`corrct._projector_backends`

Tomographic projector backends.

@author: Nicola VIGANÒ, Computational Imaging group, CWI, The Netherlands, and ESRF - The European Synchrotron, Grenoble, France

Module Contents

Classes

`ProjectorBackend`	Base abstract projector backend class. All backends should inherit from this class.
`ProjectorBackendSKimage`	Projector backend based on scikit-image.
`ProjectorBackendASTRA`	Projector backend based on astra-toolbox.
`ProjectorBackendDirectASTRA`	Experimental astra-toolbox functions projector.

Functions

compute_attenuation

Compute the attenuation volume for the given local attenuation, and angle.

API

corrct._projector_backends.compute_attenuation(vol: numpy.typing.NDArray, angle_rad: float, invert: bool = False) → numpy.typing.NDArray[source]

Compute the attenuation volume for the given local attenuation, and angle.

Parameters

vol : NDArray The local attenuation volume. angle_rad : float The angle along which to compute the attenuation. invert : bool, optional Whether to invert propagation direction. The default is False.

Returns

NDArray The attenuation volume.

class corrct._projector_backends.ProjectorBackend[source]

Bases: abc.ABC

Base abstract projector backend class. All backends should inherit from this class.

Initialization

Initialize base abstract projector backend class.

vol_geom: corrct.models.VolumeGeometry: None

vol_shape_zxy: numpy.typing.NDArray[numpy.integer]: None

angles_w_rad: numpy.typing.NDArray[numpy.floating]: None

prj_shape_vwu: numpy.typing.NDArray[numpy.integer]: None

prj_shape_vu: numpy.typing.NDArray[numpy.integer]: None

is_initialized: bool: None

is_ready: bool: None

initialize_geometry(vol_geom: corrct.models.VolumeGeometry, angles_rot_rad: Union[numpy.typing.ArrayLike, numpy.typing.NDArray], rot_axis_shift_pix: Union[numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, prj_geom: Optional[corrct.models.ProjectionGeometry] = None, create_single_projs: bool = False)[source]

Initialize the projector geometry.

Parameters

vol_geom : VolumeGeometry The volume geometry. angles_rot_rad : ArrayLike | NDArray The projection angles. rot_axis_shift_pix : float | NDArray | None, optional Relative position of the rotation center with respect to the volume center. The default is None. prj_geom : ProjectionGeometry, optional The fully specified projection geometry. When active, the rotation axis shift is ignored. The default is None. create_single_projs : bool, optional Whether to create projectors for single projections. Used for corrections and SART. The default is False.

get_vol_shape() → numpy.typing.NDArray[source]

Return the expected and produced volume shape (in ZXY coordinates).

Returns

NDArray The volume shape.

get_prj_shape() → numpy.typing.NDArray[source]

Return the expected and produced projection shape (in VWU coordinates).

Returns

NDArray The projection shape.

make_ready() → None[source]

Initialize the projector.

It should make sure that all the resources have been allocated.

dispose() → None[source]

De-initialize the projector.

It should make sure that all the resources have been de-allocated.

__del__()[source]: De-initialize projector on deletion.

__repr__() → str[source]

Build a string representation of the projector backend.

Returns

str The representation of the projector.

abstract fp(vol: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Forward-project volume.

Forward-projection interface. Derived backends need to implement this method.

Parameters

vol : NDArray The volume to forward-project. angle_ind : int, optional The angle index to foward project. The default is None.

abstract bp(prj: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Back-project data.

Back-projection interface. Derived backends need to implement this method.

Parameters

prj : NDArray The sinogram to back-project or a single line. angle_ind : int, optional The angle index to foward project. The default is None.

class corrct._projector_backends.ProjectorBackendSKimage[source]

Bases: corrct._projector_backends.ProjectorBackend

Projector backend based on scikit-image.

Initialization

Initialize scikit-image projector backend class.

initialize_geometry(vol_geom: corrct.models.VolumeGeometry, angles_rot_rad: Union[numpy.typing.ArrayLike, numpy.typing.NDArray], rot_axis_shift_pix: Union[numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, prj_geom: Optional[corrct.models.ProjectionGeometry] = None, create_single_projs: bool = False)[source]

Initialize projector backend based on scikit-image.

Parameters

vol_geom : VolumeGeometry The volume shape. angles_rot_rad : ArrayLike The projection angles. rot_axis_shift_pix : float | NDArray | None, optional Relative position of the rotation center with respect to the volume center. The default is None. NOT SUPPORTED: if anything else than None is passed, it will throw an error! prj_geom : ProjectionGeometry, optional The fully specified projection geometry. When active, the rotation axis shift is ignored. The default is None. NOT SUPPORTED: if anything else than None is passed, it will throw an error! create_single_projs : bool, optional Whether to create projectors for single projections. Used for corrections and SART. The default is False.

Raises

ValueError In case the volume dimensionality is larger than 2D, and if a rotation axis shift is passed.

static _set_filter_name(filt)[source]

static _set_bpj_size(output_size)[source]

fp(vol: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Forward-projection of the volume to the sinogram or a single sinogram line.

Parameters

vol : NDArray The volume to forward-project. angle_ind : int, optional The angle index to foward project. The default is None.

Returns

NDArray The forward-projected sinogram or sinogram line.

bp(prj: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Back-projection of a single sinogram line to the volume.

Parameters

prj : NDArray The sinogram to back-project or a single line. angle_ind : int, optional The angle index to foward project. The default is None.

Returns

NDArray The back-projected volume.

class corrct._projector_backends.ProjectorBackendASTRA(super_sampling: int = 1)[source]

Bases: corrct._projector_backends.ProjectorBackend

Projector backend based on astra-toolbox.

Initialization

Initialize the ASTRA projector backend.

Parameters

super_sampling : int, optional Super sampling factor for the pixels and voxels, by default 1.

proj_id: List: None

astra_vol_geom: Mapping: None

proj_geom_ind: Sequence[Mapping]: None

proj_geom_all: Mapping: None

initialize_geometry(vol_geom: corrct.models.VolumeGeometry, angles_rot_rad: Union[numpy.typing.ArrayLike, numpy.typing.NDArray], rot_axis_shift_pix: Union[numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, prj_geom: Optional[corrct.models.ProjectionGeometry] = None, create_single_projs: bool = False)[source]

Initialize geometry of projector backend based on astra-toolbox.

Parameters

vol_geom : VolumeGeometry The volume shape. angles_rot_rad : ArrayLike The projection angles. rot_axis_shift_pix : float | NDArray | None, optional Relative position of the rotation center with respect to the volume center. The default is None. prj_geom : ProjectionGeometry, optional The fully specified projection geometry. When active, the rotation axis shift is ignored. The default is None. create_single_projs : bool, optional Whether to create projectors for single projections. Used for corrections and SART. The default is False.

Raises

ValueError In case the volume dimensionality is larger than 2D and CUDA is not available.

make_ready() → None[source]: Initialize the ASTRA projectors.

_check_data(x: numpy.typing.NDArray, expected_shape: Union[Sequence[int], numpy.typing.NDArray[numpy.integer]]) → numpy.typing.NDArray[source]

_check_prj_shape(prj: numpy.typing.NDArray) → None[source]

dispose() → None[source]: De-initialize the ASTRA projectors.

fp(vol: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Apply forward-projection of the volume to the sinogram or a single sinogram line.

Parameters

vol : NDArray The volume to forward-project. angle_ind : int | None, optional The angle index to forward project. The default is None.

Returns

NDArray The forward-projected sinogram or sinogram line.

bp(prj: numpy.typing.NDArray, angle_ind: Optional[int] = None) → numpy.typing.NDArray[source]

Apply back-projection of a single sinogram line to the volume.

Parameters

prj : NDArray The sinogram to back-project or a single line. angle_ind : int | None, optional The angle index to forward project. The default is None.

Returns

NDArray The back-projected volume.

class corrct._projector_backends.ProjectorBackendDirectASTRA(super_sampling: int = 1)[source]

Bases: corrct._projector_backends.ProjectorBackendASTRA

Experimental astra-toolbox functions projector.

Initialization

Initialize the ASTRA projector backend.

Parameters

super_sampling : int, optional Super sampling factor for the pixels and voxels, by default 1.

astra_vol_shape: Sequence: None

astra_prj_shape: Sequence: None

astra_angle_prj_shape: Sequence: None

angle_prj_shape: Sequence: None

initialize_geometry(vol_geom: corrct.models.VolumeGeometry, angles_rot_rad: Union[numpy.typing.ArrayLike, numpy.typing.NDArray], rot_axis_shift_pix: Union[numpy.typing.ArrayLike, numpy.typing.NDArray, None] = None, prj_geom: Optional[corrct.models.ProjectionGeometry] = None, create_single_projs: bool = False)[source]

Initialize projector backend based on experimental astra-toolbox functions.

Parameters

vol_geom : VolumeGeometry The volume shape. angles_rot_rad : ArrayLike The projection angles. rot_axis_shift_pix : float, optional Relative position of the rotation center with respect to the volume center. The default is 0.0. geom : ProjectionGeometry, optional The fully specified projection geometry. When active, the rotation axis shift is ignored. The default is None. create_single_projs : bool, optional Whether to create projectors for single projections. Used for corrections and SART. The default is False.

Raises

ValueError In case CUDA is not available.

make_ready()[source]: Initialize the ASTRA projectors.

fp(vol: numpy.typing.NDArray, angle_ind: Optional[int] = None)[source]

Apply forward-projection of the volume to the sinogram or a single sinogram line.

Parameters

vol : NDArray The volume to forward-project. angle_ind : int | None, optional The angle index to forward project. The default is None.

Returns

NDArray The forward-projected sinogram or sinogram line.

bp(prj: numpy.typing.NDArray, angle_ind: Optional[int] = None)[source]

Apply back-projection of a single sinogram line to the volume.

Parameters

prj : NDArray The sinogram to back-project or a single line. angle_ind : int | None, optional The angle index to forward project. The default is None.

Returns

NDArray The back-projected volume.

corrct._projector_backends

Module Contents

Classes

Functions

API

`corrct._projector_backends`