snake.toolkit.reconstructors.pysap

Reconstructors using PySAP-fMRI toolbox.

Module Contents

Classes

ZeroFilledReconstructor	Zero Filled Reconstructor.
RestartStrategy	Restart strategies for the reconstruction.
SequentialReconstructor	Use a sequential Reconstruction.

Functions

_reconstruct_cartesian_frame

Reconstruct a single frame.

API

snake.toolkit.reconstructors.pysap._reconstruct_cartesian_frame(filename: os.PathLike, idx: int, smaps_props: snake.core.parallel.ArrayProps | None, final_props: snake.core.parallel.ArrayProps) → int

Reconstruct a single frame.

class snake.toolkit.reconstructors.pysap.ZeroFilledReconstructor

Bases: snake.toolkit.reconstructors.base.BaseReconstructor

Zero Filled Reconstructor.

__reconstructor_name__ = 'adjoint'

n_jobs: int = 10

nufft_backend: str = 'gpunufft'

density_compensation: str | bool = 'pipe'

setup(sim_conf: snake.core.simulation.SimConfig) → None

Initialize Reconstructor.

reconstruct(data_loader: snake.mrd_utils.MRDLoader, sim_conf: snake.core.simulation.SimConfig = None) → numpy.typing.NDArray

Reconstruct data with zero-filled method.

_reconstruct_cartesian(data_loader: snake.mrd_utils.CartesianFrameDataLoader) → numpy.typing.NDArray

_reconstruct_nufft(data_loader: snake.mrd_utils.NonCartesianFrameDataLoader) → numpy.typing.NDArray

Reconstruct data with nufft method.

class snake.toolkit.reconstructors.pysap.RestartStrategy

Bases: snake._meta.NoCaseEnum

Restart strategies for the reconstruction.

WARM = 'warm'

COLD = 'cold'

REFINE = 'refine'

class snake.toolkit.reconstructors.pysap.SequentialReconstructor

Bases: snake.toolkit.reconstructors.base.BaseReconstructor

Use a sequential Reconstruction.

Parameters:

• max_iter_frame – Number of iteration to allow per frame.

• optimizer – Optimizer name, available are pogm and fista.

• threshold – Threshold value for the wavelet regularisation.

__reconstructor_name__ = 'sequential'

max_iter_per_frame: int = 15

optimizer: str = 'pogm'

wavelet: str = 'db4'

threshold: float | str = 'sure'

nufft_backend: str = 'gpunufft'

density_compensation: str | bool = 'pipe'

restart_strategy: snake.toolkit.reconstructors.pysap.RestartStrategy = None

compute_backend: str = 'cupy'

__str__() → str

Return a string representation of the reconstructor.

setup(sim_conf: snake.core.simulation.SimConfig = None, shape: tuple[int] = None) → None

Set up the reconstructor.

reconstruct(data_loader: snake.mrd_utils.MRDLoader) → numpy.ndarray

Reconstruct with Sequential.

_reconstruct_frame(grad_op: Any, x_init: numpy.typing.NDArray, n_iter: int = 15, progbar: tqdm.auto.tqdm | None = None) → numpy.typing.NDArray