diff --git a/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h b/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h index 9632a5f126d..bb68433ad66 100644 --- a/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h +++ b/Modules/Core/SpatialObjects/include/itkGaussianSpatialObject.h @@ -29,13 +29,13 @@ namespace itk * * The Gaussian function G(x) is given by * \f[ - * G(\vec{x}) = m e^{-\|\S^{-1} \vec{x}\|^2 / 2}, + * G(\vec{x}) = m e^{-\|S^{-1} \vec{x}\|^2 / 2}, * \f] - * where m is a scaling factor set by SetMaximum(), and \f$\S\f$ is the + * where m is a scaling factor set by SetMaximum(), and \f$S\f$ is the * (invertible) matrix associated to the IndexToObjectTransform of the object - * multiplied by the Sigma parameter. If \f$\S\f$ is symmetric and positive + * multiplied by the Sigma parameter. If \f$S\f$ is symmetric and positive * definite, and m is chosen so that the integral of G(x) is 1, then G will - * denote a normal distribution with mean 0 and covariance matrix \f$\S \times + * denote a normal distribution with mean 0 and covariance matrix \f$S \times * Sigma\f$. * \ingroup ITKSpatialObjects */ @@ -117,7 +117,7 @@ class ITK_TEMPLATE_EXPORT GaussianSpatialObject : public SpatialObject::Pointer GetEllipsoid() const; diff --git a/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h b/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h index fc9da5d0b0a..ce425ff1785 100644 --- a/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h +++ b/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h @@ -93,7 +93,6 @@ class ITK_TEMPLATE_EXPORT ElasticBodySplineKernelTransform : public KernelTransf using typename Superclass::GMatrixType; /** Compute G(x) * For the elastic body spline, this is: - * \f$ G(x) = [alpha*r(x)^2*I - 3*x*x']*r(x) \f$ * \f$ G(x) = [\alpha*r(x)^2*I - 3*x*x']*r(x) \f$ * where * \f$\alpha = 12 ( 1 - \nu ) - 1\f$ diff --git a/Modules/Core/Transform/include/itkScaleSkewVersor3DTransform.h b/Modules/Core/Transform/include/itkScaleSkewVersor3DTransform.h index 1a84f9580b3..24e6ff40720 100644 --- a/Modules/Core/Transform/include/itkScaleSkewVersor3DTransform.h +++ b/Modules/Core/Transform/include/itkScaleSkewVersor3DTransform.h @@ -46,7 +46,7 @@ namespace itk * where \f$\textbf{R}_v\f$ is the rotation matrix given the versor, * \f$S=\left( \begin{array}{ccc}s_0-1 & 0 & 0 \\ 0 & s_1-1 & 0 \\ 0 & 0 & s_2-1 \end{array} \right) \f$ * , and - * \f$K=\left( \begin{array}{ccc}0 & k_0 & k_1 \\ k_2 & 0 & k_3 \\ k_4 & k_5 & 0 \end{array} \right)\ \f$. + * \f$K=\left( \begin{array}{ccc}0 & k_0 & k_1 \\ k_2 & 0 & k_3 \\ k_4 & k_5 & 0 \end{array} \right) \f$. * * \ingroup ITKTransform */ diff --git a/Modules/Core/Transform/include/itkScaleVersor3DTransform.h b/Modules/Core/Transform/include/itkScaleVersor3DTransform.h index 65f9d879d86..ec7bd2d90b0 100644 --- a/Modules/Core/Transform/include/itkScaleVersor3DTransform.h +++ b/Modules/Core/Transform/include/itkScaleVersor3DTransform.h @@ -30,7 +30,7 @@ namespace itk * The transform can be described as: * \f$ (\textbf{R}_v + \textbf{S})\textbf{x} \f$ where \f$\textbf{R}_v\f$ is the * rotation matrix given the versor, and - * \f$S=\left( \begin{array}{ccc}s_0-1 & 0 & 0 \\ 0 & s_1-1 & 0 \\ 0 & 0 & s_2-1 \end{array} \right)\ \f$ + * \f$S=\left( \begin{array}{ccc}s_0-1 & 0 & 0 \\ 0 & s_1-1 & 0 \\ 0 & 0 & s_2-1 \end{array} \right) \f$ * * * \note This transform's scale parameters are not related to the diff --git a/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h b/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h index 3ba06d8c6b8..6d2c555b77c 100644 --- a/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h +++ b/Modules/Filtering/Deconvolution/include/itkInverseDeconvolutionImageFilter.h @@ -32,7 +32,7 @@ namespace itk * equivalent to multiplying the Fourier transform of the two images, * the inverse filter consists of inverting the multiplication. In * other words, this filter computes the following: - * \f[ hat{F}(\omega) = + * \f[ \hat{F}(\omega) = * \begin{cases} * G(\omega) / H(\omega) & \text{if $|H(\omega)| \geq \epsilon$} \\ * 0 & \text{otherwise} diff --git a/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h b/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h index 7304e1c275e..88f8fb15bb3 100644 --- a/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h +++ b/Modules/Filtering/FastMarching/include/itkFastMarchingNumberOfElementsStoppingCriterion.h @@ -31,7 +31,7 @@ namespace itk * * \note For itk::Image, one element is one pixel. So the number of elements is directly * linked to the physical size of the object, i.e. - * \f$ PhysicalSize = TargetNumberOfElements \cdot \prod_{i=1}{dim} Spacing_{i} \f$ + * \f$ PhysicalSize = TargetNumberOfElements \cdot \prod_{i=1}^{dim} Spacing_{i} \f$ * * \note For itk::QuadEdgeMesh, one element is one vertex. * diff --git a/Modules/Filtering/ImageNoise/include/itkSaltAndPepperNoiseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkSaltAndPepperNoiseImageFilter.h index 45c08150ae3..c1014a8219b 100644 --- a/Modules/Filtering/ImageNoise/include/itkSaltAndPepperNoiseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkSaltAndPepperNoiseImageFilter.h @@ -44,7 +44,7 @@ namespace itk * \begin{cases} * M, & \quad \text{if } U < p/2 \\ * m, & \quad \text{if } U > 1 - p/2 \\ - * I_0, & \quad \text{if } p/2 \geq U \leq 1 - p/2 + * I_0, & \quad \text{if } p/2 \geq U \leq 1 - p/2 * \end{cases} \f$ * * \par diff --git a/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h b/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h index 810fbb8f410..648fcf18172 100644 --- a/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h +++ b/Modules/Filtering/ImageNoise/include/itkSpeckleNoiseImageFilter.h @@ -35,14 +35,14 @@ namespace itk * It can be modeled as: * * \par - * \f$ I = I_0 \ast G \f$ + * \f$ I = I_0 \ast G \f$ * * \par * where \f$ G \f$ is a is a gamma distributed random variable of mean 1 and * variance proportional to the noise level: * * \par - * \f$ G \sim \Gamma(\frac{1}{\sigma^2}, \sigma^2) \f$ + * \f$ G \sim \Gamma(\frac{1}{\sigma^2}, \sigma^2) \f$ * * \author Gaetan Lehmann * diff --git a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h index 84c5e6f2454..9005730f8c0 100644 --- a/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h +++ b/Modules/Filtering/QuadEdgeMeshFiltering/include/itkSmoothingQuadEdgeMeshFilter.h @@ -33,7 +33,7 @@ namespace itk * * For one iteration the location of one vertex is computed as follows: * \f[ - * \boldsymbol{ v' }_i = v_i + m_RelaxationFactor \cdot \frac{ \sum_j w_{ij} ( \boldsymbol{ v_j } - \boldsymbol{ v_i } ) + * \boldsymbol{ v' }_i = v_i + m_{RelaxationFactor} \cdot \frac{ \sum_j w_{ij} ( \boldsymbol{ v_j } - \boldsymbol{ v_i } ) * }{ \sum_j w_{ij} } \f] * * where \f$ w_{ij} \f$ is computed by the means of the set functor diff --git a/Modules/Numerics/Optimizers/include/itkLBFGSOptimizer.h b/Modules/Numerics/Optimizers/include/itkLBFGSOptimizer.h index 238063b0ebc..620a3028767 100644 --- a/Modules/Numerics/Optimizers/include/itkLBFGSOptimizer.h +++ b/Modules/Numerics/Optimizers/include/itkLBFGSOptimizer.h @@ -43,9 +43,9 @@ namespace itk * The step size \f$ s \f$ is determined through line search with the approach * by More and Thuente \cite more1994. This line search approach finds a step size such that * \f[ - * \lVert \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \rVert + * \| \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \| * \le - * \nu \lVert \nabla f(x) \rVert + * \nu \| \nabla f(x) \| * \f] * The parameter \f$ \nu \f$ is set through SetLineSearchAccuracy() (default 0.9) * The default step length, i.e. starting step length for the line search, @@ -53,7 +53,7 @@ namespace itk * * The optimization stops when either the gradient satisfies the condition * \f[ - * \lVert \nabla f(x) \rVert \le \epsilon \max(1, \lVert X \rVert) + * \| \nabla f(x) \| \le \epsilon \max(1, \| X \|) * \f] * or a maximum number of function evaluations has been reached. * The tolerance \f$\epsilon\f$ is set through SetGradientConvergenceTolerance() diff --git a/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h index e47e224c97d..68191cb93e3 100644 --- a/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkLBFGS2Optimizerv4.h @@ -105,9 +105,9 @@ extern ITKOptimizersv4_EXPORT std::ostream & * the approach by More and Thuente \cite more1994. This line search approach finds a step * size such that * \f[ - * \lVert \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \rVert + * \| \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \| * \le - * \nu \lVert \nabla f(x) \rVert + * \nu \| \nabla f(x) \| * \f] * The parameter \f$\nu\f$ is set through SetLineSearchAccuracy() (default 0.9) * and SetGradientLineSearchAccuracy() @@ -120,7 +120,7 @@ extern ITKOptimizersv4_EXPORT std::ostream & * * The optimization stops when either the gradient satisfies the condition * \f[ - * \lVert \nabla f(x) \rVert \le \epsilon \max(1, \lVert X \rVert) + * \| \nabla f(x) \| \le \epsilon \max(1, \| X \|) * \f] * or a maximum number of function evaluations has been reached. * The tolerance \f$\epsilon\f$ is set through SetSolutionAccuracy() @@ -380,7 +380,7 @@ class ITK_TEMPLATE_EXPORT LBFGS2Optimizerv4Template * problems. Setting this parameter to a positive value activates * Orthant-Wise Limited-memory Quasi-Newton (OWL-QN) method, which * minimizes the objective function F(x) combined with the L1 norm |x| - * of the variables, \f$F(x) + C |x|}. \f$. This parameter is the coefficient + * of the variables, \f$F(x) + C |x| \f$. This parameter is the coefficient * for the |x|, i.e., C. As the L1 norm |x| is not differentiable at * zero, the library modifies function and gradient evaluations from * a client program suitably; a client program thus have only to return diff --git a/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h b/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h index 3a9b9d2a624..462434c3ced 100644 --- a/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h +++ b/Modules/Numerics/Optimizersv4/include/itkLBFGSOptimizerv4.h @@ -42,9 +42,9 @@ namespace itk * The step size \f$ s \f$ is determined through line search with the approach * by More and Thuente [4]. This line search approach finds a step size such that * \f[ - * \lVert \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \rVert + * \| \nabla f(x + s (\nabla^2 f(x_n) )^{-1} \nabla f(x) ) \| * \le - * \nu \lVert \nabla f(x) \rVert + * \nu \| \nabla f(x) \| * \f] * The parameter \f$ \nu \f$ is set through SetLineSearchAccuracy() (default 0.9) * The default step length, i.e. starting step length for the line search, @@ -52,7 +52,7 @@ namespace itk * * The optimization stops when either the gradient satisfies the condition * \f[ - * \lVert \nabla f(x) \rVert \le \epsilon \max(1, \lVert X \rVert) + * \| \nabla f(x) \| \le \epsilon \max(1, \| X \|) * \f] * or a maximum number of function evaluations has been reached. * The tolerance \f$\epsilon\f$ is set through SetGradientConvergenceTolerance() diff --git a/Modules/Registration/Metricsv4/include/itkCorrelationImageToImageMetricv4HelperThreader.h b/Modules/Registration/Metricsv4/include/itkCorrelationImageToImageMetricv4HelperThreader.h index 09659141245..f55725b69b4 100644 --- a/Modules/Registration/Metricsv4/include/itkCorrelationImageToImageMetricv4HelperThreader.h +++ b/Modules/Registration/Metricsv4/include/itkCorrelationImageToImageMetricv4HelperThreader.h @@ -29,8 +29,8 @@ namespace itk * \brief Helper class for CorrelationImageToImageMetricv4 \c * To compute the average pixel intensities of the fixed image and the moving image * on the sampled points or inside the virtual image region: - * \f$ \bar f (CorrelationImageToImageMetricv4::m_AverageFix ) \f$ - * \f$ \bar m (CorrelationImageToImageMetricv4::m_AverageMov ) \f$ + * \f$ \bar f (CorrelationImageToImageMetricv4::m\_AverageFix ) \f$ + * \f$ \bar m (CorrelationImageToImageMetricv4::m\_AverageMov ) \f$ * * \ingroup ITKMetricsv4 */ diff --git a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h index ffb277ee203..b44c5428901 100644 --- a/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h +++ b/Modules/Segmentation/KLMRegionGrowing/include/itkKLMSegmentationRegion.h @@ -55,7 +55,7 @@ namespace itk * surrounded by four borders. * * Initial regions of a 8 by 9 image with a 4 by 3 grid partition. - * \f[\begin{tabular}{|c|c|c|c|c|c|c|c|c|} + * \f[\begin{array}{|c|c|c|c|c|c|c|c|c|} * \hline * 1 & 1 & 1 & 2 & 2 & 2 & 3 & 3 & 3 \\ \hline * 1 & 1 & 1 & 2 & 2 & 2 & 3 & 3 & 3 \\ \hline @@ -65,10 +65,10 @@ namespace itk * 7 & 7 & 7 & 8 & 8 & 8 & 9 & 9 & 9 \\ \hline * a & a & a & b & b & b & c & c & c \\ \hline * a & a & a & b & b & b & c & c & c \\ \hline - * \end{tabular}\f] + * \end{array}\f] * * Region borders are shown as "E". - * \f[\begin{tabular}{|c|c|c|c|c|c|c|c|c|c|c|} + * \f[\begin{array}{|c|c|c|c|c|c|c|c|c|c|c|} * \hline * C & C & C & & C & C & C & & C & C & C \\ \hline * C & C & C & E & C & C & C & E & C & C & C \\ \hline @@ -81,7 +81,7 @@ namespace itk * & E & & & & E & & & & E & \\ \hline * C & C & C & & C & C & C & & C & C & C \\ \hline * C & C & C & E & C & C & C & E & C & C & C \\ \hline - * \end{tabular}\f] + * \end{array}\f] * * \ingroup RegionGrowingSegmentation * \ingroup ITKKLMRegionGrowing @@ -206,11 +206,11 @@ class ITKKLMRegionGrowing_EXPORT KLMSegmentationRegion : public SegmentationRegi * Lambda set to -1.0. * * For example, take an image with 3 regions A, B, C - * \f[\begin{tabular}{|c|c|} + * \f[\begin{array}{|c|c|} * \hline * A & A \\ \hline * B & C \\ \hline - * \end{tabular}\f] + * \end{array}\f] * where region A has region borders A-B and A-C; * region B has region borders A-B and B-C; and * region C has region borders A-C and B-C. diff --git a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h index b806da8379e..9d9773c30c2 100644 --- a/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h +++ b/Modules/Segmentation/LevelSets/include/itkThresholdSegmentationLevelSetFunction.h @@ -46,7 +46,7 @@ namespace itk * \f$ U \f$ and lower threshold \f$ L \f$ according to the following formula. * * \par - * \f$ f(x) = \left\{ \begin{array}{ll} g(x) - L & \mbox{if $(g)x < (U-L)/2 + L$} \\ U - g(x) & \mbox{otherwise} + * \f$ f(x) = \left\{ \begin{array}{ll} g(x) - L & \mbox{if g(x) < (U-L)/2 + L} \\ U - g(x) & \mbox{otherwise} * \end{array} \right. \f$ * * \sa SegmentationLevelSetImageFunction diff --git a/Modules/Segmentation/MarkovRandomFieldsClassifiers/include/itkMRFImageFilter.h b/Modules/Segmentation/MarkovRandomFieldsClassifiers/include/itkMRFImageFilter.h index 32ee3764c3f..76429245bb9 100644 --- a/Modules/Segmentation/MarkovRandomFieldsClassifiers/include/itkMRFImageFilter.h +++ b/Modules/Segmentation/MarkovRandomFieldsClassifiers/include/itkMRFImageFilter.h @@ -97,23 +97,23 @@ extern ITKMarkovRandomFieldsClassifiers_EXPORT std::ostream & * assigned a weight 1.5. A weight of 1.3 is assigned to the influence of * the north, south, east, west, and diagonal pixels in the previous and next * slices. - * \f[\begin{tabular}{ccc} - * \begin{tabular}{|c|c|c|} + * \f[\begin{array}{ccc} + * \begin{array}{|c|c|c|} * 1.3 & 1.3 & 1.3 \\ * 1.3 & 1.5 & 1.3 \\ * 1.3 & 1.3 & 1.3 \\ - * \end{tabular} & - * \begin{tabular}{|c|c|c|} + * \end{array} & + * \begin{array}{|c|c|c|} * 1.7 & 1.7 & 1.7 \\ * 1.7 & 0 & 1.7 \\ * 1.7 & 1.7 & 1.7 \\ - * \end{tabular} & - * \begin{tabular}{|c|c|c|} + * \end{array} & + * \begin{array}{|c|c|c|} * 1.3 & 1.3 & 1.3 \\ * 1.5 & 1.5 & 1.3 \\ * 1.3 & 1.3 & 1.3 \\ - * \end{tabular} \\ - * \end{tabular}\f] + * \end{array} \\ + * \end{array}\f] * * The user needs to set the neighborhood size using the SetNeighborhoodRadius * function. The details on the semantics of a neighborhood can be found diff --git a/Utilities/Doxygen/DoxygenConfig.cmake b/Utilities/Doxygen/DoxygenConfig.cmake index 2d4e62d2739..2c9dc2e2ceb 100644 --- a/Utilities/Doxygen/DoxygenConfig.cmake +++ b/Utilities/Doxygen/DoxygenConfig.cmake @@ -74,6 +74,7 @@ set(DOXYGEN_DOCSET_PUBLISHER_NAME "InsightConsortium") set(DOXYGEN_ECLIPSE_DOC_ID "org.itk.ITK") set(DOXYGEN_ENUM_VALUES_PER_LINE "1") set(DOXYGEN_USE_MATHJAX "YES") +set(DOXYGEN_MATHJAX_VERSION "MathJax_2") set(DOXYGEN_MATHJAX_RELPATH "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/") if(ITK_DOXYGEN_SERVER_BASED_SEARCH) set(DOXYGEN_SERVER_BASED_SEARCH "YES")