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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Show inline comments

 -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.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* Added: tutorial3_init.xml
 	tutorial4_init.xml
 	tutorial5_init.xml
 	* Removed: bend.xml
 	circ.xml
 	explant.xml
 	init.xml
 	one_acc_point_van3.xml
 	one_acc_point_van3_growth.xml
 	one_acc_point_van3_growth2.xml
 	tissue.xml

data/leaves/auxin_growth.xml

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Show inline comments

@@ @@ -6,49 +6,49 @@ @@
   $Source$:  Source file
   $Date$:  Date of last commit
   This file is part of the Virtual Leaf.
   The Virtual Leaf 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.
   The Virtual Leaf 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.
 -->
 <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"/>
     <par name="cellnumsize" val="1"/>
     <par name="nodenumsize" val="1"/>
     <par name="node_mag" val="1"/>
     <par name="outlinewidth" val="1"/>
     <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"/>

doc/v1.html

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@@ @@ -523,83 +523,73 @@ Traceback (most recent call last): @@
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py&quot;, line 163, in __call__
    self.app, new_environ, catch_exc_info=True)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py&quot;, line 48, in call_wsgi_application
    app_iter = application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py&quot;, line 156, in __call__
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py&quot;, line 55, in __call__
    return self.application(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py&quot;, line 152, in __call__
    return self.wrap_app(environ, session_start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py&quot;, line 131, in __call__
    response = self.app(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 98, in __call__
    self.setup_app_env(environ, start_response)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py&quot;, line 203, in setup_app_env
    pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
  File &quot;/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py&quot;, line 165, in _get_translator
    raise LanguageError('IOError: %s' % ioe)
 LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
 </pre>
 </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>
 <li>cd src</li>
 <li>hg clone <a class="reference external" href="http://www.riverbankcomputing.com/hg/sip">http://www.riverbankcomputing.com/hg/sip</a></li>
 <li>cd sip</li>
 <li>python build.py prepare</li>
 <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>
 <li>make</li>
 <li>make install</li>
 <li>cd ..</li>
 <li>hg clone <a class="reference external" href="https://litsol&#64;bitbucket.org/bfrog/cutehg">https://litsol&#64;bitbucket.org/bfrog/cutehg</a></li>
 <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
 I think that the <tt class="docutils literal">easy_install rhodecode</tt> invocation is necessary to
 install the various subsidiary packages, moving the cloned rhodecode
 into the site-packages directory seems to have made most functionality
 work. e.g. graphical logs and diff highlighting.</p>
 </div>
 </div>
 <div class="section" id="tuesday-12-october-2010">
 <h1>Tuesday 12 October 2010</h1>
 <div class="section" id="rhodecode">
 <h2>RhodeCode</h2>
 <p>I think that if Chris can install RhodeCode, I can serve individual
 instance from my home directory.</p>
 </div>
 <div class="section" id="sed-ml-l1v1rc1">
 <h2>SED-ML L1V1RC1</h2>
 <p>Walking through the new SED-ML schema I see that they've dropped the
 generic simulation class and added AddXML and RemoveXML model change
 classes. Adding several more SED-ML examples for the symposium might
 still be justified - though they become obsolete the moment I
 introduce the new schema changes.</p>
 </div>

doc/v1.pdf

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 trailer
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  % ReportLab generated PDF document -- digest (http://www.reportlab.com)
- [(\330\333`\005z4\302y^2~\371\223\241\231\341) (\330\333`\005z4\302y^2~\371\223\241\231\341)]
+ [(\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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  /Size 67 >>
 startxref
 %%EOF

doc/v1.rst

➞

Show inline comments

@@ @@ -262,86 +262,91 @@ All goes tolerably until you tick in the @@
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py", line 163, in __call__
     self.app, new_environ, catch_exc_info=True)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py", line 48, in call_wsgi_application
     app_iter = application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py", line 156, in __call__
     return self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py", line 55, in __call__
     return self.application(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py", line 152, in __call__
     return self.wrap_app(environ, session_start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py", line 131, in __call__
     response = self.app(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 98, in __call__
     self.setup_app_env(environ, start_response)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 203, in setup_app_env
     pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
   File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py", line 165, in _get_translator
     raise LanguageError('IOError: %s' % ioe)
  LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
 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
 . make
 . make install
 . cd ..
 . hg clone https://litsol@bitbucket.org/bfrog/cutehg
 . 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.
 However, upon inspection I saw that the i18n directory was missing
 from my build but present in the rhodecode clone from bitbucket. While
 I think that the ``easy_install rhodecode`` invocation is necessary to
 install the various subsidiary packages, moving the cloned rhodecode
 into the site-packages directory seems to have made most functionality
 work. e.g. graphical logs and diff highlighting.
 Tuesday 12 October 2010
 -----------------------
 RhodeCode
 +++++++++
 I think that if Chris can install RhodeCode, I can serve individual
 instance from my home directory.
 SED-ML L1V1RC1
 ++++++++++++++
 Walking through the new SED-ML schema I see that they've dropped the
 generic simulation class and added AddXML and RemoveXML model change
 classes. Adding several more SED-ML examples for the symposium might
 still be justified - though they become obsolete the moment I
 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

➞

Show inline comments

 -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

src/TutorialCode/Tutorial3/ChangeLog

➞

Show inline comments

 -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

➞

Show inline comments

@@ @@ -32,29 +32,32 @@ class Tutorial3 : public QObject, SimPlu @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	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

➞

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

➞

Show inline comments

@@ @@ -34,29 +34,32 @@ class Tutorial4 : public QObject, SimPlu @@
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	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);
 	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

➞

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

➞

Show inline comments

@@ @@ -34,29 +34,32 @@ class Tutorial5 : public QObject, SimPlu @@
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(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)
 	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);
 	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

➞

Show inline comments

@@ @@ -104,25 +104,25 @@ mu = 0. / double @@
 nu = 0. / double
 rho0 = 0. / double
 rho1 = 0. / double
 c0 = 0. / double
 gamma = 0. / double
 eps = 0. / double
 label = / label
 label = <b>User-defined parameters</b> / label
 k = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 i1 = 0 / int
 i2 = 0 / int
 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

➞

Show inline comments

@@ @@ -69,48 +69,49 @@ @@
 #include "nodeitem.h"
 #include "cellitem.h"
 #include "wallitem.h"
 #include "mesh.h"
 #include "xmlwrite.h"
 #include "miscq.h"
 #include "OptionFileDialog.h"
 #include <cstdlib>
 #include <cstdio>
 #include "modelcatalogue.h"
 #include <algorithm>
 // 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(
 			   QGraphicsScene& c, Mesh &m, QWidget* parent,
 			   const char* name, Qt::WindowFlags f) :
   QGraphicsView(&c,parent), mesh(m)
+{
   intersection_line = 0;
   //angle_line = 0;
   setInteractive(true);
   moving = 0;
   rotation_mode = false;
+}
@@ @@ -459,49 +460,49 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   mesh(m)
+{
   editor = new FigureEditor(canvas,mesh, this);
 #ifdef QDEBUG
   qDebug() << "Interactive = " << editor->isEnabled();
 #endif
   working_dir = 0;
   QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));
   QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));
   QMenuBar* menu = menuBar();
   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()) );
   edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));
   menu->insertItem("&Edit", edit);
   run = new Q3PopupMenu( menu );
   running = false;
   paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
   menu->insertItem("&Run", run);
   view = new Q3PopupMenu( menu );
   view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);
@@ @@ -1144,74 +1145,68 @@ void Main::print() @@
 #endif
     double cw = (bbur.x - bbll.x);
     double ch = (bbur.y - bbll.y);
     QPainter pp(printer);
     QRect vp=pp.viewport();
 #ifdef QDEBUG
     qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;
 #endif
     // Note that Cell is also translated...
     pp.translate(-bbur.x,-bbur.y);
     if (cw>ch) {
       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;
     //    extern Mesh mesh;
     mesh.Clear();
     Init();
     Plot();
     editor->FullRedraw();
+  }
   //startSimulation();
+}
 void Main::FitCanvasToWindow(void)
+{

src/canvas.h

➞

Show inline comments

@@ @@ -206,50 +206,48 @@ class Main : public Q3MainWindow, public @@
   void readPrevStateXML();
   void readFirstStateXML();
   void readLastStateXML();
   void exportCellData();
   void exportCellData(QString);
   void saveStateXML();
   void snapshot();
   void savePars();
   void readPars();
   void clear();
   void init();
   virtual void CutSAM() { MainBase::CutSAM(); Refresh();}
   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;
   Q3PopupMenu *run;
   QMenu *modelmenu;
   Q3PopupMenu *helpmenu;
   QPrinter* printer;
   const QDir *working_dir;
   QString currentFile;
   //  toggle item states
   int dbf_id; // options->Double Buffer
   int com_id; // view->Show centers
   int mesh_id; // view->Show mesh
   int node_number_id; // view->Show Node numbers

src/parameter.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.
+ *
  */
 // 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>
 #include <QDir>
 #include <QStringList>
 using namespace std;
 static const std::string _module_id("$Id$");
 Parameter::Parameter() {
   arrowcolor = strdup("white");
   arrowsize = 100;
   textcolor = strdup("red");
   cellnumsize = 1;
@@ @@ -165,50 +165,50 @@ Parameter::Parameter() { @@
   k[5] = 0.;
   k[6] = 0.;
   k[7] = 0.;
   k[8] = 0.;
   k[9] = 0.;
   k[10] = 0.;
   k[11] = 0.;
   k[12] = 0.;
   k[13] = 0.;
   k[14] = 0.;
   i1 = 0;
   i2 = 0;
   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);
   if (textcolor)
      free(textcolor);
   if (cell_outline_color)
      free(cell_outline_color);
   if (D)
      free(D);
   if (initval)
      free(initval);
   if (datadir)
      free(datadir);
   if (k)
      free(k);
@@ @@ -326,50 +326,50 @@ void Parameter::Read(const char *filenam @@
   rho0 = fgetpar(fp, "rho0", 0., true);
   rho1 = fgetpar(fp, "rho1", 0., true);
   c0 = fgetpar(fp, "c0", 0., true);
   gamma = fgetpar(fp, "gamma", 0., true);
   eps = fgetpar(fp, "eps", 0., true);
   k = dgetparlist(fp, "k", 15, true);
   i1 = igetpar(fp, "i1", 0, true);
   i2 = igetpar(fp, "i2", 0, true);
   i3 = igetpar(fp, "i3", 0, true);
   i4 = igetpar(fp, "i4", 0, true);
   i5 = igetpar(fp, "i5", 0, true);
   s1 = sgetpar(fp, "s1", "", true);
   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;
+}
 void Parameter::Write(ostream &os) const {
   if (arrowcolor)
   os << " arrowcolor = " << arrowcolor << endl;
   os << " arrowsize = " << arrowsize << endl;
   if (textcolor)
   os << " textcolor = " << textcolor << endl;
   os << " cellnumsize = " << cellnumsize << endl;
   os << " nodenumsize = " << nodenumsize << endl;
   os << " node_mag = " << node_mag << endl;
@@ @@ -1872,25 +1872,24 @@ if (!strcmp(namec, "D")) { @@
      D[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "initval")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      initval[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "k")) {
   int i=0;
   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

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 // 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:
    Parameter();
    ~Parameter();
    void CleanUp(void);
    void Read(const char *filename);
    void Write(ostream &os) const;
    void XMLAdd(xmlNode *root) const;
    void XMLRead(xmlNode *root);
    void AssignValToPar(const char *namec, const char *valc);
    void AssignValArrayToPar(const char *namec, vector<double> valarray);
   char * arrowcolor;
   double arrowsize;
   char * textcolor;

src/pardialog.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.
+ *
  */
 // 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("$Id$");
 ParameterDialog::ParameterDialog(QWidget *parent, const char *name, Qt::WindowFlags f) : QDialog(parent,name,false,f) {
     extern Parameter par;
   arrowcolor_edit = new QLineEdit( QString("%1").arg(par.arrowcolor), this, "arrowcolor_edit" );
   arrowsize_edit = new QLineEdit( QString("%1").arg(par.arrowsize), this, "arrowsize_edit" );
   textcolor_edit = new QLineEdit( QString("%1").arg(par.textcolor), this, "textcolor_edit" );
   cellnumsize_edit = new QLineEdit( QString("%1").arg(par.cellnumsize), this, "cellnumsize_edit" );
   nodenumsize_edit = new QLineEdit( QString("%1").arg(par.nodenumsize), this, "nodenumsize_edit" );
   node_mag_edit = new QLineEdit( QString("%1").arg(par.node_mag), this, "node_mag_edit" );
   outlinewidth_edit = new QLineEdit( QString("%1").arg(par.outlinewidth), this, "outlinewidth_edit" );
   cell_outline_color_edit = new QLineEdit( QString("%1").arg(par.cell_outline_color), this, "cell_outline_color_edit" );
   resize_stride_edit = new QLineEdit( QString("%1").arg(par.resize_stride), this, "resize_stride_edit" );
   T_edit = new QLineEdit( QString("%1").arg(par.T), this, "T_edit" );
@@ @@ -797,25 +798,24 @@ void ParameterDialog::Reset(void) { @@
   c0_edit->setText( QString("%1").arg(par.c0) );
   gamma_edit->setText( QString("%1").arg(par.gamma) );
   eps_edit->setText( QString("%1").arg(par.eps) );
   QString k_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   k_string = k_string.arg(par.k[0]).arg(par.k[1]).arg(par.k[2]).arg(par.k[3]).arg(par.k[4]).arg(par.k[5]).arg(par.k[6]).arg(par.k[7]).arg(par.k[8]).arg(par.k[9]).arg(par.k[10]).arg(par.k[11]).arg(par.k[12]).arg(par.k[13]).arg(par.k[14]);
   k_edit->setText( k_string );
   i1_edit->setText( QString("%1").arg(par.i1) );
   i2_edit->setText( QString("%1").arg(par.i2) );
   i3_edit->setText( QString("%1").arg(par.i3) );
   i4_edit->setText( QString("%1").arg(par.i4) );
   i5_edit->setText( QString("%1").arg(par.i5) );
   s1_edit->setText( QString("%1").arg(par.s1) );
   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

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 // 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
       public:
 	ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0);
     virtual ~ParameterDialog(void);
     public slots:
     void Reset(void);
     private slots:
     void write(void);
   private:
   QLineEdit *arrowcolor_edit;
@@ @@ -127,25 +127,24 @@ class ParameterDialog : public QDialog { @@
   QLineEdit *rho0_edit;
   QLineEdit *rho1_edit;
   QLineEdit *c0_edit;
   QLineEdit *gamma_edit;
   QLineEdit *eps_edit;
   QLineEdit *k_edit;
   QLineEdit *i1_edit;
   QLineEdit *i2_edit;
   QLineEdit *i3_edit;
   QLineEdit *i4_edit;
   QLineEdit *i5_edit;
   QLineEdit *s1_edit;
   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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