tomopy.sim.project

Module for simulation of x-rays.

Functions:

angles(nang[, ang1, ang2])

Return uniformly distributed projection angles in radian.

project(obj, theta[, center, emission, pad, ...])

Project x-rays through a given 3D object.

fan_to_para(tomo, dist, geom)

Convert fan-beam data to parallel-beam data.

para_to_fan(tomo, dist, geom)

Convert parallel-beam data to fan-beam data.

add_gaussian(tomo[, mean, std])

Add Gaussian noise.

add_poisson(tomo)

Add Poisson noise.

add_salt_pepper(tomo[, prob, val])

Add salt and pepper noise.

add_focal_spot_blur(tomo, spotsize)

Add focal spot blur.
tomopy.sim.project.add_drift(tomo, amp=0.2, period=50, mean=1)[source]

Add illumination drift.

Illumination drift is caused by the beam instability as the object rotates.

This drift is modeled using a sinusoid. Which alters the illumination along the rotation dimension. The vertical dimension is constant.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • amp (float) – The amplitude of the drift.

  • period (float) – The period of the drift.

Returns

ndarray – Tomographic data with zingers added.

tomopy.sim.project.add_focal_spot_blur(tomo, spotsize)[source]

Add focal spot blur.

Warning

Not implemented yet.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • spotsize (float) – Focal spot size of circular x-ray source.

tomopy.sim.project.add_gaussian(tomo, mean=0, std=None)[source]

Add Gaussian noise.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • mean (float, optional) – Mean of the Gaussian distribution.

  • std (float, optional) – Standard deviation of the Gaussian distribution.

Returns

ndarray – 3D tomographic data after Gaussian noise added.

tomopy.sim.project.add_poisson(tomo)[source]

Add Poisson noise.

Parameters

tomo (ndarray) – 3D tomographic data.

Returns

ndarray – 3D tomographic data after Poisson noise added.

tomopy.sim.project.add_rings(tomo, std=0.05)[source]

Add rings.

Rings are caused by inconsistent pixel sensitivity across the detector.

The sensitivity of the pixels is modeled as normally distributed with an average sensitivity of 1 and a standard deviation given.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • std (float) – The standard deviation of the pixel sensitivity

Returns

ndarray – Tomographic data with zingers added.

tomopy.sim.project.add_salt_pepper(tomo, prob=0.01, val=None)[source]

Add salt and pepper noise.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • prob (float, optional) – Independent probability that each element of a pixel might be corrupted by the salt and pepper type noise.

  • val (float, optional) – Value to be assigned to the corrupted pixels.

Returns

ndarray – 3D tomographic data after salt and pepper noise added.

tomopy.sim.project.add_zingers(tomo, f=0.01, sat=65536)[source]

Add zingers.

Zingers are caused by stray X-rays hitting the detector and causing pixels to saturate.

The zingers are uniformly distributed across the data set with the given frequency.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • f (float) – The fraction of measurements that are zingers.

  • sat (float) – The pixel saturation value.

Returns

ndarray – Tomographic data with zingers added.

tomopy.sim.project.angles(nang, ang1=0.0, ang2=180.0)[source]

Return uniformly distributed projection angles in radian.

Parameters

  • nang (int, optional) – Number of projections.

  • ang1 (float, optional) – First projection angle in degrees.

  • ang2 (float, optional) – Last projection angle in degrees.

Returns

array – Projection angles

tomopy.sim.project.fan_to_para(tomo, dist, geom)[source]

Convert fan-beam data to parallel-beam data.

Warning

Not implemented yet.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • dist (float) – Distance from fan-beam vertex to rotation center.

  • geom (str) – Fan beam geometry. ‘arc’ or ‘line’.

Returns

ndarray – Transformed 3D tomographic data.

tomopy.sim.project.para_to_fan(tomo, dist, geom)[source]

Convert parallel-beam data to fan-beam data.

Warning

Not implemented yet.

Parameters

  • tomo (ndarray) – 3D tomographic data.

  • dist (float) – Distance from fan-beam vertex to rotation center.

  • geom (str) – Fan beam geometry. ‘arc’ or ‘line’.

Returns

ndarray – Transformed 3D tomographic data.

tomopy.sim.project.project(obj, theta, center=None, emission=True, pad=True, sinogram_order=False, ncore=None, nchunk=None)[source]

Project x-rays through a given 3D object.

Parameters

  • obj (ndarray) – Voxelized 3D object.

  • theta (array) – Projection angles in radian.

  • center (array, optional) – Location of rotation axis.

  • emission (bool, optional) – Determines whether output data is emission or transmission type.

  • pad (bool, optional) – Determines if the projection image width will be padded or not. If True, then the diagonal length of the object cross-section will be used for the output size of the projection image width.

  • sinogram_order (bool, optional) – Determines whether output data is a stack of sinograms (True, y-axis first axis) or a stack of radiographs (False, theta first axis).

  • ncore (int, optional) – Number of cores that will be assigned to jobs.

  • nchunk (int, optional) – Chunk size for each core.

Returns

ndarray – 3D tomographic data.

tomopy.sim.project.project2(objx, objy, theta, center=None, emission=True, pad=True, sinogram_order=False, axis=0, ncore=None, nchunk=None)[source]

Project x-rays through a given 3D object.

Parameters

  • objx (ndarray) – (x, y) components of vector of a voxelized 3D object.

  • theta (array) – Projection angles in radian.

  • center (array, optional) – Location of rotation axis.

  • emission (bool, optional) – Determines whether output data is emission or transmission type.

  • pad (bool, optional) – Determines if the projection image width will be padded or not. If True, then the diagonal length of the object cross-section will be used for the output size of the projection image width.

  • sinogram_order (bool, optional) – Determines whether output data is a stack of sinograms (True, y-axis first axis) or a stack of radiographs (False, theta first axis).

  • ncore (int, optional) – Number of cores that will be assigned to jobs.

  • nchunk (int, optional) – Chunk size for each core.

Returns

ndarray – 3D tomographic data.

tomopy.sim.project.project3(objx, objy, objz, theta, center=None, emission=True, pad=True, sinogram_order=False, axis=0, ncore=None, nchunk=None)[source]

Project x-rays through a given 3D object.

Parameters

  • objx (ndarray) – (x, y) components of vector of a voxelized 3D object.

  • theta (array) – Projection angles in radian.

  • center (array, optional) – Location of rotation axis.

  • emission (bool, optional) – Determines whether output data is emission or transmission type.

  • pad (bool, optional) – Determines if the projection image width will be padded or not. If True, then the diagonal length of the object cross-section will be used for the output size of the projection image width.

  • sinogram_order (bool, optional) – Determines whether output data is a stack of sinograms (True, y-axis first axis) or a stack of radiographs (False, theta first axis).

  • ncore (int, optional) – Number of cores that will be assigned to jobs.

  • nchunk (int, optional) – Chunk size for each core.

Returns

ndarray – 3D tomographic data.