Stimulus¶

Schema for stimulation protocols / source terms¶

class pigreads.schema.stimulus.SignalStep(**data)¶

Bases: BaseModel

Within a time interval, increase the value of variables by a given amounts.

The start and duration of the signal are given in time units of the simulation. The variables are given as a dictionary with the variable names as keys and the amount to increase the variable by as values:

start: 100 # ms
duration: 10 # ms
variables:
  u: 1
  v: 2

The interval is defined mathematically as \(t \in [\text{start}, \text{start} + \text{duration})\).

Parameters:: data (Any)

__call__(signal, times, varidx)¶

Modify the signal array.

The signal array is modified in place to increase the values of the variables by the given amounts within the time interval.

Parameters:

signal (ndarray[Any, Any]) – Signal array to modify.
times (ndarray[Any, Any]) – Times of the signal steps.
varidx (dict[str, int]) – Mapping of variable names to indices in the signal array, see pigreads.schema.simulation.Simulation.varidx().

Return type:

ndarray[Any, Any]

Returns:

Modified signal array.

duration: float¶: Duration of the signal.

model_config: ClassVar[ConfigDict]¶: Configuration for pydantic.BaseModel.

start: float¶: Starting time of the signal.

variables: dict[str, float]¶: Variables to modify and the amount to modify them by.

class pigreads.schema.stimulus.Stimulus(**data)¶

Bases: BaseModel

A stimulus is a combination of a shape and a signal.

The shape is defined by a list of pigreads.schema.setter.Setter objects and defines where the stimulus is applied. The signal is defined by a list of SignalStep objects and defines how the stimulus changes over time.

Parameters:: data (Any)

model_config: ClassVar[ConfigDict]¶: Configuration for pydantic.BaseModel.

classmethod normalise_shape(shape)¶

Normalise the setters in the shape.

See pigreads.schema.setter.normalise_list_of_setters() for details.

Parameters:: shape (Any) – Any data to try to interpret.
Return type:: Any
Returns:: Normalised data.

shape: list[SetterFile | SetterSlices | SetterSpherical]¶: Shape of the stimulus.

signal: list[SignalStep]¶: Signal of the stimulus.