Mathematical Expressions
Mathematical expressions are permitted on different sections of the
Parameter Tree. Such expressions may contain typical math
operations such as +, -, *, ^, sin, tan, etc. The complete list of
possibilities is found here.
That is, the muParser built in operators.
Furthermore, we provide extra variables/functions that may be included on the math expressions.
Variables
Context-Independent
The following list of variables are unconditionally available when defining expressions:
| Variable | Description |
|---|---|
t | Time |
x | First dimension in the cartesian coordinate system |
y | Second dimension in the cartesian coordinate system |
z | Third dimension in the cartesian coordinate system (only in 3D) |
dim | Dimension of the euclidean space |
pi | Approximation to the number π |
Context-Dependent
Additionally, there are other variables that are conditionally available to
define the expression. These variables depend on the context of its definition.
An example of it is the reaction expressions within a compartment. If the
section [model.nucleus.reaction] defines expressions u, v, and w,
then, they all will be available to each other. E.g.
[model.nucleus.reaction]
u = u*v*w
v = u*v*w
w = u*v*w
Functions
Context-Dependent
There are also functions that may be conditionally available depending on the context. In such case, the function will have a custom name and fixed number of arguments and will be available for use on the mathematical expression.
Currently we only provide these for defining TIFF input images as 2D functions for initial conditions (See Input Data section).