Some last fine-tuning
- File dialogs start from appropriate data directories
- XML files contain right values for datadir
- Reordered parameter dialog
- Added new "make perl" heading to the makefile
- Corrected segfault for batch mode

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed data/leaves/tutorial1_init.xml
changed data/leaves/tutorial2_init.xml
changed data/leaves/tutorial3_init.xml
changed data/leaves/tutorial4_init.xml
changed data/leaves/tutorial5_init.xml
changed src/Makefile
changed src/VirtualLeaf.cpp
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h

Replaced getIterations() with getTime().

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user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/canvas.cpp
changed src/mesh.h

Synchronise leaf movie frame and cell export data timestep references.

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user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.h

Corrected Compactness algorithm. Added algorithms to calculate circumference of convex hull and of the whole morph/

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'

In DrawCell class (VirtualLeaf.cpp) - iterate over NChem to construct info_string. Additional cleanup.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/Neighbor.cpp
changed src/Neighbor.h
changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/UniqueMessage.h
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/cellitem.cpp
changed src/cellitem.h
changed src/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/libplugin.pro
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.h
changed src/mesh.cpp
changed src/mesh.h
changed src/miscq.cpp
changed src/miscq.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeitem.h
changed src/nodeset.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/parse.cpp
changed src/parse.h
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
changed src/simplugin.h
changed src/sqr.h
changed src/tiny.h
changed src/transporterdialog.cpp
changed src/transporterdialog.h
changed src/vector.cpp
changed src/vector.h
changed src/wall.cpp
changed src/wall.h
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp
changed src/xmlwrite.h

* Added functionality for numerical output (CSV) format. See functions starting with "CSV" in mesh.cpp. External code hull.cpp is responsible for convex hull calculations.
- ToDo: adopt menu item "File->export cell areas" so user can choose a file name or set up periodic output of numerical data.
- ToDo: add parameters re: periodic numeric output to "<settings>" block of LeafML-file, so it becomes possible to set up numeric output interactively, then write the LeafML file and run the program in batch mode to retrieve periodic numeric output.

* Added new functionality to plugin interface. It becomes possible to define a default LeafML init file for a plugin. It is read whenever the model plugin is loaded.
- ToDo: define default LeafML files for all plugins, according to the LeafML files mentioned in the Plant Phys. tutorial.


user: Roeland Merks <merks@cwi.nl>
branch 'default'
added src/hull.cpp
added src/hull.h
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.cpp
changed src/simplugin.h
changed src/xmlwrite.cpp

Reformatted the source files and generally straighten up the code.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/Neighbor.cpp
changed src/Neighbor.h
changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/UniqueMessage.h
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
changed src/build_models/translate_plugin.pl
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/cellitem.cpp
changed src/cellitem.h
changed src/curvecolors.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/far_mem_5.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.h
changed src/maxmin.h
changed src/mesh.cpp
changed src/mesh.h
changed src/miscq.cpp
changed src/miscq.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/modelelement.h
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeitem.h
changed src/nodeset.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/parse.cpp
changed src/parse.h
changed src/perl/deployapp.pl
changed src/perl/histogram.pl
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
changed src/perl/make_xmlwritecode.pl
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rseed.cpp
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
changed src/simplugin.cpp
changed src/simplugin.h
changed src/sqr.h
changed src/tiny.h
changed src/transporterdialog.cpp
changed src/transporterdialog.h
changed src/vector.cpp
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wall.h
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp
changed src/xmlwrite.h

Cleanup: e.g. removed commented out and otherwise disabled code.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parse.cpp
changed src/parse.h
changed src/random.cpp
changed src/random.h
changed src/sqr.h
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp

Wrapped diagnostic messages in QDEBUG blocks. Information messages still go to stderr.

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user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/forwardeuler.cpp
changed src/mesh.cpp
changed src/mesh.h
changed src/random.cpp
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallitem.cpp

Added to new menu options: edit->ResetChemicals and edit->ResetTransporters, which allows you to set only the chemicals or only the transporters to the initial values. I needed this for preparing a suitable initial condition for Tutorial 6 and thought it would be useful for the main distribution.

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user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h

Changed interface for model plugins to make usage of pointers and references consistent.
Added codes for tutorial belonging to VLeaf manuscript.
Something changed in modelcatalogue. I'm not sure what...

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial0/mymodel.cpp
added src/TutorialCode/Tutorial0/mymodel.h
added src/TutorialCode/Tutorial0/mymodel.pro
added src/TutorialCode/Tutorial1/mymodel.cpp
added src/TutorialCode/Tutorial1/mymodel.h
added src/TutorialCode/Tutorial1/mymodel.pro
added src/TutorialCode/Tutorial2/mymodel.cpp
added src/TutorialCode/Tutorial2/mymodel.h
added src/TutorialCode/Tutorial2/mymodel.pro
added src/TutorialCode/Tutorial3/mymodel.cpp
added src/TutorialCode/Tutorial3/mymodel.h
added src/TutorialCode/Tutorial3/mymodel.pro
added src/TutorialCode/Tutorial4/mymodel.cpp
added src/TutorialCode/Tutorial4/mymodel.h
added src/TutorialCode/Tutorial4/mymodel.pro
added src/TutorialCode/Tutorial5/mymodel.cpp
added src/TutorialCode/Tutorial5/mymodel.h
added src/TutorialCode/Tutorial5/mymodel.pro
added src/build_models/translate_plugin.pl
changed src/VirtualLeafpar.tmpl
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h

Roeland's recent improvements - especially a more robust Mesh::Derivatives().

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user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/mesh.cpp
changed src/mesh.h