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
|
/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkMissingStructurePenalty_h
#define itkMissingStructurePenalty_h
#include "itkSingleValuedPointSetToPointSetMetric.h"
#include "itkPoint.h"
#include "itkPointSet.h"
#include "itkImage.h"
#include "itkMesh.h"
#include "itkVectorContainer.h"
#include "vnl_adjugate_fixed.h"
namespace itk
{
/** \class MissingVolumeMeshPenalty
* \brief Computes the (pseudo) volume of the transformed surface mesh of a structure.\n
*
* \author F.F. Berendsen, Image Sciences Institute, UMC Utrecht, The Netherlands
* \note If you use the MissingStructurePenalty anywhere we would appreciate if you cite the following article:\n
* F.F. Berendsen, A.N.T.J. Kotte, A.A.C. de Leeuw, I.M. Juergenliemk-Schulz,\n
* M.A. Viergever and J.P.W. Pluim "Registration of structurally dissimilar \n
* images in MRI-based brachytherapy ", Phys. Med. Biol. 59 (2014) 4033-4045.\n
* http://stacks.iop.org/0031-9155/59/4033
* \ingroup RegistrationMetrics
*/
template <class TFixedPointSet, class TMovingPointSet>
class ITK_TEMPLATE_EXPORT MissingVolumeMeshPenalty
: public SingleValuedPointSetToPointSetMetric<TFixedPointSet, TMovingPointSet>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(MissingVolumeMeshPenalty);
/** Standard class typedefs. */
using Self = MissingVolumeMeshPenalty;
using Superclass = SingleValuedPointSetToPointSetMetric<TFixedPointSet, TMovingPointSet>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** Type used for representing point components */
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(MissingVolumeMeshPenalty, SingleValuedPointSetToPointSetMetric);
/** Types transferred from the base class */
using typename Superclass::TransformType;
using typename Superclass::TransformPointer;
using typename Superclass::TransformParametersType;
using typename Superclass::TransformJacobianType;
using typename Superclass::MeasureType;
using typename Superclass::DerivativeType;
using typename Superclass::DerivativeValueType;
using typename Superclass::InputPointType;
using typename Superclass::OutputPointType;
using CoordRepType = typename OutputPointType::CoordRepType;
using VnlVectorType = vnl_vector<CoordRepType>;
using typename Superclass::NonZeroJacobianIndicesType;
/** Constants for the pointset dimensions. */
itkStaticConstMacro(FixedPointSetDimension, unsigned int, Superclass::FixedPointSetDimension);
itkStaticConstMacro(MovingPointSetDimension, unsigned int, Superclass::MovingPointSetDimension);
/** Typedefs. */
using DummyMeshPixelType = unsigned char;
using MeshTraitsType =
DefaultStaticMeshTraits<DummyMeshPixelType, FixedPointSetDimension, FixedPointSetDimension, CoordRepType>;
using FixedMeshType = Mesh<DummyMeshPixelType, FixedPointSetDimension, MeshTraitsType>;
using FixedMeshPointIdentifier = typename FixedMeshType::PointIdentifier;
using FixedMeshConstPointer = typename FixedMeshType::ConstPointer;
using FixedMeshPointer = typename FixedMeshType::Pointer;
using CellInterfaceType = typename MeshTraitsType::CellType;
using MeshPointType = typename FixedMeshType::PointType;
using VectorType = typename FixedMeshType::PointType::VectorType;
using VectorConstPointer = typename VectorType::const_pointer;
using SubVectorType = itk::Vector<typename VectorType::ValueType, FixedPointSetDimension - 1>;
using MeshPointsContainerType = typename FixedMeshType::PointsContainer;
using MeshPointsContainerPointer = typename MeshPointsContainerType::Pointer;
using MeshPointsContainerConstPointer = typename MeshPointsContainerType::ConstPointer;
using MeshPointsContainerConstIteratorType = typename FixedMeshType::PointsContainerConstIterator;
using MeshPointsContainerIteratorType = typename FixedMeshType::PointsContainerIterator;
using MeshPointDataContainerType = typename FixedMeshType::PointDataContainer;
using MeshPointDataContainerConstPointer = typename FixedMeshType::PointDataContainerConstPointer;
using MeshPointDataContainerPointer = typename FixedMeshType::PointDataContainerPointer;
// typedef typename FixedMeshType::PointDataContainerConstIterator MeshPointDataContainerConstIteratorType;
using MeshPointDataContainerConstIteratorType = typename FixedMeshType::PointDataContainerIterator;
using MeshPointDataContainerIteratorType = typename MeshPointDataContainerType::Iterator;
using MeshIdType = unsigned int;
using FixedMeshContainerType = VectorContainer<MeshIdType, FixedMeshConstPointer>;
using FixedMeshContainerPointer = typename FixedMeshContainerType::Pointer;
using FixedMeshContainerConstPointer = typename FixedMeshContainerType::ConstPointer;
using FixedMeshContainerElementIdentifier = typename FixedMeshContainerType::ElementIdentifier;
using MappedMeshContainerType = VectorContainer<MeshIdType, FixedMeshPointer>;
using MappedMeshContainerPointer = typename MappedMeshContainerType::Pointer;
using MappedMeshContainerConstPointer = typename MappedMeshContainerType::ConstPointer;
using MeshPointsDerivativeValueType = Array<DerivativeValueType>;
itkSetConstObjectMacro(FixedMeshContainer, FixedMeshContainerType);
itkGetConstObjectMacro(FixedMeshContainer, FixedMeshContainerType);
itkSetObjectMacro(MappedMeshContainer, MappedMeshContainerType);
itkGetModifiableObjectMacro(MappedMeshContainer, MappedMeshContainerType);
/** Initialize the Metric by making sure that all the components are
* present and plugged together correctly.
*/
void
Initialize() override;
/** Set the fixed mask. */
// \todo: currently not used
// itkSetConstObjectMacro( FixedImageMask, FixedImageMaskType );
/** Get the fixed mask. */
// itkGetConstObjectMacro( FixedImageMask, FixedImageMaskType );
/** Get the value for single valued optimizers. */
MeasureType
GetValue(const TransformParametersType & parameters) const override;
/** Get the derivatives of the match measure. */
void
GetDerivative(const TransformParametersType & parameters, DerivativeType & Derivative) const override;
/** Get value and derivatives for multiple valued optimizers. */
void
GetValueAndDerivative(const TransformParametersType & parameters,
MeasureType & Value,
DerivativeType & Derivative) const override;
protected:
MissingVolumeMeshPenalty();
~MissingVolumeMeshPenalty() override = default;
/** PrintSelf. */
// void PrintSelf(std::ostream& os, Indent indent) const;
/** Member variables. */
FixedMeshConstPointer m_FixedMesh{};
mutable FixedMeshContainerConstPointer m_FixedMeshContainer{};
mutable MappedMeshContainerPointer m_MappedMeshContainer{};
private:
void
SubVector(const VectorType & fullVector, SubVectorType & subVector, const unsigned int leaveOutIndex) const;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkMissingStructurePenalty.hxx"
#endif
#endif
|
