EI/VirtualLeaf Changeset - c32457e84c7f · Centrum Wiskunde & Informatica (CWI)

Changeset - c32457e84c7f

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0 14 0

Roeland Merks - 15 years ago 2010-10-14 11:56:01
roeland.merks@cwi.nl

Commit changes

user: Roeland Merks <roeland.merks@cwi.nl>
branch merge
branch 'default'
changed src/ChangeLog
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3.h
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/tutorial4.h
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/tutorial5.h
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h

13 files changed with 39 insertions and 27 deletions:

src/TutorialCode/Tutorial3/ChangeLog

src/TutorialCode/Tutorial3/tutorial3.h

src/TutorialCode/Tutorial4/ChangeLog

src/TutorialCode/Tutorial4/tutorial4.h

src/TutorialCode/Tutorial5/ChangeLog

src/TutorialCode/Tutorial5/tutorial5.h

src/VirtualLeafpar.tmpl

src/canvas.cpp

src/canvas.h

src/parameter.cpp

src/parameter.h

src/pardialog.cpp

src/pardialog.h

0 comments (0 inline, 0 general)

src/TutorialCode/Tutorial3/ChangeLog

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 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3.h (SimPluginInterface): Added default LeafML file.
 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3.pro: Corrected windows library path.

src/TutorialCode/Tutorial3/tutorial3.h

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@@ @@ -44,17 +44,20 @@ public: @@
 	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);
 	// default LeafML file
 	virtual QString DefaultLeafML(void) { return QString("tutorial3_init.xml"); }
 };

src/TutorialCode/Tutorial4/ChangeLog

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Show inline comments

 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* tutorial4.h (SimPluginInterface): Added default LeafML file.
 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial4.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial4.pro: Corrected windows library path.

src/TutorialCode/Tutorial4/tutorial4.h

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@@ @@ -46,17 +46,20 @@ public: @@
 	// 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);
 	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w);
 	// default LeafML file
 	virtual QString DefaultLeafML(void) { return QString("tutorial4_init.xml"); }
 };

src/TutorialCode/Tutorial5/ChangeLog

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Show inline comments

 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* tutorial5.h (SimPluginInterface): Added default LeafML file.
 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* tutorial5.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* tutorial5.pro: Corrected windows library path.

src/TutorialCode/Tutorial5/tutorial5.h

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Show inline comments

@@ @@ -46,17 +46,20 @@ public: @@
 	// 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);
 	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w);
 	// default LeafML file
 	virtual QString DefaultLeafML(void) { return QString("tutorial5_init.xml"); }
 };

src/VirtualLeafpar.tmpl

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@@ @@ -116,13 +116,13 @@ i3 = 0 / int @@
 i4 = 0 / int
 i5 = 0 / int
 s1 =  / string
 s2 =  / string
 s3 =  / string
 b1 = false / bool
 b2 = false / bool
 b3 = false / bool
 b4 = false / bool
 dir1 = . / directory
 dir2 = . / directory
 export_interval = 0 / int
-export_fn_prefix = CellData_ / string
+export_fn_prefix = cell. / string

src/canvas.cpp

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@@ @@ -81,24 +81,25 @@ @@
 // Include VIB and PSB logos
 #include "psb.xpm"
 #include "cwi.xpm"
 static const std::string _module_id("$Id$");
 using namespace std;
 // We use a global variable to save memory - all the brushes and pens in
 // the mesh are shared.
 #define FNAMESIZE 100
 #define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)
 #define QUOTE_ME_2NDLEV(s) #s
 static QColor dark_red("darkRed");
 static const int imageRTTI = 984376;
 extern Parameter par;
 const QString Main::caption("Virtual leaf");
 const QString Main::caption_with_file("Virtual leaf: %1");
 FigureEditor::FigureEditor(
@@ @@ -471,25 +472,25 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   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->insertItem("Export cell data", 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()) );
@@ @@ -1156,50 +1157,44 @@ void Main::print() @@
       pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));
     } else {
       pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));
+    }
     canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));
+  }
+}
 void Main::TimeStepWrap(void)
+{
   static int t=0;
   stringstream fname;
   TimeStep();
   t++;
   if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){
     this->exportCellData(QString(par.datadir) + QString('/') + QString(par.export_fn_prefix) + this->TimeStamp());
     fname << par.datadir << "/" << par.export_fn_prefix;
     fname.fill('0');
     fname.width(6);
     fname << t << ".csv";
     this->exportCellData(QString(fname.str().c_str()));
+  }
   // check number of timesteps
   if (t==par.nit) {
     emit SimulationDone();
+  }
+}
 QString Main::TimeStamp(){
   time_t rawtime;
   struct tm * timeinfo;
   char buffer [15];
   time ( &rawtime );
   timeinfo = localtime ( &rawtime );
   strftime (buffer,15,"%Y%m%d%H%M%S",timeinfo);
   return QString(buffer);
+}
 void Main::RestartSim(void)
+{
   stopSimulation();
   if ( QMessageBox::question(
 			     this,
 			     tr("Restart simulation?"),
 			     tr("Restart simulation.\n"
 				"Are you sure?"),
 			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
     cerr << "Restarting simulation" << endl;

src/canvas.h

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@@ @@ -218,26 +218,24 @@ class Main : public Q3MainWindow, public @@
   void enlarge();
   void shrink();
   void zoomIn();
   void zoomOut();
   void CleanMesh();
   void CleanMeshChemicals(void);
   void CleanMeshTransporters(void);
   void RandomizeMesh();
   QString TimeStamp();
  signals:
   void SimulationDone(void);
   void ParsChanged(void);
  protected:
   Mesh &mesh;
  private:
   NodeSet *node_set;
   FigureEditor *editor;
   Q3PopupMenu* options;
   Q3PopupMenu *view;

src/parameter.cpp

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@@ @@ -10,27 +10,27 @@ @@
  *  VirtualLeaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 // WARNING: This file is automatically generated by make_parameter_source.pl.
 // Do not edit. All edits will be discarded.
 #include "parameter.h"
 #include <cstdio>
 #include <cstring>
 #include <cstdlib>
 #include <cerrno>
 #include <iostream>
 #include <sstream>
 #include "output.h"
 #include "parse.h"
 #include "xmlwrite.h"
 #include "warning.h"
 #include <QLocale>
@@ @@ -177,26 +177,26 @@ Parameter::Parameter() { @@
   i3 = 0;
   i4 = 0;
   i5 = 0;
   s1 = strdup("");
   s2 = strdup("");
   s3 = strdup("");
   b1 = false;
   b2 = false;
   b3 = false;
   b4 = false;
   dir1 = strdup(".");
   dir2 = strdup(".");
   export_interval = 100;
   export_fn_prefix = strdup("CELLDATA");
   export_interval = 0;
   export_fn_prefix = strdup("cell.");
+}
 Parameter::~Parameter() {
 // destruct parameter object
 // free string parameter
 CleanUp();
+}
 void Parameter::CleanUp(void) {
   if (arrowcolor)
      free(arrowcolor);
@@ @@ -338,26 +338,26 @@ void Parameter::Read(const char *filenam @@
   s2 = sgetpar(fp, "s2", "", true);
   s3 = sgetpar(fp, "s3", "", true);
   b1 = bgetpar(fp, "b1", false, true);
   b2 = bgetpar(fp, "b2", false, true);
   b3 = bgetpar(fp, "b3", false, true);
   b4 = bgetpar(fp, "b4", false, true);
   dir1 = sgetpar(fp, "dir1", ".", true);
   if (strcmp(dir1, "."))
     MakeDir(dir1);
   dir2 = sgetpar(fp, "dir2", ".", true);
   if (strcmp(dir2, "."))
     MakeDir(dir2);
   export_interval = igetpar(fp, "export_interval", 100, true);
   export_fn_prefix = sgetpar(fp, "export_fn_prefix", "CELLDATA", true);
   export_interval = igetpar(fp, "export_interval", 0, true);
   export_fn_prefix = sgetpar(fp, "export_fn_prefix", "cell.", true);
+}
 const char *sbool(const bool &p) {
   const char *true_str="true";
   const char *false_str="false";
   if (p)
     return true_str;
   else
     return false_str;
+}
@@ @@ -1884,13 +1884,12 @@ if (!strcmp(namec, "k")) { @@
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      k[i++]=*(v++);
+  }
+}
+}
 ostream &operator<<(ostream &os, Parameter &p) {
     p.Write(os);
     return os;
+}
 /* finis */

src/parameter.h

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@@ @@ -13,25 +13,25 @@ @@
  *  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.
+ *
  */
 // WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.
 // All edits will be discarded.
+// Do not edit. All edits will be discarded.
 #ifndef _PARAMETER_H_
 #define _PARAMETER_H_
 #include "vector.h"
 #include <vector>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
  class Parameter {
  public:

src/pardialog.cpp

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@@ @@ -10,24 +10,25 @@ @@
  *  VirtualLeaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 // WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.
 // Do not edit. All edits will be discarded.
 #include "pardialog.h"
 #include "parameter.h"
 #include <cstring>
 #include <qdialog.h>
 #include <qlabel.h>
 #include <qlineedit.h>
 #include <qmessagebox.h>
 static const std::string _module_id("$Id$");
@@ @@ -809,13 +810,12 @@ void ParameterDialog::Reset(void) { @@
   s2_edit->setText( QString("%1").arg(par.s2) );
   s3_edit->setText( QString("%1").arg(par.s3) );
   b1_edit->setText( QString("%1").arg(sbool(par.b1)));
   b2_edit->setText( QString("%1").arg(sbool(par.b2)));
   b3_edit->setText( QString("%1").arg(sbool(par.b3)));
   b4_edit->setText( QString("%1").arg(sbool(par.b4)));
   dir1_edit->setText( QString("%1").arg(par.dir1) );
   dir2_edit->setText( QString("%1").arg(par.dir2) );
   export_interval_edit->setText( QString("%1").arg(par.export_interval) );
   export_fn_prefix_edit->setText( QString("%1").arg(par.export_fn_prefix) );
+}
 /* finis */

src/pardialog.h

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@@ @@ -13,25 +13,25 @@ @@
  *  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.
+ *
  */
 // WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.
 // All edits will be discarded.
+// Do not edit. All edits will be discarded.
 #ifndef PARAMETER_DIALOG_H
 #define PARAMETER_DIALOG_H
 #include <qdialog.h>
 #include <qspinbox.h>
 #include <qlineedit.h>
 #include <qlayout.h>
 #include <qpushbutton.h>
 #include <iostream>
 class ParameterDialog : public QDialog {
     Q_OBJECT
@@ @@ -139,13 +139,12 @@ class ParameterDialog : public QDialog { @@
   QLineEdit *s2_edit;
   QLineEdit *s3_edit;
   QLineEdit *b1_edit;
   QLineEdit *b2_edit;
   QLineEdit *b3_edit;
   QLineEdit *b4_edit;
   QLineEdit *dir1_edit;
   QLineEdit *dir2_edit;
   QLineEdit *export_interval_edit;
   QLineEdit *export_fn_prefix_edit;
 };
 #endif

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