itkOrientationDistributionFunction.h
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00001 /*========================================================================= 00002 00003 Program: Medical Imaging & Interaction Toolkit 00004 Language: C++ 00005 Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ 00006 Version: $Revision: 18127 $ 00007 00008 Copyright (c) German Cancer Research Center, Division of Medical and 00009 Biological Informatics. All rights reserved. 00010 See MITKCopyright.txt or https://www.mitk.org/copyright.html for details. 00011 00012 This software is distributed WITHOUT ANY WARRANTY; without even 00013 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00014 PURPOSE. See the above copyright notices for more information. 00015 00016 =========================================================================*/ 00017 00018 #ifndef __itkOrientationDistributionFunction_h 00019 #define __itkOrientationDistributionFunction_h 00020 00022 //#ifdef OrientationDistributionFunction 00023 //#undef OrientationDistributionFunction 00024 //#endif 00025 00026 #include "MitkDiffusionImagingExports.h" 00027 #include "itkIndent.h" 00028 #include "itkFixedArray.h" 00029 #include "itkMatrix.h" 00030 #include "itkSymmetricEigenAnalysis.h" 00031 #include "itkSimpleFastMutexLock.h" 00032 #include "itkDiffusionTensor3D.h" 00033 00034 #include "vtkPolyData.h" 00035 #include "vtkPoints.h" 00036 #include "vtkCellArray.h" 00037 #include "vtkDelaunay2D.h" 00038 #include "vtkCleanPolyData.h" 00039 #include "vtkAppendPolyData.h" 00040 #include "vtkPlane.h" 00041 00042 namespace itk 00043 { 00044 00055 template < typename TComponent, unsigned int NOdfDirections > 00056 class OrientationDistributionFunction: public 00057 FixedArray<TComponent,NOdfDirections> 00058 { 00059 public: 00060 00061 enum InterpolationMethods { 00062 ODF_NEAREST_NEIGHBOR_INTERP, 00063 ODF_TRILINEAR_BARYCENTRIC_INTERP, 00064 ODF_SPHERICAL_GAUSSIAN_BASIS_FUNCTIONS 00065 }; 00066 00068 typedef OrientationDistributionFunction Self; 00069 typedef FixedArray<TComponent,NOdfDirections> Superclass; 00070 00072 itkStaticConstMacro(InternalDimension, unsigned int, NOdfDirections); 00073 00075 typedef FixedArray<TComponent, 00076 itkGetStaticConstMacro(InternalDimension)> BaseArray; 00077 00079 typedef TComponent ComponentType; 00080 typedef typename Superclass::ValueType ValueType; 00081 typedef typename NumericTraits<ValueType>::RealType AccumulateValueType; 00082 typedef typename NumericTraits<ValueType>::RealType RealValueType; 00083 00084 typedef Matrix<TComponent, NOdfDirections, NOdfDirections> MatrixType; 00085 00086 typedef vnl_matrix_fixed<double, 3, NOdfDirections> DirectionsType; 00087 00089 OrientationDistributionFunction() {this->Fill(0);} 00090 00091 OrientationDistributionFunction (const ComponentType& r) { this->Fill(r); } 00092 00093 typedef ComponentType ComponentArrayType[ itkGetStaticConstMacro(InternalDimension) ]; 00094 00096 OrientationDistributionFunction(const Self& r): BaseArray(r) {} 00097 OrientationDistributionFunction(const ComponentArrayType r): BaseArray(r) {} 00098 00100 Self& operator= (const Self& r); 00101 Self& operator= (const ComponentType& r); 00102 Self& operator= (const ComponentArrayType r); 00103 00105 Self operator+(const Self &vec) const; 00106 Self operator-(const Self &vec) const; 00107 const Self & operator+=(const Self &vec); 00108 const Self & operator-=(const Self &vec); 00109 00111 Self operator*(const RealValueType & scalar ) const; 00112 Self operator/(const RealValueType & scalar ) const; 00113 const Self & operator*=(const RealValueType & scalar ); 00114 const Self & operator/=(const RealValueType & scalar ); 00115 00117 static DirectionsType* GetDirections() 00118 { 00119 return itkGetStaticConstMacro(m_Directions); 00120 } 00121 00123 static unsigned int GetNumberOfComponents() 00124 { 00125 return itkGetStaticConstMacro(InternalDimension); 00126 } 00127 00129 ComponentType GetNthComponent(int c) const 00130 { return this->operator[](c); } 00131 00133 ComponentType GetInterpolatedComponent( vnl_vector_fixed<double,3> dir, InterpolationMethods method ) const; 00134 00136 void SetNthComponent(int c, const ComponentType& v) 00137 { this->operator[](c) = v; } 00138 00140 ValueType & operator()( unsigned int row, unsigned int col ); 00141 const ValueType & operator()( unsigned int row, unsigned int col ) const; 00142 00144 void SetIsotropic(); 00145 00146 void InitFromTensor(itk::DiffusionTensor3D<TComponent> tensor); 00147 00149 Self PreMultiply( const MatrixType & m ) const; 00150 00152 Self PostMultiply( const MatrixType & m ) const; 00153 00154 void Normalize(); 00155 00156 Self MinMaxNormalize() const; 00157 00158 Self MaxNormalize() const; 00159 00160 int GetPrincipleDiffusionDirection() const; 00161 00162 int GetNthDiffusionDirection(int n, vnl_vector_fixed<double,3> rndVec) const; 00163 00164 TComponent GetGeneralizedFractionalAnisotropy() const; 00165 00166 TComponent GetGeneralizedGFA(int k, int p) const; 00167 00168 TComponent GetNormalizedEntropy() const; 00169 00170 TComponent GetNematicOrderParameter() const; 00171 00172 TComponent GetStdDevByMaxValue() const; 00173 00174 TComponent GetPrincipleCurvature(double alphaMinDegree, double alphaMaxDegree, int invert) const; 00175 00176 static std::vector<int> GetNeighbors(int idx); 00177 00178 static vtkPolyData* GetBaseMesh(){ComputeBaseMesh(); return m_BaseMesh;} 00179 00180 static void ComputeBaseMesh(); 00181 00182 static double GetMaxChordLength(); 00183 00184 static vnl_vector_fixed<double,3> GetDirection(int i); 00185 00186 private: 00187 00188 static vtkPolyData* m_BaseMesh; 00189 00190 static double m_MaxChordLength; 00191 00192 static DirectionsType* m_Directions; 00193 00194 static std::vector< std::vector<int>* >* m_NeighborIdxs; 00195 00196 static std::vector< std::vector<int>* >* m_AngularRangeIdxs; 00197 00198 static std::vector<int>* m_HalfSphereIdxs; 00199 00200 static itk::SimpleFastMutexLock m_MutexBaseMesh; 00201 static itk::SimpleFastMutexLock m_MutexHalfSphereIdxs; 00202 static itk::SimpleFastMutexLock m_MutexNeighbors; 00203 static itk::SimpleFastMutexLock m_MutexAngularRange; 00204 00205 }; 00206 00209 typedef std::ostream OutputStreamType; 00210 typedef std::istream InputStreamType; 00211 00212 template< typename TComponent, unsigned int NOdfDirections > 00213 MitkDiffusionImaging_EXPORT OutputStreamType& operator<<(OutputStreamType& os, 00214 const OrientationDistributionFunction<TComponent,NOdfDirections> & c); 00215 template< typename TComponent, unsigned int NOdfDirections > 00216 MitkDiffusionImaging_EXPORT InputStreamType& operator>>(InputStreamType& is, 00217 OrientationDistributionFunction<TComponent,NOdfDirections> & c); 00218 00219 00220 00221 } // end namespace itk 00222 00223 //#include "itkNumericTraitsTensorPixel.h" 00224 00225 00226 // Define instantiation macro for this template. 00227 #define ITK_TEMPLATE_OrientationDistributionFunction(_, EXPORT, x, y) namespace itk { \ 00228 _(2(class MitkDiffusionImaging_EXPORT EXPORT OrientationDistributionFunction< ITK_TEMPLATE_2 x >)) \ 00229 namespace Templates { typedef OrientationDistributionFunction< ITK_TEMPLATE_2 x > \ 00230 OrientationDistributionFunction##y; } \ 00231 } 00232 00233 #if ITK_TEMPLATE_EXPLICIT 00234 # include "Templates/itkOrientationDistributionFunction+-.h" 00235 #endif 00236 00237 #if ITK_TEMPLATE_TXX 00238 # include "itkOrientationDistributionFunction.txx" 00239 #endif 00240 00241 00242 #endif //__itkOrientationDistributionFunction_h
