DOC: replace explicit references to papers with citations.

zivy · hjmjohnson · commit 657e16e0ba0e · 2025-03-18T17:34:56.000-05:00
Replace the explicit references with citations to Lehmann_2006_a,
Tustison_2009_d, Mosaliganti_2009_a, Mosaliganti_2009_b, and
Mosaliganti_2009_c.
diff --git a/Documentation/Doxygen/doxygen.bib b/Documentation/Doxygen/doxygen.bib
@@ -1591,7 +1591,7 @@ @article{Tustison_2009_d
   year={2009},
   month=dec }
 @article{Mosaliganti_2009_a,
-  title={level set segmentation using coupled active surfaces},
+  title={Level set segmentation using coupled active surfaces},
   ISSN={2327-770X},
   url={https//dx.doi.org/10.54294/23ugmy},
   DOI={10.54294/23ugmy},
diff --git a/Modules/Core/Common/include/itkAtanRegularizedHeavisideStepFunction.h b/Modules/Core/Common/include/itkAtanRegularizedHeavisideStepFunction.h
@@ -28,21 +28,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKCommon
  */
diff --git a/Modules/Core/Common/include/itkHeavisideStepFunction.h b/Modules/Core/Common/include/itkHeavisideStepFunction.h
@@ -34,21 +34,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKCommon
  */
diff --git a/Modules/Core/Common/include/itkHeavisideStepFunctionBase.h b/Modules/Core/Common/include/itkHeavisideStepFunctionBase.h
@@ -29,21 +29,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKCommon
  */
diff --git a/Modules/Core/Common/include/itkRegularizedHeavisideStepFunction.h b/Modules/Core/Common/include/itkRegularizedHeavisideStepFunction.h
@@ -28,21 +28,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKCommon
  */
diff --git a/Modules/Core/Common/include/itkSinRegularizedHeavisideStepFunction.h b/Modules/Core/Common/include/itkSinRegularizedHeavisideStepFunction.h
@@ -28,21 +28,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKCommon
  */
diff --git a/Modules/Filtering/ImageStatistics/include/itkBinaryProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkBinaryProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class BinaryProjectionImageFilter
  * \brief Binary projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  *  INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkLabelOverlapMeasuresImageFilter.h
@@ -30,10 +30,8 @@ namespace itk
  * \brief Computes overlap measures between the same set of labels of
  * pixels of two images. Background is assumed to be 0.
  *
- * This code was contributed in the Insight Journal paper:
- * "Introducing Dice, Jaccard, and Other Label Overlap Measures To ITK"
- * by Nicholas J. Tustison, James C. Gee
- * https://doi.org/10.54294/1vixgg
+ * This code was contributed in the Insight Journal paper
+ * \cite Tustison_2009_d.
  *
  * \author Nicholas J. Tustison
  * \sa LabelOverlapMeasuresImageFilter
diff --git a/Modules/Filtering/ImageStatistics/include/itkMaximumProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkMaximumProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class MaximumProjectionImageFilter
  * \brief Maximum projection
  *
- * This class was contributed to the insight journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the insight journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la reproduction,
  *  inra de jouy-en-josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkMeanProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkMeanProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class MeanProjectionImageFilter
  * \brief Mean projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkMedianProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkMedianProjectionImageFilter.h
@@ -29,9 +29,8 @@ namespace itk
 /** \class MedianProjectionImageFilter
  * \brief Median projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkMinimumProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkMinimumProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class MinimumProjectionImageFilter
  * \brief Minimum projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkProjectionImageFilter.h
@@ -42,8 +42,7 @@ namespace itk
  * the type of the output image.
  *
  * This class was contributed to the Insight Journal by Emiliano Beronich and
- * Gaetan Lehmann. The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * Gaetan Lehmann \cite Lehmann_2006_a.
  *
  * \author Emiliano Beronich
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
diff --git a/Modules/Filtering/ImageStatistics/include/itkStandardDeviationProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkStandardDeviationProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class StandardDeviationProjectionImageFilter
  * \brief Mean projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/ImageStatistics/include/itkSumProjectionImageFilter.h b/Modules/Filtering/ImageStatistics/include/itkSumProjectionImageFilter.h
@@ -26,9 +26,8 @@ namespace itk
 /** \class SumProjectionImageFilter
  * \brief Sum projection
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * The original paper can be found at
- * https://doi.org/10.54294/0pjyho
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h b/Modules/Filtering/Thresholding/include/itkBinaryThresholdProjectionImageFilter.h
@@ -28,10 +28,8 @@ namespace itk
  * \brief BinaryThreshold projection
  *
  *
- * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * the original paper can be found at
- * https://doi.org/10.54294/0pjyho
- *
+ * This class was contributed to the Insight Journal by Gaetan Lehmann
+ * \cite Lehmann_2006_a.
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
diff --git a/Modules/Nonunit/Review/include/itkConstrainedRegionBasedLevelSetFunctionSharedData.h b/Modules/Nonunit/Review/include/itkConstrainedRegionBasedLevelSetFunctionSharedData.h
@@ -32,21 +32,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKReview
  */
diff --git a/Modules/Nonunit/Review/include/itkMultiphaseDenseFiniteDifferenceImageFilter.h b/Modules/Nonunit/Review/include/itkMultiphaseDenseFiniteDifferenceImageFilter.h
@@ -70,21 +70,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ImageFilters
  * \sa FiniteDifferenceImageFilter
diff --git a/Modules/Nonunit/Review/include/itkMultiphaseFiniteDifferenceImageFilter.h b/Modules/Nonunit/Review/include/itkMultiphaseFiniteDifferenceImageFilter.h
@@ -129,21 +129,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
- *
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ImageFilter
  * \ingroup LevelSetSegmentation
diff --git a/Modules/Nonunit/Review/include/itkMultiphaseSparseFiniteDifferenceImageFilter.h b/Modules/Nonunit/Review/include/itkMultiphaseSparseFiniteDifferenceImageFilter.h
@@ -142,20 +142,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * \ingroup ITKReview
  */
diff --git a/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunction.h b/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunction.h
@@ -35,20 +35,9 @@ namespace itk
  *
  * \author Mosaliganti K., Smith B., Gelas A., Gouaillard A., Megason S.
  *
- *  This code was taken from the Insight Journal paper:
- *
- *      "Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes"
- *      https://doi.org/10.54294/wvwmf8
- *
- *  That is based on the papers:
- *
- *      "Level Set Segmentation: Active Contours without edge"
- *      https://doi.org/10.54294/8jk6oy
- *
- *      and
- *
- *      "Level set segmentation using coupled active surfaces"
- *      https://doi.org/10.54294/23ugmy
+ *  This code was taken from the Insight Journal paper \cite Mosaliganti_2009_c
+ *  that is based on the papers \cite Mosaliganti_2009_a and
+ *  \cite  Mosaliganti_2009_b.
  *
  * NOTE: The convention followed is
  * inside of the level-set function is negative and outside is positive.
diff --git a/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionData.h b/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionData.h
diff --git a/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionSharedData.h b/Modules/Nonunit/Review/include/itkRegionBasedLevelSetFunctionSharedData.h
diff --git a/Modules/Nonunit/Review/include/itkScalarChanAndVeseDenseLevelSetImageFilter.h b/Modules/Nonunit/Review/include/itkScalarChanAndVeseDenseLevelSetImageFilter.h
diff --git a/Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunction.h b/Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunction.h
diff --git a/Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunctionData.h b/Modules/Nonunit/Review/include/itkScalarChanAndVeseLevelSetFunctionData.h
diff --git a/Modules/Nonunit/Review/include/itkScalarChanAndVeseSparseLevelSetImageFilter.h b/Modules/Nonunit/Review/include/itkScalarChanAndVeseSparseLevelSetImageFilter.h
diff --git a/Modules/Nonunit/Review/include/itkScalarRegionBasedLevelSetFunction.h b/Modules/Nonunit/Review/include/itkScalarRegionBasedLevelSetFunction.h
diff --git a/Modules/Nonunit/Review/include/itkUnconstrainedRegionBasedLevelSetFunctionSharedData.h b/Modules/Nonunit/Review/include/itkUnconstrainedRegionBasedLevelSetFunctionSharedData.h

Original file line number	Diff line number	Diff line change
`@@ -26,9 +26,8 @@ namespace itk`
`26`	`26`	`/** \class BinaryProjectionImageFilter`
`27`	`27`	`* \brief Binary projection`
`28`	`28`	`*`
`29`		`- * This class was contributed to the Insight Journal by Gaetan Lehmann.`
`30`		`- * The original paper can be found at`
`31`		`- * https://doi.org/10.54294/0pjyho`
	`29`	`+ * This class was contributed to the Insight Journal by Gaetan Lehmann`
	`30`	`+ * \cite Lehmann_2006_a.`
`32`	`31`	`*`
`33`	`32`	`* \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,`
`34`	`33`	`* INRA de Jouy-en-Josas, France.`
Original file line number	Diff line number	Diff line change
`@@ -30,10 +30,8 @@ namespace itk`
`30`	`30`	`* \brief Computes overlap measures between the same set of labels of`
`31`	`31`	`* pixels of two images. Background is assumed to be 0.`
`32`	`32`	`*`
`33`		`- * This code was contributed in the Insight Journal paper:`
`34`		`- * "Introducing Dice, Jaccard, and Other Label Overlap Measures To ITK"`
`35`		`- * by Nicholas J. Tustison, James C. Gee`
`36`		`- * https://doi.org/10.54294/1vixgg`
	`33`	`+ * This code was contributed in the Insight Journal paper`
	`34`	`+ * \cite Tustison_2009_d.`
`37`	`35`	`*`
`38`	`36`	`* \author Nicholas J. Tustison`
`39`	`37`	`* \sa LabelOverlapMeasuresImageFilter`