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%OPTOMO Wrapper for ASTRA tomography projector
%
% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM) generates a Spot operator OP for
% the ASTRA forward and backprojection operations. The string TYPE
% determines the model used for the projections. Possible choices are:
% TYPE: * using the CPU
% 'line' - use a line kernel
% 'linear' - use a Joseph kernel
% 'strip' - use the strip kernel
% * using the GPU
% 'cuda' - use a Joseph kernel, on the GPU, currently using
% 'cuda' is the only option in 3D.
% The PROJ_GEOM and VOL_GEOM structures are projection and volume
% geometries as used in the ASTRA toolbox.
%
% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM, GPU_INDEX) also specify the
% index of the GPU that should be used, if multiple GPUs are present in
% the host system. By default GPU_INDEX is 0.
%
% Note: this code depends on the Matlab toolbox
% "Spot - A Linear-Operator Toolbox" which can be downloaded from
% http://www.cs.ubc.ca/labs/scl/spot/
%--------------------------------------------------------------------------
% This file is part of the ASTRA Toolbox
%
% Copyright: 2010-2018, imec Vision Lab, University of Antwerp
% 2014-2018, CWI, Amsterdam
% License: Open Source under GPLv3
% Contact: astra@astra-toolbox.com
% Website: http://www.astra-toolbox.com/
%--------------------------------------------------------------------------
classdef opTomo < opSpot
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Properties
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
properties ( Access = private )
% multiplication function
funHandle
% ASTRA identifiers
sino_id
vol_id
fp_alg_id
bp_alg_id
proj_id
% ASTRA IDs handle
astra_handle
end % properties
properties ( SetAccess = private, GetAccess = public )
proj_size
vol_size
proj_geom
vol_geom
end % properties
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Methods - public
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
methods
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% opTomo - constructor
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function op = opTomo(type, proj_geom, vol_geom, gpu_index)
if nargin < 4 || isempty(gpu_index), gpu_index = 0; end
proj_size = astra_geom_size(proj_geom);
vol_size = astra_geom_size(vol_geom);
% construct operator
op = op@opSpot('opTomo', prod(proj_size), prod(vol_size));
% determine the dimension
is2D = ~isfield(vol_geom, 'GridSliceCount');
gpuEnabled = strcmpi(type, 'cuda');
if is2D
% create a projector
proj_id = astra_create_projector(type, proj_geom, vol_geom);
% create a function handle
op.funHandle = @opTomo_intrnl2D;
% Initialize ASTRA data objects.
% projection data
sino_id = astra_mex_data2d('create', '-sino', proj_geom, 0);
% image data
vol_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
% Setup forward and back projection algorithms.
if gpuEnabled
fp_alg = 'FP_CUDA';
bp_alg = 'BP_CUDA';
else
fp_alg = 'FP';
bp_alg = 'BP';
end
% configuration for ASTRA fp algorithm
cfg_fp = astra_struct(fp_alg);
cfg_fp.ProjectorId = proj_id;
cfg_fp.ProjectionDataId = sino_id;
cfg_fp.VolumeDataId = vol_id;
% configuration for ASTRA bp algorithm
cfg_bp = astra_struct(bp_alg);
cfg_bp.ProjectionDataId = sino_id;
cfg_bp.ProjectorId = proj_id;
cfg_bp.ReconstructionDataId = vol_id;
% set GPU index
if gpuEnabled
cfg_fp.option.GPUindex = gpu_index;
cfg_bp.option.GPUindex = gpu_index;
end
fp_alg_id = astra_mex_algorithm('create', cfg_fp);
bp_alg_id = astra_mex_algorithm('create', cfg_bp);
% Create handle to ASTRA objects, so they will be deleted
% if opTomo is deleted.
op.astra_handle = opTomo_helper_handle([sino_id, ...
vol_id, proj_id, fp_alg_id, bp_alg_id]);
op.fp_alg_id = fp_alg_id;
op.bp_alg_id = bp_alg_id;
op.sino_id = sino_id;
op.vol_id = vol_id;
else
% 3D
% only gpu/cuda code for 3D
if ~gpuEnabled
error(['Only type ' 39 'cuda' 39 ' is supported ' ...
'for 3D geometries.'])
end
% setup projector
cfg = astra_struct('cuda3d');
cfg.ProjectionGeometry = proj_geom;
cfg.VolumeGeometry = vol_geom;
cfg.option.GPUindex = gpu_index;
% create projector
op.proj_id = astra_mex_projector3d('create', cfg);
% create handle to ASTRA object, for cleaning up
op.astra_handle = opTomo_helper_handle(op.proj_id);
% create a function handle
op.funHandle = @opTomo_intrnl3D;
end
% pass object properties
op.proj_size = proj_size;
op.vol_size = vol_size;
op.cflag = false;
op.sweepflag = false;
op.proj_geom = proj_geom;
op.vol_geom = vol_geom;
end % opTomo - constructor
end % methods - public
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Methods - protected
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
methods( Access = protected )
% multiplication
function y = multiply(op,x,mode)
% ASTRA cannot handle sparse vectors
if issparse(x)
x = full(x);
end
if isa(x, 'double')
isdouble = true;
x = single(x);
else
isdouble = false;
end
% the multiplication
y = op.funHandle(op, x, mode);
% make sure output is column vector
y = y(:);
if isdouble
y = double(y);
end
end % multiply
end % methods - protected
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Methods - private
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
methods( Access = private )
% 2D projection code
function y = opTomo_intrnl2D(op,x,mode)
if mode == 1
% x is passed as a vector, reshape it into an image.
x = reshape(x, op.vol_size);
% Matlab data copied to ASTRA data
astra_mex_data2d('store', op.vol_id, x);
% forward projection
astra_mex_algorithm('iterate', op.fp_alg_id);
% retrieve Matlab array
y = astra_mex_data2d('get_single', op.sino_id);
else
% x is passed as a vector, reshape it into a sinogram.
x = reshape(x, op.proj_size);
% Matlab data copied to ASTRA data
astra_mex_data2d('store', op.sino_id, x);
% backprojection
astra_mex_algorithm('iterate', op.bp_alg_id);
% retrieve Matlab array
y = astra_mex_data2d('get_single', op.vol_id);
end
end % opTomo_intrnl2D
% 3D projection code
function y = opTomo_intrnl3D(op,x,mode)
if mode == 1
% x is passed as a vector, reshape it into an image
x = reshape(x, op.vol_size);
% forward projection
y = astra_mex_direct('FP3D', op.proj_id, x);
else
% x is passed as a vector, reshape it into projection data
x = reshape(x, op.proj_size);
y = astra_mex_direct('BP3D', op.proj_id, x);
end
end % opTomo_intrnl3D
end % methods - private
end % classdef
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