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
|
%--------------------------------------------------------------------------
% 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 MaskingDefault < matlab.mixin.Copyable
% Default policy class for masking for DART.
%----------------------------------------------------------------------
properties (Access=public)
radius = 1; % SETTING: Radius of masking kernel.
conn = 8; % SETTING: Connectivity window. For 2D: 4 or 8. For 3D: 6 or 26.
edge_threshold = 1; % SETTING: Number of pixels in the window that should be different.
random = 0.1; % SETTING: Percentage of random points. Between 0 and 1.
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.masking.getsettings();
settings.radius = this.radius;
settings.conn = this.conn;
settings.edge_threshold = this.edge_threshold;
settings.random = this.random;
end
%------------------------------------------------------------------
function Mask = apply(this, ~, S)
% Applies masking.
% >> Mask = DART.segmentation.apply(DART, S);
% 2D, one slice
if size(S,3) == 1
if strcmp(this.gpu,'yes')
Mask = this.apply_2D_gpu(S);
else
Mask = this.apply_2D(S);
end
% 3D, slice by slice
elseif this.conn == 4 || this.conn == 8
Mask = zeros(size(S));
for slice = 1:size(S,3)
if strcmp(this.gpu,'yes')
Mask(:,:,slice) = this.apply_2D_gpu(S(:,:,slice));
else
Mask(:,:,slice) = this.apply_2D(S(:,:,slice));
end
end
% 3D, full
else
if strcmp(this.gpu,'yes')
Mask = this.apply_3D_gpu(S);
else
Mask = this.apply_3D(S);
end
end
end
end
%----------------------------------------------------------------------
methods (Access=protected)
%------------------------------------------------------------------
function Mask = apply_2D_gpu(this, S)
vol_geom = astra_create_vol_geom(size(S));
data_id = astra_mex_data2d('create', '-vol', vol_geom, S);
mask_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
cfg = astra_struct('DARTMASK_CUDA');
cfg.SegmentationDataId = data_id;
cfg.MaskDataId = mask_id;
cfg.option.GPUindex = this.gpu_core;
cfg.option.Connectivity = this.conn;
cfg.option.Threshold = this.edge_threshold;
cfg.option.Radius = this.radius;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate',alg_id,1);
Mask = astra_mex_data2d('get', mask_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data2d('delete', data_id, mask_id);
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Mask, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_2D(this, S)
r = this.radius;
w = 2 * r + 1;
kernel = Kernels.BinaryPixelKernel(r, this.conn);
% edges
Xlarge = zeros(size(S,1)+w-1, size(S,2)+w-1);
Xlarge(1+r:end-r, 1+r:end-r) = S;
Edges = zeros(size(S));
for s = -r:r
for t = -r:r
if kernel(s+r+1, t+r+1) == 0
continue
end
Temp = abs(Xlarge(1+r:end-r, 1+r:end-r) - Xlarge(1+r+s:end-r+s, 1+r+t:end-r+t));
Edges(Temp > eps) = Edges(Temp > eps) + 1;
end
end
Edges = Edges > this.edge_threshold;
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Edges, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_3D(this, S)
r = this.radius;
w = 2 * r + 1;
kernel = Kernels.BinaryPixelKernel(r, this.conn);
% edges
Xlarge = zeros(size(S,1)+w-1, size(S,2)+w-1, size(S,3)+w-1);
Xlarge(1+r:end-r, 1+r:end-r, 1+r:end-r) = S;
Edges = zeros(size(S));
for s = -r:r
for t = -r:r
for u = -r:r
if kernel(s+r+1, t+r+1, u+r+1) == 0
continue
end
Temp = abs(Xlarge(1+r:end-r, 1+r:end-r, 1+r:end-r) - Xlarge(1+r+s:end-r+s, 1+r+t:end-r+t, 1+r+u:end-r+u));
Edges(Temp > eps) = 1;
end
end
end
clear Xlarge;
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Edges, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_3D_gpu(this, S)
vol_geom = astra_create_vol_geom(size(S,2), size(S,1), size(S,3));
data_id = astra_mex_data3d('create', '-vol', vol_geom, S);
cfg = astra_struct('DARTMASK3D_CUDA');
cfg.SegmentationDataId = data_id;
cfg.MaskDataId = data_id;
cfg.option.GPUindex = this.gpu_core;
cfg.option.Connectivity = this.conn;
cfg.option.Threshold = this.edge_threshold;
cfg.option.Radius = this.radius;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate',alg_id,1);
Mask = astra_mex_data3d('get', data_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data3d('delete', data_id);
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Mask, RandomField);
end
%------------------------------------------------------------------
end
end
|
