell wall yielding)
     if ( (-dh) < par.energy_threshold) {
       mesh.IncreaseCellCapacityIfNecessary();
       mesh.DoCellHouseKeeping();
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       // Reaction diffusion
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
+    }
   } else {
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e){}
 /* Custom message handler - Default appends a newline character to the end of each line. */
 void vlMessageOutput(QtMsgType type, const char *msg)
+{
   switch (type) {
   case QtDebugMsg:
     //fprintf(stderr, "Debug: %s\n", msg);
     cerr << msg << flush;
     break;
   case QtWarningMsg:
     //fprintf(stderr, "Warning: %s\n", msg);
     cerr << "Warning: " << msg << flush;
     break;
   case QtCriticalMsg:
     fprintf(stderr, "Critical: %s\n", msg);
     cerr << "Critical: " << msg << flush;
     break;
   case QtFatalMsg:
     //fprintf(stderr, "Fatal: %s\n", msg);
     cerr << "Fatal: " << msg << flush;
     abort();
+  }
+}
 Parameter par;
 int main(int argc,char **argv) {
   try {
     int c;
     char *leaffile=0;
     char *modelfile=0;
     while (1) {
@@ @@ -320,145 +325,145 @@ int main(int argc,char **argv) { @@
       };
       // short option 'p' creates trouble for non-commandline usage on MacOSX. Option -p changed to -P (capital)
       static char *short_options = "blm";
       c = getopt_long (argc, argv, "bl:m:",
 		       long_options, &option_index);
       if (c == -1)
 	break;
       if (c==0) {
 	printf ("option %s", long_options[option_index].name);
 	if (optarg)
 	  printf (" with arg %s", optarg);
 	printf ("\n");
 	c = short_options[option_index];
+      }
       switch (c) {
       case 'b':
 	cerr << "Running in batch mode\n";
 	batch=true;
 	break;
       case 'l':
 	leaffile=strdup(optarg);
 	if (!leaffile) {
 	  throw("Out of memory");
+	}
 	printf("Reading leaf state file '%s'\n", leaffile);
 	break;
       case 'm':
 	modelfile=strdup(optarg);
 	if (!modelfile) {
 	  throw("Out of memory");
+	}
 	break;
       case '?':
 	break;
       default:
 	printf ("?? getopt returned character code 0%o ??\n", c);
+      }
+    }
     if (optind < argc) {
       printf ("non-option ARGV-elements: ");
       while (optind < argc)
 	printf ("%s ", argv[optind++]);
       printf ("\n");
+    }
     bool useGUI = !batch;
     qInstallMsgHandler(vlMessageOutput); // custom message handler
     QApplication app(argc,argv,useGUI);
     QPalette tooltippalette = QToolTip::palette();
     QColor transparentcolor = QColor(tooltippalette.brush(QPalette::Window).color());
     tooltippalette.setBrush (QPalette::Window, QBrush (transparentcolor) );
     QToolTip::setPalette( tooltippalette );
     QGraphicsScene canvas(0,0,8000,6000);
     if (useGUI) {
       main_window=new Main(canvas, mesh);
       if ( QApplication::desktop()->width() > ((Main *)main_window)->width() + 10
 	   && QApplication::desktop()->height() > ((Main *)main_window)->height() +30 ) {
 	((Main *)main_window)->show();
 	((Main *)main_window)->resize( ((Main *)main_window)->sizeHint());
       } else {
         ((Main *)main_window)->showMaximized();
+      }
       // 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) {
     if (batch) {
       cerr << "Exception caught:" << endl;
       cerr << message << endl;
       abort();
     } else {
       QString qmess=QString("Exception caught: %1").arg(message);
       QMessageBox::critical(0, "Critical Error", qmess);
       abort();
+    }
   } catch (ios_base::failure) {
     stringstream error_message;
     error_message << "I/O failure: " << strerror(errno);
     if (batch) {
       cerr << error_message.str() <<endl;
       abort();
     } else {
       QString qmess(error_message.str().c_str());
       QMessageBox::critical(0, "I/O Error", qmess );
       abort();
+    }
+  }
+}
 /* finis */

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
 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
 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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@@ @@ -552,260 +552,264 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   // Menu of models
   modelmenu = new QMenu( menu );
   menu->insertItem("&Models", modelmenu);
   menu->insertSeparator();
   helpmenu = new Q3PopupMenu( menu );
   tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));
   helpmenu->setItemChecked(tooltips_id, true);
   helpmenu->insertSeparator();
     //helpmenu->insertSeparator();
   helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );
   helpmenu->insertItem("About", this, SLOT(about()) ); //, Key_F1);
 	menu->insertItem("&Help",helpmenu);
   statusBar();
   setCentralWidget(editor);
   printer = 0;
   init();
   // Start timer which repetitively invokes
   // a simulation time step
   timer = new QTimer( this );
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
 void Main::init()
+{
   clear();
   static int r=24;
   srand(++r);
   mainCount++;
+}
 Main::~Main()
+{
   delete printer;
   if ( !--mainCount ) {
+  }
   //EndGifAnim();
+}
 void Main::newView()
+{
   // Open a new view... have it delete when closed.
   Main *m = new Main(canvas, mesh, 0, 0, Qt::WDestructiveClose);
   qApp->setMainWidget(m);
   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 ),
 			       QMessageBox::Yes, QMessageBox::No
 			       ) == QMessageBox::No
 	 ) {
       return snapshot();
     } else {
       // Save bitmaps at 1024x768
       Save((const char *)fileName, extension, 1024, 768);
       QString status_message = QString("Wrote snapshot to %1").arg(fileName);
       cerr << status_message.toStdString() << endl;
       statusBar()->showMessage(status_message);
+    }
+  }
+}
 void Main::readPrevStateXML()
+{
   // 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 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     if (f==xml_files.begin()) {
       QMessageBox mb( "Read previous leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
 #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
@@ @@ -817,206 +821,245 @@ int Main::readStateXML(const char *filen @@
     statusBar()->message(status_message);
     emit ParsChanged();
 #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
 #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
 		    QMessageBox::Ok | QMessageBox::Default,
 		    Qt::NoButton,
 		    Qt::NoButton);
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML()
+{
   // 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 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     ++f;
     if (f==xml_files.end()) {
       QMessageBox mb( "Read next leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *f;
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readLastStateXML()
+{
   // 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.back();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 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
     ( "VirtualLeaf V1.0",
       "<h3>VirtualLeaf V1.0</h3>"
       "<p>"
       "An Open Source framework for cell-based modeling of plant tissue growth and development <br>"
       "(c) 2005-2008, Roeland Merks <i>et al.</i><br>"
       "    <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>, "
       "Ghent, Belgium <br>"
       "(c) 2008-2010, <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a> <br>"
       "    <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica</a> and <a href=\"http://www.ncsb.nl\">Netherlands Consortium for Systems Biology</a>, Amsterdam, Netherlands <br>"
 "<br>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.<br>"
       "<br>If you use this code for your projects, please cite our paper:"
 "<br>Merks, Guravage, Inze, and Beemster. An Open Source framework for cell-based modeling of plant tissue growth and development. <i>Plant Physiology,</i> submitted.<br> . <br>"
       "<br>Please share your model plugins and extensions at <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
 void Main::gpl()
+{
   static QMessageBox* gpl = new QMessageBox ( "GPL License", "",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   QDir docDir(QApplication::applicationDirPath());
   docDir.cd("../doc"); // Where Linux expects gpl3.txt
   QString path = docDir.filePath("gpl3.txt");
   if (!docDir.exists("gpl3.txt")){
     docDir = QApplication::applicationDirPath();
     docDir.cd("doc"); // Where Windows expects gpl3.txt
     path = docDir.filePath("gpl3.txt");
+  }
   // At this point path points either to the linux variant, which
   // exists, or the windows variant, which may exist. Testing the
   // ifstream object will determine whether we've found gpl3.txt.
   std::ifstream file(path.toStdString().c_str());
   std::string str;
   if (file) {
     file.seekg(0, std::ios::end);
     str.reserve(file.tellg());
     file.seekg(0, std::ios::beg);
     str.assign((std::istreambuf_iterator<char>(file)),
 	       std::istreambuf_iterator<char>());
     gpl->setDetailedText(QString(str.c_str()));
+  }
   gpl->setText(QString( "<h3>GNU GENERAL PUBLIC LICENSE</h3>"
 			"<p>Version 3, 29 June 2007</p>"
 			"<p>Copyright &copy; 2007 Free Software Foundation, Inc. "
 			"&lt;<a href=\"http://fsf.org/\">http://fsf.org/</a>&gt;</p><p>"
 			"Everyone is permitted to copy and distribute verbatim copies "
 			"of this license document, but changing it is not allowed.</p>"
 			"<h2>GNU GENERAL PUBLIC LICENSE</h2>"));
   gpl->setButtonText( 1, "Dismiss" );
   gpl->show();
+}
 void Main::aboutQt(){
   QMessageBox::aboutQt( this, "Virtual Leaf" );
+}
 void Main::toggleShowCellCenters()
+{
   Plot();
+}
@@ @@ -1302,170 +1345,169 @@ void Main::CleanMeshChemicals(void) @@
   vector<double> clean_chem(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshTransporters(void)
+{
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_transporters[i]=0.;
+  }
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::RandomizeMesh(void)
+{
   vector<double> max_chem(Cell::NChem());
   vector<double> max_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     max_transporters[i]=0.;
     max_chem[i]=par.initval[i];
+  }
   // Amount of PIN1 at walls
   max_transporters[1] = 0.01;
   mesh.RandomizeChemicals(max_chem, max_transporters);
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
   view->setItemChecked(com_id, showcentersp);
   view->setItemChecked(mesh_id, showmeshp);
   view->setItemChecked(border_id, showbordercellp);
   view->setItemChecked(node_number_id, shownodenumbersp);
   view->setItemChecked(cell_number_id, showcellnumbersp);
   view->setItemChecked(cell_axes_id, showcellsaxesp);
   view->setItemChecked(cell_strain_id, showcellstrainp);
   view->setItemChecked(movie_frames_id, movieframesp);
   view->setItemChecked(only_boundary_id, showboundaryonlyp);
   view->setItemChecked(fluxes_id, showfluxesp);
   view->setItemChecked(hide_cells_id, hidecellsp);
   options->setItemChecked(dyn_cells_id, dynamicscellsp);
   view->setItemChecked( cell_walls_id, showwallsp);
  // view->setItemChecked( apoplasts_id, showapoplastsp);
   editor->setTransform(viewport);
+}
 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
 	  ) {
 	return exportCellData();
       } else {
 	fileName.replace(extension,"csv");
 	extension="csv";
+      }
+    }
     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 ),
 			       QMessageBox::Yes, QMessageBox::No
 			       ) == QMessageBox::No
 	 ) {
       return exportCellData();
     } else {
       exportCellData(fileName);
       QString status_message = QString("Wrote data file to %1").arg(fileName);
       statusBar()->showMessage(status_message);
+    }
+  }
+}
   /* finis */

src/canvas.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  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.
+ *
  */
 #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"
 #else
 #define PREFIX "crtl"
 #endif
 class QFile;
 class QDir;
 class ModelCatalogue;
 class InfoBar;
 class FigureEditor : public QGraphicsView {
   Q_OBJECT
     friend class Main;
  public:
   FigureEditor(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   void clear();
   void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
   void FullRedraw(void);
  protected:
   void mousePressEvent(QMouseEvent*);
   void mouseMoveEvent(QMouseEvent*);
   void mouseReleaseEvent(QMouseEvent*);
   void wheelEvent(QWheelEvent *event);
   void scaleView(qreal scaleFactor);
   vector <CellItem *> getIntersectedCells(void);
   void insertNode(QPointF p);
   NodeItem *selectedNodeItem(QList<QGraphicsItem *> l) const;
  signals:
   void status(const QString&);
   void MousePressed(void);
   void MouseReleased(void);
  protected:
   Mesh &mesh;
  private:
   //NodeItem* moving;
   SimItemBase *moving;
   QPointF moving_start;
   QGraphicsLineItem *intersection_line;
   bool rotation_mode;
   bool insert_mode;
   double rot_angle;
 };
 class Main : public Q3MainWindow, public MainBase {
   Q_OBJECT
     friend class ModelCatalogue; // needs to populate menu item models
  public:
   Main(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   ~Main();
   virtual bool ShowCentersP(void) {return view->isItemChecked(com_id);}
   virtual bool ShowMeshP(void) {return view->isItemChecked(mesh_id);}
   virtual bool ShowBorderCellsP(void) {return view->isItemChecked(border_id);}
   virtual bool PausedP(void) {return run->isItemChecked(paused_id);}
   virtual bool ShowNodeNumbersP(void) {return view->isItemChecked(node_number_id);}
   virtual bool ShowCellNumbersP(void) {return view->isItemChecked(cell_number_id);}
   virtual bool ShowCellAxesP(void) {return view->isItemChecked(cell_axes_id);}
   virtual bool ShowCellStrainP(void) {return view->isItemChecked(cell_strain_id);}
   virtual bool MovieFramesP(void) {return view->isItemChecked(movie_frames_id);}
   virtual bool ShowBoundaryOnlyP(void) {return view->isItemChecked(only_boundary_id);}
   virtual bool ShowWallsP(void) {return view->isItemChecked(cell_walls_id);}
  // virtual bool ShowApoplastsP(void) { return view->isItemChecked(apoplasts_id);}
   virtual bool ShowFluxesP(void) { return view->isItemChecked(fluxes_id); }
   virtual bool DynamicCellsP(void) { return options->isItemChecked(dyn_cells_id); }
   virtual bool RotationModeP(void) { return options->isItemChecked(rotation_mode_id); }
   virtual bool InsertModeP(void) { return options->isItemChecked(insert_mode_id); }
   virtual bool ShowToolTipsP(void) { return helpmenu->isItemChecked(tooltips_id); }
   virtual bool HideCellsP(void) { return view->isItemChecked(hide_cells_id); }
   void scale(double factor);
   virtual double getFluxArrowsize(void)
+  {
     return flux_arrow_size;
+  }
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   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();
  signals:
   void SimulationDone(void);
   void ParsChanged(void);
  protected:
   Mesh &mesh;
  private:
   NodeSet *node_set;
   FigureEditor *editor;
   Q3PopupMenu* options;
   Q3PopupMenu *view;
   Q3PopupMenu *run;
   QMenu *modelmenu;
   Q3PopupMenu *helpmenu;
   QPrinter* printer;
   const QDir *working_dir;
   QString currentFile;
   //  toggle item states
   int dbf_id; // options->Double Buffer
   int com_id; // view->Show centers
   int mesh_id; // view->Show mesh
   int node_number_id; // view->Show Node numbers
   int cell_number_id; // view->Show Cell numbers
   int border_id; // view->Show border cells
   int paused_id; // run->Simulation paused
   int cell_axes_id; // view->Show cell axes
   int cell_strain_id; // view->Show cell strain
   int only_boundary_id; // view ->Show only leaf boundary
   int cell_walls_id; // view -> Show transporters
   //int apoplasts_id; // view -> Show apoplasts
   int tooltips_id; // help -> Show Cell Info
   int hide_cells_id; // view->Hide Cells
   double flux_arrow_size;
   int movie_frames_id;
   int fluxes_id;
   int dyn_cells_id;
   int rotation_mode_id;
   int insert_mode_id;
   QTimer *timer;
   QFile *gifanim;
   bool running;
   virtual xmlNode *XMLSettingsTree(void);
   static const QString caption;
   static const QString caption_with_file;
   InfoBar *infobar;
 };
 #endif
 /* finis*/

src/mesh.cpp

➞

Show inline comments

@@ @@ -1972,110 +1972,146 @@ void Mesh::StandardInit(void) { @@
 double Mesh::Compactness(double *res_compactness, double *res_area, double *res_cell_area, double *res_circumference) {
   // Calculate compactness using the convex hull of the cells
   // We use Andrew's Monotone Chain Algorithm (see hull.cpp)
   // Step 1. Prepare data for 2D hull code - get boundary polygon
   int pc=0;
   Point *p=new Point[boundary_polygon->nodes.size()+1];
   for (list<Node *>::const_iterator i = boundary_polygon->nodes.begin();
        i!=boundary_polygon->nodes.end(); i++) {
     p[pc++]=Point((*i)->x,(*i)->y);
+  }
   // chainHull algorithm requires sorted points
   qSort( p, p+pc );
   // Step 2: call 2D Hull code
   int np=boundary_polygon->nodes.size();
   Point *hull=new Point[np+1];
   int nph=chainHull_2D(p,np,hull);
   // Step 3: calculate area and circumference of convex hull
   double hull_area=0.;
   double hull_circumference=0.;
   for (int i=0;i<nph-1;i++) {
     hull_area+=hull[i].x * hull[i+1].y - hull[i+1].x * hull[i].y;
     double s_dx=(hull[i+1].x-hull[i].x);
     double s_dy=(hull[i+1].y-hull[i].y);
     double l=sqrt(s_dx*s_dx+s_dy*s_dy);
     //    f << hull[i].x << " " << hull[i].y << " " << hull[i+1].x << " " << hull[i+1].y << " " << l << endl;
     hull_circumference+=l;
+  }
   hull_area/=2.;
   // Step 4: get area of bounary polygon
   double boundary_pol_area = boundary_polygon->CalcArea();
   /*  ofstream datastr("hull.dat");
   for (int i=0;i<nph<i++) {
     datastr << hull.x << " " << hull.y << endl;
+  }
   ofstream polstr("pol.dat");
   for (int i=0;i<np;h*/
   delete[] p;
   delete[] hull;
   // put intermediate results into optional pointers
   if (res_compactness) {
     *res_compactness = boundary_pol_area/hull_area;
+  }
   if (res_area) {
     *res_area = hull_area;
+  }
   if (res_cell_area) {
     *res_cell_area = boundary_pol_area;
+  }
   if (res_circumference) {
     *res_circumference = hull_circumference;
+  }
   // return compactness
   return boundary_pol_area/hull_area;
+}
 // 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

@@ @@ -295,143 +295,144 @@ class Mesh { @@
+    }
+  }
   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();
+    }
+  }
   void Clear();
   void ReactDiffuse( double delta_t = 1 );
   double SumChemical(int ch);
   void SetChemical(int ch, double value) {
     for (vector<Cell *>::iterator c=cells.begin();
 	 c!=cells.end();
 	 c++) {
       (*c)->chem[ch]=value;
+    }
+  }
   // used for interacing with ODE-solvers (e.g. NRCRungeKutta)
   void setValues(double x, double *y);
   double *getValues(int *neqs);
   void Derivatives(double *derivs);
 #ifdef QTGRAPHICS
   inline void DrawBoundary(QGraphicsScene *c) {
     boundary_polygon->Draw(c);
+  }
   void DrawNodes(QGraphicsScene *c) const;
 #endif
   double max_chem;
   void XMLSave(const char *docname, xmlNode *settings=0) const;
   void XMLRead(const char *docname, xmlNode **settings=0, bool geometry = true, bool pars = true, bool simtime = true);
   void XMLReadPars(const xmlNode * root_node);
   void XMLReadGeometry(const xmlNode *root_node);
   void XMLReadSimtime(const xmlNode *root_node);
   void XMLReadNodes(xmlNode *cur);
   void XMLReadCells(xmlNode *cur);
   void XMLParseTree(const xmlNode * root_node);
   void XMLReadWalls(xmlNode *cur, vector<Wall *> *tmp_cells);
   void XMLReadWallsToCells(xmlNode *root, vector<Wall *> *tmp_walls);
   void XMLReadNodeSets(xmlNode *root);
   void XMLReadNodeSetsToNodes(xmlNode *root);
   void PerturbChem(int chemnum, double range);
   void CleanUpCellNodeLists(void);
   void CleanUpWalls(void);
   void CutAwayBelowLine( Vector startpoint, Vector endpoint );
   void CutAwaySAM(void);
   void RepairBoundaryPolygon(void);
   void Rotate(double angle, Vector center);
   void PrintWallList( void );
   void TestIllegalWalls(void);
   Vector FirstConcMoment(int chem);
   inline Vector Centroid(void) {
     return boundary_polygon->Centroid();
+  }
   inline Vector Offset(void) {
     return boundary_polygon->Offset();
+  }
   inline double Factor(void) {
     return boundary_polygon->Factor();
+  }
   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);
   inline Node *AddNode(Node *n) {
     nodes.push_back(n);
     shuffled_nodes.push_back(n);
     n->m=this;
     return n;
+  }
   inline Cell *AddCell(Cell *c) {
     cells.push_back(c);
     shuffled_cells.push_back(c);
     //cerr << "Shuffled cell indices:  ";
     /*copy(shuffled_cells.begin(),shuffled_cells.end(),ostream_iterator<int>(cerr," "));
       cerr << endl;*/
     c->m=this;
     return c;
+  }
   void CircumCircle(double x1,double y1,double x2,double y2,double x3,double y3,
 		    double *xc,double *yc,double *r);
 };
 #endif
 /* finis */

src/modelcatalogue.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  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();
     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 {
       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!");
+  }
   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") {
 	pluginDir.cdUp();
+      }
       cerr << "pluginDir: " << pluginDir.dirName().toStdString().c_str() << endl;
       if (!pluginDir.cd("data/leaves")) {
 	MyWarning::warning("Directory 'data/leaves' not found! Cannot load LeafML file '%s'. Reverting to standard initial condition now...",plugin->DefaultLeafML().toStdString().c_str());
 	mainwin->Init(0);
       } else {
 	if (!pluginDir.exists(plugin->DefaultLeafML())) {
 	  MyWarning::error("LeafML file '%s' not found - hint: is file in data/leaves folder? Reverting to standard initial condition now...",plugin->DefaultLeafML().toStdString().c_str());
 	  mainwin->Init(0);
 	} else {
 	  // Initialize simulation using default LeafML file referenced in plugin.
 	  //mainwin->Init(0);
 	  cerr << "Default LeafML: " << plugin->DefaultLeafML().toStdString().c_str() << endl;
 	  mainwin->Init(pluginDir.absFilePath(plugin->DefaultLeafML()).toStdString().c_str());
+	}
+      }
+    }
+  }
+}

src/modelcatalogue.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  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.
+ *
  */
 #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 */

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