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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@@ @@ -32,7 +32,7 @@ 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}

src/VirtualLeaf.cpp

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@@ @@ -226,6 +226,13 @@ INIT { @@
   } else {
     mesh.StandardInit();
+  }
   Cell::SetMagnification(1);
   Cell::setOffset(0,0);
   FitLeafToCanvas();
   Plot();
+}
 TIMESTEP {
@@ @@ -412,22 +419,25 @@ int main(int argc,char **argv) { @@
       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 {

src/VirtualLeaf.pro

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@@ @@ -19,8 +19,8 @@ @@
 #  Copyright 2010 Roeland Merks.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG -= release
 CONFIG += debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions
@@ @@ -82,6 +82,7 @@ HEADERS += \ @@
  cell.h \
  cellitem.h \
  forwardeuler.h \
        hull.h \
  infobar.h \
  mainbase.h \
  mainbase.h \
@@ @@ -123,6 +124,7 @@ SOURCES += \ @@
  cell.cpp \
  cellitem.cpp \
  forwardeuler.cpp \
  hull.cpp \
  mainbase.cpp \
  matrix.cpp \
  mesh.cpp \

src/build_models/auxingrowthplugin.cpp

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@@ @@ -257,6 +257,9 @@ void AuxinGrowthPlugin::CellDynamics(Cel @@
+  }
+}
 Q_EXPORT_PLUGIN2(auxingrowthplugin, AuxinGrowthPlugin)
 /* finis */

src/build_models/auxingrowthplugin.h

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@@ @@ -55,7 +55,9 @@ class AuxinGrowthPlugin : public QObject @@
   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);
 };

src/canvas.cpp

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@@ @@ -477,6 +477,7 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   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);
@@ @@ -1353,4 +1354,18 @@ xmlNode *Main::XMLSettingsTree(void) @@
   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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@@ @@ -206,6 +206,7 @@ class Main : public Q3MainWindow, public @@
   void readPrevStateXML();
   void readFirstStateXML();
   void readLastStateXML();
   void exportCellData();
   void saveStateXML();
   void snapshot();
   void savePars();

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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@@ @@ -63,7 +63,7 @@ class MainBase { @@
   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; }
@@ @@ -133,7 +133,7 @@ class MainBase { @@
 //#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

src/mesh.cpp

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@@ @@ -46,6 +46,7 @@ @@
 #include <set>
 #include <iostream>
 #include <iterator>
 #include <QTextStream>
 static const std::string _module_id("$Id$");
@@ @@ -467,7 +468,10 @@ void Mesh::Clear(void) { @@
   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++) {
@@ @@ -1995,8 +1999,10 @@ void Mesh::Clean(void) { @@
   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
@@ @@ -2027,4 +2033,97 @@ void Mesh::StandardInit(void) { @@
+  }
+}
 #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

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@@ @@ -41,6 +41,7 @@ @@
 #include <QVector>
 #include <QPair>
 #include <QDebug>
 #include <QTextStream>
 using namespace std;
 // new queue which rejects duplicate elements
@@ @@ -81,9 +82,13 @@ class Mesh { @@
     time = 0.;
     plugin = 0;
     boundary_polygon=0;
   };
   ~Mesh(void) {
     delete boundary_polygon;
     if (boundary_polygon) {
       delete boundary_polygon;
       boundary_polygon=0;
+    }
   };
   void Clean(void);
@@ @@ -380,7 +385,10 @@ class Mesh { @@
+  }
   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:

src/modelcatalogue.cpp

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@@ @@ -147,14 +147,58 @@ void ModelCatalogue::InstallModel(QActio @@
 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

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@@ @@ -20,6 +20,7 @@ @@
  */
 #include <string>
 #include <QString>
 #include "simplugin.h"
 static const std::string _module_id("$Id$");
@@ @@ -34,4 +35,6 @@ void SimPluginInterface::SetCellsStaticD @@
   CellBase::static_data_members = cells_static_data_members_of_main;
+}
 QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
 /* finis */

src/simplugin.h

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@@ @@ -65,6 +65,9 @@ class SimPluginInterface { @@
   // 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);
@@ @@ -73,7 +76,7 @@ class SimPluginInterface { @@
   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

src/xmlwrite.cpp

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@@ @@ -1446,7 +1446,10 @@ void Mesh::XMLReadCells(xmlNode *root) @@
   cells.clear();
   Cell::NCells() = 0;
   delete boundary_polygon;
   if (boundary_polygon) {
     delete boundary_polygon;
     boundary_polygon=0;
+  }
   xmlNode *cur = root->xmlChildrenNode;

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