What is a Steppable? (SteppableBasePy class)

SteppableBasePy has built-in functions that are called automatically during the simulation. The most important functions are start and step.

Functions

def __init__(self, frequency=1): This code runs as the simulation is set up, and, in most cases, you will not need to edit it.

def start(self): This is called after cells are created but before the simulation starts, so use it to assign custom cell properties or create plots.

def step(self, mcs): Almost everything will happen here. For example, you might grow, divide, or kill your cells here.

def on_stop(self): This runs when you click the stop button.

def finish(self): This function is called at the end of the simulation, but it is used very infrequently. Be careful: it will only run if the simulation reaches the maximum number of steps as specified by the XML attribute <Steps>.

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A very common line in a Python steppable will read:

for cell in self.cell_list:

cell_list is a variable of the SteppableBasePy class, which means that every steppable you create will automatically store every cell it creates in that list.

All steppables in CompuCell3D are extensions of SteppableBasePy, so they, too, can use cell_list.

If you’re new to programming: The word self refers to the class we’re inside, which would the steppable. Please see chapters on classes and inheritance from any Python manual if this looks unfamiliar. Also, if you want a full list of the cell attributes, see Appendix B.

If you’re a programmer: Under the hood, the self.cell_list is a handle, or a “pointer”, to the C++ object that stores all cells in the simulation. The content of cell inventory and cell ordering of cells there is fully managed by C++ code. You can easily see what member variables the C++ cell object has by calling dir(cell) with one of the cells from the self.cell_list or by checking out Appendix B.

Note

Old syntax like self.cellList is still supported.