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nabu.reconstruction.mlem

source module nabu.reconstruction.mlem

Classes

Functions

  • has_corrct — corrct will create a cuda context upon importing any module. On the other hand, python will crash if creating a subprocess when cuda is already initialized. So to check whether corrct is available, we do the "try import" in a subprocess

source class CCTMLEMReconstructor(data_vwu_shape, angles_rad, shifts_uv=None, cor=None, n_iterations=50, extra_options=None)

A reconstructor for MLEM reconstruction using the CorrCT toolbox.

Parameters

  • data_vwu_shape : tuple — Shape of the input data, expected to be (n_slices, n_angles, n_dets). Raises an error if the shape is not 3D.

  • angles_rad : numpy.ndarray — Angles in radians for the projections. Must match the second dimension of data_vwu_shape.

  • shifts_vu : numpy.ndarray, optional. — Shifts in the v and u directions for each angle. If provided, must have the same number of cols as angles_rad. Each col is (tv,tu)

  • cor : float, optional — Center of rotation, which will be adjusted based on the sinogram width.

  • n_iterations : int, optional — Number of iterations for the MLEM algorithm. Default is 50.

  • extra_options : dict, optional — Additional options for the reconstruction process. Default options include:

    • scale_factor (float, default is 1.0): Scale factor for the reconstruction.
    • compute_shifts (boolean, default is False): Whether to compute shifts.
    • tomo_consistency (boolean, default is False): Whether to enforce tomographic consistency.
    • v_min_for_v_shifts (number, default is 0): Minimum value for vertical shifts.
    • v_max_for_v_shifts (number, default is None): Maximum value for vertical shifts.
    • v_min_for_u_shifts (number, default is 0): Minimum value for horizontal shifts.
    • v_max_for_u_shifts (number, default is None): Maximum value for horizontal shifts.

Methods

  • reset_rot_center

  • reconstruct — data_align_vwu: numpy.ndarray or cupy array Raw data, with shape (n_sinograms, n_angles, width) output: optional Output array. If not provided, a new numpy array is returned

source method CCTMLEMReconstructor.reset_rot_center(cor)

source method CCTMLEMReconstructor.reconstruct(data_vwu, x0=None)

data_align_vwu: numpy.ndarray or cupy array Raw data, with shape (n_sinograms, n_angles, width) output: optional Output array. If not provided, a new numpy array is returned

source has_corrct(safe=True)

corrct will create a cuda context upon importing any module. On the other hand, python will crash if creating a subprocess when cuda is already initialized. So to check whether corrct is available, we do the "try import" in a subprocess

source class NabuMLEMReconstructor(sino_shape, slice_shape=None, angles=None, rot_center=None, halftomo=False, extra_options=None, cuda_options=None)

Methods

source method NabuMLEMReconstructor.reconstruct(sino, n_iterations=10, output=None, eps=1e-06)