Merge pull request InsightSoftwareConsortium#5215 from zivy/doxygenBib3

DOC: Convert from raw in-code citations to bibtex (3/N)

Author: zivy

Documentation/Doxygen/doxygen.bib

@@ -35,9 +35,7 @@ namespace itk
  * volume) while attribute closings fill dark regions that meet the
  * attribute criteria.
  *
- * This filter is implemented using the method of Wilkinson, "A
- * comparison of algorithms for Connected set openings and Closings",
- * A. Meijster and M. H. Wilkinson, PAMI, vol 24, no. 4, April 2002.
+ * This filter is implemented using the method describe in \cite meijster2002.
  *
  * This code was contributed in the Insight Journal paper
  *

Modules/Nonunit/Review/include/itkAttributeMorphologyBaseImageFilter.h

@@ -28,11 +28,7 @@ namespace itk
  *
  * This class holds cache data used during the computation of the LevelSet updates.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkConstrainedRegionBasedLevelSetFunctionSharedData.h

@@ -66,11 +66,7 @@ namespace itk
  * subclass it to a specific instance that supplies a function and Halt()
  * method.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkMultiphaseDenseFiniteDifferenceImageFilter.h

@@ -125,11 +125,7 @@ namespace itk
  * (or ThreadedHalt) method returns a true value to stop iteration.
  *
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkMultiphaseFiniteDifferenceImageFilter.h

@@ -136,20 +136,9 @@ namespace itk
  *  FiniteDifferenceFunction to use for calculations.  This is set using the
  *  method SetDifferenceFunction in the parent class.
  *
- * \par REFERENCES
- * Whitaker, Ross. A Level-Set Approach to 3D Reconstruction from Range Data.
- * International Journal of Computer Vision.  V. 29 No. 3, 203-231. 1998.
+ * For algorithmic details see \cite whitaker1998 and \sethian1996.
  *
- * \par
- * Sethian, J.A. Level Set Methods. Cambridge University Press. 1996.
- *
- *
- *
- * This code was adapted from the paper
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * This code was adapted from \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkMultiphaseSparseFiniteDifferenceImageFilter.h

@@ -31,11 +31,7 @@ namespace itk
  * This class implements a level set function that computes the speed image by
  * integrating values on the image domain.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
@@ -459,12 +455,7 @@ class ITK_TEMPLATE_EXPORT RegionBasedLevelSetFunction : public FiniteDifferenceF
 
   /** \brief Compute the laplacian term
       \return \f$ \Delta \phi - \div(\frac{\nabla \phi}{|\nabla \phi|}) \f$
-      For details see
-
-      \par REFERENCE
-      Li, C.M. and Xu, C.Y. and Gui, C. and Fox, M.D.
-      "Level Set Evolution without Re-Initialization: A New Variational Formulation",
-      CVPR05. 2005. pp. 430-436.
+      For details see \cite li2005.
   */
 
   /** \brief Compute the laplacian

Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunction.h

@@ -35,11 +35,7 @@ namespace itk
  *
  * This class holds cache data used during the computation of the LevelSet updates.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionData.h

@@ -35,11 +35,7 @@ namespace itk
  *
  * This class holds cache data used during the computation of the LevelSet updates.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionSharedData.h

@@ -27,11 +27,7 @@ namespace itk
 /** \class ScalarChanAndVeseDenseLevelSetImageFilter
  * \brief Dense implementation of the Chan and Vese multiphase level set image filter.
  *
- * This code was adapted from the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * This code was adapted from the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkScalarChanAndVeseDenseLevelSetImageFilter.h

@@ -33,16 +33,7 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- * Based on the papers:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
- *
- *         "Segmenting and Tracking Fluorescent Cells in Dynamic 3-D
- *          Microscopy With Coupled Active Surfaces"
- *          Dufour, Shinin, Tajbakhsh, Guillen-Aghion, Olivo-Marin
- *          In IEEE Transactions on Image Processing, vol. 14, No 9, Sep. 2005
+ * Based on the papers \cite chan1999 and \cite dufour2005.
  *
  *  This code was taken from the Insight Journal paper:
  *

Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunction.h

@@ -28,11 +28,8 @@ namespace itk
  *
  * This class holds cache data used during the computation of the LevelSet updates.
  *
- * Based on the paper:
+ * Based on the paper \cite chan1999.
  *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunctionData.h

@@ -27,11 +27,7 @@ namespace itk
 /** \class ScalarChanAndVeseSparseLevelSetImageFilter
  * \brief Sparse implementation of the Chan and Vese multiphase level set image filter.
  *
- * This code was adapted from the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * This code was adapted from the paper \cite chan1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkScalarChanAndVeseSparseLevelSetImageFilter.h

@@ -33,11 +33,7 @@ namespace itk
  * integrating values on the image domain. NOTE: The convention followed is
  * inside of the level-set function is negative and outside is positive.
  *
- * Based on the paper:
- *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
+ * Based on the paper \cite chan2001.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkScalarRegionBasedLevelSetFunction.h

@@ -28,11 +28,8 @@ namespace itk
  *
  * This class holds cache data used during the computation of the LevelSet updates.
  *
- * Based on the paper:
+ * Based on the paper \cite chan1999.
  *
- *        "An active contour model without edges"
- *         T. Chan and L. Vese.
- *         In Scale-Space Theories in Computer Vision, pages 141-151, 1999.
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *

Modules/Nonunit/Review/include/itkUnconstrainedRegionBasedLevelSetFunctionSharedData.h

@@ -62,19 +62,7 @@ namespace fem
  *
  * \author Yixun Liu
  *
- * \par REFERENCE
- * O. Clatz, H. Delingette, I.-F. Talos, A. Golby, R. Kikinis, F. Jolesz,
- * N. Ayache, and S. Warfield, "Robust non-rigid registration to capture
- * brain shift from intra-operative MRI", IEEE Trans. Med. Imag., vol. 24,
- * no. 11, pp. 1417-1427, 2005.
- *
- *
- * \par REFERENCE
- * Yixun Liu, Andriy Fedorov, Ron Kikinis and Nikos Chrisochoides, "Real-time Non-rigid
- * Registration of Medical Images on a Cooperative Parallel Architecture",
- * IEEE International Conference on Bioinformatics & Biomedicine, pp. 401- 4,
- * November 2009.
- *
+ * For algorithmic details see \cite clatz2005 and \cite liu2009.
  *
  * \ingroup ITKFEM
  */

Modules/Numerics/FEM/include/itkFEMRobustSolver.h

@@ -106,17 +106,7 @@ namespace fem
  *
  * \author Yixun Liu
  *
- * \par REFERENCE
- * O. Clatz, H. Delingette, I.-F. Talos, A. Golby, R. Kikinis, F. Jolesz,
- * N. Ayache, and S. Warfield, "Robust non-rigid registration to capture brain
- * shift from intra-operative MRI", IEEE Trans. Med. Imag.,
- * 24(11);1417-27, 2005.
- *
- * \par REFERENCE
- * Yixun Liu, Andriy Fedorov, Ron Kikinis and Nikos Chrisochoides,
- * "Real-time Non-rigidRegistration of Medical Images on a Cooperative Parallel
- * Architecture", IEEE International Conference on Bioinformatics & Biomedicine,
- * pp. 401-404, November 2009.
+ * For algorithmic details see \cite clatz2005 and \cite liu2009.
  *
  * \sa FEMRobustSolver
  *

Modules/Numerics/FEM/include/itkFEMScatteredDataPointSetToImageFilter.h

@@ -61,8 +61,7 @@ namespace itk
  *  FiniteDifferenceFunction to use for calculations.  This is set using the
  *  method SetDifferenceFunction in the parent class.
  *
- * \par REFERENCES
- * Sethian, J.A. Level Set Methods. Cambridge University Press. 1996.
+ * For algorithmic details see \cite sethian1996.
  *
  * \ingroup ITKNarrowBand
  */

Modules/Numerics/NarrowBand/include/itkNarrowBandImageFilterBase.h

@@ -28,11 +28,7 @@ namespace itk
  * \brief Implementation of a biased/regularized Particle Swarm Optimization
  *        (PSO) algorithm.
  *
- * This PSO algorithm was originally described in:
- * M. P. Wachowiak, R. Smolikova, Y. Zheng, J. M. Zurada, A. S. Elmaghraby,
- * "An approach to multimodal biomedical image registration utilizing particle
- * swarm optimization", IEEE Transactions on Evolutionary Computing,
- * vol. 8(3): 289-301, 2004.
+ * This PSO algorithm was originally described in \cite wachowiak2004.
  *
  * The algorithm uses a stochastic optimization approach. Optimization
  * is performed by maintaining a swarm (flock) of

Modules/Numerics/Optimizers/include/itkInitializationBiasedParticleSwarmOptimizer.h

@@ -45,18 +45,7 @@ class ITK_FORWARD_EXPORT LBFGSBOptimizerHelper;
  *
  * See also the documentation in Numerics/lbfgsb.c
  *
- * References:
- *
- * [1] R. H. Byrd, P. Lu and J. Nocedal.
- * A Limited Memory Algorithm for Bound Constrained Optimization, (1995),
- * SIAM Journal on Scientific and Statistical Computing ,
- * 16, 5, pp. 1190-1208.
- *
- * [2] C. Zhu, R. H. Byrd and J. Nocedal.
- * L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale
- * bound constrained optimization (1997),
- * ACM Transactions on Mathematical Software,
- * Vol 23, Num. 4, pp. 550 - 560.
+ * For algorithmic details see \cite byrd1995 and \cite zhu1997.
  *
  * \ingroup Numerics Optimizers
  * \ingroup ITKOptimizers

Modules/Numerics/Optimizers/include/itkLBFGSBOptimizer.h

@@ -27,7 +27,8 @@ namespace itk
 {
 /** \class LBFGSOptimizer
  * \brief Wrap of the vnl_lbfgs algorithm for use in ITKv4 registration framework.
- * The vnl_lbfgs is a wrapper for the NETLIB fortran code by Nocedal [1].
+ * The vnl_lbfgs is a wrapper for the NETLIB fortran code by Nocedal
+ * [NETLIB lbfgs](http://users.iems.northwestern.edu/~nocedal/lbfgs.html).
  *
  * LBFGS is a quasi-Newton method. Quasi-Newton methods use an approximate estimate
  * of the inverse Hessian \f$ (\nabla^2 f(x) )^{-1} \f$ to scale the gradient step:
@@ -40,7 +41,7 @@ namespace itk
  * thus only the gradient of the objective function is required.
  *
  * 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
+ * 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
  *   \le
@@ -64,21 +65,9 @@ namespace itk
  * optimizer is unlikely to find a minima.
  *
  *
- * References:
- *
- * [1] [NETLIB lbfgs](http://users.iems.northwestern.edu/~nocedal/lbfgs.html)
- *
- * [2] Jorge Nocedal.
- * Updating Quasi-Newton Matrices with Limited Storage.
- * Mathematics of Computation, Vol. 35, No. 151, pp. 773-782, 1980.
- *
- * [3] Dong C. Liu and Jorge Nocedal.
- * On the limited memory BFGS method for large scale optimization.
- * Mathematical Programming B, Vol. 45, No. 3, pp. 503-528, 1989.
- *
- * [4] More, J. J. and D. J. Thuente.
- * Line Search Algorithms with Guaranteed Sufficient Decrease.
- * ACM Transactions on Mathematical Software 20, no. 3 (1994): 286-307.
+ * For algorithmic details see:
+ * [NETLIB lbfgs](http://users.iems.northwestern.edu/~nocedal/lbfgs.html),
+ * \cite nocedal1980, \cite liu1989, and \cite more1994.
  *
  * \ingroup Numerics Optimizers
  * \ingroup ITKOptimizers

Modules/Numerics/Optimizers/include/itkLBFGSOptimizer.h

@@ -52,15 +52,8 @@ namespace itk
  * by Martin Styner, Univ. of North Carolina at Chapel Hill, and his
  * colleagues.
  *
- * For more details. refer to the following articles.
- * "Parametric estimate of intensity inhomogeneities applied to MRI"
- * Martin Styner, G. Gerig, Christian Brechbuehler, Gabor Szekely,
- * IEEE TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000,
- * (https://www.cs.unc.edu/~styner/docs/tmi00.pdf)
- *
- * "Evaluation of 2D/3D bias correction with 1+1ES-optimization"
- * Martin Styner, Prof. Dr. G. Gerig (IKT, BIWI, ETH Zuerich), TR-197
- * (https://www.cs.unc.edu/~styner/docs/StynerTR97.pdf)
+ * For more details refer to the following articles \cite styner2000
+ * and \cite styner1997.
  *
  * \ingroup Numerics Optimizers
  *

Modules/Numerics/Optimizers/include/itkOnePlusOneEvolutionaryOptimizer.h

@@ -26,9 +26,7 @@ namespace itk
 /** \class ParticleSwarmOptimizer
  * \brief Implementation of a Particle Swarm Optimization (PSO) algorithm.
  *
- * The PSO algorithm was originally presented in:<br>
- * J. Kennedy, R. Eberhart, "Particle Swarm Optimization",
- * Proc. IEEE Int. Neural Networks, 1995.<br>
+ * The PSO algorithm was originally presented in \cite kennedy1995.
  *
  * The algorithm uses a stochastic optimization approach. Optimization
  * is performed by maintaining a swarm (flock) of

Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizer.h

@@ -28,9 +28,7 @@ namespace itk
 /** \class ParticleSwarmOptimizerBase
  * \brief Abstract implementation of a Particle Swarm Optimization (PSO) algorithm.
  *
- * The PSO algorithm was originally presented in:<br>
- * J. Kennedy, R. Eberhart, "Particle Swarm Optimization",
- * Proc. IEEE Int. Neural Networks, 1995.<br>
+ * The PSO algorithm was originally presented in \cite kennedy1995.
  *
  * The algorithm is a stochastic global search optimization approach.
  * Optimization is performed by maintaining a swarm of particles that traverse

Modules/Numerics/Optimizers/include/itkParticleSwarmOptimizerBase.h

@@ -50,13 +50,8 @@ extern ITKOptimizers_EXPORT std::ostream &
  * \brief An optimizer based on simultaneous perturbation...
  *
  * This optimizer is an implementation of the Simultaneous
- * Perturbation Stochastic Approximation method, described in:
- *
- * - https://www.jhuapl.edu/SPSA/
- *
- * - Spall, J.C. (1998), "An Overview of the Simultaneous
- * Perturbation Method for Efficient Optimization," Johns
- * Hopkins APL Technical Digest, vol. 19, pp. 482-492
+ * Perturbation Stochastic Approximation method, described in
+ * \cite spall1998.
  *
  * \ingroup Optimizers
  * \ingroup ITKOptimizers