VTK output problem when running AdhesionFlexPython


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19 days ago by
JJ Yeo  
Dear Admins,

I tried running the AdhesionFlexPython demo on both CC3D 3.7.7 and 3.7.6 in Mac OSX High Sierra. I encountered a strange problem where the moment the adhesions are changed by the AdhesionFlexSteppables.py script, the VTK outputs all zeroes for all entries (such as CellID, CellType, ClusterID).

I verified this by changing the original script to
# Same as demo until this point....

if mcs==100:
            for cell in self.cellList:
                print "CELL ID=",cell.id, " CELL TYPE=",cell.type
                if cell.type==1:
                    # accessing adhesion molecule density using its name
                    print "NCad=", self.adhesionFlexPlugin.getAdhesionMoleculeDensity(cell,"NCad")

                    # accessing adhesion molecule density using its index -
                    # molecules are indexed in the sdame order they are listed in the xml file
                    print "Int=", self.adhesionFlexPlugin.getAdhesionMoleculeDensityByIndex(cell,1)

# And so on....​
Once the MCS reaches 100 and changes the adhesions, the VTK outputs become matrices of zeroes. Also, the adhesions do not change at all if I change the condition to
# Same as demo until this point....

if mcs==101:
            for cell in self.cellList:
                print "CELL ID=",cell.id, " CELL TYPE=",cell.type
                if cell.type==1:
                    # accessing adhesion molecule density using its name
                    print "NCad=", self.adhesionFlexPlugin.getAdhesionMoleculeDensity(cell,"NCad")

                    # accessing adhesion molecule density using its index -
                    # molecules are indexed in the sdame order they are listed in the xml file
                    print "Int=", self.adhesionFlexPlugin.getAdhesionMoleculeDensityByIndex(cell,1)

# And so on....​​
 
Am I missing something here or something has to be changed in the settings? I am running the demo using the command
runScript.command -i $working_dir/$working_script -f 100 --currentDir $working_dir -o $working_dir/movies --exitWhenDone​


Here's a video of the default run, I don't understand what's happening here, why are all the cells becoming type 0 (medium)?

File attached: AdhesionFlex.mpg (2.61 MB)

Community: CompuCell3D
Did anyone else see this problem or it's only an issue with my simulations? Any response is greatly appreciated so that I can troubleshoot the problem.
written 14 days ago by JJ Yeo  

1 Answer


0
4 days ago by
I ran the AdhesionFlex Simulation with the VTK output but could not reproduce the problem. Could you post the exact simulation that you ran?
I ran the default AdhesionFlexPython demo on both Mac OSX High Sierra and Ubuntu 14.04 with CC3D 3.7.7. The CC3D on Ubuntu was compiled by myself. Both these cases showed the same result of Type 1 disappearing slowly.

I have attached the .zip file of the demo that I ran just to be sure:
https://mega.nz/#!5AoCSDwB!Jw9SXf2yDz3wV0hNIQKInEtLqN_yGnCa6NvJS7v0rw8
written 3 days ago by JJ Yeo  
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