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
|
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* 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 itkTimeVaryingVelocityFieldIntegrationImageFilter_h
#define itkTimeVaryingVelocityFieldIntegrationImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkVectorInterpolateImageFunction.h"
namespace itk
{
/**
* \class TimeVaryingVelocityFieldIntegrationImageFilter
* \brief Integrate a time-varying velocity field using 4th order Runge-Kutta.
*
* Diffeomorphisms are topology-preserving mappings that are useful for
* describing biologically plausible deformations. Mathematically, a
* diffeomorphism, \f$ \phi \f$, is generated from a time-varying velocity field, v, as
* described by the integral equation:
*
* \f[
* \phi(t_b) = \phi(t_a) + \int_{t_a}^{t_b} v(\phi(t),t) dt
* \f]
*
* In this class, the input is the time-varying velocity field and an initial
* diffeomorophism. The output diffeomorphism is produced using fourth order
* Runge-Kutta.
*
* \warning The output deformation field needs to have dimensionality of 1
* less than the input time-varying velocity field.
*
* \author Nick Tustison
* \author Brian Avants
*
* \ingroup ITKDisplacementField
*/
template<typename TTimeVaryingVelocityField, typename TDisplacementField =
Image<typename TTimeVaryingVelocityField::PixelType,
TTimeVaryingVelocityField::ImageDimension - 1> >
class ITK_TEMPLATE_EXPORT TimeVaryingVelocityFieldIntegrationImageFilter :
public ImageToImageFilter<TTimeVaryingVelocityField, TDisplacementField>
{
public:
typedef TimeVaryingVelocityFieldIntegrationImageFilter Self;
typedef ImageToImageFilter
<TTimeVaryingVelocityField, TDisplacementField> 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( TimeVaryingVelocityFieldIntegrationImageFilter, ImageToImageFilter );
/**
* Dimensionality of input data is assumed to be one more than the output
* data the same. */
itkStaticConstMacro( InputImageDimension, unsigned int,
TTimeVaryingVelocityField::ImageDimension );
itkStaticConstMacro( OutputImageDimension, unsigned int,
TDisplacementField::ImageDimension );
typedef TTimeVaryingVelocityField TimeVaryingVelocityFieldType;
typedef TDisplacementField DisplacementFieldType;
typedef typename DisplacementFieldType::Pointer DisplacementFieldPointer;
typedef typename DisplacementFieldType::PixelType VectorType;
typedef typename VectorType::RealValueType RealType;
typedef typename VectorType::ValueType ScalarType;
typedef typename DisplacementFieldType::PointType PointType;
typedef typename DisplacementFieldType::RegionType OutputRegionType;
typedef VectorInterpolateImageFunction
<TimeVaryingVelocityFieldType, ScalarType> VelocityFieldInterpolatorType;
typedef typename VelocityFieldInterpolatorType::Pointer
VelocityFieldInterpolatorPointer;
typedef VectorInterpolateImageFunction<DisplacementFieldType, ScalarType> DisplacementFieldInterpolatorType;
typedef typename DisplacementFieldInterpolatorType::Pointer DisplacementFieldInterpolatorPointer;
/** Get/Set the time-varying velocity field interpolator. Default = linear. */
itkSetObjectMacro( VelocityFieldInterpolator, VelocityFieldInterpolatorType );
itkGetModifiableObjectMacro(VelocityFieldInterpolator, VelocityFieldInterpolatorType );
/**
* Get/Set the deformation field interpolator for the initial diffeomorphism
* (if set). Default = linear.
*/
itkSetObjectMacro( DisplacementFieldInterpolator, DisplacementFieldInterpolatorType );
itkGetModifiableObjectMacro(DisplacementFieldInterpolator, DisplacementFieldInterpolatorType );
/**
* Get/Set the initial diffeomorphism
*/
itkSetObjectMacro( InitialDiffeomorphism, DisplacementFieldType );
itkGetModifiableObjectMacro(InitialDiffeomorphism, DisplacementFieldType );
/**
* Set the lower time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkSetClampMacro( LowerTimeBound, RealType, 0, 1 );
/**
* Get the lower time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkGetConstMacro( LowerTimeBound, RealType );
/**
* Set the upper time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkSetClampMacro( UpperTimeBound, RealType, 0, 1 );
/**
* Get the upper time bound defining the integration domain of the transform.
* We assume that the total possible time domain is [0,1].
*/
itkGetConstMacro( UpperTimeBound, RealType );
/**
* Set the number of integration steps used in the Runge-Kutta solution of the
* initial value problem. Default = 10.
*/
itkSetMacro( NumberOfIntegrationSteps, unsigned int );
/**
* Get the number of integration steps used in the Runge-Kutta solution of the
* initial value problem. Default = 10.
*/
itkGetConstMacro( NumberOfIntegrationSteps, unsigned int );
protected:
TimeVaryingVelocityFieldIntegrationImageFilter();
~TimeVaryingVelocityFieldIntegrationImageFilter() ITK_OVERRIDE;
void PrintSelf( std::ostream & os, Indent indent ) const ITK_OVERRIDE;
virtual void GenerateOutputInformation() ITK_OVERRIDE;
virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
virtual void ThreadedGenerateData( const OutputRegionType &, ThreadIdType ) ITK_OVERRIDE;
VectorType IntegrateVelocityAtPoint( const PointType &initialSpatialPoint, const TimeVaryingVelocityFieldType * inputField );
RealType m_LowerTimeBound;
RealType m_UpperTimeBound;
DisplacementFieldPointer m_InitialDiffeomorphism;
unsigned int m_NumberOfIntegrationSteps;
unsigned int m_NumberOfTimePoints;
DisplacementFieldInterpolatorPointer m_DisplacementFieldInterpolator;
private:
ITK_DISALLOW_COPY_AND_ASSIGN(TimeVaryingVelocityFieldIntegrationImageFilter);
VelocityFieldInterpolatorPointer m_VelocityFieldInterpolator;
};
}
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkTimeVaryingVelocityFieldIntegrationImageFilter.hxx"
#endif
#endif
|
