Merge pull request #6411 from hjmjohnson/fix-doxygen-warnings

hjmjohnson · web-flow · commit a449d5703d42 · 2026-06-09T07:45:14.000-05:00
DOC: Clear Doxygen documentation warnings (CDash Linux-Ubuntu-GCC-Doxygen)
diff --git a/Modules/Filtering/AnisotropicDiffusionLBR/itk-module.cmake b/Modules/Filtering/AnisotropicDiffusionLBR/itk-module.cmake
@@ -3,8 +3,8 @@ set(
   "This module provides coherence-enhancing (CED) and edge-enhancing
 (EED) anisotropic diffusion filters built on the
 Lattice-Basis-Reduction (LBR) stencil scheme by Jean-Marie Mirebeau.
-See the Doxygen on \\\\ref AnisotropicDiffusionLBRImageFilter and
-\\\\ref CoherenceEnhancingDiffusionImageFilter for the algorithm and
+See the Doxygen on \\\\ref itk::AnisotropicDiffusionLBRImageFilter and
+\\\\ref itk::CoherenceEnhancingDiffusionImageFilter for the algorithm and
 citations, and the module README for in-tree vs archived-upstream
 scope."
 )
diff --git a/Modules/Filtering/BoneEnhancement/include/itkKrcahEigenToMeasureParameterEstimationFilter.h b/Modules/Filtering/BoneEnhancement/include/itkKrcahEigenToMeasureParameterEstimationFilter.h
@@ -45,7 +45,7 @@ namespace itk
  * \f$ \gamma \f$. This is done to seperate parameter estimation from the unary
  * functor. The modification is very simple. If the average of the trace is
  * denoted \f$ T \f$ the new parameter becomes:
- *  \f{
+ *  \f{eqnarray*}{
  *      \gamma &=& 0.25 \cdot T
  *  \f}
  *
diff --git a/Modules/Filtering/BoneEnhancement/include/itkKrcahPreprocessingImageToImageFilter.h b/Modules/Filtering/BoneEnhancement/include/itkKrcahPreprocessingImageToImageFilter.h
@@ -32,8 +32,8 @@ namespace itk
  *
  * This filters performs an unsharp filter as defined by Krcah
  * et al. The unsharp filter is defined by:
- *  \f{
- *      J = I+k*(I-(I*G))
+ *  \f{eqnarray*}{
+ *      J &=& I+k*(I-(I*G))
  *  \f}
  *
  * Where \f$ k \f$ is a scaling constant set to 5 and the Guassian
diff --git a/Modules/Filtering/FixedPointInverseDisplacementField/include/itkFixedPointInverseDisplacementFieldImageFilter.h b/Modules/Filtering/FixedPointInverseDisplacementField/include/itkFixedPointInverseDisplacementFieldImageFilter.h
@@ -50,7 +50,6 @@ Medical Physics, vol. 35, issue 1, p. 81
  *
  * \author Marcel Lüthi, Computer Science Department, University of Basel
  *
- * \ingroup ImageToImageFilter
  * \ingroup FixedPointInverseDisplacementField
  */
 
diff --git a/Modules/Filtering/GenericLabelInterpolator/itk-module.cmake b/Modules/Filtering/GenericLabelInterpolator/itk-module.cmake
@@ -6,7 +6,7 @@ independently with any underlying ordinary image interpolator and
 returns the label with the highest interpolated value at each
 point.  Generalizes the Gaussian-only behavior of
 itkLabelImageGaussianInterpolateImageFunction.  See the Doxygen on
-\\\\ref LabelImageGenericInterpolateImageFunction for the algorithm
+\\\\ref itk::LabelImageGenericInterpolateImageFunction for the algorithm
 and the Insight Journal article (Schaerer, Roche, Belaroussi, 2014,
 https://hdl.handle.net/10380/3506) for derivation, and the module
 README for in-tree vs archived-upstream scope."
diff --git a/Modules/Filtering/IsotropicWavelets/include/itkRieszRotationMatrix.h b/Modules/Filtering/IsotropicWavelets/include/itkRieszRotationMatrix.h
@@ -78,12 +78,13 @@ class RieszRotationMatrix : public itk::VariableSizeMatrix<std::complex<double>>
 
   /**
    * Multi-index notation
-   * S[n = (n1,...,nd)][m = (m1,...,md)]
    *
-   * S[n = (n1,...,nd)][m = (m1,...,md)] =
-   *  sqrt(\frac{m!}{n!}) \sum_{|k1| = n1} \cdots \sum_{|kd| = nd}
-   *  \delta_{k1 + k2 + k3, m} x
-   *  \\frac{n!}{k1! \cdots kd!} r_1^{k_1} \cdots r_d^{k_d}
+   * \f[
+   *  S[n = (n_1, \cdots, n_d)][m = (m_1, \cdots, m_d)] =
+   *  \sqrt{\frac{m!}{n!}} \sum_{|k_1| = n_1} \cdots \sum_{|k_d| = n_d}
+   *  \delta_{k_1 + \cdots + k_d, m} x
+   *  \frac{n!}{k_1! \cdots k_d!} r_1^{k_1} \cdots r_d^{k_d}
+   * \f]
    *
    * The indices are ordered in descending order:
    * For example, for order = 2:
diff --git a/Modules/Filtering/MinimalPathExtraction/include/itkArrivalFunctionToPathFilter.h b/Modules/Filtering/MinimalPathExtraction/include/itkArrivalFunctionToPathFilter.h
@@ -137,8 +137,6 @@ class ITK_TEMPLATE_EXPORT ArrivalFunctionToPathCommand : public itk::Command
  *
  * \author Dan Mueller, Queensland University of Technology, dan.muel[at]gmail.com
  *
- * \ingroup ImageToPathFilters
- *
  * \ingroup MinimalPathExtraction
  */
 template <typename TInputImage, typename TOutputPath = PolyLineParametricPath<TInputImage::ImageDimension>>
diff --git a/Modules/Filtering/MinimalPathExtraction/include/itkSpeedFunctionToPathFilter.h b/Modules/Filtering/MinimalPathExtraction/include/itkSpeedFunctionToPathFilter.h
@@ -61,8 +61,6 @@ namespace itk
  * \author Dan Mueller, Queensland University of Technology, dan.muel[at]gmail.com
  *
  * \sa ArrivalFunctionToPathFilter
- * \ingroup ImageToPathFilters
- *
  * \ingroup MinimalPathExtraction
  */
 template <typename TInputImage, typename TOutputPath = PolyLineParametricPath<TInputImage::ImageDimension>>
diff --git a/Modules/Filtering/ParabolicMorphology/include/itkMorphSDTHelperImageFilter.h b/Modules/Filtering/ParabolicMorphology/include/itkMorphSDTHelperImageFilter.h
@@ -30,7 +30,7 @@ namespace itk
  *
  * \ingroup ParabolicMorphology
  *
- * \ingroup IntensityImageFilters  Multithreaded
+ * \ingroup IntensityImageFilters  MultiThreaded
  */
 namespace Function
 {
diff --git a/Modules/Filtering/PolarTransform/include/itkCartesianToPolarTransform.h b/Modules/Filtering/PolarTransform/include/itkCartesianToPolarTransform.h
@@ -50,7 +50,7 @@ namespace itk
  * \author Jakub Bican, Department of Image Processing, Institute of Information Theory and Automation, Academy of
  * Sciences of the Czech Republic.
  *
- * \ingroup Transforms
+ * \ingroup GeometricTransform
  * \ingroup PolarTransform
  */
 template <typename TParametersValueType = double, // Data type for scalars (float or double)
diff --git a/Modules/Filtering/PolarTransform/include/itkPolarToCartesianTransform.h b/Modules/Filtering/PolarTransform/include/itkPolarToCartesianTransform.h
@@ -48,7 +48,7 @@ namespace itk
  * \author Jakub Bican, Department of Image Processing, Institute of Information Theory and Automation, Academy of
  * Sciences of the Czech Republic.
  *
- * \ingroup Transforms
+ * \ingroup GeometricTransform
  * \ingroup PolarTransform
  */
 template <typename TParametersValueType = double, // Data type for scalars (float or double)
diff --git a/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h b/Modules/IO/IOMeshSTL/include/itkSTLMeshIO.h
@@ -55,8 +55,8 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
   /**-------- This part of the interfaces deals with reading data. ----- */
 
   /** Determine if the file can be read with this MeshIO implementation.
-   * \param FileNameToRead The name of the file to test for reading.
-   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \param fileName The name of the file to test for reading.
+   * \post Sets classes MeshIOBase::m_FileName variable to be fileName
    * \return Returns true if this MeshIO can read the file specified.
    */
   bool
@@ -96,8 +96,8 @@ class IOMeshSTL_EXPORT STLMeshIO : public MeshIOBase
 
   /*-------- This part of the interfaces deals with writing data. ----- */
   /** Determine if the file can be written with this MeshIO implementation.
-   * \param FileNameToWrite The name of the file to test for writing.
-   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \param fileName The name of the file to test for writing.
+   * \post Sets classes MeshIOBase::m_FileName variable to be fileName
    * \return Returns true if this MeshIO can write the file specified.
    */
   bool
diff --git a/Modules/IO/IOMeshSWC/include/itkSWCMeshIO.h b/Modules/IO/IOMeshSWC/include/itkSWCMeshIO.h
@@ -84,8 +84,8 @@ class IOMeshSWC_EXPORT SWCMeshIO : public MeshIOBase
   /*-------- This part of the interfaces deals with reading data. ----- */
 
   /** Determine if the file can be read with this MeshIO implementation.
-   * \param FileNameToRead The name of the file to test for reading.
-   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \param fileName The name of the file to test for reading.
+   * \post Sets classes MeshIOBase::m_FileName variable to be fileName
    * \return Returns true if this MeshIO can read the file specified.
    */
   bool
@@ -111,8 +111,8 @@ class IOMeshSWC_EXPORT SWCMeshIO : public MeshIOBase
   /*-------- This part of the interfaces deals with writing data. ----- */
 
   /** Determine if the file can be written with this MeshIO implementation.
-   * \param FileNameToWrite The name of the file to test for writing.
-   * \post Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite
+   * \param fileName The name of the file to test for writing.
+   * \post Sets classes MeshIOBase::m_FileName variable to be fileName
    * \return Returns true if this MeshIO can write the file specified.
    */
   bool
diff --git a/Modules/IO/MGHIO/include/itkMGHImageIO.h b/Modules/IO/MGHIO/include/itkMGHImageIO.h
@@ -56,7 +56,7 @@ class MGHIO_EXPORT MGHImageIO : public ImageIOBase
 
   /** Determine if the file can be read with this ImageIO implementation.
    * \param FileNameToRead The name of the file to test for reading.
-   * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
+   * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToRead
    * \return Returns true if this ImageIO can read the file specified.
    */
   bool
@@ -73,8 +73,8 @@ class MGHIO_EXPORT MGHImageIO : public ImageIOBase
   /*-------- This part of the interfaces deals with writing data. ----- */
 
   /** Determine if the file can be written with this ImageIO implementation.
-   * \param FileNameToWrite The name of the file to test for writing.
-   * \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
+   * \param name The name of the file to test for writing.
+   * \post Sets classes ImageIOBase::m_FileName variable to be name
    * \return Returns true if this ImageIO can write the file specified.
    */
   bool
diff --git a/Modules/Registration/Montage/itk-module.cmake b/Modules/Registration/Montage/itk-module.cmake
@@ -3,8 +3,8 @@ set(
   "This module provides Montage: mosaic-stitching and 3D
 reconstruction of large datasets from a collection of partially
 overlapping 2D slices via phase-correlation image registration.
-Core pieces are \\\\ref PhaseCorrelationImageRegistrationMethod,
-\\\\ref TileMontage, and \\\\ref TileMergeImageFilter.
+Core pieces are \\\\ref itk::PhaseCorrelationImageRegistrationMethod,
+\\\\ref itk::TileMontage, and \\\\ref itk::TileMergeImageFilter.
 See the module README for in-tree vs archived-upstream scope."
 )
 
diff --git a/Modules/Registration/RANSAC/include/itkRANSAC.h b/Modules/Registration/RANSAC/include/itkRANSAC.h
@@ -94,7 +94,7 @@ class ITK_TEMPLATE_EXPORT RANSAC : public Object
    * Set/Get the number of threads used by the RANSAC implementation.
    *
    * @param numberOfThreads Number of threads the algorithm uses. Valid values
-   *                        are in [1, #cores].
+   *                        are in [1, \#cores].
    */
   void
   SetNumberOfThreads(unsigned int numberOfThreads);
@@ -163,7 +163,7 @@ class ITK_TEMPLATE_EXPORT RANSAC : public Object
 protected:
   /**
    * Construct an instance of the RANSAC algorithm. The number of threads used
-   * in the computation is 1, valid values are in [1, #cores].
+   * in the computation is 1, valid values are in [1, \#cores].
    *
    */
   RANSAC();
diff --git a/Modules/Registration/VariationalRegistration/include/itkContinuousBorderWarpImageFilter.h b/Modules/Registration/VariationalRegistration/include/itkContinuousBorderWarpImageFilter.h
@@ -46,7 +46,7 @@ namespace itk
  *  and displacement field type all have the same number of dimensions.
  *
  *  \ingroup VariationalRegistration
- *  \ingroup GeometricTransforms
+ *  \ingroup GeometricTransform
  *  \ingroup MultiThreaded
  *
  *  \note This class was developed with funding from the German Research
diff --git a/Modules/Segmentation/GrowCut/include/FibHeap.h b/Modules/Segmentation/GrowCut/include/FibHeap.h
@@ -161,7 +161,7 @@ class GrowCut_EXPORT FibHeapNode
 // FibHeap class can then be used to Insert(), ExtractMin(), etc.,
 // instances of FibHeapNode class.
 
-/// \ingroup Slicer_QtModules_Segmentations
+/// \ingroup GrowCut
 
 class GrowCut_EXPORT FibHeap
 {
diff --git a/Utilities/Doxygen/DoxygenConfig.cmake b/Utilities/Doxygen/DoxygenConfig.cmake
@@ -16,6 +16,7 @@ set(DOXYGEN_NUM_PROC_THREADS "0")
 set(
   DOXYGEN_ALIASES
   "starteraliasnotused=@par not used"
+  "doxygen{1}=\\ref \\1"
   "sphinx=\\par ITK Sphinx Examples: ^^ \\li <a href=\\\"https://itk.org/ITKExamples\\\">All ITK Sphinx Examples</a> ^^"
   "sphinxexample{2}=\\li <a href=\\\"https://itk.org/ITKExamples/src/\\1/Documentation.html\\\">\\2</a> ^^"
   "endsphinx=^^ ^^ ^^"
@@ -209,7 +210,7 @@ set(
 )
 set(DOXYGEN_GRAPHICAL_HIERARCHY "NO")
 set(DOXYGEN_DOT_IMAGE_FORMAT "svg")
-set(DOXYGEN_DOT_GRAPH_MAX_NODES "250")
+set(DOXYGEN_DOT_GRAPH_MAX_NODES "300")
 set(DOXYGEN_INTERACTIVE_SVG "YES")
 set(DOXYGEN_DOT_MULTI_TARGETS "YES")
 set(

Original file line number	Diff line number	Diff line change
`@@ -45,7 +45,7 @@ namespace itk`
`45`	`45`	`* \f$ \gamma \f$. This is done to seperate parameter estimation from the unary`
`46`	`46`	`* functor. The modification is very simple. If the average of the trace is`
`47`	`47`	`* denoted \f$ T \f$ the new parameter becomes:`
`48`		`- * \f{`
	`48`	`+ * \f{eqnarray*}{`
`49`	`49`	`* \gamma &=& 0.25 \cdot T`
`50`	`50`	`* \f}`
`51`	`51`	`*`
Original file line number	Diff line number	Diff line change
`@@ -32,8 +32,8 @@ namespace itk`
`32`	`32`	`*`
`33`	`33`	`* This filters performs an unsharp filter as defined by Krcah`
`34`	`34`	`* et al. The unsharp filter is defined by:`
`35`		`- * \f{`
`36`		`- * J = I+k(I-(IG))`
	`35`	`+ * \f{eqnarray*}{`
	`36`	`+ * J &=& I+k(I-(IG))`
`37`	`37`	`* \f}`
`38`	`38`	`*`
`39`	`39`	`* Where \f$ k \f$ is a scaling constant set to 5 and the Guassian`
Original file line number	Diff line number	Diff line change
`@@ -50,7 +50,6 @@ Medical Physics, vol. 35, issue 1, p. 81`
`50`	`50`	`*`
`51`	`51`	`* \author Marcel Lüthi, Computer Science Department, University of Basel`
`52`	`52`	`*`
`53`		`- * \ingroup ImageToImageFilter`
`54`	`53`	`* \ingroup FixedPointInverseDisplacementField`
`55`	`54`	`*/`
`56`	`55`
Original file line number	Diff line number	Diff line change
`@@ -137,8 +137,6 @@ class ITK_TEMPLATE_EXPORT ArrivalFunctionToPathCommand : public itk::Command`
`137`	`137`	`*`
`138`	`138`	`* \author Dan Mueller, Queensland University of Technology, dan.muel[at]gmail.com`
`139`	`139`	`*`
`140`		`- * \ingroup ImageToPathFilters`
`141`		`- *`
`142`	`140`	`* \ingroup MinimalPathExtraction`
`143`	`141`	`*/`
`144`	`142`	`template <typename TInputImage, typename TOutputPath = PolyLineParametricPath<TInputImage::ImageDimension>>`
Original file line number	Diff line number	Diff line change
`@@ -61,8 +61,6 @@ namespace itk`
`61`	`61`	`* \author Dan Mueller, Queensland University of Technology, dan.muel[at]gmail.com`
`62`	`62`	`*`
`63`	`63`	`* \sa ArrivalFunctionToPathFilter`
`64`		`- * \ingroup ImageToPathFilters`
`65`		`- *`
`66`	`64`	`* \ingroup MinimalPathExtraction`
`67`	`65`	`*/`
`68`	`66`	`template <typename TInputImage, typename TOutputPath = PolyLineParametricPath<TInputImage::ImageDimension>>`
Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,7 @@ namespace itk`
`30`	`30`	`*`
`31`	`31`	`* \ingroup ParabolicMorphology`
`32`	`32`	`*`
`33`		`- * \ingroup IntensityImageFilters Multithreaded`
	`33`	`+ * \ingroup IntensityImageFilters MultiThreaded`
`34`	`34`	`*/`
`35`	`35`	`namespace Function`
`36`	`36`	`{`
Original file line number	Diff line number	Diff line change
`@@ -50,7 +50,7 @@ namespace itk`
`50`	`50`	`* \author Jakub Bican, Department of Image Processing, Institute of Information Theory and Automation, Academy of`
`51`	`51`	`* Sciences of the Czech Republic.`
`52`	`52`	`*`
`53`		`- * \ingroup Transforms`
	`53`	`+ * \ingroup GeometricTransform`
`54`	`54`	`* \ingroup PolarTransform`
`55`	`55`	`*/`
`56`	`56`	`template <typename TParametersValueType = double, // Data type for scalars (float or double)`