Plugins

Ancillary features are added to the mrfmsim ecosystem through plugin packages. The separation of the core functionality and the plugins allows for an easy maintenance of the mrfmsim package. The core functionalities do not depend on the plugins.

mrfmsim-ymal: YAML configuration plugin

mrfmsim classes can be fully defined using YAML configuration files. The plugin creates a MrfmSimLoader and a MrfmSimDumper that can be used to load and dump the mrfmsim classes to and from YAML files. For detailed usage of the package see the mrfmsim-ymal.

To define an experiment or experiment group with YAML files, the available tags are: “!func”, “!import”, “!nodes”, “!Graph”, “!Experiment”, and “!ExperimentGroup”.

Tag	Usage	Description
!func	!func:<name> ‘<expression>’	Define function object or expression.
!import (function)	!import ‘<module>’	Import an object.
!import (with applied arguments)	!import:<module> {<arg1>: <value1>, <arg2>: <value2>, …}	Import an object and pass arguments to it.
!nodes	!nodes name: {<node1>: {func: <value1>, output: <value2>, …}, <node2>: …}	Define a dictionary of node objects.
!Graph	!Graph:<name> {grouped_edges: <value1>, node_objects: !nodes: <value2>, …}	Define a graph object.
!Experiment	!Experiment:<name> {graph: !Graph:<value1>, components: <value2>, …}	Define an experiment object.
!ExperimentGroup	!ExperimentGroup:<name> {node_objects: <value1>, …}	A tag to define an experiment group object.

The following is an example of a YAML configuration file:

# experiment.yaml
!Experiment:test_experiment
graph: !Graph:test_graph
    grouped_edges:
    - [add, [subtract, power, log]]
    - [[subtract, power], multiply]
    node_objects: !nodes
        add:
            func: !func:add 'lambda a, h: a + h'
            output: c
        subtract:
            func: !import '_operator.sub'
            inputs: [c, d]
            output: e
        power:
            func: !import 'math.pow'
            inputs: [c, f]
            output: g
        log:
            func: !import 'math.log'
            inputs: [c, b]
            output: m
        multiply:
            func: !import 'numpy.multiply'
            inputs: [e, g]
            output: k
            output_unit: m^2
    graph_module: mrfmsim
components:
    replace_obj: [a, b]
modifiers: [!import:mmodel.modifier.loop_input {parameter: d}]
doc: Test experiment with components.
param_defaults:
    h: 2

To load the experiment:

from mrfmsim_yaml import MrfmSimLoader
import yaml

with open('experiment.yaml', 'r') as f:
    experiment = yaml.load(f, MrfmSimLoader)

>>> print(experiment)
test_experiment(d_loop, f, replace_obj, h=2)
returns: (k, m)
return_units: {'k': 'm^2'}
graph: test_graph
handler: MemHandler
modifiers:
- loop_input(parameter='d')

Test experiment with components.

Or to dump an experiment object to a YAML file:

from mrfmsim_yaml import MrfmSimDumper
import yaml

with open('experiment.yaml', 'w') as f:
    yaml.dump(experiment, f, Dumper=MrfmSimDumper)

mrfmsim-cli: command line interface plugin

The command line interface is provided by the mrfmsim-cli plugin. See readme of the mrfmsim-cli project for more examples.

To view the CLI options:

mrfmsim --help

To show the experiment metadata:

mrfmsim metadata --expt name_of_exp

To draw the experiment graph:

mrfmsim visualize --expt name_of_exp

mrfmsim-unit: unit plugin

mrfmsim-unit plugin is a package that handles units and unit conversions for the mrfmsim base unit system. The plugin is installed by default.

The plugin is based on the pint package, and provides a registry with mrfmsim base units pre-defined. The quantity also has quick conversion method to_base_units() to convert to the base units.

from mrfmsim_unit.unit import MRFMUnitRegistry

mureg = MRFMUnitRegistry()
a = 0.1 * mureg.micrometer
b = 1.0 * mureg.nanometer

>>> a * b
0.1 nm µm

>>> (a * b).to_base_units()
100.0 nm^2

>>> # (a * b).to_base_units().magnitude
>>> # (a * b).base_magnitude
>>> (a * b).bm
100.0

The mrfmsim components do not accept pint.Quantity. Only the magnitude should be supplied to the components. The plugin provides a getattr method to access the quantity with units.

magnet = SphereMagnet(magnet_radius=50.0, mu0_Ms=1800.0, magnet_origin=[0.0, 0.0, 50.0])
r = mureg.getattr(magnet, "radius")

>>> r
50.0 nm
>>> r ** 2
2500.0 nm^2

mrfmsim-plot: plot plugin

To facilitate the visualization of three-dimensional experiment results, for example, the magnetic field, polarization, and signal distribution, we created the mrfmsim-plot plugin that provides conversion from the experiment data to the mayavi mlab and PyVista data objects.