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
|
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkDiffeomorphicDemonsRegistrationFilter.h
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkDiffeomorphicDemonsRegistrationFilter_h
#define __itkDiffeomorphicDemonsRegistrationFilter_h
#include "itkPDEDeformableRegistrationFilter.h"
#include "itkESMDemonsRegistrationFunction.h"
#include "itkMultiplyByConstantImageFilter.h"
#include "itkExponentialDeformationFieldImageFilter.h"
#include "itkWarpVectorImageFilter.h"
#include "itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.h"
#include "itkAddImageFilter.h"
namespace itk {
/** \class DiffeomorphicDemonsRegistrationFilter
* \brief Deformably register two images using a diffeomorphic demons algorithm.
*
* This class was contributed by Tom Vercauteren, INRIA & Mauna Kea Technologies,
* based on a variation of the DemonsRegistrationFilter. The basic modification
* is to use diffeomorphism exponentials.
*
* See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
* "Non-parametric Diffeomorphic Image Registration with the Demons Algorithm",
* Proc. of MICCAI 2007.
*
* DiffeomorphicDemonsRegistrationFilter implements the demons deformable algorithm that
* register two images by computing the deformation field which will map a
* moving image onto a fixed image.
*
* A deformation field is represented as a image whose pixel type is some
* vector type with at least N elements, where N is the dimension of
* the fixed image. The vector type must support element access via operator
* []. It is assumed that the vector elements behave like floating point
* scalars.
*
* This class is templated over the fixed image type, moving image type
* and the deformation field type.
*
* The input fixed and moving images are set via methods SetFixedImage
* and SetMovingImage respectively. An initial deformation field maybe set via
* SetInitialDeformationField or SetInput. If no initial field is set,
* a zero field is used as the initial condition.
*
* The output deformation field can be obtained via methods GetOutput
* or GetDeformationField.
*
* This class make use of the finite difference solver hierarchy. Update
* for each iteration is computed in DemonsRegistrationFunction.
*
* \author Tom Vercauteren, INRIA & Mauna Kea Technologies
*
* \warning This filter assumes that the fixed image type, moving image type
* and deformation field type all have the same number of dimensions.
*
* This implementation was taken from the Insight Journal paper:
* http://hdl.handle.net/1926/510
*
* \sa DemonsRegistrationFilter
* \sa DemonsRegistrationFunction
* \ingroup DeformableImageRegistration MultiThreaded
*/
template<class TFixedImage, class TMovingImage, class TDeformationField>
class ITK_EXPORT DiffeomorphicDemonsRegistrationFilter :
public PDEDeformableRegistrationFilter< TFixedImage, TMovingImage,
TDeformationField>
{
public:
/** Standard class typedefs. */
typedef DiffeomorphicDemonsRegistrationFilter Self;
typedef PDEDeformableRegistrationFilter<
TFixedImage, TMovingImage,TDeformationField> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro( DiffeomorphicDemonsRegistrationFilter,
PDEDeformableRegistrationFilter );
/** FixedImage image type. */
typedef typename Superclass::FixedImageType FixedImageType;
typedef typename Superclass::FixedImagePointer FixedImagePointer;
/** MovingImage image type. */
typedef typename Superclass::MovingImageType MovingImageType;
typedef typename Superclass::MovingImagePointer MovingImagePointer;
/** Deformation field type. */
typedef typename Superclass::DeformationFieldType DeformationFieldType;
typedef typename Superclass::DeformationFieldPointer DeformationFieldPointer;
/** FiniteDifferenceFunction type. */
typedef typename
Superclass::FiniteDifferenceFunctionType FiniteDifferenceFunctionType;
/** Take timestep type from the FiniteDifferenceFunction. */
typedef typename
FiniteDifferenceFunctionType::TimeStepType TimeStepType;
/** DemonsRegistrationFilterFunction type. */
typedef ESMDemonsRegistrationFunction<
FixedImageType,
MovingImageType, DeformationFieldType> DemonsRegistrationFunctionType;
typedef typename
DemonsRegistrationFunctionType::GradientType GradientType;
/** Get the metric value. The metric value is the mean square difference
* in intensity between the fixed image and transforming moving image
* computed over the the overlapping region between the two images.
* This value is calculated for the current iteration */
virtual double GetMetric() const;
virtual const double &GetRMSChange() const;
virtual void SetUseGradientType( GradientType gtype );
virtual GradientType GetUseGradientType() const;
/** Use a first-order approximation of the exponential.
* This amounts to using an update rule of the type
* s <- s o (Id + u) instead of s <- s o exp(u) */
itkSetMacro( UseFirstOrderExp, bool );
itkGetConstMacro( UseFirstOrderExp, bool );
itkBooleanMacro( UseFirstOrderExp );
/** Set/Get the threshold below which the absolute difference of
* intensity yields a match. When the intensities match between a
* moving and fixed image pixel, the update vector (for that
* iteration) will be the zero vector. Default is 0.001. */
virtual void SetIntensityDifferenceThreshold(double);
virtual double GetIntensityDifferenceThreshold() const;
/** Set/Get the maximum length in terms of pixels of
* the vectors in the update buffer. */
virtual void SetMaximumUpdateStepLength(double);
virtual double GetMaximumUpdateStepLength() const;
protected:
DiffeomorphicDemonsRegistrationFilter();
~DiffeomorphicDemonsRegistrationFilter() {}
void PrintSelf(std::ostream& os, Indent indent) const;
/** Initialize the state of filter and equation before each iteration. */
virtual void InitializeIteration();
/** This method allocates storage in m_UpdateBuffer. It is called from
* FiniteDifferenceFilter::GenerateData(). */
virtual void AllocateUpdateBuffer();
/** Apply update. */
virtual void ApplyUpdate(TimeStepType dt);
private:
DiffeomorphicDemonsRegistrationFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
/** Downcast the DifferenceFunction using a dynamic_cast to ensure that it is of the correct type.
* this method will throw an exception if the function is not of the expected type. */
DemonsRegistrationFunctionType * DownCastDifferenceFunctionType();
const DemonsRegistrationFunctionType * DownCastDifferenceFunctionType() const;
/** Exp and composition typedefs */
typedef MultiplyByConstantImageFilter<
DeformationFieldType,
TimeStepType, DeformationFieldType > MultiplyByConstantType;
typedef ExponentialDeformationFieldImageFilter<
DeformationFieldType, DeformationFieldType > FieldExponentiatorType;
typedef WarpVectorImageFilter<
DeformationFieldType,
DeformationFieldType, DeformationFieldType> VectorWarperType;
typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction<
DeformationFieldType, double> FieldInterpolatorType;
typedef AddImageFilter<
DeformationFieldType,
DeformationFieldType, DeformationFieldType> AdderType;
typedef typename MultiplyByConstantType::Pointer MultiplyByConstantPointer;
typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;
typedef typename VectorWarperType::Pointer VectorWarperPointer;
typedef typename FieldInterpolatorType::Pointer FieldInterpolatorPointer;
typedef typename FieldInterpolatorType::OutputType FieldInterpolatorOutputType;
typedef typename AdderType::Pointer AdderPointer;
MultiplyByConstantPointer m_Multiplier;
FieldExponentiatorPointer m_Exponentiator;
VectorWarperPointer m_Warper;
AdderPointer m_Adder;
bool m_UseFirstOrderExp;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDiffeomorphicDemonsRegistrationFilter.txx"
#endif
#endif
|
