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elxStatisticalShapePenalty.h
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1 /*=========================================================================
2  *
3  * Copyright UMC Utrecht and contributors
4  *
5  * Licensed under the Apache License, Version 2.0 (the "License");
6  * you may not use this file except in compliance with the License.
7  * You may obtain a copy of the License at
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10  *
11  * Unless required by applicable law or agreed to in writing, software
12  * distributed under the License is distributed on an "AS IS" BASIS,
13  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14  * See the License for the specific language governing permissions and
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16  *
17  *=========================================================================*/
18 #ifndef __elxStatisticalShapePenalty_H__
19 #define __elxStatisticalShapePenalty_H__
20 
21 #include "elxIncludes.h" // include first to avoid MSVS warning
23 
24 #include <vnl/vnl_matrix.h>
25 #include <vnl/vnl_vector.h>
26 #include <vcl_iostream.h>
27 
28 namespace elastix
29 {
30 using namespace itk;
31 
58 template< class TElastix >
61  typename MetricBase< TElastix >::FixedPointSetType,
62  typename MetricBase< TElastix >::MovingPointSetType >,
63  public MetricBase< TElastix >
64 {
65 public:
66 
74  typedef SmartPointer< const Self > ConstPointer;
75 
77  itkNewMacro( Self );
78 
80  itkTypeMacro( StatisticalShapePenalty,
82 
87  elxClassNameMacro( "StatisticalShapePenalty" );
88 
95 
96 // typedef typename Superclass1::FixedImageRegionType FixedImageRegionType;
103 // typedef typename Superclass1::RealType RealType;
111 
112  typedef typename OutputPointType::CoordRepType CoordRepType;
114 
116  typedef itk::Object ObjectType;
117  /*typedef itk::AdvancedTransform<
118  CoordRepType,
119  itkGetStaticConstMacro( FixedImageDimension ),
120  itkGetStaticConstMacro( MovingImageDimension ) > ITKBaseType;
121  */
123  itkGetStaticConstMacro( FixedImageDimension ) > CombinationTransformType;
124  typedef typename
126 
137 
139  itkStaticConstMacro( FixedImageDimension, unsigned int,
140  FixedImageType::ImageDimension );
141 
143  itkStaticConstMacro( MovingImageDimension, unsigned int,
144  MovingImageType::ImageDimension );
145 
151 
155  virtual void Initialize( void ) throw ( ExceptionObject );
156 
161  virtual void BeforeRegistration( void );
162 
163  virtual void BeforeEachResolution( void );
164 
166  unsigned int ReadLandmarks(
167  const std::string & landmarkFileName,
168  typename PointSetType::Pointer & pointSet,
169  const typename ImageType::ConstPointer image );
170 
171  unsigned int ReadShape(
172  const std::string & ShapeFileName,
173  typename PointSetType::Pointer & pointSet,
174  const typename ImageType::ConstPointer image );
175 
177  virtual void SelectNewSamples( void ){}
178 
179 protected:
180 
185 
186 private:
187 
189  StatisticalShapePenalty( const Self & ); // purposely not implemented
191  void operator=( const Self & ); // purposely not implemented
192 
193 };
194 
195 } // end namespace elastix
196 
197 #ifndef ITK_MANUAL_INSTANTIATION
198 #include "elxStatisticalShapePenalty.hxx"
199 #endif
200 
201 #endif // end #ifndef __elxStatisticalShapePenalty_H__
elastix::StatisticalShapePenalty::TransformPointer
Superclass1::TransformPointer TransformPointer
Definition: elxStatisticalShapePenalty.h:98
elastix::StatisticalShapePenalty::OutputPointType
Superclass1::OutputPointType OutputPointType
Definition: elxStatisticalShapePenalty.h:100
itk::StatisticalShapePointPenalty::TransformParametersType
Superclass::TransformParametersType TransformParametersType
Definition: itkStatisticalShapePointPenalty.h:79
elastix::StatisticalShapePenalty::FixedImageType
Superclass2::FixedImageType FixedImageType
Definition: elxStatisticalShapePenalty.h:135
elastix::StatisticalShapePenalty::elxClassNameMacro
elxClassNameMacro("StatisticalShapePenalty")
itk::SingleValuedPointSetToPointSetMetric::MovingImageMaskType
SpatialObject< itkGetStaticConstMacro(MovingPointSetDimension) > MovingImageMaskType
Definition: itkSingleValuedPointSetToPointSetMetric.h:110
elastix::StatisticalShapePenalty
An metric based on the itk::StatisticalShapePointPenalty.
Definition: elxStatisticalShapePenalty.h:64
elastix::MetricBase::ITKBaseType
itk::SingleValuedCostFunction ITKBaseType
Definition: elxMetricBase.h:100
itkStatisticalShapePointPenalty.h
elastix::StatisticalShapePenalty::ConfigurationPointer
Superclass2::ConfigurationPointer ConfigurationPointer
Definition: elxStatisticalShapePenalty.h:131
elastix::MetricBase::RegistrationPointer
Superclass::RegistrationPointer RegistrationPointer
Definition: elxMetricBase.h:89
elastix::StatisticalShapePenalty::InputPointType
Superclass1::InputPointType InputPointType
Definition: elxStatisticalShapePenalty.h:99
itk::StatisticalShapePointPenalty
Computes the Mahalanobis distance between the transformed shape and a mean shape. A model mean and co...
Definition: itkStatisticalShapePointPenalty.h:59
SmartPointer< Self >
elastix::StatisticalShapePenalty::~StatisticalShapePenalty
virtual ~StatisticalShapePenalty()
Definition: elxStatisticalShapePenalty.h:184
elastix::MetricBase
This class is the elastix base class for all Metrics.
Definition: elxMetricBase.h:73
itk::StatisticalShapePointPenalty::TransformJacobianType
Superclass::TransformJacobianType TransformJacobianType
Definition: itkStatisticalShapePointPenalty.h:80
elastix::StatisticalShapePenalty::MovingImageType
Superclass2::MovingImageType MovingImageType
Definition: elxStatisticalShapePenalty.h:136
itk::StatisticalShapePointPenalty::MovingPointSetConstPointer
Superclass::MovingPointSetConstPointer MovingPointSetConstPointer
Definition: itkStatisticalShapePointPenalty.h:89
itk::StatisticalShapePointPenalty::InputPointType
Superclass::InputPointType InputPointType
Definition: itkStatisticalShapePointPenalty.h:94
elastix::StatisticalShapePenalty::Initialize
virtual void Initialize(void)
elastix::StatisticalShapePenalty::MovingPointSetConstPointer
Superclass1::MovingPointSetConstPointer MovingPointSetConstPointer
Definition: elxStatisticalShapePenalty.h:94
elastix::StatisticalShapePenalty::StatisticalShapePenalty
StatisticalShapePenalty()
Definition: elxStatisticalShapePenalty.h:182
elastix::StatisticalShapePenalty::PointSetType
FixedPointSetType PointSetType
Definition: elxStatisticalShapePenalty.h:149
elastix::StatisticalShapePenalty::FixedPointSetType
Superclass1::FixedPointSetType FixedPointSetType
Definition: elxStatisticalShapePenalty.h:91
elastix::MetricBase::MovingPointSetType
itk::PointSet< CoordinateRepresentationType, MovingImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, MovingImageDimension, MovingImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > > MovingPointSetType
Definition: elxMetricBase.h:125
itk::StatisticalShapePointPenalty::MeasureType
Superclass::MeasureType MeasureType
Definition: itkStatisticalShapePointPenalty.h:83
itk::StatisticalShapePointPenalty::FixedPointSetType
Superclass::FixedPointSetType FixedPointSetType
Definition: itkStatisticalShapePointPenalty.h:86
elastix::StatisticalShapePenalty::ConfigurationType
Superclass2::ConfigurationType ConfigurationType
Definition: elxStatisticalShapePenalty.h:130
elastix::StatisticalShapePenalty::FixedImageMaskType
Superclass1::FixedImageMaskType FixedImageMaskType
Definition: elxStatisticalShapePenalty.h:104
vnl_vector< CoordRepType >
itk::SingleValuedPointSetToPointSetMetric::FixedImageMaskType
SpatialObject< itkGetStaticConstMacro(FixedPointSetDimension) > FixedImageMaskType
Definition: itkSingleValuedPointSetToPointSetMetric.h:106
elastix::StatisticalShapePenalty::operator=
void operator=(const Self &)
elastix::StatisticalShapePenalty::ReadShape
unsigned int ReadShape(const std::string &ShapeFileName, typename PointSetType::Pointer &pointSet, const typename ImageType::ConstPointer image)
itk::AdvancedCombinationTransform
This class combines two transforms: an 'initial transform' with a 'current transform'.
Definition: itkAdvancedCombinationTransform.h:58
elastix::StatisticalShapePenalty::ReadLandmarks
unsigned int ReadLandmarks(const std::string &landmarkFileName, typename PointSetType::Pointer &pointSet, const typename ImageType::ConstPointer image)
elastix::StatisticalShapePenalty::ImageType
FixedImageType ImageType
Definition: elxStatisticalShapePenalty.h:150
elastix::StatisticalShapePenalty::ITKBaseType
Superclass2::ITKBaseType ITKBaseType
Definition: elxStatisticalShapePenalty.h:134
elastix::StatisticalShapePenalty::ElastixPointer
Superclass2::ElastixPointer ElastixPointer
Definition: elxStatisticalShapePenalty.h:129
elastix::StatisticalShapePenalty::RegistrationType
Superclass2::RegistrationType RegistrationType
Definition: elxStatisticalShapePenalty.h:132
elastix::StatisticalShapePenalty::TransformParametersType
Superclass1::TransformParametersType TransformParametersType
Definition: elxStatisticalShapePenalty.h:101
elastix::StatisticalShapePenalty::VnlVectorType
vnl_vector< CoordRepType > VnlVectorType
Definition: elxStatisticalShapePenalty.h:113
elastix::StatisticalShapePenalty::itkStaticConstMacro
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
itk::SingleValuedPointSetToPointSetMetric::MovingImageMaskPointer
MovingImageMaskType::Pointer MovingImageMaskPointer
Definition: itkSingleValuedPointSetToPointSetMetric.h:111
itk::StatisticalShapePointPenalty::OutputPointType
Superclass::OutputPointType OutputPointType
Definition: itkStatisticalShapePointPenalty.h:95
itk::StatisticalShapePointPenalty::TransformPointer
Superclass::TransformPointer TransformPointer
Definition: itkStatisticalShapePointPenalty.h:78
elastix::MetricBase::ConfigurationPointer
Superclass::ConfigurationPointer ConfigurationPointer
Definition: elxMetricBase.h:87
itk::StatisticalShapePointPenalty::FixedPointSetConstPointer
Superclass::FixedPointSetConstPointer FixedPointSetConstPointer
Definition: itkStatisticalShapePointPenalty.h:88
elastix::StatisticalShapePenalty::CombinationTransformType
itk::AdvancedCombinationTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension) > CombinationTransformType
Definition: elxStatisticalShapePenalty.h:123
elastix::StatisticalShapePenalty::BeforeRegistration
virtual void BeforeRegistration(void)
elastix::StatisticalShapePenalty::CoordRepType
OutputPointType::CoordRepType CoordRepType
Definition: elxStatisticalShapePenalty.h:112
itk::AdvancedTransform< TScalarType, NDimensions, NDimensions >
elastix::StatisticalShapePenalty::ObjectType
itk::Object ObjectType
Definition: elxStatisticalShapePenalty.h:116
itk::SingleValuedPointSetToPointSetMetric::ParametersType
Superclass::ParametersType ParametersType
Definition: itkSingleValuedPointSetToPointSetMetric.h:118
elastix::MetricBase::FixedPointSetType
itk::PointSet< CoordinateRepresentationType, FixedImageDimension, itk::DefaultStaticMeshTraits< CoordinateRepresentationType, FixedImageDimension, FixedImageDimension, CoordinateRepresentationType, CoordinateRepresentationType, CoordinateRepresentationType > > FixedPointSetType
Definition: elxMetricBase.h:118
elastix::StatisticalShapePenalty::CoordinateRepresentationType
Superclass1::CoordinateRepresentationType CoordinateRepresentationType
Definition: elxStatisticalShapePenalty.h:90
elastix::MetricBase::ConfigurationType
Superclass::ConfigurationType ConfigurationType
Definition: elxMetricBase.h:86
elastix::StatisticalShapePenalty::BeforeEachResolution
virtual void BeforeEachResolution(void)
elastix::StatisticalShapePenalty::FixedImageMaskPointer
Superclass1::FixedImageMaskPointer FixedImageMaskPointer
Definition: elxStatisticalShapePenalty.h:105
elastix::StatisticalShapePenalty::DerivativeType
Superclass1::DerivativeType DerivativeType
Definition: elxStatisticalShapePenalty.h:109
elastix::StatisticalShapePenalty::Pointer
SmartPointer< Self > Pointer
Definition: elxStatisticalShapePenalty.h:73
elastix::StatisticalShapePenalty::FixedPointSetConstPointer
Superclass1::FixedPointSetConstPointer FixedPointSetConstPointer
Definition: elxStatisticalShapePenalty.h:92
elastix::StatisticalShapePenalty::StatisticalShapePenalty
StatisticalShapePenalty(const Self &)
elxIncludes.h
elastix::StatisticalShapePenalty::ParametersType
Superclass1::ParametersType ParametersType
Definition: elxStatisticalShapePenalty.h:110
itk::StatisticalShapePointPenalty::DerivativeType
Superclass::DerivativeType DerivativeType
Definition: itkStatisticalShapePointPenalty.h:84
itk::StatisticalShapePointPenalty::TransformType
Superclass::TransformType TransformType
Definition: itkStatisticalShapePointPenalty.h:74
elastix::StatisticalShapePenalty::MovingPointSetType
Superclass1::MovingPointSetType MovingPointSetType
Definition: elxStatisticalShapePenalty.h:93
elastix::MetricBase::ElastixPointer
Superclass::ElastixPointer ElastixPointer
Definition: elxMetricBase.h:85
elastix::StatisticalShapePenalty::MovingImageMaskPointer
Superclass1::MovingImageMaskPointer MovingImageMaskPointer
Definition: elxStatisticalShapePenalty.h:107
elastix::StatisticalShapePenalty::Superclass1
StatisticalShapePointPenalty< typename MetricBase< TElastix >::FixedPointSetType, typename MetricBase< TElastix >::MovingPointSetType > Superclass1
Definition: elxStatisticalShapePenalty.h:71
elastix::StatisticalShapePenalty::Self
StatisticalShapePenalty Self
Definition: elxStatisticalShapePenalty.h:68
elastix::StatisticalShapePenalty::InitialTransformType
CombinationTransformType::InitialTransformType InitialTransformType
Definition: elxStatisticalShapePenalty.h:125
itk
Definition: itkAdvancedImageToImageMetric.h:40
elastix::StatisticalShapePenalty::RegistrationPointer
Superclass2::RegistrationPointer RegistrationPointer
Definition: elxStatisticalShapePenalty.h:133
elastix::StatisticalShapePenalty::ElastixType
Superclass2::ElastixType ElastixType
Definition: elxStatisticalShapePenalty.h:128
elastix::MetricBase::FixedImageType
ElastixType::FixedImageType FixedImageType
Definition: elxMetricBase.h:92
itk::SingleValuedPointSetToPointSetMetric::FixedImageMaskPointer
FixedImageMaskType::Pointer FixedImageMaskPointer
Definition: itkSingleValuedPointSetToPointSetMetric.h:107
elastix::StatisticalShapePenalty::ConstPointer
SmartPointer< const Self > ConstPointer
Definition: elxStatisticalShapePenalty.h:74
elastix::MetricBase::MovingImageType
ElastixType::MovingImageType MovingImageType
Definition: elxMetricBase.h:95
elastix::StatisticalShapePenalty::MovingImageMaskType
Superclass1::MovingImageMaskType MovingImageMaskType
Definition: elxStatisticalShapePenalty.h:106
elastix::MetricBase::ElastixType
Superclass::ElastixType ElastixType
Definition: elxMetricBase.h:81
elastix::StatisticalShapePenalty::itkStaticConstMacro
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
itk::SingleValuedPointSetToPointSetMetric::CoordinateRepresentationType
Superclass::ParametersValueType CoordinateRepresentationType
Definition: itkSingleValuedPointSetToPointSetMetric.h:74
elastix::StatisticalShapePenalty::MeasureType
Superclass1::MeasureType MeasureType
Definition: elxStatisticalShapePenalty.h:108
elastix::StatisticalShapePenalty::Superclass2
MetricBase< TElastix > Superclass2
Definition: elxStatisticalShapePenalty.h:72
elastix::StatisticalShapePenalty::SelectNewSamples
virtual void SelectNewSamples(void)
Definition: elxStatisticalShapePenalty.h:177
elastix::StatisticalShapePenalty::TransformJacobianType
Superclass1::TransformJacobianType TransformJacobianType
Definition: elxStatisticalShapePenalty.h:102
elastix
Definition: elxFixedGenericPyramid.h:25
elastix::StatisticalShapePenalty::TransformType
Superclass1::TransformType TransformType
Definition: elxStatisticalShapePenalty.h:97
elastix::MetricBase::RegistrationType
Superclass::RegistrationType RegistrationType
Definition: elxMetricBase.h:88
itk::StatisticalShapePointPenalty::MovingPointSetType
Superclass::MovingPointSetType MovingPointSetType
Definition: itkStatisticalShapePointPenalty.h:87


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