1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
|
%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: 2014-2015, CWI, Amsterdam
% License: Open Source under GPLv3
% Author: Folkert Bleichrodt
% Contact: F.Bleichrodt@cwi.nl
% Website: http://sf.net/projects/astra-toolbox
%--------------------------------------------------------------------------
% $Id$
classdef opTomo < opSpot
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Properties
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
properties ( Access = private )
% multiplication function
funHandle
% ASTRA identifiers
sino_id
vol_id
fp_alg_id
bp_alg_id
% ASTRA IDs handle
astra_handle
% geometries
proj_geom;
vol_geom;
end % properties
properties ( SetAccess = private, GetAccess = public )
proj_size
vol_size
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';
proj_id = [];
else
fp_alg = 'FP';
bp_alg = 'BP';
proj_id = astra_create_projector(type, proj_geom, vol_geom);
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
% create a function handle
op.funHandle = @opTomo_intrnl3D;
end
% pass object properties
op.proj_size = proj_size;
op.vol_size = vol_size;
op.proj_geom = proj_geom;
op.vol_geom = vol_geom;
op.cflag = false;
op.sweepflag = false;
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
% convert input to single
if isa(x, 'single') == false
x = single(x);
end
% the multiplication
y = op.funHandle(op, x, mode);
% make sure output is column vector
y = y(:);
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);
% initialize output
y = zeros(op.proj_size, 'single');
% link matlab array to ASTRA
vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, x, 0);
sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, y, 1);
% initialize fp algorithm
cfg = astra_struct('FP3D_CUDA');
cfg.ProjectionDataId = sino_id;
cfg.VolumeDataId = vol_id;
alg_id = astra_mex_algorithm('create', cfg);
% forward projection
astra_mex_algorithm('iterate', alg_id);
% cleanup
astra_mex_data3d('delete', vol_id);
astra_mex_data3d('delete', sino_id);
else
% X is passed as a vector, reshape it into projection data
x = reshape(x, op.proj_size);
% initialize output
y = zeros(op.vol_size,'single');
% link matlab array to ASTRA
vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, y, 1);
sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, x, 0);
% initialize bp algorithm
cfg = astra_struct('BP3D_CUDA');
cfg.ProjectionDataId = sino_id;
cfg.ReconstructionDataId = vol_id;
alg_id = astra_mex_algorithm('create', cfg);
% backprojection
astra_mex_algorithm('iterate', alg_id);
% cleanup
astra_mex_data3d('delete', vol_id);
astra_mex_data3d('delete', sino_id);
end
end % opTomo_intrnl3D
end % methods - private
end % classdef
|
