nabu.reconstruction.sinogram

source module nabu.reconstruction.sinogram

Classes

• SinoBuilder — A class to build sinograms.

• SinoMult — A class for preparing a sinogram for half-tomography reconstruction, without stitching the two parts

• SinoNormalization — A class for sinogram normalization utilities.

Functions

• convert_halftomo — Converts a sinogram into a sinogram with extended FOV with the "half tomography" setting.

• match_half_sinos_parts — Modifies the lower part of the half-acquisition sinogram so that each projection pair is separated by exactly 180 degrees. This means that new_sino[k] and new_sino[k + n_angles//2] will be 180 degrees apart.

• get_extended_sinogram_width — Compute the width (in pixels) of the extended sinogram for half-acquisition setting.

• prepare_half_tomo_sinogram

source class SinoBuilder(sinos_shape=None, radios_shape=None, rot_center=None, halftomo=False, angles=None, interpolate=False)

A class to build sinograms.

Initialize a SinoBuilder instance.

Parameters

• sinos_shape : tuple of int — Shape of the stack of sinograms, in the form (n_z, n_angles, n_x). If not provided, it is derived from radios_shape.

• radios_shape : tuple of int — Shape of the chunk of radios, in the form (n_angles, n_z, n_x). If not provided, it is derived from sinos_shape.

• rot_center : int or array — Rotation axis position. A scalar indicates the same rotation axis position for all the projections.

• halftomo : bool — Whether "half tomography" is enabled. Default is False.

• interpolate : bool, optional — Only used if halftomo=True. Whether to re-grid the second part of sinograms to match projection k with projection k + n_a/2. This forces each pair of projection (k, k + n_a/2) to be separated by exactly 180 degrees.

• angles : array, optional — Rotation angles (in radians). Used and required only when halftomo and interpolate are True.

Attributes

• output_shape — Get the output sinograms shape.

Methods

• set_rot_center — Set the rotation axis position for the current radios/sinos stack.

• get_sino — The the sinogram at a given index.

• convert_sino

• get_sinos

• radios_to_sinos — DEPRECATED. Use get_sinos() or get_sino() instead.

source method SinoBuilder.set_rot_center(rot_center)

Set the rotation axis position for the current radios/sinos stack.

rot_center: int or array Rotation axis position. A scalar indicates the same rotation axis position for all the projections.

Raises

• ValueError

source property SinoBuilder.output_shape

Get the output sinograms shape.

source method SinoBuilder.get_sino(radios, i, output=None)

The the sinogram at a given index.

Parameters

• radios : array — 3D array with shape (n_z, n_angles, n_x)

• i : int — Sinogram index

Returns

• sino : array — Two dimensional array with shape (n_angles2, n_x2) where the dimensions are determined by the current settings.

source method SinoBuilder.convert_sino(sino, output=None)

source method SinoBuilder.get_sinos(radios, output=None)

source method SinoBuilder.radios_to_sinos(radios, output=None, copy=False)

DEPRECATED. Use get_sinos() or get_sino() instead.

source class SinoMult(sino_shape, rot_center)

A class for preparing a sinogram for half-tomography reconstruction, without stitching the two parts

Methods

• prepare_sino

source method SinoMult.prepare_sino(sino)

source convert_halftomo(sino, extended_width, transition_width=None)

Converts a sinogram into a sinogram with extended FOV with the "half tomography" setting.

source match_half_sinos_parts(sino, angles, output=None)

Modifies the lower part of the half-acquisition sinogram so that each projection pair is separated by exactly 180 degrees. This means that new_sino[k] and new_sino[k + n_angles//2] will be 180 degrees apart.

Parameters

• sino : numpy.ndarray — Two dimensional array with the sinogram in the form (n_angles, n_x)

• angles : numpy.ndarray — One dimensional array with the rotation angles.

• output : numpy.array, optional — Output sinogram. By default, the array 'sino' is modified in-place.

Notes

This function assumes that the angles are in an increasing order.

source get_extended_sinogram_width(sino_width, rotation_axis_position)

Compute the width (in pixels) of the extended sinogram for half-acquisition setting.

source prepare_half_tomo_sinogram(sino, rot_center, get_extended_sino=True)

source class SinoNormalization(kind='chebyshev', sinos_shape=None, radios_shape=None, normalization_array=None)

A class for sinogram normalization utilities.

Initialize a SinoNormalization class.

Parameters

• kind : str, optional — Normalization type. They can be the following: - chebyshev: Each sinogram line is estimated by a Chebyshev polynomial of degree 2. This estimation is then subtracted from the sinogram. - subtraction: Each sinogram is subtracted with a user-provided array. The array can be 1D (angle-independent) and 2D (angle-dependent) - division: same as previously, but with a division operation. Default is "chebyshev"

• sinos_shape : tuple, optional — Shape of the sinogram or sinogram stack. Either this parameter or 'radios_shape' has to be provided.

• radios_shape : tuple, optional — Shape of the projections or projections stack. Either this parameter or 'sinos_shape' has to be provided.

• normalization_array : numpy.ndarray, optional — Normalization array when kind='subtraction' or kind='division'.

Methods

• normalize — Normalize a sinogram or stack of sinogram. The process is done in-place, meaning that the sinogram content is overwritten.

source method SinoNormalization.normalize(sino)

Normalize a sinogram or stack of sinogram. The process is done in-place, meaning that the sinogram content is overwritten.