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
|
%--------------------------------------------------------------------------
% This file is part of the ASTRA Toolbox
%
% Copyright: 2010-2022, imec Vision Lab, University of Antwerp
% 2014-2022, CWI, Amsterdam
% License: Open Source under GPLv3
% Contact: astra@astra-toolbox.com
% Website: http://www.astra-toolbox.com/
%--------------------------------------------------------------------------
classdef SmoothingDefault < matlab.mixin.Copyable
% Default policy class for smoothing for DART.
%----------------------------------------------------------------------
properties (Access=public)
radius = 1; % SETTING: Radius of smoothing kernel.
b = 0.1; % SETTING: Intensity of smoothing. Between 0 and 1.
full3d = 'yes'; % SETTING: smooth in 3D? {'yes','no'}
gpu = 'yes'; % SETTING: Use gpu? {'yes', 'no'}
gpu_core = 0; % SETTING: Which gpu core to use, only when gpu='yes'.
end
%----------------------------------------------------------------------
methods (Access=public)
%------------------------------------------------------------------
function settings = getsettings(this)
% Returns a structure containing all settings of this object.
% >> settings = DART.smoothing.getsettings();
settings.radius = this.radius;
settings.b = this.b;
settings.full3d = this.full3d;
end
%------------------------------------------------------------------
function V_out = apply(this, ~, V_in)
% Applies smoothing.
% >> V_out = DART.smoothing.apply(DART, V_in);
% 2D, one slice
if size(V_in,3) == 1
if strcmp(this.gpu,'yes')
V_out = this.apply_2D_gpu(V_in);
else
V_out = this.apply_2D(V_in);
end
% 3D, slice by slice
elseif ~strcmp(this.full3d,'yes')
V_out = zeros(size(V_in));
for slice = 1:size(V_in,3)
if strcmp(this.gpu,'yes')
V_out(:,:,slice) = this.apply_2D_gpu(V_in(:,:,slice));
else
V_out(:,:,slice) = this.apply_2D(V_in(:,:,slice));
end
end
% 3D, full
else
if strcmp(this.gpu,'yes')
V_out = this.apply_3D_gpu(V_in);
else
V_out = this.apply_3D(V_in);
end
end
end
end
%----------------------------------------------------------------------
methods (Access=protected)
%------------------------------------------------------------------
function V_out = apply_2D(this, V_in)
r = this.radius;
w = 2 * r + 1;
% Set Kernel
K = ones(w) * this.b / (w.^2-1); % edges
K(r+1,r+1) = 1 - this.b; % center
% output window
V_out = zeros(size(V_in,1) + w-1, size(V_in,2) + w - 1);
% blur convolution
for s = -r:r
for t = -r:r
V_out(1+r+s:end-r+s, 1+r+t:end-r+t) = V_out(1+r+s:end-r+s, 1+r+t:end-r+t) + K(r+1+s, r+1+t) * V_in;
end
end
% shrink output window
V_out = V_out(1+r:end-r, 1+r:end-r);
end
%------------------------------------------------------------------
function V_out = apply_2D_gpu(this, V_in)
vol_geom = astra_create_vol_geom(size(V_in));
in_id = astra_mex_data2d('create', '-vol', vol_geom, V_in);
out_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
cfg = astra_struct('DARTSMOOTHING_CUDA');
cfg.InDataId = in_id;
cfg.OutDataId = out_id;
cfg.option.Intensity = this.b;
cfg.option.Radius = this.radius;
cfg.option.GPUindex = this.gpu_core;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate',alg_id,1);
V_out = astra_mex_data2d('get', out_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data2d('delete', in_id, out_id);
end
%------------------------------------------------------------------
function I_out = apply_3D(this, I_in)
r = this.radius;
w = 2 * r + 1;
% Set Kernel
K = ones(w,w,w) * this.b / (w.^3-1); % edges
K(r+1,r+1,r+1) = 1 - this.b; % center
% output window
I_out = zeros(size(I_in,1)+w-1, size(I_in,2)+w-1, size(I_in,3)+w-1);
% blur convolution
for s = -r:r
for t = -r:r
for u = -r:r
I_out(1+r+s:end-r+s, 1+r+t:end-r+t, 1+r+u:end-r+u) = I_out(1+r+s:end-r+s, 1+r+t:end-r+t, 1+r+u:end-r+u) + K(r+1+s, r+1+t, r+1+u) * I_in;
end
end
end
% shrink output window
I_out = I_out(1+r:end-r, 1+r:end-r, 1+r:end-r);
end
%------------------------------------------------------------------
function V_out = apply_3D_gpu(this, V_in)
vol_geom = astra_create_vol_geom(size(V_in,2),size(V_in,1),size(V_in,3));
data_id = astra_mex_data3d('create', '-vol', vol_geom, V_in);
cfg = astra_struct('DARTSMOOTHING3D_CUDA');
cfg.InDataId = data_id;
cfg.OutDataId = data_id;
cfg.option.Intensity = this.b;
cfg.option.Radius = this.radius;
cfg.option.GPUindex = this.gpu_core;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate', alg_id, 1);
V_out = astra_mex_data3d('get', data_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data3d('delete', data_id);
end
%------------------------------------------------------------------
end
end
|
