corrct.projectors
Tomographic projectors.
@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France
Module Contents
Classes
Projector that uses an explicit projection matrix. |
|
Base projection class. |
|
Attenuation corrected projection class for XRF, with multi-detector support. |
Data
API
- corrct.projectors.num_threads
‘round(…)’
- corrct.projectors.astra_available
None
- class corrct.projectors.ProjectorMatrix(A: Union[numpy.typing.NDArray, scipy.sparse.spmatrix], vol_shape: numpy.typing.ArrayLike, prj_shape: numpy.typing.ArrayLike)[source]
Bases:
corrct.operators.ProjectorOperatorProjector that uses an explicit projection matrix.
Initialization
Initialize the matrix projector.
Parameters
A : NDArray | spmatrix The projection matrix. vol_shape : ArrayLike Volume shape. prj_shape : ArrayLike Projection shape.
- A: Union[numpy.typing.NDArray, scipy.sparse.spmatrix]
None
- _transpose() corrct.operators.ProjectorOperator[source]
Create the transpose operator.
Returns
operators.ProjectorOperator The transpose operator.
- absolute() corrct.operators.ProjectorOperator[source]
Return the projection operator using the absolute value of the projection coefficients.
Returns
operators.ProjectorOperator The absolute value operator.
- class corrct.projectors.ProjectorUncorrected(vol_geom: typing.Union[collections.abc.Sequence[int], numpy.typing.NDArray[numpy.integer], corrct.models.VolumeGeometry], angles_rot_rad: typing.Union[collections.abc.Sequence[float], numpy.typing.NDArray], rot_axis_shift_pix: typing.Union[float, numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, *, prj_geom: typing.Optional[corrct.models.ProjectionGeometry] = None, prj_intensities: typing.Optional[numpy.typing.ArrayLike] = None, psf: typing.Optional[numpy.typing.ArrayLike] = None, backend: typing.Union[str, corrct._projector_backends.ProjectorBackend] = 'astra' if astra_available else 'skimage', create_single_projs: bool = False)[source]
Bases:
corrct.operators.ProjectorOperatorBase projection class.
Initialization
Initialize the base projection class.
It implements the forward and back projection of the single lines of a sinogram. It takes care of initializing and disposing the ASTRA projectors when used in a with statement. It supports both 2D and 3D geometries.
Parameters
vol_geom : Sequence[int] | NDArray[np.integer] | models.VolumeGeometry The volume shape in Y X and optionally Z. angles_rot_rad : Sequence[float] | NDArray The rotation angles. rot_axis_shift_pix : float | ArrayLike | NDArray, optional The rotation axis shift(s) in pixels, by default None. prj_geom : models.ProjectionGeometry | None, optional The fully specified projection geometry. When active, the rotation axis shift is ignored, by default None. prj_intensities : ArrayLike | NDArray | None, optional Projection scaling factor, by default None. psf : ArrayLike | NDArray | None, optional The “point spread function” of the detector, by default None. backend : bool, optional Whether to use ASTRA or fall back to scikit-image. The default is True if CUDA and ASTRA are available, otherwise False. create_single_projs : bool, optional Whether to create projectors for single projections. Used for corrections and SART, by default False.
Raises
ValueError When the geometry is not correct.
- vol_geom: corrct.models.VolumeGeometry
None
- projector_backend: corrct._projector_backends.ProjectorBackend
None
- prj_intensities: Union[numpy.typing.NDArray[numpy.floating], None]
None
- psf: Union[numpy.typing.NDArray[numpy.floating], float, None]
None
- property angles_rot_rad: numpy.typing.NDArray
Simplify access to the rotation angles (in radians).
Returns
NDArray The rotation angles (in radians).
- get_pre_weights() Union[numpy.typing.NDArray, None][source]
Compute the pre-weights of the projector geometry (notably for cone-beam geometries).
Returns
Union[NDArray, None] The computed detector weights
- fp_angle(vol: numpy.typing.NDArray, angle_ind: int) numpy.typing.NDArray[source]
Forward-project a volume to a single sinogram line.
Parameters
vol : NDArray The volume to forward-project. angle_ind : int The angle index to forward project.
Returns
x : NDArray The forward-projected sinogram line.
- bp_angle(prj_vu: numpy.typing.NDArray, angle_ind: int) numpy.typing.NDArray[source]
Back-project a single sinogram line to the volume.
Parameters
prj_vu : NDArray The sinogram to back-project or a single line. angle_ind : int The angle index to forward project.
Returns
NDArray The back-projected volume.
- class corrct.projectors.ProjectorAttenuationXRF(vol_geom: typing.Union[collections.abc.Sequence[int], numpy.typing.NDArray[numpy.integer], corrct.models.VolumeGeometry], angles_rot_rad: typing.Union[collections.abc.Sequence[float], numpy.typing.NDArray], rot_axis_shift_pix: typing.Union[float, numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, *, prj_geom: typing.Optional[corrct.models.ProjectionGeometry] = None, prj_intensities: typing.Optional[numpy.typing.ArrayLike] = None, backend: typing.Union[str, corrct._projector_backends.ProjectorBackend] = 'astra' if astra_available else 'skimage', att_maps: typing.Optional[numpy.typing.NDArray[numpy.floating]] = None, att_in: typing.Optional[numpy.typing.NDArray[numpy.floating]] = None, att_out: typing.Optional[numpy.typing.NDArray[numpy.floating]] = None, angles_detectors_rad: typing.Union[float, numpy.typing.ArrayLike] = np.pi / 2, weights_detectors: typing.Optional[numpy.typing.ArrayLike] = None, psf: typing.Optional[numpy.typing.ArrayLike] = None, is_symmetric: bool = False, weights_angles: typing.Optional[numpy.typing.ArrayLike] = None, use_multithreading: bool = True, data_type: numpy.typing.DTypeLike = np.float32, verbose: bool = True)[source]
Bases:
corrct.projectors.ProjectorUncorrectedAttenuation corrected projection class for XRF, with multi-detector support.
It includes the computation of the attenuation volumes.
Initialization
Initialize the (attenuation corrected) XRF dedicated projector.
Parameters
vol_geom : Sequence[int] | NDArray[np.integer] | models.VolumeGeometry The volume shape in X Y and optionally Z. angles_rot_rad : Sequence[float] | NDArray The rotation angles. rot_axis_shift_pix : float | ArrayLike | NDArray | None, optional The rotation axis shift(s) in pixels. The default is None. prj_geom : Optional[models.ProjectionGeometry], optional The fully specified projection geometry. When active, the rotation axis shift is ignored. The default is None. prj_intensities : Optional[ArrayLike], optional Projection scaling factor. The default is None. backend : str | prj_backends.ProjectorBackend, optional Projector backend to use, by default “astra” if astra is available, otherwise “skimage”. att_maps : Optional[NDArray[np.floating]], optional Precomputed attenuation maps for each angle, by default None att_in : Optional[ArrayLike], optional Attenuation volume of the incoming beam. The default is None. att_out : Optional[ArrayLike], optional Attenuation volume of the outgoing beam. The default is None. angles_detectors_rad : float | ArrayLike, optional Angles of the detector elements with respect to incident beam. The default is (np.pi / 2). weights_detectors : Optional[ArrayLike], optional Weights (e.g. solid angle, efficiency, etc) of the detector elements. The default is None. psf : Optional[ArrayLike], optional Optical system’s point spread function (PSF). The default is None. is_symmetric : bool, optional Whether the projector is symmetric or not. The default is False. weights_angles : Optional[ArrayLike], optional Projection weight for a given element at a given angle. The default is None. use_multithreading : bool, optional Whether to use multiple threads or not. The default is True. data_type : DTypeLike, optional Output data type. The default is np.float32. verbose : bool, optional Whether to produce verbose output. The default is True.
Raises
ValueError When given inconsistent numbers of detector weights and detector angles.
- att_vol_angles: numpy.typing.NDArray[numpy.floating]
None
- executor: Union[concurrent.futures.ThreadPoolExecutor, None]
None
- fp_angle(vol: numpy.typing.NDArray, angle_ind: int) numpy.typing.NDArray[source]
Forward-project the volume to a single sinogram line.
It applies the attenuation corrections.
Parameters
vol : NDArray The volume to forward-project. angle_ind : int The angle index to forward project.
Returns
sino_line : NDArray The forward-projected sinogram line.
- bp_angle(sino: numpy.typing.NDArray, angle_ind: int, single_line: bool = False) numpy.typing.NDArray[source]
Back-project a single sinogram line to the volume.
It only applies the attenuation corrections if the projector is symmetric.
Parameters
sino : NDArray The sinogram to back-project or a single line. angle_ind : int The angle index to forward project. single_line : bool, optional Whether the input is a single sinogram line. The default is False.
Returns
NDArray The back-projected volume.