DSRunner

DSRunner#

class brainpy.DSRunner(target, inputs=(), monitors=None, numpy_mon_after_run=True, jit=True, dyn_vars=None, memory_efficient=False, dt=None, t0=0.0, progress_bar=True, data_first_axis=None, fun_inputs=None, fun_monitors=None)[source]#

The runner for DynamicalSystem.

Parameters:

  • target (DynamicalSystem) – The target model to run.

  • inputs (list, tuple, callable) –

    The inputs for variables in the target model.

    Note

    This argument can be used to set the inputs to the Variable instances in the target. If you peruse to give time-dependent inputs, please use DSRunner.predict() or DSRunner.run() function.

    • It can be a list/tuple with the format of [(target, value, [type, operation])], where target is the input target, value is the input value, type is the input type (such as “fix”, “iter”, “func”), operation is the operation for inputs (such as “+”, “-”, “*”, “/”, “=”).

      • target: should be a string or Variable. Can be specified by the absolute access or relative access.

      • value: should be a scalar, vector, matrix.

      • type: should be a string. “fix” means the input value is a constant. “iter” means the input value can be changed over time. “func” mean the input is obtained through the functional call.

      • operation: should be a string, support +, -, *, /, =.

      • Also, if you want to specify multiple inputs, just give multiple (target, value, [type, operation]), for example [(target1, value1), (target2, value2)].

    • It can also be a callable function which receives the shared argument. In this functional input, users can manually specify the inputs for the target variables. This input function should receive one argument shared which contains the shared arguments like time t, time step dt, and index i.

      Changed in version 2.3.1: fun_inputs are merged into inputs.

  • fun_inputs (callable) –

    The functional inputs. Manually specify the inputs for the target variables. This input function should receive one argument shared which contains the shared arguments like time t, time step dt, and index i.

    Deprecated since version 2.3.1: Will be removed since version 2.4.0.

  • monitors (Optional, sequence of str, dict, Monitor) –

    Variables to monitor.

    • A list of string. Like monitors=['a', 'b', 'c'].

    • A list of string with index specification. Like monitors=[('a', 1), ('b', [1,3,5]), 'c']

    • A dict with the explicit monitor target, like: monitors={'a': model.spike, 'b': model.V}

    • A dict with the index specification, like: monitors={'a': (model.spike, 0), 'b': (model.V, [1,2])}

    • A dict with the callable function, like monitors={'a': lambda: model.spike[:5]}

    Changed in version 2.3.1: fun_monitors are merged into monitors.

  • fun_monitors (dict) –

    Monitoring variables by a dict of callable functions. The dict key should be a string for the later retrieval by runner.mon[key]. The dict value should be a callable function which receives two arguments: t and dt. .. code-block:

    fun_monitors = {'spike': lambda: model.spike[:10],
                'V10': lambda: model.V[10]}

    Deprecated since version 2.3.1: Will be removed since version 2.4.0.

  • jit (bool, dict) – The JIT settings. Using dict is able to set the jit mode at different phase, for instance, jit={'predict': True, 'fit': False}.

  • progress_bar (bool) – Use progress bar to report the running progress or not?

  • dyn_vars (Optional, dict) – The dynamically changed variables. Instance of Variable. These variables together with variable retrieved from the target constitute all dynamical variables in this runner.

  • numpy_mon_after_run (bool) – When finishing the network running, transform the JAX arrays into numpy ndarray or not?

  • data_first_axis (str) –

    Set the default data dimension arrangement. To indicate whether the first axis is the batch size (data_first_axis='B') or the time length (data_first_axis='T'). In order to be compatible with previous API, default is set to be False.

    Added in version 2.3.1.

  • memory_efficient (bool) –

    Whether using the memory-efficient way to just-in-time compile the given target. Default is False.

    Added in version 2.3.8.

predict(duration=None, inputs=None, reset_state=False, eval_time=False, shared_args=None, inputs_are_batching=None)[source]#

Running a duration with the given target model. See .predict() function for more details.

This function use the JIT compilation to accelerate the model simulation. Moreover, it can automatically monitor the node variables, states, inputs, and its output.

Parameters:

  • duration (float) – The simulation time length. If you have provided inputs, there is no longer need to provide duration.

  • inputs (ArrayType, dict of ArrayType, sequence of ArrayType) –

    The input data.

    • If the mode of target is instance of BatchingMode, inputs must be a PyTree of data with two dimensions: (batch, time, ...) when data_first_axis='B', or (time, batch, ...) when data_first_axis='T'.

    • If the mode of target is instance of NonBatchingMode, the inputs should be a PyTree of data with one dimension: (time, ...).

  • inputs_are_batching (bool) –

    Whether the inputs are batching. If True, the batching axis is the first dimension.

    Deprecated since version 2.3.1: Will be removed after version 2.4.0.

  • reset_state (bool) – Whether reset the model states.

  • eval_time (bool) – Whether ro evaluate the running time.

  • shared_args (optional, dict) – The shared arguments across different layers.

Returns:

output – The model output.

Return type:

ArrayType, dict, sequence

reset_state()[source]#

Reset state of the DSRunner.

run(*args, **kwargs)[source]#

Same as predict().

Return type:

Union[TypeVar(Output), Tuple[float, TypeVar(Output)]]