ConfigSimulator¶

class mrsimulator.simulator.ConfigSimulator(*, name: str = None, description: str = None, label: str = None, property_units: Dict = {}, number_of_sidebands: ConstrainedIntValue = 64, number_of_gamma_angles: ConstrainedIntValue = 1, integration_volume: Literal['octant', 'hemisphere', 'sphere'] = 'octant', integration_density: ConstrainedIntValue = 70, decompose_spectrum: Literal['none', 'spin_system'] = 'none', isotropic_interpolation: Literal['linear', 'gaussian'] = 'linear', custom_sampling: Optional[CustomSampling] = None, is_complex: bool = True)¶

Bases: Parseable

The configurable attributes for the Simulator class used in the simulation.

number_of_sidebands¶

Number of sidebands to evaluate in the simulation. The default value is 64. Value cannot be negative or zero.

Type:: int (optional).

number_of_gamma_angles¶

Number of gamma angles averages in the simulation. The default value is 1. Value cannot be negative or zero.

Type:: int (optional).

integration_volume¶

The spatial volume over which the spectral frequency integration/averaging is performed. The valid literals of this enumeration are

octant (default),
hemisphere, and
sphere

Type:: enum (optional).

integration_density¶

The integration/sampling density or equivalently the number of (alpha, beta) orientations over which the frequency spatial averaging is performed within the given volume. If \(n\) is the integration_density, then the total number of orientations is given as

(56)¶\[n_\text{octants} \frac{(n+1)(n+2)}{2} n_\gamma,\]

where \(n_\text{octants}\) is the number of octants in the given volume and \(n_\gamma\) is the number of gamma angles. The default value is 70.

Type:: int (optional).

decompose_spectrum¶

The value specifies how a simulation result is decomposed into an array of spectra. The valid literals of this enumeration are

none (default): When the value is none, the resulting simulation is a single spectrum, which is an integration of the spectra over all spin systems.
spin_system: When the value is spin_system, the resulting simulation is an array of spectra, where each spectrum arises from a spin system within the Simulator object.

Type:: enum (optional).

isotropic_interpolation¶

Interpolation scheme for isotropic binning. The valid literals are

linear (default): linear interpolation.
gaussian: Gaussian interpolation with sigma=0.25*bin_width.

Type:: enum (optional).

custom_sampling¶

A CustomSampling object specifying the coordinates and weights used in powder averaging.

Type:: CustomSampling

is_complex¶

When True, the simulation computes both real and imaginary components of the signal. When False, only the real component is computed. Default is True.

Type:: bool

Example

>>> a = Simulator()
>>> a.config.number_of_sidebands = 128
>>> a.config.number_of_gamma_angles = 10
>>> a.config.integration_density = 96
>>> a.config.integration_volume = 'hemisphere'
>>> a.config.decompose_spectrum = 'spin_system'

get_orientations_count()¶

Return the total number of orientations.

Example

>>> a = Simulator()
>>> a.config.integration_density = 20
>>> a.config.integration_volume = 'hemisphere'
>>> a.config.get_orientations_count() # (4 * 21 * 22 / 2) = 924
924

json(exclude={}, units=True) → dict¶

Parse the class object to a JSON compliant Python dictionary object.

Parameters:

exclude – Set of keys that will be excluded from the result.
units – If true, the attribute value is a physical quantity expressed as a string with a number and a unit, else a float.

Returns: dict

classmethod parse_dict_with_units(json_dict: dict)¶

Parse the physical quantity from a dictionary representation of the class object, where the physical quantity is expressed as a string with a number and a unit.

Parameters:: json_dict (dict) – A required python dict object.

reduced_dict(exclude={}) → dict¶

Returns a reduced dictionary representation of the class object by removing all key-value pairs corresponding to keys listed in the exclude argument, and keys with a value of None.

Parameters:: exclude – A list of keys to exclude from the dictionary.

Return: A dict.

CustomSampling¶

class mrsimulator.simulator.config.CustomSampling(*, alpha: Optional[ndarray] = None, beta: Optional[ndarray] = None, weight: Optional[ndarray] = None, vertex_indexes: Optional[ndarray] = None)¶

Bases: BaseModel

Custom orientational sampling for powder averaging.

alpha¶

An array of size N of \(\alpha\) angle coordinates in radians.

Type:: ndarray

beta¶

An array of size N of \(\beta\) angle coordinates in radians.

Type:: ndarray

weight¶

An array of size N of weights corresponding to \((\alpha, \beta)\) coordinates.

Type:: ndarray

vertex_indexes¶

A 2D array of shape (N, 3) with each row listing the three indexes of \((\alpha, \beta)\) coordinates that forms a triangular mesh on a unit sphere. The indexes are used in frequency interpolation. The default value is None and corresponds to no interpolation.

Type:: ndarray (optional)