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 SecretionBasePy. 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

Direct (but somewhat naive) Implementation

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])

Tracking Amount of Secreted (Uptaken) Chemical

While the ability to have fine control over how the chemicals get secreted/uptaken is a useful feature, quite often we would like to know the total amount of the chemical that was added to the simulation as a result of the call to one of the secrete or uptake functions from he secretor object.

Let us rewrite previous example using the API ythat facilitates tracking of the amount of chemical that was added:

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:

                res = attrSecretor.secreteInsideCellTotalCount(cell,300)
                print 'secreted  ', res.tot_amount, ' inside cell'
                res = attrSecretor.secreteInsideCellAtBoundaryTotalCount(cell,300)
                print 'secreted  ', res.tot_amount, ' inside cell at the boundary'
                res = attrSecretor.secreteOutsideCellAtBoundaryTotalCount(cell,500)
                print 'secreted  ', res.tot_amount, ' outside the cell at the boundary'
                res = attrSecretor.secreteInsideCellAtCOMTotalCount(cell,300)
                print 'secreted  ', res.tot_amount, ' inside the cell at the COM'

As you can see the calls to that return the total amount of chemical added/uptaked are the same calls as we used in our previous example except we add TotalCount to the name of the function. The new function e.g. secreteInsideCellTotalCount returns object res that is an instance of FieldSecretorResult class that contains the summary of the secreion/uptake operation. Most importantly when we access total_amount member of the res object we get the total amount that was added/uptaken from the chemical field e.g. :

res = attrSecretor.secreteInsideCellTotalCount(cell,300)
print 'secreted  ', res.tot_amount, ' inside cell'

For cmpleteness we present a complete list of C++ signatures of all the functions that can be used to fine-control how uptake/secretion happens in CC3D. All those functions are members of the secretor object and are accessible from Python

bool _secreteInsideCellConstantConcentration(CellG * _cell, float _amount);

FieldSecretorResult _secreteInsideCellConstantConcentrationTotalCount(CellG * _cell, float _amount);

bool _secreteInsideCell(CellG * _cell, float _amount);

FieldSecretorResult _secreteInsideCellTotalCount(CellG * _cell, float _amount);

bool _secreteInsideCellAtBoundary(CellG * _cell, float _amount);

FieldSecretorResult _secreteInsideCellAtBoundaryTotalCount(CellG * _cell, float _amount);

bool _secreteInsideCellAtBoundaryOnContactWith(CellG * _cell, float _amount,
const std::vector<unsigned char> & _onContactVec);

FieldSecretorResult _secreteInsideCellAtBoundaryOnContactWithTotalCount(CellG * _cell,
float _amount, const std::vector<unsigned char> & _onContactVec);

bool _secreteOutsideCellAtBoundary(CellG * _cell, float _amount);

FieldSecretorResult _secreteOutsideCellAtBoundaryTotalCount(CellG * _cell, float _amount);

bool _secreteOutsideCellAtBoundaryOnContactWith(CellG * _cell, float _amount,
const std::vector<unsigned char> & _onContactVec);

FieldSecretorResult  _secreteOutsideCellAtBoundaryOnContactWithTotalCount(CellG * _cell,
float _amount, const std::vector<unsigned char> & _onContactVec);

bool secreteInsideCellAtCOM(CellG * _cell, float _amount);

FieldSecretorResult secreteInsideCellAtCOMTotalCount(CellG * _cell, float _amount);

bool _uptakeInsideCell(CellG * _cell, float _maxUptake, float _relativeUptake);

FieldSecretorResult _uptakeInsideCellTotalCount(CellG * _cell, float _maxUptake, float _relativeUptake);

bool _uptakeInsideCellAtBoundary(CellG * _cell, float _maxUptake, float _relativeUptake);

FieldSecretorResult _uptakeInsideCellAtBoundaryTotalCount(CellG * _cell, float _maxUptake, float _relativeUptake);

bool _uptakeInsideCellAtBoundaryOnContactWith(CellG * _cell, float _maxUptake,
float _relativeUptake,const std::vector<unsigned char> & _onContactVec);

FieldSecretorResult _uptakeInsideCellAtBoundaryOnContactWithTotalCount(CellG * _cell,
float _maxUptake, float _relativeUptake, const std::vector<unsigned char> & _onContactVec);

bool _uptakeOutsideCellAtBoundary(CellG * _cell, float _maxUptake, float _relativeUptake);

FieldSecretorResult _uptakeOutsideCellAtBoundaryTotalCount(CellG * _cell, float _maxUptake, float _relativeUptake);

bool _uptakeOutsideCellAtBoundaryOnContactWith(CellG * _cell, float _maxUptake,
 float _relativeUptake,const std::vector<unsigned char> & _onContactVec);

FieldSecretorResult _uptakeOutsideCellAtBoundaryOnContactWithTotalCount(CellG * _cell,
float _maxUptake, float _relativeUptake, const std::vector<unsigned char> & _onContactVec);

bool uptakeInsideCellAtCOM(CellG * _cell, float _maxUptake, float _relativeUptake);

FieldSecretorResult  uptakeInsideCellAtCOMTotalCount(CellG * _cell, float _maxUptake, float _relativeUptake);

For example if we want to use uptakeInsideCellAtCOMTotalCount(CellG * _cell, float _maxUptake, float _relativeUptake); from python we would use the following code:

In this case _cell is a cell object that we normally deal with in Python, _maxUptake has value of 3 and _relativeUptake is set to 0.1

In similar fashion we could use remaining functions listed above