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
|
/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkSplineWarpXform.h>
namespace
cmtk
{
/** \addtogroup Segmentation */
//@{
/** Class for integrated atlas-based segmentation.
* This class encapsulates the following stages of atlas-based image segmentation: 1) linear image-to-atlas registration, 2) non-linear
* image-to-atlas registration, 3) label map reformatting.
*/
class AtlasSegmentation
{
public:
/// Constructor: compute registrations.
AtlasSegmentation( UniformVolume::SmartPtr& targetImage, UniformVolume::SmartPtr& atlasImage, UniformVolume::SmartPtr& atlasLabels );
/// Get affine transformation.
AffineXform::SmartPtr& GetAffineXform()
{
if ( ! this->m_AffineXform )
this->RegisterAffine();
return this->m_AffineXform;
}
/// Get nonrigid transformation.
WarpXform::SmartPtr GetWarpXform()
{
if ( ! this->m_WarpXform )
this->RegisterSpline();
return this->m_WarpXform;
}
/// Get nonrigid spline transformation.
SplineWarpXform::SmartPtr GetSplineWarpXform()
{
return SplineWarpXform::SmartPtr::DynamicCastFrom( this->GetWarpXform() );
}
/// Get reformatted label map.
UniformVolume::SmartPtr& GetLabelMap()
{
if ( ! this->m_LabelMap )
this->ReformatLabels();
return this->m_LabelMap;
}
/// Set fast flag.
void SetFast( const bool fast )
{
this->m_Fast = fast;
}
private:
/// Flag for "fast" computation.
bool m_Fast;
/// Target image.
UniformVolume::SmartPtr m_TargetImage;
/// Atlas image.
UniformVolume::SmartPtr m_AtlasImage;
/// Atlas labels.
UniformVolume::SmartPtr m_AtlasLabels;
/// Affine registration transformation.
AffineXform::SmartPtr m_AffineXform;
/// Compute affine registration.
void RegisterAffine();
/// Nonrigid, B-spline transformation.
WarpXform::SmartPtr m_WarpXform;
/// Compute spline registration.
void RegisterSpline();
/// Output label map.
UniformVolume::SmartPtr m_LabelMap;
/// Compute label map.
void ReformatLabels();
};
//@}
} // namespace cmtk
|
