Import CompuCell3D 3.3.1 into CompuCell3D 3.7.6


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11 days ago by
Hi, I'm a student and I want to import the code of the aticle: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007190 into new CompuCell3D, but in this code base there is not a .cc3d file. How can I do?
Community: CompuCell3D

3 Answers


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11 days ago by
The easiest thing to do is to just create a new model in Twedit++ (basically just pick a few items at random), then cut and paste the XML and python from the published model into the appropriate files in your newly created model.
I try with this method and I have this error in console:
projectFullPath= /home/nic/CompucellAutomaticProject/CompucellAutomaticProject.cc3d
NEW SIMULATION reply= ?NEWSIMULATION�/home/nic/CompucellAutomaticProject/CompucellAutomaticProject.cc3d
starting CC3D
READING RESPONSE CC3D SENDER
self.socket.bytesAvailable()= 168
self.nextBlockSize= 166
self.socket.bytesAvailable()= 166




 messageType= NEWSIMULATION
self.errorConsole.playerMainWidget= <Plugins.ViewManagerPlugins.SimpleTabView.SimpleTabView object at 0x7f6c1b500770>
​
In the code base of article theris also a file .txt how can import it in compucell?
written 10 days ago by nicolalandro  
Hi, I have solved some prolems, but now I have this:
messageType= NEWSIMULATION
self.errorConsole.playerMainWidget= <Plugins.ViewManagerPlugins.SimpleTabView.SimpleTabView object at 0x7f62a0e80a68>
processIncommingSimulation =  /home/mint/compuCellWorkspace/NewSimulation/NewSimulation.cc3d  _stopCurrentSim= True
GOT NEW SIMULATION  /home/mint/compuCellWorkspace/NewSimulation/NewSimulation.cc3d
NEWSIMULATIONRECEIVED SIMULATION NAME SENT SUCCESFULLY​
In compucell3D seams run, but I do not see nothing. What is the problem?
written 10 days ago by nicolalandro  
1
11 days ago by
Typically this is what a .cc3d file looks like

<Simulation version="version number">
<XMLScript Type="XMLScript">XML_File_Name</XMLScript>
<PythonScript Type="PythonScript">Python_File_Name</PythonScript>
<Resource Type="Python">Python_Steppable_File_Name</Resource>
</Simulation>

You might need to add additional location information in the file names if they are in different directories.
Hi, I try but do not work, the error in console is:
FILE NAME= Traceback (most recent call last):
  File "/usr/lib/compucell3d/Twedit++/Plugins/PluginCCDProject.py", line 2443, in __openCC3DProject
    self.showOpenProjectDialogAndLoad(currentFilePath)
  File "/usr/lib/compucell3d/Twedit++/Plugins/PluginCCDProject.py", line 2430, in showOpenProjectDialogAndLoad
    print "FILE NAME=",fileName
UnicodeEncodeError: 'ascii' codec can't encode character u'\xe0' in position 34: ordinal not in range(128)​
The folder Hierarchy is:
  /CompucellProject
     /CompucellProject.cc3d
     /script
       /angio_growth_plugins.py
       /angio_growth.py
       /angio_growth_steppables.py
       /TumorVasc3D_180x180x180.txt
       /XML_Template_TumorVasc3D_Movie.xml

CompucellProject.cc3d
<Simulation version="3.6.2">
   <XMLScript Type="XMLScript">Simulation/XML_Template_TumorVasc3D_Movie.xml</XMLScript>
   <PythonScript Type="PythonScript">Simulation/angio_growth.py</PythonScript>
   <Resource Type="Python">Simulation/angio_growth_steppables.py</Resource>
   <Resource Type="Python">Simulation/angio_growth_plugins.py</Resource>
</Simulation>
​
written 10 days ago by nicolalandro  
I believe this error is due to encoding mismatch with value in string 'fileName'. I suspect this occurred due to the .cc3d file is not saved with UTF-8 encoding.

Can you try after saving it with UTF-8 encoding? Google how to save it in UTF-8 encoding with whichever text editor you are using. Instructions for notepad++ are here.
written 10 days ago by Anwar  
0
11 days ago by
Anwar  
Basically .cc3d is a XML file enlisting all related files and resources for the simulation. I believe you can generate a .cc3d file manually referring to demos in CompuCell3D 3.7.6.

Please let us know if you need further help with that.
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