4.7.2. pde.trackers.interactive module

Special module for defining an interactive tracker that uses napari to display fields

class InteractivePlotTracker(interval: Union[ConstantIntervals, float, int, str] = '0:01', close: bool = True, show_time: bool = False)[source]

Bases: pde.trackers.base.TrackerBase

Tracker showing the state interactively in napari

Note

The interactive tracker uses the python multiprocessing module to run napari externally. The multiprocessing module has limitations on some platforms, which requires some care when writing your own programs. In particular, the main method needs to be safe-guarded so that the main module can be imported again after spawning a new process. An established pattern that works is to introduce a function main in your code, which you call using the following pattern

def main():
    # here goes your main code

if __name__ == "__main__":
    main()

The last two lines ensure that the main function is only called when the module is run initially and not again when it is re-imported.

Parameters
  • interval – Determines how often the tracker interrupts the simulation. Simple numbers are interpreted as durations measured in the simulation time variable. Alternatively, a string using the format ‘hh:mm:ss’ can be used to give durations in real time. Finally, instances of the classes defined in intervals can be given for more control.

  • close (bool) – Flag indicating whether the napari window is closed automatically at the end of the simulation. If False, the tracker blocks when finalize is called until the user closes napari manually.

  • show_time (bool) – Whether to indicate the time

finalize(info: dict = None) None[source]

finalize the tracker, supplying additional information

Parameters

info (dict) – Extra information from the simulation

handle(state: FieldBase, t: float) None[source]

handle data supplied to this tracker

Parameters
  • state (FieldBase) – The current state of the simulation

  • t (float) – The associated time

initialize(state: FieldBase, info: dict = None) float[source]

initialize the tracker with information about the simulation

Parameters
  • state (FieldBase) – An example of the data that will be analyzed by the tracker

  • info (dict) – Extra information from the simulation

Returns

The first time the tracker needs to handle data

Return type

float

name = 'interactive'
class NapariViewer(state: FieldBase, t_initial: float = None)[source]

Bases: object

allows viewing and updating data in a separate napari process

Parameters
close(force: bool = True)[source]

closes the napari process

Parameters

force (bool) – Whether to force closing of the napari program. If this is False, this method blocks until the user closes napari manually.

update(state: FieldBase, t: float)[source]

update the state in the napari viewer

Parameters
napari_process(data_channel: multiprocessing.context.BaseContext.Queue, initial_data: Dict[str, dict], t_initial: float = None, viewer_args: dict = None)[source]

multiprocessing.Process running napari

Parameters
  • data_channel (multiprocessing.Queue) – queue instance to receive data to view

  • initial_data (dict) – Initial data to be shown by napari. The layers are named according to the keys in the dictionary. The associated value needs to be a tuple, where the first item is a string indicating the type of the layer and the second carries the associated data

  • t_initial (float) – Initial time

  • viewer_args (dict) – Additional arguments passed to the napari viewer