SIRT3D_CUDA

This is a GPU implementation of the SIRT algorithm for 3D data sets. It takes projection data and an initial reconstruction as input, and returns the reconstruction after a specified number of SIRT iterations.

Supported geometries: all 3D geometries.

Configuration options

Name	Description
ProjectionDataId	Projection data object ID.
ReconstructionDataId	ID of data object to store the result. The content of this data is used as the initial reconstruction.
option.MinConstraint	If specified, all values below MinConstraint will be set to MinConstraint. This can, for example, be used to enforce non-negative reconstructions.
option.MaxConstraint	If specified, all values above MaxConstraint will be set to MaxConstraint.
option.SinogramMaskId	If specified, data object ID of a projection-data-sized volume to be used as a mask.
option.ReconstructionMaskId	If specified, data object ID of a volume-data-sized volume to be used as a mask.
option.DetectorSuperSampling	During forward projection, each detector pixel will be subdivided by this factor along each dimension. This should only be used if detector pixels are larger than the voxels in the volume (default: 1).
option.VoxelSuperSampling	During backprojection, each voxel in the volume will be subdivided by this factor along each dimension. This should only be used if voxels in the volume are larger than the detector pixels (default: 1).
option.GPUindex	The index of the GPU to use (default: 0).

Example

import astra
import matplotlib.pyplot as plt
import numpy as np

# Create geometries
N = 256
N_ANGLES = 180
det_spacing = 1.0
angles = np.linspace(0, np.pi, N_ANGLES)
proj_geom = astra.create_proj_geom('parallel3d', det_spacing, det_spacing, N, N, angles)
vol_geom = astra.create_vol_geom(N, N, N)

# Generate phantom image
phantom_id, phantom = astra.data3d.shepp_logan(vol_geom)

# Create forward projection
sinogram_id, sinogram = astra.create_sino3d_gpu(phantom_id, proj_geom, vol_geom)

# Reconstruct
recon_id = astra.data3d.create('-vol', vol_geom)
cfg = astra.astra_dict('SIRT3D_CUDA')
cfg['ProjectionDataId'] = sinogram_id
cfg['ReconstructionDataId'] = recon_id
cfg['option'] = {'MinConstraint': 0.0}
algorithm_id = astra.algorithm.create(cfg)

astra.algorithm.run(algorithm_id, iterations=100)

reconstruction = astra.data3d.get(recon_id)
plt.imshow(reconstruction[N//2], cmap='gray')

# Clean up
astra.data3d.delete([sinogram_id, recon_id, phantom_id])
astra.algorithm.delete(algorithm_id)

%% Create phantom
N = 256;
phantom_ = repmat(phantom(N), [1, 1, N]);

%% Create geometries
det_spacing = 1.0;
N_ANGLES = 180;
angles = linspace(0, pi, N_ANGLES);
proj_geom = astra_create_proj_geom('parallel3d', det_spacing, det_spacing, N, N, angles);
vol_geom = astra_create_vol_geom(N, N, N);

%% Create forward projection
[sinogram_id, sinogram] = astra_create_sino3d_cuda(phantom_, proj_geom, vol_geom);

%% Reconstruct
recon_id = astra_mex_data3d('create', '-vol', vol_geom);
cfg = astra_struct('SIRT3D_CUDA');
cfg.ProjectionDataId = sinogram_id;
cfg.ReconstructionDataId = recon_id;
cfg.option.MinConstraint = 0.0;
algorithm_id = astra_mex_algorithm('create', cfg);

astra_mex_algorithm('iterate', algorithm_id, 100);

reconstruction = astra_mex_data3d('get', recon_id);
imshow(reconstruction(:, :, N/2), []);

%% Clean up
astra_mex_data3d('delete', sinogram_id, recon_id);
astra_mex_algorithm('delete', algorithm_id);

Extra features

SIRT3D_CUDA supports astra.algorithm.get_res_norm() / astra_mex_algorithm('get_res_norm') command to get the 2-norm of the residual for the reconstruction (the square root of the sum of squares of differences between the input and the projection of the result).