Modifying attributes of CellG object

So far, the only attributes of a cell we have been modifying were those that we attached during runtime, members of the cell dictionary. However, CC3D allows users to modify core cell attributes i.e. those which are visible to the C++ portion of the CC3D code. Those attributes are members of CellG object (see Potts3D/Cell.h in the CC3D source code) define properties of a CC3D cell. The full list of the attributes is shown in Appendix B. Here we will show a simple example how to modify some of those attributes using Python and thus alter the course of the simulation. As a matter of fact, the way to build “dynamic” simulation where cellular properties change in response to simulation events is to write a Python function/class which alters CellG object variables as simulation runs.

CAUTION: CC3D does not allow you to modify certain attributes, e.g. cell volume, and in case you try you will get warning and simuation will stop. Given that CC3D is under constant development with many new features being added continuously, it may happen that CC3D will let you modify attribute that should be read-only. In such a case you will most likely get cryptic error and the simulation will crash. Therefore you should be careful and double-check CC3D documentation to see which attributes can be modified.

The steppable below shows how to change targetVolume and lambdaVolume of a cell and how to implement cell differentiation (changing cell type):

class TypeSwitcherAndVolumeParamSteppable(SteppableBasePy):
    def __init__(self, _simulator, _frequency=100):
        SteppableBasePy.__init__(self, _simulator, _frequency)

    def start(self):
        for cell in self.cellList:
            if cell.type == 1:
                cell.targetVolume = 25
                cell.lambdaVolume = 2.0
            elif cell.type == 2:
                cell.targetVolume = 50
                cell.lambdaVolume = 2.0

    def step(self, mcs):
        for cell in self.cellList:
            if cell.type == 1:
                cell.type = 2
            elif cell.type == 2:
                cell.type = 1

As you can see in the step function we check if cell is of type 1. If it is we change it to type 2 and do analogous check/switch for cell of type 2. In the start function we initialize target volume of type 1 cells to 25 and type 2 cells will get target volume 50. The only other thing we need to remember is to change definition of Volume plugin in the XML from:

<Plugin Name="Volume">


<Plugin Name="Volume"/>

to tell CC3D that volume constraint energy term will be calculated using local values (i.e. those stored in CellG object – exactly the ones we have modified using Python) rather than global settings.

Notice that we have referred to cell types using numbers. This is OK but as we have mentioned earlier using type aliases leads to much cleaner code.