EI/VirtualLeaf Changeset - 5ec450ff7c49 · Centrum Wiskunde & Informatica (CWI)

Changeset - 5ec450ff7c49

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Michael Guravage - 15 years ago 2010-10-19 12:56:46
michael.guravage@cwi.nl

Render PNGs instead of JPGs. See ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3_init.xml
changed src/VirtualLeaf.cpp
changed src/mainbase.cpp

5 files changed with 25 insertions and 29 deletions:

src/ChangeLog

src/TutorialCode/Tutorial3/ChangeLog

src/TutorialCode/Tutorial3/tutorial3_init.xml

src/VirtualLeaf.cpp

src/mainbase.cpp

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src/ChangeLog

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 -10-19    <guravage@caterpie.sen.cwi.nl>
 	* mainbase.cpp (Save): Use format specified in function prototype.
 	* VirtualLeaf.cpp (Plot): Render PNG instead of JPEG. Write image
 	and XML files dependent only on getTime().
 -10-18    <guravage@caterpie.sen.cwi.nl>
 	* mainbase.cpp (Save): QDir::toNativeSeparators(fname). Invoke
 	save with format argument set to zero to force QImage to guess the
 	format by looking at fileName's suffix.
 	* VirtualLeaf-install.nsi: Put uninstaller in top directory.
 	* modelcatalogue.cpp (InstallModel): For all OS-es. Move from "bin" directory to root application folder.
 	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.
 	* Makefile (Makefile.libplugin): Removed -makefile qmake option.
 	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().
 	* mesh.h (Mesh): Removed {increment,get}Iterations().
 	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().
 -10-15    <guravage@caterpie.sen.cwi.nl>
 	* mesh.h (Mesh): Added iterations. incrementIterations() and
 	getIterations().
 	* VirtualLeaf.cpp (Plot): Replaced local frame counter with
 	mesh.incrementIterations().
 	* canvas.cpp (TimeStepWrap): Replaced local counter with
 	mesh.incrementIterations().
 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Turned debug off to make all profiles must be
 	consistant.
 	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX
 	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the
 	uninstaller all go in the bin directory. And leaves directory
 	placed under data directory.
 	* canvas.cpp (exportCellData): Added a check to inquire before
 	overwritting an existing file.
 -10-14    <merks@cwi.nl>
 	* mesh.cpp: In response to referees' comments, added new parameter

src/TutorialCode/Tutorial3/ChangeLog

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 -10-19    <guravage@caterpie.sen.cwi.nl>
 	* tutorial3_init.xml (public): Render PNG instead of JPEG.
 -10-18    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (Makefile.tutorial3): Removed -makefile qmake option.
 -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_init.xml

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@@ @@ -294,107 +294,107 @@ void MainBase::Plot(int resize_stride) { @@
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &amp;Node::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawAxis), &amp;canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawStrain), &amp;canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::Draw ), &amp;canvas ) );
 	if (ShowApoplastsP())
 		mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::DrawApoplast ), &amp;canvas ) );
 	if (ShowMeshP())
     mesh.DrawNodes(&amp;canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&amp;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 &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			/*
 			 fname &lt;&lt; frame &lt;&lt; ".pdf";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
-			// Write high-res JPG snapshot every plot step
+			// Write high-res PDF snapshot every plot step
 			Save(fname.str().c_str(), "PDF");
 			*/
-			fname &lt;&lt; frame &lt;&lt; ".jpg";
+			fname &lt;&lt; frame &lt;&lt; ".png";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "JPEG",1024,768);
 			// Write high-res PNG snapshot every plot step
 			Save(fname.str().c_str(), "PNG",1024,768);
+		}
 		if (!(count%par.xml_storage_stride)) {
 			stringstream fname;
 			fname &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			fname &lt;&lt; frame &lt;&lt; ".xml";
 			if (par.xml_storage_stride &lt; par.storage_stride) {
 				frame++;
+			}
 			// Write XML file every ten plot steps
 			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+		}
+	}
+}
 void Cell::Flux(double *flux, double *D)  {
   // loop over cell edges
   for (int c=0;c&lt;Cell::nchem;c++) flux[c]=0.;
   for (list&lt;Wall *&gt;::iterator i=walls.begin();
        i!=walls.end();
        i++) {
     // leaf cannot take up chemicals from environment ("no flux boundary")
     if ((*i)-&gt;c2-&gt;BoundaryPolP()) continue;
     // flux depends on edge length and concentration difference
     for (int c=0;c&lt;Cell::nchem;c++) {
       double phi = (*i)-&gt;length * ( D[c] ) * ( (*i)-&gt;c2-&gt;chem[c] - chem[c] );
       if ((*i)-&gt;c1!=this) {
 	cerr &lt;&lt; "Warning, bad cells boundary: " &lt;&lt; (*i)-&gt;c1-&gt;index &lt;&lt; ", " &lt;&lt; index &lt;&lt; endl;
+      }
       flux[c] += phi;
+    }
+  }

src/VirtualLeaf.cpp

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@@ @@ -101,168 +101,153 @@ public: @@
       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());
 		QString info_string=QString("Cell %1, chemicals(%2): ").arg(c.Index()).arg(Cell::NChem());
 		for (int i=0;i<Cell::NChem();i++) {
 			info_string += QString("%1 ").arg(c.Chemical(i));
+		}
 		info_string += QString("\nArea is %1\n Circumference is %2\n Boundary type is %3").arg(c.Area()).arg(c.WallCircumference()).arg(c.BoundaryStr());
 	  info_string += "\nNodes: " + 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;
   int count=(int)mesh.getTime();
   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) )  {
     if (!(count%par.storage_stride) ) {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame = (int)mesh.getTime();
+      }
       // Write high-res JPG snapshot every plot step
       Save(fname.str().c_str(), "JPEG",1024,768);
       fname << count << ".png";
       // Write high-res PNG snapshot every plot step
       Save(fname.str().c_str(), "PNG", 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 = (int)mesh.getTime();
+      }
       fname << count << ".xml";
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+    }
+  }
  count++;
+}
 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
     // and cell expansion
     mesh.InsertNodes(); // (this amounts to cell wall yielding)

src/mainbase.cpp

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@@ @@ -299,70 +299,70 @@ void MainBase::XMLReadSettings(xmlNode * @@
       }*/
       if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {
 	movieframesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_only_leaf_boundary")) {
 	showboundaryonlyp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"cell_growth")) {
 	dynamicscellsp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name,(const xmlChar *)"hide_cells")) {
 	hidecellsp = strtobool( (const char *)val );
+      }
       xmlFree(name);
       xmlFree(val);
+    }
     cur=cur->next;
+  }
+}
 void MainBase::Save(const char *fname, const char *format, int sizex, int sizey)
+{
   Vector ll,ur;
   mesh.BoundingBox(ll, ur);
   if (QString(fname).isEmpty()) {
     MyWarning::warning("No output filename given. Saving nothing.\n");
     return;
+  }
   ll*=Cell::Magnification(); ur*=Cell::Magnification();
   // give the leaf some space
   Vector border = ((ur-ll)/5.);
   if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {
     QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);
     image->fill(QColor(Qt::white).rgb());
     QPainter *painter=new QPainter(image);
     canvas.render(painter);
 #ifdef QDEBUG
     qDebug() << "Native Image Filename: " << QDir::toNativeSeparators(QString(fname)) << endl;
 #endif
-    if (!image->save(QDir::toNativeSeparators(QString(fname)), 0, -1)) {
+    if (!image->save(QDir::toNativeSeparators(QString(fname)), format)) {
       MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");
-    };
+    }
     delete painter;
     delete image;
   } else {
     QPrinter pdf(QPrinter::HighResolution);
     pdf.setOutputFileName(fname);
     pdf.setOutputFormat(QPrinter::PdfFormat);
     QPainter painter(&pdf);
     canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));
     cerr << "Rendering to printer\n";
+  }
+}
 void MainBase::CutSAM()
+{
   mesh.CutAwaySAM();
+}
 /* finis */

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