EI/VirtualLeaf Changeset - c2962c0745f8 · Centrum Wiskunde & Informatica (CWI)

Changeset - c2962c0745f8

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Michael Guravage - 15 years ago 2010-10-14 11:19:03
michael.guravage@cwi.nl

Use iteration number instead of time stamp to tag exported cell data files. Added default LeafML files to tutorials 3-5. See respective ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
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

19 files changed with 309 insertions and 262 deletions:

data/leaves/ChangeLog

data/leaves/auxin_growth.xml

doc/v1.html

doc/v1.pdf

235

208

doc/v1.rst

src/ChangeLog

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)

data/leaves/ChangeLog

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 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* auxin_growth.xml: Changed export_fn_prefix to 'cell.'
 -10-08    <guravage@caterpie.sen.cwi.nl>
 	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.

data/leaves/auxin_growth.xml

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@@ @@ -27,7 +27,7 @@ @@
 <leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">
   <parameter>
     <par name="export_interval" val="1000"/>
-    <par name="export_fn_prefix" val="CELLDATA_"/>
+    <par name="export_fn_prefix" val="cell."/>
     <par name="arrowcolor" val="white"/>
     <par name="arrowsize" val="10"/>
     <par name="textcolor" val="red"/>

doc/v1.html

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@@ @@ -544,7 +544,6 @@ LanguageError: IOError: [Errno 2] No tra @@
 </div>
 <div class="section" id="re-install">
 <h2>RE-INSTALL</h2>
 <blockquote>
 <ol class="arabic simple">
 <li>easy_install mercurial</li>
 <li>mkdir src</li>
@@ @@ -555,14 +554,8 @@ LanguageError: IOError: [Errno 2] No tra @@
 <li>python configure.py</li>
 <li>make</li>
 <li>make install</li>
 </ol>
 </blockquote>
 <div class="system-message">
 <p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">v1.rst</tt>, line 295)</p>
 Block quote ends without a blank line; unexpected unindent.</div>
 <ol class="arabic simple" start="10">
 <li>cd ..</li>
-<li>curl <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
+<li>wget <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
 <li>tar xzf PyQt-x11-gpl-4.7.7</li>
 <li>cd PyQt-x11-gpl-4.7.7</li>
 <li>python configure.py</li>
@@ @@ -573,12 +566,9 @@ Block quote ends without a blank line; u @@
 <li>cd cutehg</li>
 <li>python setup.py build</li>
 <li>python setup.py install</li>
 <li>cd ..</li>
 <li>easy_install rhodecode, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc2">http://pypi.python.org/pypi/RhodeCode/1.0.0rc2</a></li>
 </ol>
 <div class="system-message">
 <p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">v1.rst</tt>, line 307)</p>
 Enumerated list ends without a blank line; unexpected unindent.</div>
 <p>22. cd ..
 . easy_install rhodecode, <a class="reference external" href="http://pypi.python.org/pypi/RhodeCode/1.0.0rc2">http://pypi.python.org/pypi/RhodeCode/1.0.0rc2</a></p>
 <p>This procedure fails as before.</p>
 <p>However, upon inspection I saw that the i18n directory was missing
 from my build but present in the rhodecode clone from bitbucket. While

doc/v1.pdf

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 trailer
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+ [(\002\015b\216\002\016\216\222,\316k\030\021\317\316@) (\002\015b\216\002\016\216\222,\316k\030\021\317\316@)]
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 startxref
 %%EOF

doc/v1.rst

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@@ @@ -283,17 +283,17 @@ All goes tolerably until you tick in the @@
 RE-INSTALL
 ++++++++++
 . easy_install mercurial
 . mkdir src
 . cd src
 . hg clone http://www.riverbankcomputing.com/hg/sip
 . cd sip
 . python build.py prepare
 . python configure.py
 . make
 . make install
 . easy_install mercurial
 . mkdir src
 . cd src
 . hg clone http://www.riverbankcomputing.com/hg/sip
 . cd sip
 . python build.py prepare
 . python configure.py
 . make
 . make install
 . cd ..
-. curl http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
+. wget http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
 . tar xzf PyQt-x11-gpl-4.7.7
 . cd PyQt-x11-gpl-4.7.7
 . python configure.py
@@ @@ -305,7 +305,7 @@ 19. cd cutehg @@
 . python setup.py build
 . python setup.py install
 . cd ..
-. easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
+. easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
 This procedure fails as before.
@@ @@ -339,9 +339,14 @@ still be justified - though they become @@
 introduce the new schema changes.
 Wednesday 13 October 2010
 -------------------------
 Tweaked ``.bashrc`` and ``virtualenvwrapper.sh`` to facilitate
 virtualenv and virtualenvwrapper - many unbound variables!
 Pushed recent changes to repository from where Roeland can retrieve
 and test them.
 OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.

src/ChangeLog

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 -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>

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.

src/TutorialCode/Tutorial3/tutorial3.h

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@@ @@ -53,6 +53,9 @@ public: @@
 	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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 -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.

src/TutorialCode/Tutorial4/tutorial4.h

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@@ @@ -55,6 +55,9 @@ public: @@
 	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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 -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.

src/TutorialCode/Tutorial5/tutorial5.h

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@@ @@ -55,6 +55,9 @@ public: @@
 	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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@@ @@ -125,4 +125,4 @@ 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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@@ @@ -90,6 +90,7 @@ 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
@@ @@ -480,7 +481,7 @@ 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->insertItem("Export cell data", this, SLOT(exportCellData()));
   file->insertSeparator();
   file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);
@@ @@ -1165,11 +1166,17 @@ void Main::print() @@
 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
@@ @@ -1179,18 +1186,6 @@ void Main::TimeStepWrap(void) @@
+}
 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)
+{

src/canvas.h

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@@ @@ -227,8 +227,6 @@ class Main : public Q3MainWindow, public @@
   void RandomizeMesh();
   QString TimeStamp();
  signals:
   void SimulationDone(void);
   void ParsChanged(void);

src/parameter.cpp

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@@ @@ -19,9 +19,9 @@ @@
+ *
  */
 // 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>
@@ @@ -186,8 +186,8 @@ Parameter::Parameter() { @@
   b4 = false;
   dir1 = strdup(".");
   dir2 = strdup(".");
   export_interval = 100;
   export_fn_prefix = strdup("CELLDATA");
   export_interval = 0;
   export_fn_prefix = strdup("cell.");
+}
 Parameter::~Parameter() {
@@ @@ -347,8 +347,8 @@ void Parameter::Read(const char *filenam @@
   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) {
@@ @@ -1893,4 +1893,3 @@ ostream &operator<<(ostream &os, Paramet @@
     return os;
+}
 /* finis */

src/parameter.h

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@@ @@ -22,7 +22,7 @@ @@
  */
 // 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_

src/pardialog.cpp

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@@ @@ -19,6 +19,7 @@ @@
+ *
  */
 // 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"
@@ @@ -818,4 +819,3 @@ void ParameterDialog::Reset(void) { @@
   export_fn_prefix_edit->setText( QString("%1").arg(par.export_fn_prefix) );
+}
 /* finis */

src/pardialog.h

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@@ @@ -22,7 +22,7 @@ @@
  */
 // 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
@@ @@ -148,4 +148,3 @@ class ParameterDialog : public QDialog { @@
   QLineEdit *export_fn_prefix_edit;
 };
 #endif

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