Adding and managing extra fields for visualization purposes¶
Quite often in your simulation you will want to label cells using scalar field, vector fields or simply create your own scalar or vector fields which are fully managed by you from the Python level. CC3D allows you to create four kinds of fields:
- Scalar Field – to display scalar quantities associated with single pixels
- Cell Level Scalar Field – to display scalar quantities associated with cells
- Vector Field - to display vector quantities associated with single pixels
- Cell Level Vector Field - to display vector quantities associated with cells
You can take look at
CompuCellPythonTutorial/ExtraFields to see an
example of a simulation that uses all four kinds of fields. The Python
syntax used to create and manipulate custom fields is relatively simple
but quite hard to memorize. Fortunately Twedit++ has
menu that inserts code snippets to create/manage fields.
Scalar Field – pixel based¶
Let’s look at the steppable that creates and manipulates scalar cell field. This field is implemented as Numpy float array and you can use Numpy functions to manipulate this field.
from cc3d.core.PySteppables import * from random import random from math import sin class ExtraFieldVisualizationSteppable(SteppableBasePy): def __init__(self, frequency=10): SteppableBasePy.__init__(self, frequency) self.create_scalar_field_py("ExtraField") def step(self, mcs): cell = self.field.Cell_Field[20, 20, 0] print('cell=', cell) # clear field self.field.ExtraField[:, :, :] = 10.0 for x, y, z in self.every_pixel(4, 4, 1): if not mcs % 20: self.field.ExtraField[x, y, z] = x * y else: self.field.ExtraField[x, y, z] = sin(x * y)
The scalar field (we called it
ExtraField) is declared in the
__init__ function of the steppable using
Ideally you would declare exrta fields in the
__init__ function but if you create them elsewhere they will work as well. HOwever in certain situations you may notice that fields declared outside
__init__ may be missing
from e.g. player menus. Normally it is not a big deal but if you want to have full functionality associated with the fields declare them inside
In the step function we initialize
ExtraField using slicing operation:
self.field.ExtraField[:, :, :] = 10.0
In Python slicing convention, a single colon means all indices – here we
put three colons for each axis which is equivalent to selecting all
pixels. Notice how we use
self.field.ExtraField construct to access the field.
It is perfectly fine (and faster too if you acces field repeatedly) to split this int two lines:
extra_field = self.field.ExtraField extra_field[:, :, :] = 10
Following lines in the step functions iterate over every pixel in the
simulation and if MCS is divisible by 20 then self.scalarField is
x*y value if MCS is not divisible by 20 than we
initialize scalar field with
sin(x*y) function. Notice, that we
imported all functions from the
math Python module so that we can get
sin function to work.
SteppableBasePy provides convenience function called
CC3D Python->Visit->All Lattice Pixels) that facilitates compacting triple loop to just one line:
for x,y,z in self.every_pixel(): if not mcs % 20: self.field.ExtraField[x, y, z]=x*y else: self.field.ExtraField[x, y, z]=sin(x*y)
If we would like to iterate over x axis indices with step 5, over y indices with step 10 and over z axis indices with step 4 we would replace first line in the above snippet with.
for x, y, z in self.every_pixel(5,10,4):
You can still use triple loops if you like but shorter syntax leads to a cleaner code.
Vector Field – pixel based¶
By analogy to pixel based scalar field we can create vector field. Let’s look at the example code:
class VectorFieldVisualizationSteppable(SteppableBasePy): def __init__(self, frequency=10): SteppableBasePy.__init__(self, frequency) self.create_vector_field_py("VectorField") def step(self, mcs): vec_field = self.field.VectorField # clear vector field vec_field[:, :, :, :] = 0.0 for x, y, z in self.everyPixel(10, 10, 5): vec_field[x, y, z] = [x * random(), y * random(), z * random()]
Th code is very similar to the previous steppable. In the
function we create pixel based vector field , in the step function we
initialize it first to with zero vectors and later we iterate over
pixels using steps
axes respectively and to these select lattice pixels we assign
[x*random(), y*random(), z*random()]
self.field.VectorField is implemented as
np.zeros(shape=(_dim.x, _dim.y, _dim.z,3), dtype=np.float32)
Scalar Field – cell level¶
Pixel based fields are appropriate for situations where we want to assign scalar of vector to particular lattice locations. If, on the other hand, we want to label cells with a scalar or a vector we need to use cell level field (scalar or vector). It is still possible to use pixel-based fields but we assure you that the code you would write would be ver ugly at best.
Internally cell-based scalar field is implemented as a map or a dictionary indexed by cell id (although in Python instead of passing cell id we pass cell object to make syntax cleaner). Let us look at an example code:
class IdFieldVisualizationSteppable(SteppableBasePy): def __init__(self, frequency=10): SteppableBasePy.__init__(self, frequency) def start(self): # note if you create field outside constructor this field will not be properly # initialized if you are using restart snapshots. It is OK as long as you are aware of this limitation self.create_scalar_field_cell_level_py("IdFieldNew") def step(self, mcs): # clear id field try: id_field = self.field.IdFieldNew id_field.clear() except KeyError: # an exception might occur if you are using restart snapshots to restart simulation # because field has been created outside constructor self.create_scalar_field_cell_level_py("IdFieldNew") id_field = self.field.IdFieldNew for cell in self.cell_list: id_field[cell] = cell.id * random()
As it was the case with other fields we create cell level scalar field
__init__ function using
the step function we first clear the field – this simply removes all
entries from the dictionary. If you forget to clean dictionary before
putting new values you may end up with stray values from the previous
step. Inside the loop over all cells we assign random value to each cell.
When we plot
IdFieldNew in the player we will see that cells have different
color labels. If we used pixel-based field to accomplish same task we
would have to manually assign same value to all pixels belonging to a
given cell. Using cell level fields we save ourselves a lot of work and
make code more readable.
Vector Field – cell level¶
We can also associate vectors with cells. The code below is analogous to the previous example:
__init__ function we create cell-level vector field using
self.create_vector_field_cell_level_py function. In the step function we
clear field and then iterate over all cells and assign random vector to
each cell. When we plot this field on top cell borders you will see that
vectors are anchored in “cells’ corners” and not at the COM. This is
because such rendering is faster.
You should remember that all those 4 kinds of field discussed here are for display purposes only. They do not participate in any calculations done by C++ core code and there is no easy way to pass values of those fields to the CC3D computational core.