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 23 insertions and 27 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
 	"yield_threshold" instead of fixed parameter '4' for yield
 	threshold.
 	* wallitem.cpp: when clicking a wall, both the wall type was
 	cycled and the transporterdialog popped up. Corrected this - for
 	wall type cycling, hold the Control button while left
 	clicking. TransporterDialog only pops up for left click. Also made
 	sure the wall is redrawn after changing the transporter values.
 	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference
 	* hull.h: added an operator< to sort Points
 	* hull.cpp: added an operator< to sort Points
 	* cellbase.cpp (ExactCircumference): I added a new function
 	ExactCircumference, yielding the circumference of the cell along
 	its wall_elements
 	* VirtualLeaf.cpp: adjust info_string to accomodate for new name
 	of function CellBase::Circumference -> CellBase::WallCircumference
 	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates
 	need to be sorted in x,y order for the convex hull algorithm
 	(thanks Margriet!). I updated CSVExportCellData so it exports the
 	circumferences of hull and boundary_polygon.
 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'
 	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data
 	filename now incorporates iteration number.
 	* canvas.h (MainBase): Removed TimeStamp().
 -10-08    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h:
 	* pardialog.cpp:
 	* parameter.h:
 	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.
 	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.
 	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.
 	* canvas.cpp:
 	(TimeStamp): New private TimeStamp() function.
 	(TimeStepWrap): Added invocation of exportCellData().
 	(exportCellData): Created two polymorphic functions: one with a
 	single QString argument, the other with no argument. The former is
 	called from TimeStepWrap() while the latter is called from the
 	"Export cell areas" item in the file menu.
 -10-07    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire
 	where to write the exportCellData.
 -06-28    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.
 	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc
 	directory (Linux) or a decedent doc directory (Windows, via the
 	binary installer).
 	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.
 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* gpl3.txt: Moved gpl3.txt from doc to src directory.
 	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 	* libplugin.pro: Ditto.
 	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.
 	* parameter.h: Ditto.
 	* output.h: Declared new function (AppendHomeDirIfPathRelative).
 	* output.cpp (AppendHomeDirIfPathRelative): Added new function.
 	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").
 	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.
 	Add missing libiconv/bin, libxml2bin and libz/bin directories.
 	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.
 	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.
 -06-24    <guravage@caterpie.sen.cwi.nl>
 	* libplugin.pro: Use correct library path.
 	* VirtualLeaf.pro: Ditto.
 	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* simitembase.cpp: Removed NULL assignments to unused variables.
 	* VirtualLeaf.cpp: Ditto.
 	* apoplastitem.cpp: Ditto.
 	* canvas.cpp: Ditto.
 	* cell.cpp: Ditto.
 	* cellbase.h: Ditto.
 	* forwardeuler.cpp: Ditto.
 	* mainbase.h: Ditto.
 	* nodeitem.cpp: Ditto.
 	* qcanvasarrow.h: Ditto.
 	* simitembase.cpp: Ditto.
 	* Makefile (clean): Add -f Makefile argument to each make invocation.
 	* VirtualLeaf-install.nsi: New gpl license text.
 	* VirtualLeaf.pro: Disabled console mode.
 	* mesh.cpp (Clear): Added parentheses to qDebug statments.
 	(TestIllegalWalls): Replaced qDebug().
 	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.
 	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (tutorials): Add tutorials target.
 -06-21    <guravage@caterpie.sen.cwi.nl>
 	* parameter.cpp: Added particular reassignment of datadir.
 	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.
 -06-18    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (gpl): Added gpl slot to display GPL license.
 	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
 	* libplugin.pro: Ditto.
 	* Makefile (clean): add if stmt not to `touch` on windows.
 -06-17    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed perl references.
 	* libplugin.pro: Ditto.
 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.
 	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.
 	* xmlwrite.h (XMLIO): Ditto!
 	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;
 	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
 	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
 	(XMLReadCells): Removed unused count variable.
 	(XMLReadSimtime): Removed unused cur variable.
 	(XMLRead): Removed unused v_str variable.
 	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
 	(SimItemBase) Ditto.
 	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.
 	* output.cpp (OpenWriteFile): Removed unused par variable.
 	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.
 	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.
 	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.
 	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
 	(mousePressEvent): Removed unused item variable.
 	* apoplastitem.cpp
 	(ApoplastItem): Removed unused par variable.
 	(OnClick): Use NULL assignment merely to obviate compilation warning.
 	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.
 	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* data_plot.cpp ditto.
 	* forwardeuler.cpp ditto.
 	* mesh.cpp ditto.
 	* mesh.h
 	* random.cpp ditto.
 	* wall.cpp ditto.
 	* wallbase.cpp ditto.
 	* wallitem.cpp ditto.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h: Added default versions of this automatically generated file.
 	* pardialog.cpp: ditto.
 	* parameter.h: ditto.
 	* parameter.cpp: ditto.
 	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
  	* libplugin.pro: dito.
 	* Makefile: Added top-level Makefile
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

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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 <?xml version="1.0" encoding="UTF-8"?>
 <leaf name="/Users/roel/VLeaf1.0/V1.0/bin/auxinfluxinit.xml" date="Mon Jun  7 15:40:43 2010" simtime="0">
   <parameter>
     <par name="arrowcolor" val="white"/>
     <par name="arrowsize" val="10"/>
     <par name="textcolor" val="red"/>
     <par name="cellnumsize" val="1"/>
     <par name="nodenumsize" val="1"/>
     <par name="node_mag" val="20"/>
     <par name="outlinewidth" val="2"/>
     <par name="cell_outline_color" val="forestgreen"/>
     <par name="resize_stride" val="10"/>
     <par name="T" val="1"/>
     <par name="lambda_length" val="100"/>
     <par name="lambda_celllength" val="0"/>
     <par name="target_length" val="60"/>
     <par name="cell_expansion_rate" val="10"/>
     <par name="cell_div_expansion_rate" val="10"/>
     <par name="auxin_dependent_growth" val="true"/>
     <par name="ode_accuracy" val="0.0001"/>
     <par name="mc_stepsize" val="0.4"/>
     <par name="mc_cell_stepsize" val="0.2"/>
     <par name="energy_threshold" val="1000"/>
     <par name="bend_lambda" val="0"/>
     <par name="alignment_lambda" val="0"/>
     <par name="rel_cell_div_threshold" val="2"/>
     <par name="rel_perimeter_stiffness" val="2"/>
     <par name="collapse_node_threshold" val="0.05"/>
     <par name="morphogen_div_threshold" val="0.2"/>
     <par name="morphogen_expansion_threshold" val="0.01"/>
     <par name="copy_wall" val="true"/>
     <par name="source" val="0"/>
     <par name="D">
       <valarray>
         <val v="0.0001"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="initval">
       <valarray>
         <val v="1"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="k1" val="1"/>
     <par name="k2" val="0.3"/>
     <par name="r" val="1"/>
     <par name="kr" val="1"/>
     <par name="km" val="1"/>
     <par name="Pi_tot" val="1"/>
     <par name="transport" val="0.36"/>
     <par name="ka" val="1"/>
     <par name="pin_prod" val="0"/>
     <par name="pin_prod_in_epidermis" val="0"/>
     <par name="pin_breakdown" val="0"/>
     <par name="pin_breakdown_internal" val="0.001"/>
     <par name="aux1prod" val="0.001"/>
     <par name="aux1prodmeso" val="0"/>
     <par name="aux1decay" val="0.001"/>
     <par name="aux1decaymeso" val="0.1"/>
     <par name="aux1transport" val="0.036"/>
     <par name="aux_cons" val="0"/>
     <par name="aux_breakdown" val="0"/>
     <par name="kaux1" val="1"/>
     <par name="kap" val="1"/>
     <par name="leaf_tip_source" val="0.001"/>
     <par name="sam_efflux" val="0.0001"/>
     <par name="sam_auxin" val="10"/>
     <par name="sam_auxin_breakdown" val="0"/>
     <par name="van3prod" val="0.002"/>
     <par name="van3autokat" val="0.1"/>
     <par name="van3sat" val="10"/>
     <par name="k2van3" val="0.3"/>
     <par name="dt" val="0.1"/>
     <par name="rd_dt" val="10"/>
     <par name="datadir" val="."/>
     <par name="movie" val="false"/>
     <par name="nit" val="100000"/>
     <par name="maxt" val="1000"/>
     <par name="storage_stride" val="10"/>
     <par name="xml_storage_stride" val="500"/>
     <par name="rseed" val="-1"/>
     <par name="constituous_expansion_limit" val="16"/>
     <par name="vessel_inh_level" val="1"/>
     <par name="vessel_expansion_rate" val="0.25"/>
     <par name="d" val="0"/>
     <par name="e" val="0"/>
     <par name="f" val="0"/>
     <par name="c" val="0"/>
     <par name="mu" val="0"/>
     <par name="nu" val="0"/>
     <par name="rho0" val="0"/>
     <par name="rho1" val="0"/>
     <par name="c0" val="0"/>
     <par name="gamma" val="0"/>
     <par name="eps" val="0"/>
     <par name="k">
       <valarray>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="i1" val="0"/>
     <par name="i2" val="0"/>
     <par name="i3" val="0"/>
     <par name="i4" val="0"/>
     <par name="i5" val="0"/>
     <par name="s1" val=""/>
     <par name="s2" val=""/>
     <par name="s3" val=""/>
     <par name="b1" val="false"/>
     <par name="b2" val="false"/>
     <par name="b3" val="false"/>
     <par name="b4" val="false"/>
     <par name="dir1" val="."/>
     <par name="dir2" val="."/>
   </parameter>
   <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;
 #include &lt;sstream&gt;
 #include &lt;cstring&gt;
 #include &lt;functional&gt;
 #include &lt;getopt.h&gt;
 #include &lt;cerrno&gt;
 #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 &lt;qwidget.h&gt;
 #include &lt;q3process.h&gt;
 #include &lt;qapplication.h&gt;
 #include &lt;QDesktopWidget&gt;
 #include &lt;QGraphicsScene&gt;
 #include &lt;QMessageBox&gt;
 //Added by qt3to4:
 #include &lt;QMouseEvent&gt;
 #include &lt;unistd.h&gt;
 #include &lt;q3textstream.h&gt;
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include &lt;QPalette&gt;
 #include &lt;QBrush&gt;
 #include &lt;QToolTip&gt;
 #include "simplugin.h"
 #include "testplugin.h"
 /* #define _xstr_(s) _str_(s)
 #define _str_(s) #s
 #include _xstr_(REACTIONS_HEADER)
 */
 extern Parameter par;
 MainBase *main_window = 0;
 double auxin_account = 0.;
 TestPlugin *plugin = new TestPlugin();
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
   void operator() (const Node &amp;n) const
+  {
     cerr &lt;&lt; n.Index() &lt;&lt; ": " &lt;&lt; n &lt;&lt;  endl;
+  }
 };
 class EdgeSource {
 public:
   void operator() (Cell &amp;c) {
     if (c.AtBoundaryP()) {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is a source cell.\n";
       c.SetSource(0,par.source);
     } else {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is _not_ a source cell.\n";
+    }
+  }
 };
 class CellInfo {
 public:
   void operator() (Cell &amp;c,std::ostream &amp;os) const {
     os &lt;&lt; "Cell " &lt;&lt; c.index &lt;&lt; " says: " &lt;&lt; endl;
     os &lt;&lt; "c.nodes.size() = " &lt;&lt; c.nodes.size() &lt;&lt; endl;
     for (list&lt;Node *&gt;::iterator i=c.nodes.begin();
 	 i!=c.nodes.end();
 	 i++) {
       cerr &lt;&lt; (*i)-&gt;Index() &lt;&lt; " ";
+    }
     cerr &lt;&lt; endl;
+  }
 };
 double PINSum(Cell &amp;c) {
 	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls&lt;double&gt;( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &amp;c,QGraphicsScene &amp;canvas, MainBase &amp;m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() &amp;&amp; !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(&amp;canvas, info_string);
 	} else {
 	  c.Draw(&amp;canvas);
+	}
       if (m.ShowCentersP())
 	c.DrawCenter(&amp;canvas);
     if (m.ShowFluxesP())
 	c.DrawFluxes(&amp;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 ( &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;
+    }
+  }
+}
 INIT {
 	if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &amp;settings);
     main_window-&gt;XMLReadSettings(settings);
     xmlFree(settings);
     main_window-&gt;UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
   } else {
 	  Cell &amp;circle=mesh.CircularCell(0,0,10,10);
     circle.SetTargetArea(circle.CalcArea());
 	  mesh.SetBaseArea();
 	// clean up chemicals
 	  for (int c=0; c&lt;Cell::NChem(); c++) {
 		  circle.SetChemical(c, 0.);
+      }
+  }
+}
 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) &lt; par.energy_threshold) {
       mesh.IncreaseCellCapacityIfNecessary();
 		mesh.LoopCurrentCells(&amp;TestPlugin::CellHouseKeeping); // this includes cell division
       // Reaction diffusion
 		/*CelltoCellTransport *transport_f = &amp;TestPlugin::CelltoCellTransport;
       CellReaction *cellreaction_f = new plugin-&gt;CellDynamics();
       WallReaction *wall_f = new WallDynamics();*/
       mesh.ReactDiffuse(plugin, par.rd_dt);
       t++;
       Plot(par.resize_stride);
 		/*QVector&lt; QPair&lt;double, int&gt; &gt; angles=mesh.VertexAnglesValues();
 		QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 		ofstream af(afname.toStdString().c_str());
 		*/
 		/*for (QVector&lt; QPair&lt;qreal, int&gt; &gt;::const_iterator v=angles.begin();
 			 v!=angles.end();
 			 v++) {
 			af &lt;&lt; v-&gt;first &lt;&lt; " " &lt;&lt; v-&gt;second &lt;&lt; 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(plugin, par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
+}
 void Wall::OnWallInsert(void) {
+}
 int main(int argc,char **argv) {
   try {
     int c;
     char *leaffile=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}
       };
       // 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:",
 		       long_options, &amp;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 &lt;&lt; "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 '?':
 	break;
       default:
 	printf ("?? getopt returned character code 0%o ??\n", c);
+      }
+    }
     if (optind &lt; argc) {
       printf ("non-option ARGV-elements: ");
       while (optind &lt; argc)
 	printf ("%s ", argv[optind++]);
       printf ("\n");
+    }
 	  MakeDir("Angles");
     bool useGUI = !batch;
     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()-&gt;width() &gt; ((Main *)main_window)-&gt;width() + 10
 	   &amp;&amp; QApplication::desktop()-&gt;height() &gt; ((Main *)main_window)-&gt;height() +30 ) {
 	((Main *)main_window)-&gt;show();
 	((Main *)main_window)-&gt;resize( ((Main *)main_window)-&gt;sizeHint());
     } else {
         ((Main *)main_window)-&gt;showMaximized();
+    }
   } else {
         main_window=new MainBase(canvas, mesh);
+ }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
     main_window-&gt;Init(leaffile);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     main_window-&gt;FitLeafToCanvas();
     main_window-&gt;Plot();
     if (batch) {
       double t=0.;
       do {
 	t = main_window-&gt;TimeStep();
       } while (t &lt; par.maxt);
     } else
       return app.exec();
   } catch (const char *message) {
     if (batch) {
       cerr &lt;&lt; "Exception caught:" &lt;&lt; endl;
       cerr &lt;&lt; message &lt;&lt; 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 &lt;&lt; "I/O failure: " &lt;&lt; strerror(errno);
     if (batch) {
       cerr &lt;&lt; error_message.str() &lt;&lt;endl;
       abort();
     } else {
       QString qmess(error_message.str().c_str());
       QMessageBox::critical(0, "I/O Error", qmess );
       abort();
+    }
+  }
+}
 </code>
   <code name="reactions_pce_growth.h">
 // Executed after the cellular mechanics steps have equillibrized
 class CellHouseKeeping {
 public:
 	void operator() (Cell &amp;c) const {
 		c.EnlargeTargetArea(par.cell_expansion_rate);
 		if (c.Area() &gt; par.rel_cell_div_threshold * c.BaseArea() ) {
 			c.Divide();
+		}
+	}
 };
 // The number of chemical species in the cels
 const int Cell::nchem = 0;
 // Differential equations describing transport of chemicals from cell to cell
 class CelltoCellTransport : public TransportFunction {
  public:
 	virtual void operator()(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)
 class WallDynamics : public WallReaction {
  public:
 	virtual void operator()(Wall *w, double *dw1, double *dw2) {};
 };
 // Differential equations describing chemical reactions inside the cells
 class CellDynamics : public CellReaction {
  public:
 	virtual void operator()(Cell *c, double *dchem) {
 	};
 };
 // Rules for cell coloring
 void Cell::SetColor(QColor &amp;color) { }
 // To be executed after cell division
 void Cell::OnDivide(ParentInfo &amp;parent_info, Cell &amp;daughter) {}
 </code>
   <nodes n="1277" target_length="3.09017">
     <node x="210.911" y="-39.9231" fixed="false" boundary="true" sam="false"/>
     <node x="191.318" y="108.843" fixed="false" boundary="true" sam="false"/>
     <node x="49.3519" y="206.243" fixed="false" boundary="true" sam="false"/>
     <node x="-116.346" y="180.886" fixed="false" boundary="true" sam="false"/>
     <node x="-174.807" y="131.435" fixed="false" boundary="true" sam="false"/>
     <node x="-205.135" y="-82.753" fixed="false" boundary="true" sam="false"/>
     <node x="-197.138" y="-88.9985" fixed="false" boundary="true" sam="false"/>
     <node x="-25.9056" y="-214.059" fixed="false" boundary="true" sam="false"/>
     <node x="46.3642" y="-206.845" fixed="false" boundary="true" sam="false"/>
     <node x="166.573" y="-142.11" fixed="false" boundary="true" sam="false"/>
     <node x="-122.758" y="172.566" fixed="false" boundary="true" sam="false"/>
     <node x="82.8058" y="-189.874" fixed="false" boundary="true" sam="false"/>

src/VirtualLeaf.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  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.
+ *
  */
 #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"
 static const std::string _module_id("$Id$");
 extern Parameter par;
 MainBase *main_window = 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());
 		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) )  {
       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)
     if ( (-dh) < par.energy_threshold) {
       mesh.IncreaseCellCapacityIfNecessary();
       mesh.DoCellHouseKeeping();
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       // Reaction diffusion
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
+    }
   } else {
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e){}
 /* 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", 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 = "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();
+      }
       // 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();
     /*    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();
+    }
+  }
+}
 /* finis */

src/mainbase.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  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.
+ *
  */
 #include <libxml/xpath.h>
 #include <libxml/xmlreader.h>
 #include "mainbase.h"
 #include "xmlwrite.h"
 #include <sstream>
 #include <string>
 #include <QLocale>
 #include <QDir>
 #include <QDebug>
 static const std::string _module_id("$Id$");
 xmlNode *MainBase::XMLViewportTree(QTransform &transform) const {
   QLocale standardlocale(QLocale::C);
   xmlNode *xmlviewport = xmlNewNode(NULL, BAD_CAST "viewport");
+  {
     xmlNewProp(xmlviewport, BAD_CAST "m11", BAD_CAST standardlocale.toString(transform.m11()).toStdString().c_str() );
     xmlNewProp(xmlviewport, BAD_CAST "m12", BAD_CAST standardlocale.toString(transform.m12()).toStdString().c_str() );
     xmlNewProp(xmlviewport, BAD_CAST "m21", BAD_CAST standardlocale.toString(transform.m21()).toStdString().c_str() );
     xmlNewProp(xmlviewport, BAD_CAST "m22", BAD_CAST standardlocale.toString(transform.m22()).toStdString().c_str() );
     xmlNewProp(xmlviewport, BAD_CAST "dx", BAD_CAST standardlocale.toString(transform.dx()).toStdString().c_str() );
     xmlNewProp(xmlviewport, BAD_CAST "dy", BAD_CAST standardlocale.toString(transform.dy()).toStdString().c_str() );
+ }
   return xmlviewport;
+}
 xmlNode *MainBase::XMLSettingsTree(void) const {
   xmlNode *xmlsettings = xmlNewNode(NULL, BAD_CAST "settings");
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_centers");
     ostringstream text;
     text << bool_name(showcentersp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_nodes");
     ostringstream text;
     text << bool_name(showmeshp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_node_numbers");
     ostringstream text;
     text << bool_name(shownodenumbersp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_numbers");
     ostringstream text;
     text << bool_name(showcellnumbersp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_border_cells");
     ostringstream text;
     text << bool_name(showbordercellp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_axes");
     ostringstream text;
     text << bool_name(showcellsaxesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_strain");
     ostringstream text;
     text << bool_name(showcellstrainp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_fluxes");
     ostringstream text;
     text << bool_name(showfluxesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_walls");
     ostringstream text;
     text << bool_name(showwallsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
  /* {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_apoplasts");
     ostringstream text;
     text << bool_name(showapoplastsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
   }*/
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "save_movie_frames");
     ostringstream text;
     text << bool_name(movieframesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_only_leaf_boundary");
     ostringstream text;
     text << bool_name(showboundaryonlyp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "cell_growth");
     ostringstream text;
     text << bool_name(dynamicscellsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "hide_cells");
     ostringstream text;
     text << bool_name(hidecellsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
   return xmlsettings;
+}
 void MainBase::XMLReadViewport(xmlNode *settings) {
   if (settings == 0) {
     return;
+  }
   qreal m11=25,m12=0,m21=0,m22=25,dx=0,dy=0;
   QLocale standardlocale(QLocale::C);
   xmlNode *cur = settings->xmlChildrenNode;
   while (cur!=NULL) {
     if (!xmlStrcmp(cur->name,(const xmlChar *)"viewport")) {
       bool ok;
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m11");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  m11=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m12");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  m12=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m21");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  m21=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m22");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  m22=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "dx");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  dx=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+      {
 	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "dy");
 	if (v_str==0) {
 	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");
+	}
 	if (v_str != NULL) {
 	  dy=standardlocale.toDouble((char *)v_str, &ok);
 	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);
 	  xmlFree(v_str);
+	}
+      }
+    }
     cur=cur->next;
+  }
   viewport = QTransform(m11,m12,m21,m22,dx,dy);
+}
 void MainBase::XMLReadSettings(xmlNode *settings)
+{
   // Many files have no settings section, so don't complain about it.
   // Defaults will be used instead.
   if (settings == 0) {
     return;
+  }
   XMLReadViewport(settings);
   xmlNode *cur = settings->xmlChildrenNode;
   while (cur!=NULL) {
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"setting"))){
       xmlChar *name = xmlGetProp(cur, BAD_CAST "name");
       xmlChar *val = xmlGetProp(cur, BAD_CAST "val");
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_centers")) {
 	showcentersp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_nodes")) {
 	showmeshp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_node_numbers")) {
 	shownodenumbersp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_numbers")) {
 	showcellnumbersp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_border_cells")) {
 	showbordercellp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_axes")) {
 	showcellsaxesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_strain")) {
 	showcellstrainp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_fluxes")) {
 	showfluxesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {
 	showwallsp = strtobool( (const char *)val );
+      }
      /* if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {
 	showapoplastsp = strtobool( (const char *)val );
       }*/
       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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