Custom Cell Attributes in Python

As you have already seen each cell object has a several attributes describing properties of model cell (e.g. volume, surface, target surface, type, id etc...). However, in almost every simulation that you develop, you need to associate additional attributes with the cell objects. For example, you may want every cell to have a countdown clock that will be recharged once its value reaches zero. One way to accomplish this task is to add a line:

int clock

to Cell.h file and recompile entire CompuCell3D package. Cell.h is a C++ header file that defines basic properties of the CompuCell3D cells and it happened so that almost every C++ file in the CC3D source code depends on it. Consequently, any modification of this file will mean that you would need to recompile almost entire CC3D from scratch. This is inefficient. Even worse, you will not be able to share your simulation using this extra attribute, unless the other person also recompiled her/his code using your tweak. Fortunately CC3D let’s you easily attach any type of Python object as cell attribute. Each cell, by default, has a Python dictionary attached to it. This allows you to store any object that has Python interface as a cell attribute. Let’s take a look at the following implementation of the step function:

def step(self,mcs):

    for cell in self.cellList:

    for cell in self.cellList:
        print '',,' dict=',cell.dict

We have two loops that iterate over list of all cells. In the first loop we access dictionary that is attached to each cell:


and then insert into a dictionary a product of 2, mcs and cell id:


In the second loop we access the dictionary and print its content to the screen. The result will look something like:


Figure 14 Simple simulation demonstrating the usage of custom cell attributes.

If you would like attach a Python list to the cell all you do it insert Python list as one of the elements of the dictionary e.g.:

for cell in self.cellList:

Thus all you really need to store additional cell attributes is the dictionary.