Field Secretion

PDE solvers in the CC3D allow users to specify secretion properties individually for each cell type. However, there are situations where you want only a single cell to secrete the chemical. In this case you have to use Secretor objects. In Twedit++, go to CC3D Python->Secretion menu to see what options are available. Let us look at the example code to understand what kind of capabilities CC3D offers in this regard (see Demos/SteppableDemos/Secretion):

class SecretionSteppable(SecretionBasePy):
    def __init__(self,_simulator,_frequency=1):
        SecretionBasePy.__init__(self,_simulator, _frequency)

    def step(self,mcs):
        attrSecretor=self.getFieldSecretor("ATTR")
        for cell in self.cellList:
            if cell.type==3:
                attrSecretor.secreteInsideCell(cell,300)
                attrSecretor.secreteInsideCellAtBoundary(cell,300)
                attrSecretor.secreteOutsideCellAtBoundary(cell,500)
                attrSecretor.secreteInsideCellAtCOM(cell,300)

In the step function we obtain a handle to field secretor object that operates on diffusing field ATTR. In the for loop where we go over all cells in the simulation we pick cells which are of type 3 (notice we use numeric value here instead of an alias). Inside the loop we use secreteInsideCell, secreteInsideCellAtBoundary, secreteOutsideCellAtBoundary, and secreteInsideCellAtCOM member functions of the secretor object to carry out secretion in the region occupied by a given cell. secreteInsideCell increases concentration by a given amount (here 300) in every pixel occupied by a cell. secreteInsideCellAtBoundary and secreteOutsideCellAtBoundary increase concentration but only in pixels which at the boundary but are inside cell or outside pixels touching cell boundary. Finally, secreteInsideCellAtCOM increases concentration in a single pixel that is closest to cell center of mass of a cell.

Notice that SecretionSteppable inherits from SecretionBasePy11. We do this to ensure that Python-based secretion plays nicely with PDE solvers. This requires that such steppable must be called before MCS, or rather before the PDE solvers start evolving the field. If we look at the definition of ``SecretionBasePy we will see that it inherits from SteppableBasePy and in the __init__ function it sets self.runBeforeMCS flag to 1:

class SecretionBasePy(SteppableBasePy):
    def __init__(self,_simulator,_frequency=1):
        SteppableBasePy.__init__(self,_simulator,_frequency)
        self.runBeforeMCS=1

Now, for the sake of completeness, let us implement cell secretion at the COM using alternative code:

self.field = self.getConcentrationField('ATTR')
lmfLength = 1.0;
xScale = 1.0
yScale = 1.0
zScale = 1.0
# FOR HEX LATTICE IN 2D
#         lmfLength=sqrt(2.0/(3.0*sqrt(3.0)))*sqrt(3.0)
#         xScale=1.0
#         yScale=sqrt(3.0)/2.0
#         zScale=sqrt(6.0)/3.0

for cell in self.cellList:
    # converting from real coordinates to pixels
    xCM = int(cell.xCOM / (lmfLength * xScale))
    yCM = int(cell.yCOM / (lmfLength * yScale))

    if cell.type == 3:
        self.field[xCM, yCM, 0] = self.field[xCM, yCM, 0] + 10.0

As you can tell, it is significantly more work than our original solution.

Lattice Conversion Factors

In the code where we manually implement secretion at the cell’sCOM we use strange looking variables lmfLength, xScale and yScale. CC3D allows users to run simulations on square (Cartesian) or hexagonal lattices. Under the hood these two lattices rely on the Cartesian lattice. However distances between neighboring pixels are different on Cartesian and hex lattice. This is what those 3 variables accomplish. The take home message is that to convert COM coordinates on hex lattice to Cartesian lattice coordinates we need to use converting factors. Please see writeup “Hexagonal Lattices in CompuCell3D” (http://www.compucell3d.org/BinDoc/cc3d_binaries/Manuals/HexagonalLattice.pdf) for more information. To convert between hex and Cartesian lattice coordinates we can use PySteppableBase built-in functions (self.cartesian2Hex, and self.hex2Cartesian) – see also Twedit++ CC3D Python menu Distances, Vectors, Transformations:

hex_coords = self.cartesian2Hex(_in=[10, 20, 11])
pt = self.hex2Cartesian(_in=[11.2, 13.1, 21.123])