SimulatedShell

from mcot.dippi.scan import SimulatedShell

class mcot.dippi.scan.SimulatedShell(scanner: mcot.dippi.scan.Scanner = <factory>, encoding: mcot.dippi.scan.Encoding = <Encoding.linear: 1>, bval: float = 3.0, gradients: Optional[numpy.ndarray] = None, ngradients_in: dataclasses.InitVar = 30, ndim_in: dataclasses.InitVar = 3, dual_echo: bool = True, t_phase: float = 30, theta_b0: float = 0.0)

Represents the scan settings and physical constants

Used in both the simulator and in fitting

This represents a single shell of diffusion-weighted susceptibility data

The main scanner parameters to be set are B0, max_gradient, slew_rate, and the duration of the readout (t_ro) and pulse (t_pulse)

The main acquisition parameters to be set are bval, t_phase, and gradients. The gradients can be initialised uniformly by settings ngradients_in.

The second refocus pulse can be removed by setting dual_echo to false (will raise an error if t_ro > t_phase)

Based on this input the following times are computed - TE1 = readout1: time of first spin echo/readout - TE2: time of second spin echo (only if dual_echo=True) - readout2: time of second readout (=echo time + t_phase) - time_done: time the second readout is finished (readout2 + t_ro/2)

__init__(scanner: mcot.dippi.scan.Scanner = <factory>, encoding: mcot.dippi.scan.Encoding = <Encoding.linear: 1>, bval: float = 3.0, gradients: Optional[numpy.ndarray] = None, ngradients_in: dataclasses.InitVar = 30, ndim_in: dataclasses.InitVar = 3, dual_echo: bool = True, t_phase: float = 30, theta_b0: float = 0.0) → None

Initialize self. See help(type(self)) for accurate signature.

Inheritance diagram

Methods

from_dict(kvs, *[, infer_missing])
from_json(s, *[, parse_float, parse_int, …])
schema(*[, infer_missing, only, exclude, …])
spherical_harmonics(lmax[, odd])
to_dict([encode_json])
to_json(*[, skipkeys, ensure_ascii, …])

Attributes

TE1	Time till first readout in ms
TE2	Time till second readout
b0_dir
b0_group
bval	Gradients orientations (1D array for angles in 2D-plane or (N, 3) array for full gradient orientations)
dataclass_json_config
dual_echo	time of phase accumulation
encoding	b-value in ms/micrometer^2
gradients	Helper parameters to define a default set of bvecs (if user does not provide one)
ndim	Whether gradients are on a circle (2) or sphere (3)
ndim_in	Whether to add a second refocus pulse
ngradients	Number of gradient orientations in this shell
ngradients_in
readout1	Time till the centre of the first readout in ms
readout2	Time till the second readout in ms
refocus1	Time of the centre of the first refocus pulse
refocus2	Time of the centre of the second refocus pulse
t_diff1	Time between end of excitation and start of refocus pulse in ms
t_diff2	Total duration of pulse (with ramp-up and ramp-down) in ms
t_phase	angle of B0 with the z-direction (assumed in x-z plane)
theta_b0
time_done	Time from the excitation pulse till the end of the second readout in ms

from_dict

classmethod SimulatedShell.from_dict(kvs: Optional[Union[dict, list, str, int, float, bool]], *, infer_missing=False) → A

from_json

classmethod SimulatedShell.from_json(s: Union[str, bytes, bytearray], *, parse_float=None, parse_int=None, parse_constant=None, infer_missing=False, **kw) → A

schema

classmethod SimulatedShell.schema(*, infer_missing: bool = False, only=None, exclude=(), many: bool = False, context=None, load_only=(), dump_only=(), partial: bool = False, unknown=None) → dataclasses_json.mm.SchemaF[A]

spherical_harmonics

SimulatedShell.spherical_harmonics(lmax, odd=True)

to_dict

SimulatedShell.to_dict(encode_json=False) → Dict[str, Optional[Union[dict, list, str, int, float, bool]]]

to_json

SimulatedShell.to_json(*, skipkeys: bool = False, ensure_ascii: bool = True, check_circular: bool = True, allow_nan: bool = True, indent: Optional[Union[str, int]] = None, separators: Optional[Tuple[str, str]] = None, default: Optional[Callable] = None, sort_keys: bool = False, **kw) → str