EI/VirtualLeaf Changeset - 9a40ab737a73 · Centrum Wiskunde & Informatica (CWI)

Changeset - 9a40ab737a73

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0 14 2

Roeland Merks - 15 years ago 2010-09-08 17:31:50
merks@cwi.nl

* Added functionality for numerical output (CSV) format. See functions starting with "CSV" in mesh.cpp. External code hull.cpp is responsible for convex hull calculations.
- ToDo: adopt menu item "File->export cell areas" so user can choose a file name or set up periodic output of numerical data.
- ToDo: add parameters re: periodic numeric output to "<settings>" block of LeafML-file, so it becomes possible to set up numeric output interactively, then write the LeafML file and run the program in batch mode to retrieve periodic numeric output.

* Added new functionality to plugin interface. It becomes possible to define a default LeafML init file for a plugin. It is read whenever the model plugin is loaded.
- ToDo: define default LeafML files for all plugins, according to the LeafML files mentioned in the Plant Phys. tutorial.

user: Roeland Merks <merks@cwi.nl>
branch 'default'
added src/hull.cpp
added src/hull.h
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.cpp
changed src/simplugin.h
changed src/xmlwrite.cpp

16 files changed with 340 insertions and 20 deletions:

src/TutorialCode/Tutorial0/tutorial0.pro

src/VirtualLeaf.cpp

src/VirtualLeaf.pro

src/build_models/auxingrowthplugin.cpp

src/build_models/auxingrowthplugin.h

src/canvas.cpp

src/canvas.h

src/hull.cpp

110

src/hull.h

src/mainbase.h

src/mesh.cpp

102

src/mesh.h

src/modelcatalogue.cpp

src/simplugin.cpp

src/simplugin.h

src/xmlwrite.cpp

0 comments (0 inline, 0 general)

src/TutorialCode/Tutorial0/tutorial0.pro

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Show inline comments

@@ @@ -11,49 +11,49 @@ @@
 #  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.
+#
 TARGET = tutorial0
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
-HEADERS = $${TARGET}.h
+HEADERS = $${TARGET}.h $${INCDIR}/simplugin.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = $${LIBDIR}\libxml2
  LIBICONVDIR = $${LIBDIR}\libiconv
  LIBZDIR = $${LIBDIR}\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}

src/VirtualLeaf.cpp

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Show inline comments

@@ @@ -205,48 +205,55 @@ void MainBase::Plot(int resize_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();
+  }
   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
@@ @@ -391,64 +398,67 @@ int main(int argc,char **argv) { @@
     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);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
     if (leaffile)
       main_window->Init(leaffile);
     Cell::SetMagnification(1);
     /*    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();

src/VirtualLeaf.pro

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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
 BINDIR = ../bin
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 TEMPLATE = app
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 !win32 {
@@ @@ -61,89 +61,91 @@ win32 { @@
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 # Input
 HEADERS += \
  apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.h \
        hull.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 \
  hull.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 \

src/build_models/auxingrowthplugin.cpp

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@@ @@ -236,27 +236,30 @@ void AuxinGrowthPlugin::CellDynamics(Cel @@
   double dPidt = 0.;
   double sum_Pij = c->SumTransporters( 1 );
   // exocytosis regulated:
   dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &AuxinGrowthPlugin::complex_PijAj ) ) + par->k2 * sum_Pij;
   // production of PIN depends on auxin concentration
   dPidt +=  (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
   // no PIN production in SAM
   if (c->Boundary() == CellBase::SAM) {
     dchem[1]=0.;
     dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);
   } else {
     dchem[1] = dPidt;
     // source of auxin
     dchem[0] = par->aux_cons - par->aux_breakdown * c->Chemical(0);
+  }
+}
 Q_EXPORT_PLUGIN2(auxingrowthplugin, AuxinGrowthPlugin)
 /* finis */

src/build_models/auxingrowthplugin.h

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@@ @@ -34,32 +34,34 @@ class AuxinGrowthPlugin : public QObject @@
   Q_INTERFACES(SimPluginInterface);
  public:
   virtual QString ModelID(void) { return QString( "Auxin accumulation and growth" ); }
   // Executed after the cellular mechanics steps have equillibrized
   virtual void CellHouseKeeping (CellBase *c);
   // Differential equations describing transport of chemicals from cell to cell
   virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
   // Differential equations describing chemical reactions taking place at or near the cell walls
   // (e.g. PIN accumulation)
   virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
   // Differential equations describing chemical reactions inside the cells
   virtual void CellDynamics(CellBase *c, double *dchem);
   // to be executed after a cell division
   virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
   // to be executed for coloring a cell
   virtual void SetCellColor(CellBase *c, QColor *color);
   // return number of chemicals
   virtual int NChem(void) { return 2; }
   virtual QString DefaultLeafML(void) { return QString("auxin_growth.xml"); }
  private:
   double complex_PijAj(CellBase *here, CellBase *nb, Wall *w);
 };
 #endif
 /* finis */

src/canvas.cpp

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@@ @@ -456,48 +456,49 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   mesh(m)
+{
   editor = new FigureEditor(canvas,mesh, this);
 #ifdef QDEBUG
   qDebug() << "Interactive = " << editor->isEnabled();
 #endif
   working_dir = 0;
   QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));
   QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));
   QMenuBar* menu = menuBar();
   Q3PopupMenu* file = new Q3PopupMenu( menu );
   file->insertItem("&Read leaf", this, SLOT(readStateXML()));
   file->insertItem("&Save leaf", this, SLOT(saveStateXML()));
   file->insertItem("Snapshot", this, SLOT(snapshot()), Qt::CTRL+Qt::SHIFT+Qt::Key_S);
   file->insertSeparator();
   file->insertItem("Read next leaf", this, SLOT(readNextStateXML()), Qt::Key_PageDown);
   file->insertItem("Read previous leaf", this, SLOT(readPrevStateXML()), Qt::Key_PageUp);
   file->insertItem("Read last leaf", this, SLOT(readLastStateXML()), Qt::Key_End);
   file->insertItem("Read first leaf", this, SLOT(readFirstStateXML()), Qt::Key_Home);
   file->insertItem("Export cell areas", this, SLOT(exportCellData()));
   file->insertSeparator();
   file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);
   file->insertSeparator();
   file->insertItem("E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q);
   menu->insertItem("&File", file);
   Q3PopupMenu* edit = new Q3PopupMenu( menu );
   edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );
   edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );
   edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );
   edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );
   edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));
   menu->insertItem("&Edit", edit);
   run = new Q3PopupMenu( menu );
   running = false;
   paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
   menu->insertItem("&Run", run);
   view = new Q3PopupMenu( menu );
   view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);
@@ @@ -1332,25 +1333,39 @@ void Main::XMLReadSettings(xmlNode *sett @@
 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;
+}
 void Main::exportCellData(void) {
   // perhaps make this more general: a popup window were user selects data he wants to export
   // can go to "settings" section of XML file as well so this can also be measured off-line
   // mesh.CSVExport would take an QMap or so to record all options
   // first line gives legenda
   QFile file("areas.csv");
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
+  }
+}
 /* finis */

src/canvas.h

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@@ @@ -185,48 +185,49 @@ class Main : public Q3MainWindow, public @@
     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();
   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 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:

src/hull.cpp

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@@ new file 100644 @@
 // Copyright 2001, softSurfer (www.softsurfer.com)
 // This code may be freely used and modified for any purpose
 // providing that this copyright notice is included with it.
 // SoftSurfer makes no warranty for this code, and cannot be held
 // liable for any real or imagined damage resulting from its use.
 // Users of this code must verify correctness for their application.
 // Assume that a class is already given for the object:
 //    Point with coordinates {float x, y;}
 //===================================================================
 // isLeft(): tests if a point is Left|On|Right of an infinite line.
 //    Input:  three points P0, P1, and P2
 //    Return: >0 for P2 left of the line through P0 and P1
 //            =0 for P2 on the line
 //            <0 for P2 right of the line
 //    See: the January 2001 Algorithm on Area of Triangles
 #include "hull.h"
 inline float
 isLeft( Point P0, Point P1, Point P2 )
+{
     return (P1.x - P0.x)*(P2.y - P0.y) - (P2.x - P0.x)*(P1.y - P0.y);
+}
 //===================================================================
 // chainHull_2D(): Andrew's monotone chain 2D convex hull algorithm
 //     Input:  P[] = an array of 2D points
 //                   presorted by increasing x- and y-coordinates
 //             n = the number of points in P[]
 //     Output: H[] = an array of the convex hull vertices (max is n)
 //     Return: the number of points in H[]
 int
 chainHull_2D( Point* P, int n, Point* H )
+{
     // the output array H[] will be used as the stack
     int    bot=0, top=(-1);  // indices for bottom and top of the stack
     int    i;                // array scan index
     // Get the indices of points with min x-coord and min|max y-coord
     int minmin = 0, minmax;
     float xmin = P[0].x;
     for (i=1; i<n; i++)
         if (P[i].x != xmin) break;
     minmax = i-1;
     if (minmax == n-1) {       // degenerate case: all x-coords == xmin
         H[++top] = P[minmin];
         if (P[minmax].y != P[minmin].y) // a nontrivial segment
             H[++top] = P[minmax];
         H[++top] = P[minmin];           // add polygon endpoint
         return top+1;
+    }
     // Get the indices of points with max x-coord and min|max y-coord
     int maxmin, maxmax = n-1;
     float xmax = P[n-1].x;
     for (i=n-2; i>=0; i--)
         if (P[i].x != xmax) break;
     maxmin = i+1;
     // Compute the lower hull on the stack H
     H[++top] = P[minmin];      // push minmin point onto stack
     i = minmax;
     while (++i <= maxmin)
+    {
         // the lower line joins P[minmin] with P[maxmin]
         if (isLeft( P[minmin], P[maxmin], P[i]) >= 0 && i < maxmin)
             continue;          // ignore P[i] above or on the lower line
         while (top > 0)        // there are at least 2 points on the stack
+        {
             // test if P[i] is left of the line at the stack top
             if (isLeft( H[top-1], H[top], P[i]) > 0)
                 break;         // P[i] is a new hull vertex
             else
                 top--;         // pop top point off stack
+        }
         H[++top] = P[i];       // push P[i] onto stack
+    }
     // Next, compute the upper hull on the stack H above the bottom hull
     if (maxmax != maxmin)      // if distinct xmax points
         H[++top] = P[maxmax];  // push maxmax point onto stack
     bot = top;                 // the bottom point of the upper hull stack
     i = maxmin;
     while (--i >= minmax)
+    {
         // the upper line joins P[maxmax] with P[minmax]
         if (isLeft( P[maxmax], P[minmax], P[i]) >= 0 && i > minmax)
             continue;          // ignore P[i] below or on the upper line
         while (top > bot)    // at least 2 points on the upper stack
+        {
             // test if P[i] is left of the line at the stack top
             if (isLeft( H[top-1], H[top], P[i]) > 0)
                 break;         // P[i] is a new hull vertex
             else
                 top--;         // pop top point off stack
+        }
         H[++top] = P[i];       // push P[i] onto stack
+    }
     if (minmax != minmin)
         H[++top] = P[minmin];  // push joining endpoint onto stack
     return top+1;
+}

src/hull.h

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@@ new file 100644 @@
 // Class point needed by 2D convex hull code
 class Point {
 public:
   Point(float xx, float yy) {
     x=xx;
     y=yy;
+  }
   Point(void) {
     x=0; y=0;
+  }
   float x,y;
 };
 int chainHull_2D( Point* P, int n, Point* H );

src/mainbase.h

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@@ @@ -42,49 +42,49 @@ using namespace std; @@
 class MainBase  {
  public:
  MainBase(QGraphicsScene &c, Mesh &m) : mesh(m), canvas(c) {
     // Standard options for batch version
     showcentersp =  false;
     showmeshp =  false;
     showbordercellp =  false;
     shownodenumbersp =  false;
     showcellnumbersp =  false;
     showcellsaxesp = false;
     showcellstrainp =  false;
     movieframesp = true;
     showboundaryonlyp =  false;
     showwallsp =  false;
     showfluxesp = false;
     dynamicscellsp = true;
     showtooltipsp = false;
     hidecellsp = false;
+  }
   virtual ~MainBase() {};
   virtual double TimeStep();
   virtual void Init(char *leaffile=0);
+  virtual void Init(const char *leaffile=0);
   virtual bool ShowCentersP(void) {return showcentersp;}
   virtual bool ShowMeshP(void) {return showmeshp; }
   virtual bool ShowBorderCellsP(void) {return showbordercellp; }
   virtual bool PausedP(void) {return false; }
   virtual bool ShowNodeNumbersP(void) {return shownodenumbersp; }
   virtual bool ShowCellNumbersP(void) {return showcellnumbersp;}
   virtual bool ShowCellAxesP(void) {return showcellsaxesp;}
   virtual bool ShowCellStrainP(void) {return showcellstrainp;}
   virtual bool MovieFramesP(void) {return movieframesp;}
   virtual bool ShowBoundaryOnlyP(void) {return showboundaryonlyp;}
   virtual bool ShowToolTipsP(void) {return showtooltipsp;}
   virtual bool ShowWallsP(void) {return showwallsp;}
   virtual bool ShowApoplastsP(void) { return showapoplastsp;}
   virtual bool ShowFluxesP(void) { return showfluxesp; }
   virtual bool DynamicCellsP(void) { return dynamicscellsp; }
   virtual void FitCanvasToWindow() {};
   virtual void FitLeafToCanvas() {};
   virtual bool HideCellsP(void) { return hidecellsp; }
   virtual void clear(void) {
     QList<QGraphicsItem *> list = canvas.items();
     QList<QGraphicsItem *>::Iterator it = list.begin();
     for (; it != list.end(); ++it) {
       if ( *it )
@@ @@ -112,29 +112,29 @@ class MainBase { @@
   QGraphicsScene &canvas;
   virtual xmlNode *XMLSettingsTree(void) const;
   virtual xmlNode *XMLViewportTree(QTransform &transform) const;
  protected:
   bool showcentersp;
   bool showmeshp;
   bool showbordercellp;
   bool shownodenumbersp;
   bool showcellnumbersp;
   bool showcellsaxesp;
   bool showcellstrainp;
   bool movieframesp;
   bool showboundaryonlyp;
   bool showwallsp;
   bool showapoplastsp;
   bool showfluxesp;
   bool dynamicscellsp;
   bool showtooltipsp;
   bool hidecellsp;
 };
 //#include <qapplication.h>
 #define TIMESTEP double MainBase::TimeStep(void)
 #define INIT void MainBase::Init(char *leaffile)
+#define INIT void MainBase::Init(const char *leaffile)
 #endif
 /* finis */

src/mesh.cpp

➞

Show inline comments

@@ @@ -25,48 +25,49 @@ @@
 #include <sstream>
 #include <cstdlib>
 //#include <cerrno>
 #include <cstring>
 #include <numeric>
 #include <functional>
 #include <fstream>
 #include <QPair>
 #include "mesh.h"
 #include "tiny.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "parse.h"
 #include "matrix.h"
 #include "sqr.h"
 #include "nodeset.h"
 #include "nodeitem.h"
 #include "simplugin.h"
 #include <QDebug>
 #include <set>
 #include <iostream>
 #include <iterator>
 #include <QTextStream>
 static const std::string _module_id("$Id$");
 extern Parameter par;
 void Mesh::AddNodeToCellAtIndex(Cell *c, Node *n, Node *nb1, Node *nb2, list<Node *>::iterator ins_pos) {
   c->nodes.insert(ins_pos, n);
   n->owners.push_back( Neighbor(c, nb1, nb2 ) );
+}
 void Mesh::AddNodeToCell(Cell *c, Node *n, Node *nb1, Node *nb2) {
   c->nodes.push_back( n );
   n->owners.push_back( Neighbor(c, nb1, nb2 ) );
+}
 void Mesh::PerturbChem(int chemnum, double range) {
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     (*i)->chem[chemnum] += range*(RANDOM()-0.5);
     if ((*i)->chem[chemnum]<0.) (*i)->chem[chemnum]=0.;
+  }
+}
@@ @@ -446,49 +447,52 @@ void Mesh::Clear(void) { @@
     delete *i;
+  }
   nodes.clear();
   Node::nnodes=0;
   node_insertion_queue.clear();
   // Clear NodeSets
   for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
+  }
   node_sets.clear();
   time = 0;
   // clear cells
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
+  }
   cells.clear();
   Cell::NCells() = 0;
   delete boundary_polygon;
   if (boundary_polygon) {
     delete boundary_polygon;
     boundary_polygon=0;
+  }
   // Clear walls
   for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
+  }
   walls.clear();
   WallBase::nwalls = 0;
   //tmp_walls->clear();
   shuffled_cells.clear();
   shuffled_nodes.clear();
   //Cell::ncells=0;
   /*    Cell::ClearNCells();
 	Node::nnodes=0;
 	cells.clear();
 	nodes.clear();
 	shuffled_cells.clear();
 	shuffled_nodes.clear();
 	node_insertion_queue.empty();
 	cerr << "Meshed cleared: cells: " << cells.size() << ", nodes: " << nodes.size() << endl;
   */
@@ @@ -1974,57 +1978,152 @@ void Mesh::Clean(void) { @@
   nodes.clear();
   Node::nnodes=0;
 #ifdef QDEBUG
   qDebug() << "Freeing node sets" << endl;
 #endif
   for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
+  }
   node_sets.clear();
 #ifdef QDEBUG
   qDebug() << "Freeing cells" << endl;
 #endif
   //CellsStaticDatamembers *old_static_data_mem = Cell::GetStaticDataMemberPointer();
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
+  }
   //Cell::static_data_members = old_static_data_mem;
   cells.clear();
   Cell::NCells()=0;
   delete boundary_polygon; // (already deleted during cleaning of cells?)
   if (boundary_polygon) {
     delete boundary_polygon; // (already deleted during cleaning of cells?)
     boundary_polygon=0;
+  }
 #ifdef QDEBUG
   qDebug() << "Freeing walls" << endl;
 #endif
   for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
+  }
   walls.clear();
   Wall::nwalls=0;
   node_insertion_queue.clear();
   shuffled_nodes.clear();
   shuffled_cells.clear();
   time = 0.0;
+}
 void Mesh::StandardInit(void) {
   boundary_polygon = new BoundaryPolygon();
   Cell &circle=CircularCell(0,0,10,10);
   circle.SetTargetArea(circle.CalcArea());
   circle.SetTargetLength(par.target_length);
   circle.SetLambdaLength(par.lambda_celllength);
   SetBaseArea();
   // clean up chemicals
   for (int c=0; c<Cell::NChem(); c++) {
     circle.SetChemical(c, 0.);
+  }
+}
 #include "hull.h"
 double Mesh::Compactness(double *res_compactness, double *res_area, double *res_cell_area) {
   // 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()];
   for (list<Node *>::const_iterator i = boundary_polygon->nodes.begin();
        i!=boundary_polygon->nodes.end(); i++) {
     p[pc++]=Point((*i)->x,(*i)->y);
+  }
   // Step 2: call 2D Hull code
   int np=boundary_polygon->nodes.size();
   Point *hull=new Point[np];
   int nph=chainHull_2D(p,np,hull);
   // Step 3: calculate area of convex hull
   double hull_area=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;
+  }
   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;
+  }
   // 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;
+  }
+}
 void Mesh::CSVExportMeshData(QTextStream &csv_stream) {
   csv_stream << "\"Mesh area\",\"Number of cells\",\"Number of nodes\",\"Compactness\",\"Hull area\",\"Cell area\"" << endl;
   double res_compactness, res_area, res_cell_area;
   Compactness(&res_compactness, &res_area, &res_cell_area);
   csv_stream << Area() << ", " << NCells() << ", " << NNodes() << ", " << res_compactness << ", " << res_area << ", " << res_cell_area  << endl;
+}
 /* finis */

src/mesh.h

➞

Show inline comments

@@ @@ -20,91 +20,96 @@ @@
  *  Copyright 2010 Roeland Merks.
+ *
  */
 // Cell derives from Vector, where Vector is simply used as a Vertex
 #ifndef _MESH_H_
 #define _MESH_H_
 #include <vector>
 #include <algorithm>
 #include <queue>
 #include <iterator>
 #include <functional>
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>
 #endif
 #include "cell.h"
 #include "node.h"
 #include "simplugin.h"
 #include <QVector>
 #include <QPair>
 #include <QDebug>
 #include <QTextStream>
 using namespace std;
 // new queue which rejects duplicate elements
 template<class T, class C = deque<T> > class unique_queue : public queue<T,C> {
  public:
  typedef typename C::value_type value_type;
  // reimplements push: reject element if it exists already
  void push(const value_type &x) {
    if (find (queue<T,C>::c.begin(),queue<T,C>::c.end(),x)==queue<T,C>::c.end()) {
      queue<T,C>::c.push_back(x);
+   }
+ }
  void clear(void) {
    queue<T,C>::c.clear();
+ }
 };
 template<class P> P& deref_ptr ( P *obj) { return *obj; }
 class Mesh {
   friend class Cell;
   friend class Node;
   friend class FigureEditor;
  public:
   Mesh(void) {
     // Make sure the reserved value is large enough if a cell is added
     // in "Divide" when the capacity is insufficient, "cells" might be
     // relocated including the current Cell (i.e. the value of *this)
     // calling "Mesh::IncreaseCapacityIfNecessary" (from another
     // object than Cell, e.g. Mesh) before entering Divide will solve
     // this issue (solved now).
     cells.reserve(2);
     nodes.reserve(500);
     time = 0.;
     plugin = 0;
     boundary_polygon=0;
   };
   ~Mesh(void) {
     delete boundary_polygon;
     if (boundary_polygon) {
       delete boundary_polygon;
       boundary_polygon=0;
+    }
   };
   void Clean(void);
   Cell &EllipticCell(double xc, double yc, double ra, double rb, int nnodes=10, double rotation=0);
   Cell &CircularCell(double xc, double yc, double r, int nnodes=10) {
     return EllipticCell(xc, yc, r, r, nnodes, 0);
+  }
   Cell &LeafPrimordium(int n, double pet_length);
   Cell &LeafPrimordium2(int n);
   Cell *RectangularCell(const Vector ll, const Vector ur, double rotation = 0);
   void CellFiles(const Vector ll, const Vector ur);
   inline Cell &getCell(int i) {
     if ((unsigned)i<cells.size())
       return *cells[i];
     else {
 #ifdef QDEBUG
       qDebug() << i << endl;
       qDebug() << "size is " << cells.size() << endl;
 #endif
       abort();
+    }
+  }
@@ @@ -359,49 +364,52 @@ class Mesh { @@
     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);
   void CSVExportCellData(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);

src/modelcatalogue.cpp

➞

Show inline comments

@@ @@ -126,35 +126,79 @@ void ModelCatalogue::InstallFirstModel() @@
+}
 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...)
   mesh->Clean();
   plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
   mesh->SetSimPlugin(plugin);
   Cell::SetNChem(plugin->NChem());
   plugin->SetParameters(&par);
   if (mainwin) {
     mainwin->RefreshInfoBar();
     mainwin->Init(0);
     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.
       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/simplugin.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 <QString>
 #include "simplugin.h"
 static const std::string _module_id("$Id$");
 void SimPluginInterface::SetParameters(Parameter *pass_pars)
+{
   par = pass_pars;
+}
 void SimPluginInterface::SetCellsStaticDatamembers( CellsStaticDatamembers *cells_static_data_members_of_main)
+{
   CellBase::static_data_members = cells_static_data_members_of_main;
+}
 QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
 /* finis */

src/simplugin.h

➞

Show inline comments

@@ @@ -44,38 +44,41 @@ class SimPluginInterface { @@
   virtual ~SimPluginInterface() { }
   // Executed after the cellular mechanics steps have equillibrized
   virtual void CellHouseKeeping(CellBase *c) = 0;
   // Differential equations describing transport of chemicals from cell to cell
   virtual void CelltoCellTransport(Wall *, double *dchem_c1, double *dchem_c2) = 0;
   // Differential equations describing chemical reactions taking place at or near the cell walls
   // (e.g. PIN accumulation)
   virtual void WallDynamics(Wall *w, double *dw1, double *dw)  = 0;
   // Differential equations describing chemical reactions inside the cells
   virtual void CellDynamics(CellBase *c, double *dchem) = 0;
   // to be executed after a cell division
   virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) = 0;
   // to be executed for coloring a cell
   virtual void SetCellColor(CellBase *c, QColor *color) = 0;
   // Number of chemicals
   virtual int NChem(void) = 0;
   // Default LeafML-file to be read after model startup
   virtual QString DefaultLeafML(void);
   // For internal use; not to be redefined by end users
   virtual void SetParameters(Parameter *pass_pars);// { par = pass_pars; }
   virtual void SetCellsStaticDatamembers (CellsStaticDatamembers *cells_static_data_members_of_main);
  protected:
   class Parameter *par;
 };
-Q_DECLARE_INTERFACE(SimPluginInterface, "nl.cwi.VirtualLeaf.SimPluginInterface/1.2")
+Q_DECLARE_INTERFACE(SimPluginInterface, "nl.cwi.VirtualLeaf.SimPluginInterface/1.3")
 Q_DECLARE_METATYPE(SimPluginInterface *)
 #endif
 /* finis */

src/xmlwrite.cpp

➞

Show inline comments

@@ @@ -1425,49 +1425,52 @@ void Mesh::XMLReadNodeSets(xmlNode *root @@
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"nodeset"))){
       new_nodeset = new NodeSet();
       node_sets.push_back(new_nodeset);
+    }
     if (new_nodeset == 0) {
       cur = cur->next;
       continue;
+    }
     new_nodeset->XMLRead(cur, this);
     cur=cur->next;
+  }
+}
 void Mesh::XMLReadCells(xmlNode *root)
+{
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
+  }
   cells.clear();
   Cell::NCells() = 0;
   delete boundary_polygon;
   if (boundary_polygon) {
     delete boundary_polygon;
     boundary_polygon=0;
+  }
   xmlNode *cur = root->xmlChildrenNode;
   while (cur!=NULL) {
     Cell *new_cell=0;
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell"))){
       new_cell = new Cell(0,0);
       new_cell->m = this;
       cells.push_back(new_cell);
     } else {
       if ((!xmlStrcmp(cur->name, (const xmlChar *)"boundary_polygon"))) {
 	new_cell = boundary_polygon = new BoundaryPolygon(0,0);
 	boundary_polygon->m = this;
+      }
+    }
     if (new_cell == 0) {
       cur = cur->next;
       continue;
+    }

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