Merge branch 'master' into feature/issue_3654

# Conflicts:
#	Modules/IO/ImageBase/include/itkImageSeriesWriter.h

Author: albert-github

.github/workflows/scorecard.yml

@@ -1,8 +1,4 @@
-# This workflow uses actions that are not certified by GitHub. They are provided
-# by a third-party and are governed by separate terms of service, privacy
-# policy, and support documentation.
-
-name: Scorecard supply-chain security
+name: Scorecard analysis workflow
 on:
   # For Branch-Protection check. Only the default branch is supported. See
   # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection
@@ -32,12 +28,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
+        uses: ossf/scorecard-action@f49aabe0b5af0936a0987cfb85d86b75731b0186 # v2.4.1
         with:
           results_file: results.sarif
           results_format: sarif
@@ -56,10 +52,11 @@ jobs:
           #     of the value entered here.
           publish_results: true
 
-      # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
-      # format to the repository Actions tab.
+      # Upload the results as artifacts (optional). Commenting out will disable
+      # uploads of run results in SARIF format to the repository Actions tab.
+      # https://docs.github.com/en/actions/advanced-guides/storing-workflow-data-as-artifacts
       - name: "Upload artifact"
-        uses: actions/upload-artifact@97a0fba1372883ab732affbe8f94b823f91727db # v3.pre.node20
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1
         with:
           name: SARIF file
           path: results.sarif
@@ -68,6 +65,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@v3
+        uses: github/codeql-action/upload-sarif@b56ba49b26e50535fa1e7f7db0f4f7b4bf65d80d # v3.28.10
         with:
           sarif_file: results.sarif

CMake/ITKModuleTest.cmake

@@ -153,14 +153,6 @@ function(itk_python_add_test)
   else()
     set(itk_wrap_python_binary_dir "${ITK_BINARY_DIR}/Wrapping/Generators/Python")
   endif()
-  # itk_wrap_python_binary_dir *MUST* contain the WrapITK.pth file
-  # Final installed version of ITK will leverage the WrapITK.pth paths, so
-  # the test environment should also use those same paths.
-  set(WrapITK_PTH_FILE "${itk_wrap_python_binary_dir}/WrapITK.pth")
-  if(NOT EXISTS ${WrapITK_PTH_FILE})
-    message(FATAL_ERROR "${WrapITK_PTH_FILE} must exist.")
-  endif()
-  unset(WrapITK_PTH_FILE)
 
   itk_add_test(
     NAME

Documentation/Doxygen/doxygen.bib

@@ -1549,58 +1549,7 @@ @article{zijdenbos1994
   doi          = {10.1109/42.363096},
   url          = {https://doi.org/10.1109/42.363096}
 }
-@book{book_2003,
-  title={Computer Aided Systems Theory - EUROCAST 2003: 9th International Workshop on Computer Aided Systems Theory Las Palmas de Gran Canaria, Spain, February 24-28, 2003 Revised Selected Papers},
-  ISBN={9783540452102},
-  ISSN={1611-3349},
-  url={https//dx.doi.org/10.1007/b13239},
-  DOI={10.1007/b13239},
-  journal={Lecture Notes in Computer Science},
-  publisher={Springer Berlin Heidelberg},
-  year={2003} }
-@inproceedings{Aylward_2016,
-  title={Ultrasound spectroscopy},
-  url={https//dx.doi.org/10.1109/ISBI.2016.7493437},
-  DOI={10.1109/isbi.2016.7493437},
-  booktitle={2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)},
-  publisher={IEEE},
-  author={Aylward, S. R. and McCormick, M. and Kang, H. J. and Razzaque, S. and Kwitt, R. and Niethammer, M.},
-  year={2016},
-  month=apr, pages={1013–1016} }
-@article{Albu_2008,
-  title={A Morphology-Based Approach for Interslice Interpolation of Anatomical Slices From Volumetric Images},
-  volume={55},
-  ISSN={1558-2531},
-  url={https//dx.doi.org/10.1109/TBME.2008.921158},
-  DOI={10.1109/tbme.2008.921158},
-  number={8},
-  journal={IEEE Transactions on Biomedical Engineering},
-  publisher={Institute of Electrical and Electronics Engineers (IEEE)},
-  author={Albu, Alexandra Branzan and Beugeling, Trevor and Laurendeau, Denis},
-  year={2008},
-  month=aug, pages={2022–2038} }
-@article{McCormick_2011,
-  title={Bayesian Regularization Applied to Ultrasound Strain Imaging},
-  volume={58},
-  ISSN={1558-2531},
-  url={https//dx.doi.org/10.1109/TBME.2011.2106500},
-  DOI={10.1109/tbme.2011.2106500},
-  number={6},
-  journal={IEEE Transactions on Biomedical Engineering},
-  publisher={Institute of Electrical and Electronics Engineers (IEEE)},
-  author={McCormick, M and Rubert, N and Varghese, T},
-  year={2011},
-  month=jun, pages={1612–1620} }
-@article{McCormick_2014,
-  title={ITK: enabling reproducible research and open science},
-  volume={8},
-  ISSN={1662-5196},
-  url={https//dx.doi.org/10.3389/fninf.2014.00013},
-  DOI={10.3389/fninf.2014.00013},
-  journal={Frontiers in Neuroinformatics},
-  publisher={Frontiers Media SA},
-  author={McCormick, Matthew and Liu, Xiaoxiao and Jomier, Julien and Marion, Charles and Ibanez, Luis},
-  year={2014} }
+
 @article{Tustison_2005,
   title={N-D $C^k$ B-Spline Scattered Data Approximation},
   ISSN={2327-770X},
@@ -1611,16 +1560,6 @@ @article{Tustison_2005
   author={Tustison, Nicholas J. and Gee, James},
   year={2005},
   month=nov }
-@article{Hernandez_Cerdan_2016,
-  title={Isotropic and Steerable Wavelets in N Dimensions. A multiresolution analysis framework.},
-  ISSN={2327-770X},
-  url={https//dx.doi.org/10.54294/0e1c0748fe24},
-  DOI={10.54294/0e1c0748fe24},
-  journal={The Insight Journal},
-  publisher={NumFOCUS - Insight Software Consortium (ITK)},
-  author={Hernandez-Cerdan, Pablo},
-  year={2016},
-  month=jul }
 @article{Lehmann_2010_b,
   title={FFT based convolution},
   ISSN={2327-770X},
@@ -1651,18 +1590,8 @@ @article{Tustison_2009_d
   author={Tustison, Nicholas J. and Gee, James},
   year={2009},
   month=dec }
-@article{Mccormick_2017,
-  title={N-Dimensional Computation of Strain Tensor Images in the Insight Toolkit},
-  ISSN={2327-770X},
-  url={https//dx.doi.org/10.54294/1wtpo8},
-  DOI={10.54294/1wtpo8},
-  journal={The Insight Journal},
-  publisher={NumFOCUS - Insight Software Consortium (ITK)},
-  author={Mccormick, Matthew},
-  year={2017},
-  month=may }
 @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},

Modules/Bridge/VtkGlue/include/itkViewImage.hxx

@@ -101,8 +101,8 @@ ViewImage<TImage>::View(const ImageType * img, const std::string & winTitle, siz
   cam->GetViewUp(vup);
   for (unsigned int i = 0; i < 3; ++i)
   {
-    pos[i] = -pos[i];
-    vup[i] = -vup[i];
+    pos[i] *= -1;
+    vup[i] *= -1;
   }
   cam->SetPosition(pos);
   cam->SetViewUp(vup);

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
  */

Modules/Core/Common/include/itkDataObject.h

@@ -59,10 +59,7 @@ class ITKCommon_EXPORT DataObjectError : public ExceptionObject
   ~DataObjectError() noexcept override = default;
 
   /** Constructor. Needed to ensure the exception object can be copied. */
-  DataObjectError(const char * file, unsigned int lineNumber);
-
-  /** Constructor. Needed to ensure the exception object can be copied. */
-  DataObjectError(const std::string & file, unsigned int lineNumber);
+  DataObjectError(std::string file, unsigned int lineNumber);
 
   /** Copy constructor. Needed to ensure the exception object can be copied. */
   DataObjectError(const DataObjectError & orig) noexcept;
@@ -118,10 +115,7 @@ class ITKCommon_EXPORT InvalidRequestedRegionError : public DataObjectError
   ~InvalidRequestedRegionError() noexcept override = default;
 
   /** Constructor. Needed to ensure the exception object can be copied. */
-  InvalidRequestedRegionError(const char * file, unsigned int lineNumber);
-
-  /** Constructor. Needed to ensure the exception object can be copied. */
-  InvalidRequestedRegionError(const std::string & file, unsigned int lineNumber);
+  InvalidRequestedRegionError(std::string file, unsigned int lineNumber);
 
   /** Copy constructor.  Needed to ensure the exception object can be copied. */
   InvalidRequestedRegionError(const InvalidRequestedRegionError & orig) noexcept;

Modules/Core/Common/include/itkExceptionObject.h

@@ -56,14 +56,10 @@ class ITKCommon_EXPORT ExceptionObject : public std::exception
   /** Explicitly-defaulted default-constructor. Creates an empty exception object. */
   ExceptionObject() noexcept = default;
 
-  explicit ExceptionObject(const char * file,
-                           unsigned int lineNumber = 0,
-                           const char * desc = "None",
-                           const char * loc = "Unknown");
   explicit ExceptionObject(std::string  file,
                            unsigned int lineNumber = 0,
-                           std::string  desc = "None",
-                           std::string  loc = "Unknown");
+                           std::string  description = "None",
+                           std::string  location = {});
 
   /** Copy-constructor. */
   ExceptionObject(const ExceptionObject &) noexcept = default;
@@ -133,7 +129,7 @@ class ITKCommon_EXPORT ExceptionObject : public std::exception
 private:
   class ExceptionData;
 
-  std::shared_ptr<const ExceptionData> m_ExceptionData{};
+  std::shared_ptr<const ExceptionData> m_ExceptionData;
 };
 
 /** Generic inserter operator for ExceptionObject and its subclasses. */
@@ -222,18 +218,9 @@ class ITKCommon_EXPORT ProcessAborted : public ExceptionObject
   }
 
   /** Constructor. Needed to ensure the exception object can be copied. */
-  ProcessAborted(const char * file, unsigned int lineNumber)
-    : ExceptionObject(file, lineNumber)
-  {
-    this->SetDescription("Filter execution was aborted by an external request");
-  }
-
-  /** Constructor. Needed to ensure the exception object can be copied. */
-  ProcessAborted(const std::string & file, unsigned int lineNumber)
-    : ExceptionObject(file, lineNumber)
-  {
-    this->SetDescription("Filter execution was aborted by an external request");
-  }
+  ProcessAborted(std::string file, unsigned int lineNumber)
+    : ExceptionObject(std::move(file), lineNumber, "Filter execution was aborted by an external request")
+  {}
 
   /** \see LightObject::GetNameOfClass() */
   itkOverrideGetNameOfClassMacro(ProcessAborted);

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
  */

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
  */

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
  */