EI/VirtualLeaf Changeset - 6d2e1692ec10 · Centrum Wiskunde & Informatica (CWI)

Changeset - 6d2e1692ec10

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Roeland Merks - 15 years ago 2010-05-26 10:47:32
roeland.merks@cwi.nl

I've repaired VLeaf's batch mode to work with dynamic model loading. There is a new option now "-m" that allows you to supply a model name.

For example:

./VirtualLeaf -l ../data/leaves/auxin_growth.xml -m libauxingrowth.so -b

or

./VirtualLeaf --leaffile ../data/leaves/auxin_growth.xml --model libauxingrowth.so --batch

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/warning.cpp

5 files changed with 92 insertions and 27 deletions:

src/VirtualLeaf.cpp

src/VirtualLeaf.pro

src/modelcatalogue.cpp

src/modelcatalogue.h

src/warning.cpp

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src/VirtualLeaf.cpp

➞

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@@ @@ -7,542 +7,550 @@ @@
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include <fstream>
 #include <sstream>
 #include <cstring>
 #include <functional>
 #include <getopt.h>
 #include <cerrno>
 #include "mesh.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "cellitem.h"
 #include "canvas.h"
 #include "cell.h"
 #include "output.h"
 #include <qwidget.h>
 #include <q3process.h>
 #include <qapplication.h>
 #include <QDesktopWidget>
 #include <QGraphicsScene>
 #include <QMessageBox>
 //Added by qt3to4:
 #include <QMouseEvent>
 #include <unistd.h>
 #include <q3textstream.h>
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include <QPalette>
 #include <QBrush>
 #include <QToolTip>
 #include "simplugin.h"
 #include <QPluginLoader>
 #include <QDir>
 #include "modelcatalogue.h"
 /* #define _xstr_(s) _str_(s)
 #define _str_(s) #s
 #include _xstr_(REACTIONS_HEADER)
 */
 static const std::string _module_id("$Id$");
 extern Parameter par;
 MainBase *main_window = 0;
 //double auxin_account = 0.;
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
   void operator() (const Node &n) const
+  {
     cerr << n.Index() << ": " << n <<  endl;
+  }
 };
 class EdgeSource {
 public:
   void operator() (Cell &c) {
     if (c.AtBoundaryP()) {
       cerr << "Cell " << c.Index() << " is a source cell.\n";
       c.SetSource(0,par.source);
     } else {
       cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";
+    }
+  }
 };
 class CellInfo {
 public:
   void operator() (Cell &c,std::ostream &os) const {
     os << "Cell " << c.index << " says: " << endl;
     os << "c.nodes.size() = " << c.nodes.size() << endl;
     for (list<Node *>::iterator i=c.nodes.begin();
 	 i!=c.nodes.end();
 	 i++) {
       cerr << (*i)->Index() << " ";
+    }
     cerr << endl;
+  }
 };
 double PINSum(Cell &c) {
 	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
+}
 class DrawCell {
 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());
 	  info_string += "\n" + 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();
   static int count=0;
   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() )) {
 		static int frame = 0;
 		// frame numbers are sequential for the most frequently written file type.
 		// for the less frequently written file type they match the other type
 		if (!(count%par.storage_stride) )  {
 			stringstream fname;
 			fname << par.datadir << "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			/*
 			 fname << frame << ".pdf";
 			if (par.storage_stride <= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "PDF");
 			*/
 			fname << frame << ".jpg";
 			if (par.storage_stride <= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "JPEG",1024,768);
+		}
 		if (!(count%par.xml_storage_stride)) {
 			stringstream fname;
 			fname << par.datadir << "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			fname << frame << ".xml";
 			if (par.xml_storage_stride < par.storage_stride) {
 				frame++;
+			}
 			// 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()));
   } else {
 	  mesh.StandardInit();
+  }
+}
 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
 		/*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
       CellReaction *cellreaction_f = new plugin->CellDynamics();
       WallReaction *wall_f = new WallDynamics();*/
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
 		/*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
 		QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 		ofstream af(afname.toStdString().c_str());
 		*/
 		/*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
 			 v!=angles.end();
 			 v++) {
 			af << v->first << " " << v->second << endl;
+			}
 			*/
+			}
 			} else {
   /*  TransportFunction *transport_f = new CelltoCellTransport();
     CellReaction *cellreaction_f = new CellDynamics();
     WallReaction *wall_f = new WallDynamics();
     mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
 				mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
   /* #ifdef HAVE_QWT
 	// Launch DataPlot window
 	QStringList curvenames;
     for (int i=0;i<NChem();i++) {
 		curvenames += QString("Chem #%1").arg(i);
+	}
     PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
     QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
                      plot, SLOT(AddValue(double,double *)));
 #endif
 	*/
 	//getMesh().plugin->OnClick(*this);
+}
 /* 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) {
       //int this_option_optind = optind ? optind : 1;
       int option_index = 0;
       static struct option long_options[] = {
 	{"batch", 0, 0, 0},
 	{"leaffile", 2, 0, 0}
 	{"batch", no_argument, NULL, 'b'},
 	{"leaffile", required_argument, NULL, 'l'},
 	{"model", required_argument, NULL, 'm'}
       };
       // short option 'p' creates trouble for non-commandline usage on MacOSX. Option -p changed to -P (capital)
       static char *short_options = "bl";
       c = getopt_long (argc, argv, "bl:",
       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();
+    }
   } else {
         main_window=new MainBase(canvas, mesh);
+ }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
 	  // Load plugins
 	  /*QVector<SimPluginInterface *> plugins = LoadPlugins();
 	  InstallPlugin(plugins[0], main_window);
 	  cerr << "List of models:" << endl;
 	  foreach (SimPluginInterface *p, plugins) {
 		  cerr << p->ModelID().toStdString() << endl;
+	  }
 	  */
 	  ModelCatalogue model_catalogue(&mesh, (Main *)main_window);
 	  model_catalogue.PopulateModelMenu();
 	  model_catalogue.InstallFirstModel();
     // Install model or read catalogue of models
     ModelCatalogue model_catalogue(&mesh, useGUI?(Main *)main_window:0,modelfile);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
-	  //main_window->Init(leaffile);
+    main_window->Init(leaffile);
     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();
+    }
+  }
+}

src/VirtualLeaf.pro

➞

Show inline comments

+#
 #  $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG -= release
 CONFIG += debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 #REACTIONS = reactions_auxin_growth.h
 #REACTIONS = reactions_meinhardt.h
 #REACTIONS = reactions_pce_growth.h
 DEFINES += QTGRAPHICS
 DEFINES += REACTIONS_HEADER=$${REACTIONS}
 DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"
 DEFINES += FLEMING
 PERLDIR = ./perl
 BINDIR = ../bin
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 TEMPLATE = app
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG += console
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  system(DEL parameter.cpp parameter.h)
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
  QMAKE_POST_LINK = "\
   C:\Bin\cp release\VirtualLeaf.exe \
   C:\Qt\4.5.3\bin\Qt3Support4.dll \
   C:\Qt\4.5.3\bin\QtGui4.dll \
   C:\Qt\4.5.3\bin\QtSql4.dll \
   C:\Qt\4.5.3\bin\QtXml4.dll \
   C:\Qt\4.5.3\bin\QtCore4.dll \
   C:\Qt\4.5.3\bin\QtNetwork4.dll \
   C:\Qt\4.5.3\bin\QtSvg4.dll \
   C:\bin\iconv.dll \
   C:\bin\libxml2.dll \
   C:\bin\zlib1.dll \
   C:\MinGW\bin\mingwm10.dll \
   $${DESTDIR}"
  LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv
+}
 # Application icons
 macx {
  ICON = leaficon.icns
  # make sure that the executable can find the libqwt share library
  QMAKE_POST_LINK = "mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
   cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/.; \
   #install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
   install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
   install_name_tool -change libqwt.5.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
   cp leaficon.icns $${DESTDIR}/$${TARGET}.app; "
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  system(rm -f parameter.cpp parameter.h)
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
 system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
 #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
 # Input
 HEADERS += \
  apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
  matrix.h \
  mesh.h \
  miscq.h \
  modelcatalogue.h \
  Neighbor.h \
  node.h \
  nodeitem.h \
  nodeset.h \
  OptionFileDialog.h \
  output.h \
  parameter.h \
  pardialog.h \
  parse.h \
  pi.h \
  qcanvasarrow.h \
  random.h \
  rungekutta.h \
  simitembase.h \
  simplugin.h \
  sqr.h \
  tiny.h \
  transporterdialog.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  wall.h \
  wallitem.h \
  warning.h \
  xmlwrite.h \
  $${PARTMPL}
 SOURCES += \
  apoplastitem.cpp \
  canvas.cpp \
  cellbase.cpp \
  cell.cpp \
  cellitem.cpp \
  forwardeuler.cpp \
  mainbase.cpp \
  matrix.cpp \
  mesh.cpp \
  miscq.cpp \
  modelcatalogue.cpp \
  Neighbor.cpp \
  node.cpp \
  nodeitem.cpp \
  nodeset.cpp \
  OptionFileDialog.cpp \
  output.cpp \
  parameter.cpp \
  pardialog.cpp \
  parse.cpp \
  random.cpp \
  rungekutta.cpp \
  simitembase.cpp \
  transporterdialog.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  wall.cpp \
  wallitem.cpp \
  warning.cpp \
  xmlwritecode.cpp \
  xmlwrite.cpp \
  $$MAINSRC
 contains( TARGET, leaf_fleming ) {
  DEFINES += FLEMING
+}
 contains(GRAPHICS, qwt) {
  #macx:LIBS += -L$$QWTDIR/lib -lqwt
  #win32:LIBS += -L$$QWTDIR/lib -lqwt5
  #LIBS += -L$$QWTDIR/lib -lqwt
  INCLUDEPATH += $$QWTDIR/include
  DEFINES += HAVE_QWT
  HEADERS += data_plot.h
  SOURCES += data_plot.cpp
+}
 contains( GRAPHICS, qt ) {
  message( "Building Qt executable" )
  QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
+}
 contains( GRAPHICS, xfig ) {
  message("Building Xfig executable (background runnable).")
  QMAKE_CXXFLAGS += -DXFIGGRAPHICS
+}
 contains( GRAPHICS, x11 ) {
  !unix {
   error("X11 graphics only available on Unix systems.")
+ }
  message("Building X11 executable")
  SOURCES += x11graph.cpp
  HEADERS += x11graph.h
  QMAKE_CXXFLAGS += -DX11GRAPHICS
  CONFIG -= qt
  CONFIG += x11
  unix:LIBS += -lpng
+}
 # finis

src/modelcatalogue.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include "modelcatalogue.h"
 #include <QVariant>
 static const std::string _module_id("$Id$");
 ModelCatalogue::ModelCatalogue(Mesh *_mesh, Main *_mainwin) {
+ModelCatalogue::ModelCatalogue(Mesh *_mesh, Main *_mainwin, const char *model=0) {
 	mesh = _mesh;
 	mainwin = _mainwin;
 	LoadPlugins();
 	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;
+	//QVector<SimPluginInterface *> plugins;
 	foreach (QString fileName, pluginDir.entryList(QDir::Files)){
 		QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
 		if (SimPluginInterface *plugin =
 			qobject_cast<SimPluginInterface *>(loader.instance())) {
 			models.append(plugin);
 		} else {
 			MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
+		}
+	}
+}
 void ModelCatalogue::LoadPlugin(const char *model) {
   QDir pluginDir(QApplication::applicationDirPath());
   QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"
 #if defined(Q_OS_WIN)
   if (pluginDir.dirName().toLower() =="debug"
       ||pluginDir.dirName().toLower() =="release")
     pluginDir.cdUp();
   //plugin_filters << "*.dll";
 #elif defined(Q_OS_MAC)
   if (pluginDir.dirName() =="MacOS"){
     pluginDir.cdUp();
     pluginDir.cdUp();
     pluginDir.cdUp();
+  }
   //plugin_filters << "*.dylib";
 #endif
   plugin_filters << model;
   pluginDir.setNameFilters(plugin_filters);
   if (!pluginDir.cd("models")) {
     MyWarning::error("Directory 'models' not found!");
+  }
   //QVector<SimPluginInterface *> plugins;
   QStringList modelnames=pluginDir.entryList(QDir::Files);
   if (modelnames.empty()) {
     MyWarning::error("Model %s not found - hint: do not include path in filename.",model);
+  }
   foreach (QString fileName, modelnames){
     QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
     if (SimPluginInterface *plugin =
 	qobject_cast<SimPluginInterface *>(loader.instance())) {
       models.append(plugin);
       MyWarning::warning("Successfully loaded model %s",fileName.toStdString().c_str());
     } else {
       MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
+    }
+  }
+}
 void ModelCatalogue::InstallFirstModel() {
 	InstallModel(models[0]);
+}
 void ModelCatalogue::PopulateModelMenu() {
 	foreach (SimPluginInterface *model, models) {
 		QAction *modelaction = new QAction(model->ModelID(), mainwin);
 		QVariant data;
 		data.setValue(model);
 		modelaction->setData(data);
 		mainwin->modelmenu->addAction(modelaction);
+	}
 	connect(mainwin->modelmenu, SIGNAL(triggered(QAction *)), this, SLOT(InstallModel(QAction *)) );
+}
 void ModelCatalogue::InstallModel(QAction *modelaction) {
 	QVariant data = modelaction->data();
 	SimPluginInterface *model = data.value<SimPluginInterface *>();
 	cerr << "You chose model " << model->ModelID().toStdString() << "!\n";
 	mesh->Clean();
 	InstallModel(model);
+}
 void ModelCatalogue::InstallModel(SimPluginInterface *plugin) {
 	// make sure both main and plugin use the same static datamembers (ncells, nchems...)
 	plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
 	mesh->SetSimPlugin(plugin);
 	Cell::SetNChem(plugin->NChem());
 	plugin->SetParameters(&par);
 	mainwin->RefreshInfoBar();
 //	mesh->StandardInit();
 	mainwin->Init(0);
 	if (mainwin) {
 		mainwin->RefreshInfoBar();
 		//mainwin->Init(0);
+	}
 	//	mesh->StandardInit();
+}

src/modelcatalogue.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _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);
+	ModelCatalogue(Mesh *mesh, Main *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;
 };
 #endif
@@ \ No newline at end of file @@
 #endif

src/warning.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include <stdarg.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <iostream>
 #include "warning.h"
 #ifdef QTGRAPHICS
 #include <qapplication.h>
 #include "canvas.h"
 #endif
 #include <QMessageBox>
 static const std::string _module_id("$Id$");
 int Quiet=0;
 /*
  * ERROR: scream and die quickly.
  */
 #ifndef QTGRAPHICS
 void MyWarning::error(char * fmt, ...)
+{
     va_list ap;
     va_start(ap, fmt);
     vfprintf(stderr, fmt, ap);		/* invoke interface to printf       */
     fprintf(stderr,"\n");     /* automatic \n by Roeland */
     fflush(stderr);			/* drain std error buffer 	    */
     va_end(ap);
     exit(1);				/* quit with error status	    */
+}
 #else
 //#include <qmessagebox.h>
 #include "UniqueMessage.h"
 void MyWarning::error(const char *fmt, ...)
+{
   va_list ap;
   if (Quiet) return;
   char *message = new char[1000];
   va_start(ap, fmt);
   vsnprintf(message, 999, fmt, ap);		/* invoke interface to printf       */
   va_end(ap);
   QString qmess(message);
   bool batch = false;
+  //  bool batch = false;
-  if (batch) {
+  if (qApp->type()==QApplication::Tty) {
     // batch mode: print the message to stderr
     fprintf(stderr, "Fatal error: %s\n",qmess.toStdString().c_str());
     exit(1);
   } else { // issue a dialog box
     /* Solve this with signal and slot...! */
 	  //extern MainBase *main_window;
     //((Main *)main_window)->stopSimulation();
 	QMessageBox::critical( 0 , "Fatal error", qmess, QMessageBox::Abort, QMessageBox::NoButton, QMessageBox::NoButton );
     fprintf(stderr, "Error: %s\n",qmess.toStdString().c_str());
     QCoreApplication::exit(1);
     std::exit(1);
+  }
   delete[] message;
+}
 #endif
 /*
  * EPRINTF: scream, but don't die yet.
  * Roeland changed this to "warning" (21/10/1998)
  * and added an automatic "\n"
  */
 #ifndef QTGRAPHICS
 void MyWarning::warning(const char * fmt, ...)
+{
   va_list ap;
   if (Quiet) return;
   va_start(ap, fmt);
   vfprintf(stderr, fmt, ap);		/* invoke interface to printf       */
   fprintf(stderr,"\n");     /* automatic \n by Roeland */
   fflush(stderr);			/* drain std error buffer 	    */
   va_end(ap);
+}
 #else
 #include <qmessagebox.h>
 void MyWarning::warning(const char *fmt, ...)
+{
   va_list ap;
   if (Quiet) return;
   char *message = new char[1000];
   va_start(ap, fmt);
   vsnprintf(message, 999, fmt, ap);		/* invoke interface to printf       */
   va_end(ap);
   QString qmess(message);
   bool batch = false;
+  //  bool batch = false;
-  if (batch) {
+  if (qApp->type()==QApplication::Tty) {
     // batch mode: print the message to stderr
     fprintf(stderr, "Warning: %s\n",qmess.toStdString().c_str());
   } else { // issue a dialog box
 	  UniqueMessageBox msgBox( QString("Warning"), qmess );
 	  msgBox.exec();
+  }
   delete[] message;
+}
 #endif
 /*! Issues a warning only once,
   by comparing it to a list of warnings issued previously. */
 void MyWarning::unique_warning(const char *fmt, ...) {
   va_list ap;
   if (Quiet) return;
   char *message = new char[1000];
   va_start(ap, fmt);
   vsnprintf(message, 999, fmt, ap);		/* invoke interface to printf       */
   va_end(ap);
   static vector<string> previous_warnings;
   // search warning in list
   if (find(
 	   previous_warnings.begin(),previous_warnings.end(),
 	   string(message))
       ==previous_warnings.end()) {
     // new warning, store in list
     previous_warnings.push_back(string(message));
     // issue warning
     warning("%s", message);
   } else {
     // don't issue warning
     return;
+  }
+}
 #ifdef TESTBED
 main(int argc, char * argv[])
+{
     eprintf("warning: foo=%f\tbar=%d\tfum=\"%s\"\n", 3.1415, 32768, "waldo");
     error("error: foo=%f\tbar=%d\tfum=\"%s\"\n", 3.1415, 32768, "waldo");
+}
 #endif

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