Michael Guravage
092543adb6c7
9 years ago
Roeland Merks
36c567b992a6
11 years ago
Roeland Merks
f4023d64bb53
11 years ago
Roeland Merks
200c37371db5
11 years ago
Michael Guravage
48a69a5303ea
14 years ago
Michael Guravage
4395ffa0b2dc
14 years ago
Michael Guravage
6d4ff3be53ef
14 years ago
Bumped up the version number to 1.0.1 -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install-windows.nsi changed src/canvas.cpp
Michael Guravage
b0797787e1b2
14 years ago
Michael Guravage
0c80cde2ff53
14 years ago
Michael Guravage
5f261c001dd0
14 years ago
Michael Guravage
ece65c3c4808
14 years ago
Michael Guravage
a38366983d90
14 years ago
Michael Guravage
6ab5fc3a2946
14 years ago
Michael Guravage
e956dea5765e
14 years ago
Michael Guravage
83d6f23dae10
14 years ago
Michael Guravage
0c3077893f1a
14 years ago
Michael Guravage
16f3c7fd245d
14 years ago
Michael Guravage
c40eef5ee706
14 years ago
Michael Guravage
658c1ca9f634
14 years ago
Michael Guravage
cc776c408f8f
14 years ago
Michael Guravage
4f181aa04894
14 years ago
Michael Guravage
ab6363909dc1
14 years ago
Added second auxin transport protocol: PIN1 recycling. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed data/leaves/myAuxin.xml changed src/protocols/MyAuxinModel/myauxinmodel.cpp
Michael Guravage
bd77d1217180
14 years ago
Added first auxin transport protocol: Auxin upstream pumping. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added data/leaves/myAuxin.xml added src/protocols/MyAuxinModel/Makefile added src/protocols/MyAuxinModel/myauxinmodel.cpp added src/protocols/MyAuxinModel/myauxinmodel.h added src/protocols/MyAuxinModel/myauxinmodel.pro changed src/protocols/Makefile
Michael Guravage
ce40edbe6273
14 years ago
Added fourth reaction-diffusion protocol: Prevent vascular cells from expanding. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/protocols/MyDiffusionModel/mydiffusionmodel.cpp
Michael Guravage
b5cc18bab697
14 years ago
Added third reaction-diffusion protocol: Diffusion in a growing domain. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added data/leaves/mygrowingleaf.xml changed src/protocols/MyDiffusionModel/mydiffusionmodel.cpp changed src/protocols/MyDiffusionModel/mydiffusionmodel.h
Michael Guravage
e730ce1f2d31
14 years ago
Added second reaction-diffusion protocol: Fick's laws of diffusion. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/protocols/MyDiffusionModel/mydiffusionmodel.cpp
Michael Guravage
9a4aa6470987
14 years ago
Added first reaction-diffusion protocol: Diffusion dependent coloring. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added data/leaves/myleaf.xml added src/protocols/MyDiffusionModel/Makefile added src/protocols/MyDiffusionModel/mydiffusionmodel.cpp added src/protocols/MyDiffusionModel/mydiffusionmodel.h added src/protocols/MyDiffusionModel/mydiffusionmodel.pro changed src/protocols/Makefile
Michael Guravage
d811502e67f8
14 years ago
Added fourth tissue growth protocol: Divide over an arbitrary axis. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/protocols/MyGrowthModel/mygrowthmodel.cpp
Michael Guravage
9b6820f9a10b
14 years ago
Added third tissue growth protocol: Divide over explicit axis. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/protocols/MyGrowthModel/mygrowthmodel.cpp
Michael Guravage
df8602459ab0
14 years ago
Added second tissue growth protocol: Divide when size doubles. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/protocols/MyGrowthModel/mygrowthmodel.cpp
Michael Guravage
854077b2d7cc
14 years ago
Added first tissue growth protocol: The expanding cell. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added src/protocols/MyGrowthModel/Makefile added src/protocols/MyGrowthModel/mygrowthmodel.cpp added src/protocols/MyGrowthModel/mygrowthmodel.h added src/protocols/MyGrowthModel/mygrowthmodel.pro changed src/protocols/Makefile
Michael Guravage
c0082ca197fb
14 years ago
Added first protocol. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added src/protocols/Makefile added src/protocols/MyEmptyModel/Makefile added src/protocols/MyEmptyModel/myemptymodel.cpp added src/protocols/MyEmptyModel/myemptymodel.h added src/protocols/MyEmptyModel/myemptymodel.pro
Michael Guravage
25054d6d05c9
14 years ago
Corrected citation text. Resolves issue
#4 .
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/canvas.cpp
Michael Guravage
f747a32958da
14 years ago
Reworked the recipe a bit. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed doc/Makefile changed doc/installation.pdf changed doc/installation.rst changed doc/recipe.rst changed doc/stylesheet.json changed doc/v1.pdf
Michael Guravage
e1209459d052
14 years ago
Michael Guravage
fe6571574827
14 years ago
Merge Roeland's recent changes to correct some problems with software deployment on MacOSX. -- user: Michael Guravage <michael.guravage@cwi.nl> branch merge branch 'default' changed doc/mac-deploy-howto.txt changed src/VirtualLeaf.pro changed src/perl/deploymodel.pl
Michael Guravage
da628cac41fc
14 years ago
Use the wallnumber (wn) to discern which cell a wallitem belongs to. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/transporterdialog.cpp changed src/wallitem.cpp
Michael Guravage
bacde69ee1b3
14 years ago
Compile leaficon_small.xpm directly into canvas.cpp and revert changes that added a separate icon directory. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added src/leaficon_small.xpm changed src/ChangeLog changed src/VirtualLeaf-install-windows.nsi changed src/canvas.cpp removed icons/leaficon.png removed icons/leaficon_small.png
Michael Guravage
825cc3737130
14 years ago
Added a small virtual icon to the About message box. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added icons/leaficon.png added icons/leaficon_small.png changed src/ChangeLog changed src/VirtualLeaf-install-windows.nsi changed src/canvas.cpp removed src/leaficon.png
Michael Guravage
4d5a298af6e9
14 years ago
Rework Transporters dialog and About message. See ChangeLog for more details. user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/canvas.cpp changed src/transporterdialog.cpp changed src/wallitem.cpp
Roeland Merks
36b188563094
15 years ago
Corrected some problems with software deployment on MacOSX. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' added doc/mac-deploy-howto.txt added src/perl/deploymodel.pl changed src/VirtualLeaf.pro
Roeland Merks
7c51085c0797
15 years ago
Merge of Michael's and Roeland's changes. -- user: Roeland Merks <roeland.merks@cwi.nl> branch merge branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install-windows.nsi changed src/canvas.cpp
Michael Guravage
fccdfd56cd6a
15 years ago
Forgot to add asterisk before our own pdf format. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/canvas.cpp
Michael Guravage
aa0e02ed3fd5
15 years ago
Preface each image format extension with an asterisk so files with those extensions to appear in the file dialogue. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/canvas.cpp
Michael Guravage
98a2c6cae168
15 years ago
Install imageformats folder alongside Windows executable. Solicit supported image formats for file dialogue filter. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install-windows.nsi changed src/canvas.cpp
Roeland Merks
d1891150036d
15 years ago
Corrected "File->Print" facility. Images did not scale well. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/canvas.cpp
Roeland Merks
3809c04020b4
15 years ago
Roeland Merks
8509673ac23b
15 years ago
Updated "saveStateXML" for consistency with snapshot() and exportData. It now suggests a default extension "xml" and produces a status message. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/canvas.cpp
Roeland Merks
931f70c7449d
15 years ago
Fixed 'flashy' bug; scene keeps on flashing up and down after switching models. We needed to reset the SceneRect of QGraphicsView after reading a new model. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/canvas.cpp
Roeland Merks
d921bb3b13ec
15 years ago
Updated Windows installer script so it adds an item to the Start menu. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/VirtualLeaf-install-windows.nsi
Roeland Merks
f2712ec0e2e8
15 years ago
Renaming the installer scripts. Note that the VirtualLeaf-install-macosx.pmdoc directory is a "bundle" for PackageMaker so it MUST have an extension. Please do not change its name. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' added src/VirtualLeaf-install-macosx.pmdoc/01virtualleaf-contents.xml added src/VirtualLeaf-install-macosx.pmdoc/01virtualleaf.xml added src/VirtualLeaf-install-macosx.pmdoc/02models-contents.xml added src/VirtualLeaf-install-macosx.pmdoc/02models.xml added src/VirtualLeaf-install-macosx.pmdoc/03leaves-contents.xml added src/VirtualLeaf-install-macosx.pmdoc/03leaves.xml added src/VirtualLeaf-install-macosx.pmdoc/index.xml added src/VirtualLeaf-install-windows.nsi removed src/VirtualLeaf-install-macosx/01virtualleaf-contents.xml removed src/VirtualLeaf-install-macosx/01virtualleaf.xml removed src/VirtualLeaf-install-macosx/02models-contents.xml removed src/VirtualLeaf-install-macosx/02models.xml removed src/VirtualLeaf-install-macosx/03leaves-contents.xml removed src/VirtualLeaf-install-macosx/03leaves.xml removed src/VirtualLeaf-install-macosx/index.xml removed src/VirtualLeaf-install.nsi removed src/vleafmacosx_installer.pmdoc/01virtualleaf-contents.xml removed src/vleafmacosx_installer.pmdoc/01virtualleaf.xml removed src/vleafmacosx_installer.pmdoc/02models-contents.xml removed src/vleafmacosx_installer.pmdoc/02models.xml removed src/vleafmacosx_installer.pmdoc/03leaves-contents.xml removed src/vleafmacosx_installer.pmdoc/03leaves.xml removed src/vleafmacosx_installer.pmdoc/index.xml
Roeland Merks
dcd49517f90b
15 years ago
Two last corrections: - Viewport was not written during automatic export of XML files, because Virtualization of XMLSettingsTree did not work due to inconsistent function definition (const vs. non-const) - Some of the default parameter-file had "Start saving movie frames" switched on by default, dramatically slowing down the example runs. Now it is switched off in all example XML files. user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed data/leaves/auxin_growth.xml changed data/leaves/tutorial5_init.xml changed src/VirtualLeaf.cpp changed src/mainbase.cpp changed src/mainbase.h
Roeland Merks
d7edbe56b125
15 years ago
The snapshot feature stopped working on Windows. The problem was in MainBase::Save, where the "format" argument was added to "image->save". On Windows the file format must be given in Capitals and in specific formats (e.g. TIFF works, TIF not). It is much safer to leave the 'format' argument out and let the system guess the format from the file extension. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/canvas.cpp changed src/mainbase.cpp changed src/mainbase.h
Michael Guravage
da350435dfe3
15 years ago
Uncompressed XML files. -- user: Michael Guravage <michael.guravage@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
Roeland Merks
1bbab6e592e6
15 years ago
Reduced XML write compression mode to 0 (no compression), because Windows seems not to be able to handle it. user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/xmlwrite.cpp
Roeland Merks
8ff9e397df2f
15 years ago
Added build scripts for MacOSX installer (PackageMaker) -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' added src/vleafmacosx_installer.pmdoc/01virtualleaf-contents.xml added src/vleafmacosx_installer.pmdoc/01virtualleaf.xml added src/vleafmacosx_installer.pmdoc/02models-contents.xml added src/vleafmacosx_installer.pmdoc/02models.xml added src/vleafmacosx_installer.pmdoc/03leaves-contents.xml added src/vleafmacosx_installer.pmdoc/03leaves.xml added src/vleafmacosx_installer.pmdoc/index.xml
Roeland Merks
74c0d6470920
15 years ago
Added "Makefile.perl" to repository. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' added src/Makefile.perl
Roeland Merks
2accd83924da
15 years ago
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
Roeland Merks
c6ad8e34e8eb
15 years ago
In response to referee's comment: "I am also afraid that the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very well in my hands, could the program be changed so that the correct file extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically." I corrected the "export cell data" dialog (it did not actually write the file in the submitted version). Also we now assume default file extensions (.jpg for snapshot and .csv for data export) if none is given. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/VirtualLeaf.pro changed src/canvas.cpp removed src/miscq.cpp removed src/miscq.h
Roeland Merks
f563ace40263
15 years ago
In response to referee's comment "I am also afraid that the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very well in my hands, could the program be changed so that the correct file extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically." I corrected the "exportCellData()" function in canvas.cpp. It did not actually call exportCellData(filename) after the user entered a filename (logic after calling QMessageBox was incorrect). -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/canvas.cpp
Roeland Merks
6bcb69712a0e
15 years ago
In response to referee's comment: "However, (although it is probably not important for model developers), I was still unable to load the model ‘Meinhardt 1976 with growth’ example from the ‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected the Meinhardt model in both the Models and the File -> Read leaf menus together, it would be preferable if the models loaded from the Models menu worked automatically. I am not sure that the update referred to in the author’s response permits the loading of ‘My First Model in Virtual Leaf’ from the ‘Models’ drop down menu; I only got a cell that wiggled." I made the following changes: - meinhardt_plugin now reads "meinhardt_init.xml" by default - changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example. - Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used. -- user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' added data/leaves/tutorial1_init.xml added data/leaves/tutorial2_init.xml changed data/leaves/auxin_growth.xml changed data/leaves/meinhardt_init.xml changed src/TutorialCode/Tutorial0/tutorial0.cpp changed src/TutorialCode/Tutorial1A/tutorial1A.h changed src/TutorialCode/Tutorial1B/tutorial1B.h changed src/TutorialCode/Tutorial1C/tutorial1C.h changed src/TutorialCode/Tutorial1D/tutorial1D.h changed src/TutorialCode/Tutorial2/tutorial2.h changed src/build_models/meinhardtplugin.h
Michael Guravage
86b2d203dbe7
15 years ago
Increased auxin_growth LeafML file's storage_slide from 10 to 100. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed data/leaves/ChangeLog changed data/leaves/auxin_growth.xml
Michael Guravage
5ec450ff7c49
15 years ago
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
Michael Guravage
3d9c788630de
15 years ago
Merged recent modelcatalogue.cpp and macosx changes. -- user: Michael Guravage <michael.guravage@cwi.nl> branch merge branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install-macosx/01virtualleaf-contents.xml changed src/VirtualLeaf-install-macosx/01virtualleaf.xml changed src/VirtualLeaf-install-macosx/02models-contents.xml changed src/VirtualLeaf-install-macosx/02models.xml changed src/VirtualLeaf-install-macosx/03leaves-contents.xml changed src/VirtualLeaf-install-macosx/03leaves.xml changed src/VirtualLeaf-install-macosx/index.xml changed src/modelcatalogue.cpp
Michael Guravage
65bd4ef0e4aa
15 years ago
Added/replaced several macosx installation files. In modelcatalogue.cpp: move from "bin" directory to root application folder. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install-macosx/01virtualleaf-contents.xml changed src/VirtualLeaf-install-macosx/01virtualleaf.xml changed src/VirtualLeaf-install-macosx/02models-contents.xml changed src/VirtualLeaf-install-macosx/02models.xml changed src/VirtualLeaf-install-macosx/03leaves-contents.xml changed src/VirtualLeaf-install-macosx/03leaves.xml changed src/VirtualLeaf-install-macosx/index.xml changed src/modelcatalogue.cpp
Michael Guravage
fba32897839a
15 years ago
Translate image fname to native format. Let QImage guess the format from the filename's suffix. Put uninstaller in root install directory. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install.nsi changed src/mainbase.cpp
Michael Guravage
67230a3743ca
15 years ago
Removed erroneous qmake -makefile option. MACOSX, look for gpl3.txt in ../doc directory. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/Makefile changed src/TutorialCode/Tutorial0/ChangeLog changed src/TutorialCode/Tutorial0/Makefile changed src/TutorialCode/Tutorial1A/ChangeLog changed src/TutorialCode/Tutorial1A/Makefile changed src/TutorialCode/Tutorial1B/ChangeLog changed src/TutorialCode/Tutorial1B/Makefile changed src/TutorialCode/Tutorial1C/ChangeLog changed src/TutorialCode/Tutorial1C/Makefile changed src/TutorialCode/Tutorial1D/ChangeLog changed src/TutorialCode/Tutorial1D/Makefile changed src/TutorialCode/Tutorial2/ChangeLog changed src/TutorialCode/Tutorial2/Makefile changed src/TutorialCode/Tutorial3/ChangeLog changed src/TutorialCode/Tutorial3/Makefile changed src/TutorialCode/Tutorial4/ChangeLog changed src/TutorialCode/Tutorial4/Makefile changed src/TutorialCode/Tutorial5/ChangeLog changed src/TutorialCode/Tutorial5/Makefile changed src/VirtualLeaf.pro changed src/build_models/ChangeLog changed src/build_models/Makefile
Michael Guravage
b85aa64a84ee
15 years ago
Replaced getIterations() with getTime(). -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf.cpp changed src/canvas.cpp changed src/mesh.h
Michael Guravage
ec439fed4af8
15 years ago
Synchronise leaf movie frame and cell export data timestep references. -- 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
Roeland Merks
ffb1f378901c
15 years ago
Merged one file - need to run now! -- user: Roeland Merks <roeland.merks@cwi.nl> branch merge branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install.nsi changed src/VirtualLeaf.pro changed src/canvas.cpp
Michael Guravage
5469f4c56a53
15 years ago
Tweaked Windows installation directories. Turned debugging off in VirtualLeaf profile - all profiles must be consistent. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install.nsi changed src/VirtualLeaf.pro
Michael Guravage
1b01e13fa5f1
15 years ago
Enquire first before overwriting an exported cell data file. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/canvas.cpp
Roeland Merks
e40119cdbdb9
15 years ago
A few last updates before submitting the revised Plant Phys. paper. Corrected the invocation of TransporterDialog and added parameter 'yield_threshold' user: Roeland Merks <roeland.merks@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeafpar.tmpl changed src/mesh.cpp changed src/parameter.cpp changed src/parameter.h changed src/pardialog.cpp changed src/pardialog.h changed src/wallitem.cpp
Roeland Merks
c32457e84c7f
15 years ago
Commit changes user: Roeland Merks <roeland.merks@cwi.nl> branch merge branch 'default' 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
Roeland Merks
4d22d3755063
15 years ago
Merged ChangeLog Enter commit message. Lines beginning with 'HG:' are removed. Leave message empty to abort commit. -- user: Roeland Merks <roeland.merks@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
Roeland Merks
8aaffb5565a2
15 years ago
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'
Michael Guravage
c2962c0745f8
15 years ago
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
Michael Guravage
fc4e80bf722d
15 years ago
Pre-push breakpoint. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed doc/v1.html changed doc/v1.pdf changed doc/v1.rst
Michael Guravage
bb80657b6912
15 years ago
Export Cell Data at interval specified in the leafML file or explicitly via the file menu. Added new parameters to VirtualLeafpar.tmpl Added GPL boilerplate to make_{parameter,pardialog}_source.pl files. Added new parameters to auxin_growth.xml. See respective ChangeLog files for details. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed data/leaves/ChangeLog changed data/leaves/auxin_growth.xml changed src/ChangeLog 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 changed src/perl/ChangeLog changed src/perl/make_parameter_source.pl changed src/perl/make_pardialog_source.pl
Michael Guravage
b3943d0b8126
15 years ago
Added a Q3FileDialog in canvas.cpp:Main::exportCellData() inquire where to write the exportCellData. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added doc/Makefile added doc/stylesheet.json added doc/v1.html added doc/v1.pdf added doc/v1.rst added src/leaficon.png changed src/ChangeLog changed src/canvas.cpp
Roeland Merks
4cb24b737683
15 years ago
Michael Guravage
d897bf22346f
15 years ago
Look for gpl3.txt in either an ancestor doc directory (Linux) or a decedent doc directory (Windows, via the binary installer). -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/canvas.cpp
Michael Guravage
03df53cdf78b
15 years ago
Grab gpl3.txt from doc directory. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf-install.nsi
Michael Guravage
6ce49db23eee
15 years ago
Moved gpl3.txt back to the doc directory, and included the doc directory in the binary distribution. Included new MAC installation data. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added doc/gpl3.txt added src/VirtualLeaf-install-macosx/01virtualleaf-contents.xml added src/VirtualLeaf-install-macosx/01virtualleaf.xml added src/VirtualLeaf-install-macosx/02models-contents.xml added src/VirtualLeaf-install-macosx/02models.xml added src/VirtualLeaf-install-macosx/03leaves-contents.xml added src/VirtualLeaf-install-macosx/03leaves.xml added src/VirtualLeaf-install-macosx/index.xml changed .hgignore changed NEWS changed src/ChangeLog changed src/VirtualLeaf-install.nsi changed src/canvas.cpp removed ChangeLog removed src/gpl3.txt removed src/vleafmacosx_installer.pmdoc/01virtualleaf-contents.xml removed src/vleafmacosx_installer.pmdoc/01virtualleaf.xml removed src/vleafmacosx_installer.pmdoc/02models-contents.xml removed src/vleafmacosx_installer.pmdoc/02models.xml removed src/vleafmacosx_installer.pmdoc/03leaves-contents.xml removed src/vleafmacosx_installer.pmdoc/03leaves.xml removed src/vleafmacosx_installer.pmdoc/index.xml
Michael Guravage
bf6b642048bc
15 years ago
Corrected problems with .hgignore file. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed .hgignore
Michael Guravage
013687d51a1d
15 years ago
Added missing libxml2 and libz bin directories; caused by my overzealous .hgignore file. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added lib/libxml2/bin/runsuite.exe added lib/libxml2/bin/runtest.exe added lib/libxml2/bin/testAutomata.exe added lib/libxml2/bin/testC14N.exe added lib/libxml2/bin/testHTML.exe added lib/libxml2/bin/testModule.exe added lib/libxml2/bin/testReader.exe added lib/libxml2/bin/testRegexp.exe added lib/libxml2/bin/testRelax.exe added lib/libxml2/bin/testSAX.exe added lib/libxml2/bin/testSchemas.exe added lib/libxml2/bin/testThreadsWin32.exe added lib/libxml2/bin/testURI.exe added lib/libxml2/bin/testXPath.exe added lib/libxml2/bin/testapi.exe added lib/libxml2/bin/xmlcatalog.exe added lib/libxml2/bin/xmllint.exe added lib/libz/bin/libz-1.dll added lib/libz/bin/zlib1.dll changed src/ChangeLog changed src/VirtualLeaf-install.nsi
Michael Guravage
caa535c40937
15 years ago
Made changes to conform to the version submitted with the Plant Physiology paper. See the individual ChangeLogs for details. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added lib/libiconv/bin/iconv.exe added lib/libiconv/bin/libcharset-1.dll added lib/libiconv/bin/libiconv-2.dll added src/gpl3.txt changed INSTALL changed src/ChangeLog changed src/TutorialCode/Tutorial0/ChangeLog changed src/TutorialCode/Tutorial0/tutorial0.pro changed src/TutorialCode/Tutorial1A/ChangeLog changed src/TutorialCode/Tutorial1A/tutorial1A.pro changed src/TutorialCode/Tutorial1B/ChangeLog changed src/TutorialCode/Tutorial1B/tutorial1B.pro changed src/TutorialCode/Tutorial1C/ChangeLog changed src/TutorialCode/Tutorial1C/tutorial1C.pro changed src/TutorialCode/Tutorial1D/ChangeLog changed src/TutorialCode/Tutorial1D/tutorial1D.pro changed src/TutorialCode/Tutorial2/ChangeLog changed src/TutorialCode/Tutorial2/tutorial2.pro changed src/TutorialCode/Tutorial3/ChangeLog changed src/TutorialCode/Tutorial3/tutorial3.pro changed src/TutorialCode/Tutorial4/ChangeLog changed src/TutorialCode/Tutorial4/tutorial4.pro changed src/TutorialCode/Tutorial5/ChangeLog changed src/TutorialCode/Tutorial5/tutorial5.pro changed src/VirtualLeaf-install.nsi changed src/VirtualLeaf.pro changed src/build_models/ChangeLog 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/libplugin.pro changed src/output.cpp changed src/output.h changed src/parameter.cpp changed src/parameter.h changed src/perl/ChangeLog changed src/perl/make_parameter_source.pl removed doc/gpl3.txt
Michael Guravage
ae58c51ca8dd
15 years ago
Use Correct library path in various project files. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf.pro changed src/build_models/ChangeLog changed src/build_models/plugin_auxingrowth.pro changed src/build_models/plugin_meinhardt.pro changed src/build_models/plugin_test.pro changed src/libplugin.pro
Michael Guravage
15d600891648
15 years ago
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
Roeland Merks
9a40ab737a73
15 years ago
* 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
Roeland Merks
c131f8cd4b54
15 years ago
Michael Guravage
59e38e5f05d2
15 years ago
Reverted NULL assignments to obviate compilation warnings. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/ChangeLog changed src/VirtualLeaf.cpp changed src/apoplastitem.cpp changed src/build_models/ChangeLog changed src/build_models/auxingrowthplugin.cpp changed src/build_models/meinhardtplugin.cpp changed src/build_models/testplugin.cpp changed src/canvas.cpp changed src/cell.cpp changed src/cellbase.h changed src/forwardeuler.cpp changed src/mainbase.h changed src/nodeitem.cpp changed src/qcanvasarrow.h changed src/simitembase.cpp
Michael Guravage
32ba6ee9c7d9
15 years ago
Corrected windows library path problem. Added -f Makefile to every make invocation. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added src/TutorialCode/ChangeLog added src/TutorialCode/Tutorial0/ChangeLog added src/TutorialCode/Tutorial1A/ChangeLog added src/TutorialCode/Tutorial1B/ChangeLog added src/TutorialCode/Tutorial1C/ChangeLog added src/TutorialCode/Tutorial1D/ChangeLog added src/TutorialCode/Tutorial2/ChangeLog added src/TutorialCode/Tutorial3/ChangeLog added src/TutorialCode/Tutorial4/ChangeLog added src/TutorialCode/Tutorial5/ChangeLog changed doc/installation.pdf changed doc/installation.rst changed src/ChangeLog changed src/Makefile changed src/TutorialCode/Makefile changed src/TutorialCode/Tutorial0/tutorial0.pro changed src/TutorialCode/Tutorial1A/tutorial1A.pro changed src/TutorialCode/Tutorial1B/tutorial1B.pro changed src/TutorialCode/Tutorial1C/tutorial1C.pro changed src/TutorialCode/Tutorial1D/tutorial1D.pro changed src/TutorialCode/Tutorial2/tutorial2.pro changed src/TutorialCode/Tutorial3/tutorial3.pro changed src/TutorialCode/Tutorial4/tutorial4.pro changed src/TutorialCode/Tutorial5/tutorial5.pro
Michael Guravage
23c0ca62df51
15 years ago
Inadvertently missed these libraries. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added lib/libiconv/lib/libcharset.a added lib/libiconv/lib/libcharset.dll.a added lib/libiconv/lib/libiconv.a added lib/libiconv/lib/libiconv.dll.a added lib/libxml2/lib/libxml2.a added lib/libz/lib/libz.a added lib/libz/lib/libz.dll.a
Michael Guravage
b117ca5d846f
15 years ago
Cleaned up leaves directory. Disabled console mode, Updated nsi script. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added data/leaves/ChangeLog added data/leaves/tutorial3_init.xml added data/leaves/tutorial4_init.xml added data/leaves/tutorial5_init.xml changed data/leaves/auxin.xml changed data/leaves/auxin_growth.xml changed data/leaves/meinhardt_init.xml changed data/leaves/schemas.xml changed data/leaves/vleaf.rnc changed data/leaves/vleaf.rng changed data/leaves/vleaf.xml changed data/leaves/vleaf.xsd changed data/leaves/vleaf2.xml changed doc/installation.pdf changed doc/installation.rst changed src/ChangeLog changed src/VirtualLeaf-install.nsi changed src/VirtualLeaf.pro removed data/leaves/bend.xml removed data/leaves/circ.xml removed data/leaves/explant.xml removed data/leaves/init.xml removed data/leaves/one_acc_point_van3.xml removed data/leaves/one_acc_point_van3_growth.xml removed data/leaves/one_acc_point_van3_growth2.xml removed data/leaves/tissue.xml
Michael Guravage
d4a19fde7f8d
15 years ago
Corrected several small problems with qDebug. See ChangeLogs for details. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed doc/installation.pdf changed doc/installation.rst changed src/ChangeLog changed src/canvas.cpp changed src/mesh.cpp changed src/random.cpp changed src/wall.cpp
Michael Guravage
23dfaeaae8f8
15 years ago
The value of QMAKE is taken from the environment - just like MAKE. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' changed src/Makefile changed src/TutorialCode/Tutorial0/Makefile changed src/TutorialCode/Tutorial1A/Makefile changed src/TutorialCode/Tutorial1B/Makefile changed src/TutorialCode/Tutorial1C/Makefile changed src/TutorialCode/Tutorial1D/Makefile changed src/TutorialCode/Tutorial2/Makefile changed src/TutorialCode/Tutorial3/Makefile changed src/TutorialCode/Tutorial4/Makefile changed src/TutorialCode/Tutorial5/Makefile changed src/build_models/Makefile
Michael Guravage
21afbd2a2c01
15 years ago
Renamed tutorial examples and added makefile, etc. -- user: Michael Guravage <michael.guravage@cwi.nl> branch 'default' added doc/gpl3.txt added doc/installation.pdf added doc/installation.rst added src/TutorialCode/Makefile added src/TutorialCode/Tutorial0/Makefile added src/TutorialCode/Tutorial0/tutorial0.cpp added src/TutorialCode/Tutorial0/tutorial0.h added src/TutorialCode/Tutorial0/tutorial0.pro added src/TutorialCode/Tutorial1A/Makefile added src/TutorialCode/Tutorial1A/tutorial1A.cpp added src/TutorialCode/Tutorial1A/tutorial1A.h added src/TutorialCode/Tutorial1A/tutorial1A.pro added src/TutorialCode/Tutorial1B/Makefile added src/TutorialCode/Tutorial1B/tutorial1B.cpp added src/TutorialCode/Tutorial1B/tutorial1B.h added src/TutorialCode/Tutorial1B/tutorial1B.pro added src/TutorialCode/Tutorial1C/Makefile added src/TutorialCode/Tutorial1C/tutorial1C.cpp added src/TutorialCode/Tutorial1C/tutorial1C.h added src/TutorialCode/Tutorial1C/tutorial1C.pro added src/TutorialCode/Tutorial1D/Makefile added src/TutorialCode/Tutorial1D/tutorial1D.cpp added src/TutorialCode/Tutorial1D/tutorial1D.h added src/TutorialCode/Tutorial1D/tutorial1D.pro added src/TutorialCode/Tutorial2/Makefile added src/TutorialCode/Tutorial2/tutorial2.cpp added src/TutorialCode/Tutorial2/tutorial2.h added src/TutorialCode/Tutorial2/tutorial2.pro added src/TutorialCode/Tutorial3/Makefile added src/TutorialCode/Tutorial3/tutorial3.cpp added src/TutorialCode/Tutorial3/tutorial3.h added src/TutorialCode/Tutorial3/tutorial3.pro added src/TutorialCode/Tutorial4/Makefile added src/TutorialCode/Tutorial4/tutorial4.cpp added src/TutorialCode/Tutorial4/tutorial4.h added src/TutorialCode/Tutorial4/tutorial4.pro added src/TutorialCode/Tutorial5/Makefile added src/TutorialCode/Tutorial5/tutorial5.cpp added src/TutorialCode/Tutorial5/tutorial5.h added src/TutorialCode/Tutorial5/tutorial5.pro added src/perl/ChangeLog changed src/ChangeLog changed src/Makefile changed src/build_models/ChangeLog changed src/build_models/Makefile changed src/canvas.cpp changed src/parameter.cpp changed src/parameter.h changed src/pardialog.cpp changed src/pardialog.h changed src/perl/make_parameter_source.pl changed src/perl/make_pardialog_source.pl changed src/perl/make_xmlwritecode.pl changed src/vleafmodel.h removed doc/GPL removed src/TutorialCode/Tutorial0/mymodel.cpp removed src/TutorialCode/Tutorial0/mymodel.h removed src/TutorialCode/Tutorial0/mymodel.pro removed src/TutorialCode/Tutorial1/mymodel.cpp removed src/TutorialCode/Tutorial1/mymodel.h removed src/TutorialCode/Tutorial1/mymodel.pro removed src/TutorialCode/Tutorial1A/mymodel.cpp removed src/TutorialCode/Tutorial1A/mymodel.h removed src/TutorialCode/Tutorial1A/mymodel.pro removed src/TutorialCode/Tutorial1B/mymodel.cpp removed src/TutorialCode/Tutorial1B/mymodel.h removed src/TutorialCode/Tutorial1B/mymodel.pro removed src/TutorialCode/Tutorial1C/mymodel.cpp removed src/TutorialCode/Tutorial1C/mymodel.h removed src/TutorialCode/Tutorial1C/mymodel.pro removed src/TutorialCode/Tutorial1D/mymodel.cpp removed src/TutorialCode/Tutorial1D/mymodel.h removed src/TutorialCode/Tutorial1D/mymodel.pro removed src/TutorialCode/Tutorial2/mymodel.cpp removed src/TutorialCode/Tutorial2/mymodel.h removed src/TutorialCode/Tutorial2/mymodel.pro removed src/TutorialCode/Tutorial3/mymodel.cpp removed src/TutorialCode/Tutorial3/mymodel.h removed src/TutorialCode/Tutorial3/mymodel.pro removed src/TutorialCode/Tutorial4/mymodel removed src/TutorialCode/Tutorial4/mymodel.cpp removed src/TutorialCode/Tutorial4/mymodel.h removed src/TutorialCode/Tutorial4/mymodel.pro removed src/TutorialCode/Tutorial5/mymodel removed src/TutorialCode/Tutorial5/mymodel.cpp removed src/TutorialCode/Tutorial5/mymodel.h removed src/TutorialCode/Tutorial5/mymodel.pro
Roeland Merks
4f82fc35a2b3
15 years ago
Roeland Merks
056581f749c0
15 years ago