Creating and Deleting Cells. Cell-Type Names

The simulation that Twedit++ Simulation Wizard generates contains some kind of initial cell layout. Sometimes however we want to be able to either create cells as simulation runs or delete some cells. CC3D makes such operations very easy and Twedit++ is of great help. Let us first start with a simulation that has no cells. All we have to do is to comment out BlobInitializer section in the CC3DML code in our cellsorting simulation:

File: C:\\CC3DProjects\\cellsorting\\Simulation\\cellsorting.xml

<CompuCell3D version="3.6.2">
    <Dimensions x="100" y="100" z="1"/>

  <Plugin Name="CellType">
    <CellType TypeId="0" TypeName="Medium"/>
    <CellType TypeId="1" TypeName="Condensing"/>
    <CellType TypeId="2" TypeName="NonCondensing"/>

  <Plugin Name="Volume">
    <VolumeEnergyParameters CellType="Condensing" LambdaVolume="2.0"
    <VolumeEnergyParameters CellType="NonCondensing" LambdaVolume="2.0"

  <Plugin Name="CenterOfMass">

  <Plugin Name="Contact">

    <Energy Type1="Medium" Type2="Medium">10.0</Energy>
    <Energy Type1="Medium" Type2="Condensing">10.0</Energy>
    <Energy Type1="Medium" Type2="NonCondensing">10.0</Energy>
    <Energy Type1="Condensing" Type2="Condensing">10.0</Energy>
    <Energy Type1="Condensing" Type2="NonCondensing">10.0</Energy>
    <Energy Type1="NonCondensing" Type2="NonCondensing">10.0</Energy>


When we run this simulation and try to iterate over list of all cells (see earlier example) we won’t see any cells:


Figure 10 Output from simulation that has no cells

To create a single cell in CC3D we type the following code snippet:

def start(self):
    self.cell_field[10:14,10:14,0] = self.new_cell(self.CONDENSING)


self.cellField still works. We can also access this field via self.field.cell_field although self.cell_field looks much simpler

In Twedit++ go to CC3D Python->Cell Manipulation->Create Cell:


Figure 11 Inserting code snippet in Twedit++ to create cells. Notice that this is a generic code that usualy needs minor customizations.

Notice that we create cell in the start function. We can create cells in step functions as well. We create a C++ cell object using the following statement:


We initialize its type using self.CONDENSING class variable that corresponds to an integer assigned to type Condensing. Cell type is an integer value from 1 to 255 and CompuCell3D automatically creates class variables corresponding to each type. By looking at the definition of the CellType plugin in CC3DML for cellsorting simulation you can easily infer that number 1 denotes cells of type Condensing and 2 denotes cells of type NonCondensing. Because it is much easier to remember names of cell types than keeping track which cell type corresponds to which number SteppableBasePy provides very convenient member variables denoting cell type numbers. The name of such variable is obtained by capitalizing all letters in the name of the cell type and prepending if with self. In our example we will have 3 such variables self.MEDIUM, self.CONDENSING, self.NONCONDENSING with values 0, 1, 2 respectively.


To ensure that cell type names are correctly translated into Python class variables avoid using spaces in cell type name.


cell.type = self.CONDENSING

is equivalent to

cell.type = 1

but the former makes the code more readable. After assigning cell type all that remains is to initialize lattice sites using newly created cell object so that atleast one lattice site points to this cell object.

The syntax which assigns cell object to 25 lattice sites

self.cell_field[10:14, 10:14, 0] = cell

is based on Numpy syntax. self.cell_field is a pointer to a C++ lattice which stores pointers to cell objects. In this example our cell is a 5x5 square collection of pixels. Notice that the 10:14 has 5 elements because the both the lower and the upper limits are included in the range. As you can probably tell, self.cellField is member of SteppableBasePy. To access cell object occupying lattice site, x, y, z, we type:


The way we access cell field is very convenient and should look familiar to anybody who has used Matlab, Octave or Numpy.

Deleting CC3D cell is easier than creating one. The only thing we have to remember is that we have to add PixelTracker Plugin to CC3DML (in case you forget this CC3D will throw error message informing you that you need to add this plugin).

The following snippet will erase all cells of type Condensing:

def step(self, mcs):
    for cell in self.cell_list:
        if cell.type == self.CONDENSING:

We use member function of SteppableBasePydeleteCell where the first argument is a pointer to cell object.