DOC: Convert from raw in-code citations to bibtex (1/N)

First PR out of N, converting raw inline citations with various styles to using a bibliography database and the doxygen cite command.
InsightSoftwareConsortium · Jan 24, 2025 · 031beda · 031beda
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diff --git a/Documentation/Doxygen/doxygen.bib b/Documentation/Doxygen/doxygen.bib
diff --git a/Modules/Core/Common/include/itkConstSliceIterator.h b/Modules/Core/Common/include/itkConstSliceIterator.h
@@ -40,8 +40,7 @@ namespace itk
  *
  * References:
  * Modeled after a slice iterator proposed by Bjarne Stroustrup
- * in C++ Programming Language, Third Edition. Bjarne Stroustrup.  Addison
- * Wesley, Reading, MA. 1997.
+ * in \cite stroustrup1997.
  *
  * \ingroup Iterators
  *

diff --git a/Modules/Core/Common/include/itkDiffusionTensor3D.h b/Modules/Core/Common/include/itkDiffusionTensor3D.h
@@ -64,10 +64,7 @@ namespace itk
  * NIA AG 17919, PI: E.V. Sullivan.
  *
  *
- * \par References
- * E. R. Melhem, S. Mori, G. Mukundan, M. A. Kraut, M. G. Pomper, and
- * P. C. M. van Zijl, "Diffusion tensor MR imaging of the brain and white
- * matter tractography," Am. J. Roentgenol., vol. 178, pp. 3-16, 2002.
+ * For algorithmic details see \cite melhem2002.
  *
  * \sa SymmetricSecondRankTensor
  *

diff --git a/Modules/Core/Common/include/itkGaussianDerivativeOperator.h b/Modules/Core/Common/include/itkGaussianDerivativeOperator.h
@@ -75,10 +75,8 @@ extern ITKCommon_EXPORT std::ostream &
  * lest the operator size become unreasonably large.
  *
  * References:
- * The Gaussian kernel contained in this operator was described
- * by Tony Lindeberg  (Discrete Scale-Space Theory and the Scale-Space
- * Primal Sketch. Dissertation. Royal Institute of Technology, Stockholm,
- * Sweden. May 1991.).
+ * The Gaussian kernel contained in this operator was described in
+ * \cite lindeberg1999.
  *
  * \author Ivan Macia, Vicomtech, Spain, https://www.vicomtech.org/en
  *

diff --git a/Modules/Core/Common/include/itkGaussianOperator.h b/Modules/Core/Common/include/itkGaussianOperator.h
@@ -47,9 +47,7 @@ namespace itk
  *
  * References:
  * The Gaussian kernel contained in this operator was described
- * by Tony Lindeberg (Discrete Scale-Space Theory and the Scale-Space
- * Primal Sketch.  Dissertation. Royal Institute of Technology, Stockholm,
- * Sweden. May 1991.).
+ * in \cite lindeberg1991.
  *
  * \note GaussianOperator does not have any user-declared "special member function",
  * following the C++ Rule of Zero: the compiler will generate them if necessary.

diff --git a/Modules/Core/Common/include/itkKernelFunctionBase.h b/Modules/Core/Common/include/itkKernelFunctionBase.h
@@ -31,10 +31,7 @@ namespace itk
  * This class encapsulates the smoothing kernel used for statistical density
  * estimation and nonparametric regression. The basic idea of the kernel
  * approach is to weight observations by a smooth function (the kernel)
- * to created a smoothed approximation.
- *
- * Reference:
- * Silverman, B. W. (1986) Density Estimation. London: Chapman and Hall.
+ * to create a smoothed approximation \cite silverman1986.
  *
  * \ingroup Functions
  * \ingroup ITKCommon

diff --git a/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h b/Modules/Core/Common/include/itkMersenneTwisterRandomVariateGenerator.h
@@ -69,10 +69,7 @@ namespace Statistics
  * division, and it benefits from caches and pipelines.  For more information
  * see the inventors' web page at http:*www.math.keio.ac.jp/~matumoto/emt.html
  *
- * Reference
- * M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623-Dimensionally
- * Equidistributed Uniform Pseudo-Random Number Generator", ACM Transactions on
- * Modeling and Computer Simulation, Vol. 8, No. 1, January 1998, pp 3-30.
+ * Algorithmic details can be found in \cite matsumoto1998.
  *
  * Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
  * Copyright (C) 2000 - 2003, Richard J. Wagner

diff --git a/Modules/Core/Common/include/itkSliceIterator.h b/Modules/Core/Common/include/itkSliceIterator.h
@@ -38,8 +38,7 @@ namespace itk
  *
  * References:
  * Modeled after a slice iterator proposed by Bjarne Stroustrup
- * in C++ Programming Language, Third Edition. Bjarne Stroustrup.  Addison
- * Wesley, Reading, MA. 1997.
+ * in \cite stroustrup1997.
  *
  * \ingroup Iterators
  * \ingroup ITKCommon

diff --git a/Modules/Core/Common/include/itkSobelOperator.h b/Modules/Core/Common/include/itkSobelOperator.h
@@ -61,9 +61,7 @@ namespace itk
  * The current implementation of the Sobel operator is for 2 and 3 dimensions only.
  * The ND version is planned for future releases.
  *
- * The extension to 3D is from the publication
- *  "Irwin Sobel. An Isotropic 3x3x3 Volume Gradient Operator.
- * Technical report, Hewlett-Packard Laboratories, April 1995."
+ * The extension to 3D was described in \cite sobel1995.
  *
  * The Sobel operator in 3D has the kernel
  *

diff --git a/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h b/Modules/Core/Common/include/itkSymmetricEigenAnalysis.h
@@ -191,10 +191,9 @@ static constexpr EigenValueOrderEnum DoNotOrder = EigenValueOrderEnum::DoNotOrde
  * netlib/tred1.c
  * netlib/tred2.c
  *
- * Reference:
- *     num. math. 11, 293-306(1968) by bowdler, martin, reinsch, and
- *     wilkinson.
- *     handbook for auto. comp., vol.ii-linear algebra, 227-240(1971).
+ * For algorithmic descriptions see \cite bowdler1968 and
+ * \cite bowdler1971.
+ *
  * \ingroup ITKCommon
  */
 
@@ -385,9 +384,8 @@ class ITK_TEMPLATE_EXPORT SymmetricEigenAnalysis
    *  Function adapted from netlib/tred1.c.
    *  [Changed: remove static vars, enforce const correctness.
    *            Use vnl routines as necessary].
-   *  Reference:
-   *  num. math. 11, 181-195(1968) by martin, reinsch, and wilkinson.
-   *    handbook for auto. comp., vol.ii-linear algebra, 212-226(1971).    */
+   *  For algorithmic descriptions see \cite martin1968 and  \cite
+   *  martin1971. */
   void
   ReduceToTridiagonalMatrix(double * a, double * d, double * e, double * e2) const;
 
@@ -409,9 +407,8 @@ class ITK_TEMPLATE_EXPORT SymmetricEigenAnalysis
    *  Function adapted from netlib/tred2.c.
    *  [Changed: remove static vars, enforce const correctness.
    *            Use vnl routines as necessary].
-   *  Reference:
-   *  num. math. 11, 181-195(1968) by martin, reinsch, and wilkinson.
-   *    handbook for auto. comp., vol.ii-linear algebra, 212-226(1971).    */
+   *  For algorithmic descriptions see \cite martin1968 and \cite
+   *  martin1971. */
   void
   ReduceToTridiagonalMatrixAndGetTransformation(const double * a, double * d, double * e, double * z) const;
 
@@ -433,9 +430,7 @@ class ITK_TEMPLATE_EXPORT SymmetricEigenAnalysis
    *
    * Reference
    *  This subroutine is a translation of the algol procedure tql1,
-   *  num. math. 11, 293-306(1968) by bowdler, martin, reinsch, and
-   *  wilkinson.
-   *  handbook for auto. comp., vol.ii-linear algebra, 227-240(1971).
+   *  \cite bowdler1968 and \cite bowdler1971.
    *
    *  Questions and comments should be directed to Burton s. Garbow,
    *  Mathematics and Computer Science Div., Argonne National Laboratory.
@@ -472,9 +467,7 @@ class ITK_TEMPLATE_EXPORT SymmetricEigenAnalysis
    *
    * Reference
    *  This subroutine is a translation of the algol procedure tql1,
-   *  num. math. 11, 293-306(1968) by bowdler, martin, reinsch, and
-   *  wilkinson.
-   *  handbook for auto. comp., vol.ii-linear algebra, 227-240(1971).
+   *  \cite bowdler1968 and \cite bowdler1971.
    *
    *  Questions and comments should be directed to Burton s. Garbow,
    *  Mathematics and Computer Science Div., Argonne National Laboratory.

diff --git a/Modules/Core/ImageFunction/include/itkBSplineDecompositionImageFilter.h b/Modules/Core/ImageFunction/include/itkBSplineDecompositionImageFilter.h
@@ -42,20 +42,8 @@ namespace itk
  * \brief Calculates the B-Spline coefficients of an image. Spline order may be from 0 to 5.
  *
  * This class defines N-Dimension B-Spline transformation.
- * It is based on:
- *    [1] M. Unser,
- *       "Splines: A Perfect Fit for Signal and Image Processing,"
- *        IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38,
- *        November 1999.
- *    [2] M. Unser, A. Aldroubi and M. Eden,
- *        "B-Spline Signal Processing: Part I--Theory,"
- *        IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 821-832,
- *        February 1993.
- *    [3] M. Unser, A. Aldroubi and M. Eden,
- *        "B-Spline Signal Processing: Part II--Efficient Design and Applications,"
- *        IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 834-848,
- *        February 1993.
- * And code obtained from bigwww.epfl.ch by Philippe Thevenaz
+ * It is based on \cite unser1999, \cite unser1993 and \cite unser1993a.
+ * Code obtained from bigwww.epfl.ch by Philippe Thevenaz
  *
  * Limitations:  Spline order must be between 0 and 5.
  *               Spline order must be set before setting the image.

diff --git a/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h
@@ -46,22 +46,8 @@ namespace itk
  * \brief Evaluates the B-Spline interpolation of an image.  Spline order may be from 0 to 5.
  *
  * This class defines N-Dimension B-Spline transformation.
- * It is based on:
-\verbatim
-[1] M. Unser,
-    "Splines: A Perfect Fit for Signal and Image Processing,"
-    IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38,
-    November 1999.
-[2] M. Unser, A. Aldroubi and M. Eden,
-    "B-Spline Signal Processing: Part I--Theory,"
-    IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 821-832,
-    February 1993.
-[3] M. Unser, A. Aldroubi and M. Eden,
-    "B-Spline Signal Processing: Part II--Efficient Design and Applications,"
-     IEEE Transactions on Signal Processing, vol. 41, no. 2, pp. 834-848,
-     February 1993.
-\endverbatim
- * And code obtained from bigwww.epfl.ch by Philippe Thevenaz
+ * It is based on \cite unser1999, \cite unser1993 and \cite unser1993a.
+ * Code obtained from bigwww.epfl.ch by Philippe Thevenaz
  *
  * The B spline coefficients are calculated through the
  * BSplineDecompositionImageFilter

diff --git a/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h b/Modules/Core/ImageFunction/include/itkWindowedSincInterpolateImageFunction.h
@@ -155,12 +155,7 @@ class ITK_TEMPLATE_EXPORT BlackmanWindowFunction
  * approximated using a limited support 'windowed' sinc filter.
  *
  * \par
- * This function is based on the following publication:
- *
- * \par
- * Erik H. W. Meijering, Wiro J. Niessen, Josien P. W. Pluim,
- * Max A. Viergever: Quantitative Comparison of Sinc-Approximating
- * Kernels for Medical Image Interpolation. MICCAI 1999, pp. 210-217
+ * This function is based on \cite meijering1999.
  *
  * \par
  * In this work, several 'windows' are estimated. In two dimensions, the

diff --git a/Modules/Core/Mesh/include/itkBinaryMask3DMeshSource.h b/Modules/Core/Mesh/include/itkBinaryMask3DMeshSource.h
@@ -46,7 +46,9 @@ namespace itk
  * final combinations. In the first table, we record the final combination that
  * can be transformed from the current combination. The entries of the second
  * table are made up of the transforming sequence that is necessary for the
- * current combination transform to one of the final combinations.
+ * current combination transform to one of the final combinations. For
+ * more details see \cite lorensen1987.
+ *
  *
  * \par
  * We then go through the 3D volume voxel by voxel, using those two tables we have defined
@@ -58,10 +60,6 @@ namespace itk
  * pixels in the object region are assigned to "1", so the default value of ObjectValue is
  * set to "1"
  *
- * \par REFERENCE
- * W. Lorensen and H. Cline, "Marching Cubes: A High Resolution 3D Surface Construction Algorithm",
- * Computer Graphics 21, pp. 163-169, 1987.
- *
  * \par INPUT
  * The input should be a 3D binary image.
  *

diff --git a/Modules/Core/Mesh/include/itkSimplexMeshVolumeCalculator.h b/Modules/Core/Mesh/include/itkSimplexMeshVolumeCalculator.h
@@ -40,9 +40,7 @@ namespace itk
  * The original implementation has been replaced with an algorithm
  * based on the discrete form of the divergence theorem.  The general
  * assumption here is that the model is of  closed surface.  For more
- * details see the following reference  (Alyassin A.M. et al,
- * "Evaluation of new algorithms for the interactive measurement of
- * surface area and volume", Med Phys 21(6) 1994.).
+ * details see \cite alyassin1994.
  * \ingroup ITKMesh
  *
  * \sphinx

diff --git a/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h b/Modules/Core/QuadEdgeMesh/include/itkQuadEdge.h
@@ -119,7 +119,7 @@ namespace itk
 /**
  * \class QuadEdge
  * \brief Base class for the implementation of a quad-edge data structure as
- * proposed in "Guibas and Stolfi 1985"
+ * proposed in \cite guibas1985.
  *
  * \author Alexandre Gouaillard, Leonardo Florez-Valencia, Eric Boix
  *

diff --git a/Modules/Core/SpatialObjects/include/itkSpatialObject.h b/Modules/Core/SpatialObjects/include/itkSpatialObject.h
@@ -38,8 +38,8 @@ namespace itk
  * \class SpatialObject
  * \brief Implementation of the composite pattern
  *
- * The purpose of this class is to implement the composite pattern [Design
- * Patterns, Gamma, 1995] within itk, so that it becomes easy to create an
+ * The purpose of this class is to implement the composite pattern
+ * \cite gamma1994 within ITK, so that it becomes easy to create an
  * environment containing objects within a scene, and to manipulate the
  * environment as a whole or any of its component objects.  An
  * object has a list of transformations to transform object coordinates

diff --git a/Modules/Core/Transform/include/itkElasticBodyReciprocalSplineKernelTransform.h b/Modules/Core/Transform/include/itkElasticBodyReciprocalSplineKernelTransform.h
@@ -25,8 +25,7 @@ namespace itk
 /** \class ElasticBodyReciprocalSplineKernelTransform
  * This class defines the elastic body spline (EBS) transformation.
  * It is implemented in as straightforward a manner as possible from
- * the IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms,
- * Vol. 16 No. 3 June 1997
+ * \cite davis1997.
  * Taken from the paper:
  * The EBS "is based on a physical model of a homogeneous, isotropic,
  * three-dimensional elastic body. The model can approximate the way

diff --git a/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h b/Modules/Core/Transform/include/itkElasticBodySplineKernelTransform.h
@@ -27,8 +27,7 @@ namespace itk
  *
  * This class defines the elastic body spline (EBS) transformation.
  * It is implemented in as straightforward a manner as possible from
- * the IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms,
- * Vol. 16 No. 3 June 1997
+ * \cite davis1997.
  * Taken from the paper:
  * The EBS "is based on a physical model of a homogeneous, isotropic,
  * three-dimensional elastic body. The model can approximate the way

diff --git a/Modules/Core/Transform/include/itkKernelTransform.h b/Modules/Core/Transform/include/itkKernelTransform.h
@@ -34,9 +34,8 @@ namespace itk
 /**
  * \class KernelTransform
  * Intended to be a base class for elastic body spline and thin plate spline.
- * This is implemented in as straightforward a manner as possible from the
- * IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms, Vol. 16,
- * No. 3 June 1997. Notation closely follows their paper, so if you have it
+ * This is implemented in as straightforward a manner as possible from
+ * \cite davis1997. Notation closely follows the paper, so if you have it
  * in front of you, this code will make a lot more sense.
  *
  * KernelTransform:
@@ -49,10 +48,7 @@ namespace itk
  * This formulation allows the stiffness of the spline to
  * be adjusted, allowing the spline to vary from interpolating the
  * landmarks to approximating the landmarks.  This part of the
- * formulation is based on the short paper by R. Sprengel, K. Rohr,
- * H. Stiehl. "Thin-Plate Spline Approximation for Image
- * Registration". In 18th International Conference of the IEEE
- * Engineering in Medicine and Biology Society. 1996.
+ * formulation is based on \cite sprengel1996.
  *
  *
  * \ingroup ITKTransform

diff --git a/Modules/Core/Transform/include/itkThinPlateR2LogRSplineKernelTransform.h b/Modules/Core/Transform/include/itkThinPlateR2LogRSplineKernelTransform.h
@@ -25,8 +25,7 @@ namespace itk
 /** \class ThinPlateR2LogRSplineKernelTransform
  * This class defines the thin plate spline (TPS) transformation.
  * It is implemented in as straightforward a manner as possible from
- * the IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms,
- * Vol. 16 No. 3 June 1997.
+ * \cite davis1997.
  *
  * The kernel used in this variant of TPS is \f$ R^2 log(R) \f$
  *

diff --git a/Modules/Core/Transform/include/itkThinPlateSplineKernelTransform.h b/Modules/Core/Transform/include/itkThinPlateSplineKernelTransform.h
@@ -25,8 +25,7 @@ namespace itk
 /** \class ThinPlateSplineKernelTransform
  * This class defines the thin plate spline (TPS) transformation.
  * It is implemented in as straightforward a manner as possible from
- * the IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms,
- * Vol. 16 No. 3 June 1997
+ * \cite davis1997.
  *
  * \ingroup ITKTransform
  */

diff --git a/Modules/Core/Transform/include/itkVolumeSplineKernelTransform.h b/Modules/Core/Transform/include/itkVolumeSplineKernelTransform.h
@@ -25,8 +25,7 @@ namespace itk
 /** \class VolumeSplineKernelTransform
  * This class defines the thin plate spline (TPS) transformation.
  * It is implemented in as straightforward a manner as possible from
- * the IEEE TMI paper by Davis, Khotanzad, Flamig, and Harms,
- * Vol. 16 No. 3 June 1997
+ * \cite davis1997.
  *
  * \ingroup ITKTransform
  */

diff --git a/Modules/Filtering/AnisotropicSmoothing/include/itkAnisotropicDiffusionFunction.h b/Modules/Filtering/AnisotropicSmoothing/include/itkAnisotropicDiffusionFunction.h
@@ -119,10 +119,7 @@ namespace itk
  * application is wholly dependent on the results you want from a specific data
  * set and the number or iterations you perform.
  *
- * \par References
- * Pietro Perona and Jitendra Malik, ``Scale-space and edge detection using
- * anisotropic diffusion,'' IEEE Transactions on Pattern Analysis Machine
- * Intelligence, vol. 12, pp. 629-639, 1990.
+ * For additional details see \cite perona1990.
  *
  * \sa VectorAnisotropicDiffusionFunction
  * \sa ScalarAnisotropicDiffusionFunction

diff --git a/Modules/Filtering/AnisotropicSmoothing/include/itkCurvatureNDAnisotropicDiffusionFunction.h b/Modules/Filtering/AnisotropicSmoothing/include/itkCurvatureNDAnisotropicDiffusionFunction.h
@@ -59,11 +59,7 @@ namespace itk
  *
  * \f[ \nabla \cdot \frac{\nabla f}{\mid \nabla f \mid} \f] .
  *
- * \par References
- *  R. Whitaker and X. Xue. Variable-Conductance, Level-Set Curvature for
- *  Image Denoising, International Conference on Image Processing, 2001
- *  pp. 142-145, Vol.3.
- *
+ * For additional information see \cite whitaker2001.
  *
  * \sa AnisotropicDiffusionFunction
  * \ingroup FiniteDifferenceFunctions

diff --git a/Modules/Filtering/AnisotropicSmoothing/include/itkGradientNDAnisotropicDiffusionFunction.h b/Modules/Filtering/AnisotropicSmoothing/include/itkGradientNDAnisotropicDiffusionFunction.h
@@ -30,7 +30,7 @@ namespace itk
  * This class implements an N-dimensional version of the classic Perona-Malik
  * anisotropic diffusion equation for scalar-valued images.  See
  * itkAnisotropicDiffusionFunction for an overview of the anisotropic diffusion
- * framework and equation.
+ * framework and equation. For additional information see \cite perona1990.
  *
  * \par
  * The conductance term for this implementation is chosen as a function of the
@@ -44,11 +44,6 @@ namespace itk
  * in the Perona-Malik paper below, but uses a more robust technique
  * for gradient magnitude estimation and has been generalized to N-dimensions.
  *
- * \par References
- * Pietro Perona and Jalhandra Malik, ``Scale-space and edge detection using
- * anisotropic diffusion,'' IEEE Transactions on Pattern Analysis Machine
- * Intelligence, vol. 12, pp. 629-639, 1990.
- *
  * \sa AnisotropicDiffusionFunction
  * \sa VectorAnisotropicDiffusionFunction
  * \sa VectorGradientAnisotropicDiffusionFunction