EI/VirtualLeaf Changeset - f563ace40263 · Centrum Wiskunde & Informatica (CWI)

Changeset - f563ace40263

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Roeland Merks - 15 years ago 2010-11-24 18:24:58
roeland.merks@cwi.nl

In response to referee's comment

"I am also afraid that the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very well in my hands, could the program be changed so that the correct file extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically."

I corrected the "exportCellData()" function in canvas.cpp. It did not actually call exportCellData(filename) after the user entered a filename (logic after calling QMessageBox was incorrect).

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/canvas.cpp

1 file changed with 7 insertions and 2 deletions:

src/canvas.cpp

0 comments (0 inline, 0 general)

src/canvas.cpp

➞

Show inline comments

@@ @@ -616,808 +616,813 @@ Main::~Main() @@
+  }
   //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)");
   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)");
   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( "XML (*.xml)");
   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->setMode( Q3FileDialog::AnyFile );
   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 snapshot();
     } else {
       // extract extension from filename
       QString extension = getExtension(fileName);
       // Save bitmaps at 1024x768
       Save((const char *)fileName, extension, 1024, 768);
+    }
+  }
+}
 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);
     Plot();
     QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
     setCaption(caption_with_file.arg(filename));
     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);
+  }
+}
 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( "XML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
+  }
   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();
+}
 void Main::toggleShowWalls()
+{
   Plot();
+}
 void Main::toggleShowApoplasts()
+{
   Plot();
+}
 void Main::toggleShowNodes()
+{
   Plot();
+}
 void Main::toggleNodeNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellAxes(void)
+{
   Plot();
+}
 void Main::toggleCellStrain(void)
+{
   Plot();
+}
 void Main::toggleShowFluxes(void)
+{
   Plot();
+}
 void Main::toggleShowBorderCells()
+{
   Plot();
+}
 void Main::toggleHideCells(void)
+{
   Plot();
   editor->FullRedraw();
+}
 void Main::toggleMovieFrames(){}
 void Main::toggleLeafBoundary(){}
 void Main::toggleDynCells() {}
 void Main::startSimulation(void)
+{
   timer->start( 0 );
   statusBar()->message("Simulation started");
   running = true;
+}
 void Main::stopSimulation(void)
+{
   timer->stop();
   cerr << "Stopping simulation" << endl;
   statusBar()->message("Simulation paused");
   running = false;
+}
 void Main::togglePaused()
+{
   bool s = run->isItemChecked(paused_id);
   if (s) {
     cerr << "Calling start simulation" << endl;
     startSimulation();
   } else {
     cerr << "Calling stop simulation" << endl;
     stopSimulation();
+  }
+}
 void Main::setFluxArrowSize(int size)
+{
   flux_arrow_size = size/100.;
+}
 void Main::enlarge()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*4./3., canvas.height()*4./3.) );
+}
 void Main::shrink()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*3/4, canvas.height()*3/4) );
+}
 void Main::scale(double factor)
+{
   QMatrix m = editor->matrix();
   m.scale(factor, factor);
   editor->setMatrix( m );
+}
 void Main::zoomIn()
+{
   QMatrix m = editor->matrix();
   m.scale( 1.1, 1.1 );
   editor->setMatrix( m );
+}
 void Main::zoomOut()
+{
   QMatrix m = editor->matrix();
   m.scale( 0.9, 0.9 );
   editor->setMatrix( m );
+}
 void Main::print()
+{
   if ( !printer ) printer = new QPrinter;
   if ( printer->setup(this) ) {
     //    extern Mesh mesh;
     Vector bbll,bbur;
     mesh.BoundingBox(bbll,bbur);
 #ifdef QDEBUG
     qDebug() << "bbll = " << bbll << endl;
     qDebug() << "bbur = " << bbur << endl;
 #endif
     double cw = (bbur.x - bbll.x);
     double ch = (bbur.y - bbll.y);
     QPainter pp(printer);
     QRect vp=pp.viewport();
 #ifdef QDEBUG
     qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;
 #endif
     // Note that Cell is also translated...
     pp.translate(-bbur.x,-bbur.y);
     if (cw>ch) {
       pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));
     } else {
       pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));
+    }
     canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));
+  }
+}
 void Main::TimeStepWrap(void)
+{
   static int t;
   stringstream fname;
   TimeStep();
   t = (int)mesh.getTime();
   if ((par.export_interval > 0) && !(t%par.export_interval)){
     fname << par.datadir << "/" << par.export_fn_prefix;
     fname.fill('0');
     fname.width(6);
     fname << t << ".csv";
     this->exportCellData(QString(fname.str().c_str()));
+  }
   // check number of timesteps
   if (t == par.nit) {
     emit SimulationDone();
+  }
+}
 void Main::RestartSim(void)
+{
   stopSimulation();
   if ( QMessageBox::question(
 			     this,
 			     tr("Restart simulation?"),
 			     tr("Restart simulation.\n"
 				"Are you sure?"),
 			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
     cerr << "Restarting simulation" << endl;
     //    extern Mesh mesh;
     mesh.Clear();
     Init();
     Plot();
     editor->FullRedraw();
+  }
   //startSimulation();
+}
 void Main::FitCanvasToWindow(void)
+{
   double scale_factor_x = (double)editor->width()/(double)canvas.width();
   double scale_factor_y = (double)editor->height()/(double)canvas.height();
   double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;
   QMatrix m = editor->matrix();
 #ifdef QDEBUG
   qDebug() << "editor->width() = " << editor->width() << endl;
   qDebug() << "editor->height() = " << editor->height() << endl;
   qDebug() << "scale_factor = " << scale_factor << endl;
   qDebug() << "scale_factor_x = " << scale_factor_x << endl;
   qDebug() << "scale_factor_y = " << scale_factor_y << endl;
 #endif
   m.scale( scale_factor, scale_factor );
   editor->setMatrix( m );
   editor->show();
+}
 void Main::PauseIfRunning(void)
+{
   if (running) {
     timer->stop();
+  }
+}
 void Main::ContIfRunning(void)
+{
   if (running) {
     timer->start( 0 );
+  }
+}
 void Main::FitLeafToCanvas(void)
+{
   Vector ll,ur;
   mesh.BoundingBox(ll, ur);
   ll*=Cell::Magnification(); ur*=Cell::Magnification();
   // give the leaf some space
   Vector border = ((ur-ll)/5.);
   QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );
   // cerr << ur << ", " << ll << endl;
   // editor->fitInView(bb, Qt::KeepAspectRatio);
   editor->ensureVisible(bb);
   //editor->setTransform(viewport);
+}
 void Main::CleanMesh(void)
+{
   vector<double> clean_chem(Cell::NChem());
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
     clean_transporters[i]=0.;
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 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.CSVExportMeshData(stream);
     file.close();
+  }
+}
 void Main::exportCellData() {
   QString fileName;
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	!QMessageBox::question(
+	 !QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Cell Data"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       this->exportCellData(fileName);
       return exportCellData();
     } else {
       exportCellData(fileName);
+    }
+  }
+}
 /* finis */

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