Merge remote-tracking branch 'upstream/release' into release-5.4

Documentation/docs/contributing/documenting_itk.md

@@ -1,15 +1,22 @@
 # Documenting ITK
 
-The ITK code documentation is available online at https://itk.org/Doxygen/html/.
+The ITK code documentation is available online at https://docs.itk.org/projects/doxygen/.
 
 By default, the latest released documentation version is displayed,
 but documentation for previous versions is available at by choosing the
-appropriate version at the bottom of the above page, e.g.
-https://itk.org/Doxygen53/html/index.html.
+appropriate version from the ReadTheDocs interface at the bottom right of a page, e.g.
+https://docs.itk.org/projects/doxygen/en/v5.3.0/.
 
 ## Using Doxygen for C++ code
 
-### Dependencies
+### Build Option 1: Use Docker
+
+The ITK Doxygen documentation can be built using Docker as described in the
+[ITKDoxygen repository](https://github.com/InsightSoftwareConsortium/ITKDoxygen).
+
+### Build Option 2: Use CMake, Doxygen Dot
+
+#### Dependencies
 
 Generating a complete Doxygen documentation requires (besides CMake and
 the ITK source code):
@@ -22,7 +29,7 @@ Preferable:
 - [Dot](https://graphviz.org/doc/info/lang.html) from [GraphViz](https://graphviz.org/)
   for generating inheritance and dependency graphs.
 
-## Generating the Doxygen documentation
+#### Generating the Doxygen documentation
 
 Generating the Doxygen documentation for ITK requires:
 

Documentation/docs/index.md

@@ -45,7 +45,7 @@ learn/fda_off_the_shelf_sw_guidelines.md
 :maxdepth: 1
 :caption: 🔨 Develop
 
-API <https://itk.org/Doxygen/html/index.html>
+API <https://docs.itk.org/projects/doxygen/en/stable/index.html>
 Discussion <https://discourse.itk.org>
 Issue tracker <https://github.com/InsightSoftwareConsortium/ITK/issues>
 supported_compilers

Documentation/docs/learn/dicom.md

@@ -59,7 +59,7 @@ $ DicomImageReadPrintTags image.dcm | grep "Image Pixel Value"
 ## Why did the header of my DICOM file change?
 
 A common question that frequently arises after using
-[`itk::GDCMImageIO`](https://itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html)
+[`itk::GDCMImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GDCMImageIO.html)
 to read, update and write out a DICOM file is: why did my header file
 change during the update mechanism?
 

Documentation/docs/learn/faq.md

@@ -13,7 +13,7 @@ optional modules (e.g. [ITKVTKGlue](https://github.com/InsightSoftwareConsortium
 
 The following table identifies the file formats that ITK can read/write
 via a factory mechanism based on the file extension
-([`itk::ImageIOFactory`](https://itk.org/Doxygen/html/classitk_1_1ImageIOFactory.html)). Some proprietary files format are only imported.
+([`itk::ImageIOFactory`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageIOFactory.html)). Some proprietary files format are only imported.
 
 More information on supported file formats is available on the
 [ITK-Wasm Image File Formats](https://wasm.itk.org/en/latest/introduction/file_formats/images.html)
@@ -32,39 +32,39 @@ images.
 | ----------- | ---------- | ------ |
 | Analyze 7.5 | `itk::AnalyzeImageIO` | |
 | [BioRad](https://www.bio-rad.com/) | | |
-| [BMP](https://en.wikipedia.org/wiki/BMP_file_format) † | [`itk::BMPImageIO`](https://itk.org/Doxygen/html/classitk_1_1BMPImageIO.html) | |
-| [DICOM](https://dicom.nema.org/) | [`itk::GDCMImageIO`](https://itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html) | |
+| [BMP](https://en.wikipedia.org/wiki/BMP_file_format) † | [`itk::BMPImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1BMPImageIO.html) | |
+| [DICOM](https://dicom.nema.org/) | [`itk::GDCMImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GDCMImageIO.html) | |
 | [DICOM Series](https://dicom.nema.org/) | | |
-| GE 4x | [`itk::GE4ImageIO`](https://itk.org/Doxygen/html/classitk_1_1GE4ImageIO.html) | |
-| GE 5x | [`itk::GE5ImageIO`](https://itk.org/Doxygen/html/classitk_1_1GE5ImageIO.html) | |
-| GE Advantage Windows | | [`itk::GEAdwImageIO`](https://itk.org/Doxygen/html/classitk_1_1GEAdwImageIO.html) |
-| [GIPL](https://www.ncbi.nlm.nih.gov/pubmed/12956259) (Guy's Image Processing Lab) (.gipl) | [`itk::GiplImageIO`](https://itk.org/Doxygen/html/classitk_1_1GiplImageIO.html) | |
-| IPLCommon | [`itk::IPLCommonImageIO`](https://itk.org/Doxygen/html/classitk_1_1IPLCommonImageIO.html) | |
+| GE 4x | [`itk::GE4ImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GE4ImageIO.html) | |
+| GE 5x | [`itk::GE5ImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GE5ImageIO.html) | |
+| GE Advantage Windows | | [`itk::GEAdwImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GEAdwImageIO.html) |
+| [GIPL](https://www.ncbi.nlm.nih.gov/pubmed/12956259) (Guy's Image Processing Lab) (.gipl) | [`itk::GiplImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1GiplImageIO.html) | |
+| IPLCommon | [`itk::IPLCommonImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1IPLCommonImageIO.html) | |
 | [ITK HDF5](https://support.hdfgroup.org/HDF5/) | | |
-| [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format) † | [`itk::JPEGImageIO`](https://itk.org/Doxygen/html/classitk_1_1JPEGImageIO.html) | |
-| [LSM](https://www.openwetware.org/wiki/Dissecting_LSM_files) | [`itk::LSMImageIO`](https://itk.org/Doxygen/html/classitk_1_1LSMImageIO.html) | |
-| [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation) (.mha/.mhd) | [`itk::MetaImageIO`](https://itk.org/Doxygen/html/classitk_1_1MetaImageIO.html) | |
-| [MINC 2.0](https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference) (Medical Image NetCDF) | [`itk::MINCImagIO`](https://itk.org/Doxygen/html/classitk_1_1MINCImageIO.html) | |
-| [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat) | [`itk:MGHImageIO`](https://itk.org/Doxygen/html/classitk_1_1MGHImageIO.html) | |
-| [MRC](http://www.ccpem.ac.uk/mrc_format/mrc_format.php) | [`itk::MRCImageIO`](https://itk.org/Doxygen/html/classitk_1_1MRCImageIO.html) | |
-| [NIfTI](https://nifti.nimh.nih.gov/nifti-1) (.nii) | [`itk::NiftiImageIO`](https://itk.org/Doxygen/html/classitk_1_1NiftiImageIO.html) | |
-| [NRRD](http://teem.sourceforge.net/nrrd/format.html) (.nhdr/.nrrd) | [`itk::NrrdImageIO`](https://itk.org/Doxygen/html/classitk_1_1NrrdImageIO.html) | |
-| [PNG](https://en.wikipedia.org/wiki/Portable_Network_Graphics) † | [`itk::PNGImageIO`](https://itk.org/Doxygen/html/classitk_1_1PNGImageIO.html) | |
-| Raw ‡ | [`itk::RawImageIO`](https://itk.org/Doxygen/html/classitk_1_1RawImageIO.html) | |
+| [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format) † | [`itk::JPEGImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1JPEGImageIO.html) | |
+| [LSM](https://www.openwetware.org/wiki/Dissecting_LSM_files) | [`itk::LSMImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1LSMImageIO.html) | |
+| [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation) (.mha/.mhd) | [`itk::MetaImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MetaImageIO.html) | |
+| [MINC 2.0](https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference) (Medical Image NetCDF) | [`itk::MINCImagIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MINCImageIO.html) | |
+| [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat) | [`itk:MGHImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MGHImageIO.html) | |
+| [MRC](http://www.ccpem.ac.uk/mrc_format/mrc_format.php) | [`itk::MRCImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MRCImageIO.html) | |
+| [NIfTI](https://nifti.nimh.nih.gov/nifti-1) (.nii) | [`itk::NiftiImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1NiftiImageIO.html) | |
+| [NRRD](http://teem.sourceforge.net/nrrd/format.html) (.nhdr/.nrrd) | [`itk::NrrdImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1NrrdImageIO.html) | |
+| [PNG](https://en.wikipedia.org/wiki/Portable_Network_Graphics) † | [`itk::PNGImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1PNGImageIO.html) | |
+| Raw ‡ | [`itk::RawImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1RawImageIO.html) | |
 | [Scanco microCT volume file format](https://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-import-export.html) | | |
-| Siemens Vision | | [`itk::SiemensVisionImageIO`](https://itk.org/Doxygen/html/classitk_1_1SiemensVisionImageIO.html) |
-| Stimulate (spr/sdt) | [`itk::StimulateImageIO`](https://itk.org/Doxygen/html/classitk_1_1TIFFImageIO.html) | |
+| Siemens Vision | | [`itk::SiemensVisionImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1SiemensVisionImageIO.html) |
+| Stimulate (spr/sdt) | [`itk::StimulateImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1TIFFImageIO.html) | |
 | [TIFF](https://en.wikipedia.org/wiki/TIFF) | [`itk::TIFFImageIO`]() | |
 | [Varian FDF](https://github.com/InsightSoftwareConsortium/ITKIOFDF) | | |
-| [VTK Structured Points](https://www.vtk.org/VTK/img/file-formats.pdf) | [`itk::VTKImageIO`](https://itk.org/Doxygen/html/classitk_1_1VTKImageIO.html) | |
+| [VTK Structured Points](https://www.vtk.org/VTK/img/file-formats.pdf) | [`itk::VTKImageIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1VTKImageIO.html) | |
 
 † BMP, PNG and JPEG are not very good formats for 3D medical images.
 They only support 2D images and a limited set of pixel types such as
 unsigned char, and unsigned short. The great advantage of BMP, PNG and
 JPEG is that you can view them with almost any image viewer. It is
 possible to read/write 3D datasets as collections of 2D slices each one
 in an independent BMP, PNG or JPEG file by using the
-[`ImageSeriesReader`](https://itk.org/Doxygen/html/classitk_1_1ImageSeriesReader.html) and [`itk::ImageSeriesWriter`](https://itk.org/Doxygen/html/classitk_1_1ImageSeriesWriter.html).
+[`ImageSeriesReader`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageSeriesReader.html) and [`itk::ImageSeriesWriter`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageSeriesWriter.html).
 
 ‡ It is higly recommended not using this format. RAW is not a format, it
 is insufficient, inconsistent and simply dangerous. A RAW file without a
@@ -81,7 +81,7 @@ contains a good set of tools for performing such conversions.
 
 You can also take advantage of the VTK readers/importers. All you need
 is then use the VTKImageToImage adaptor in order to convert the
-[`vtkImageData`](https://vtk.org/doc/nightly/html/classvtkImageData.html) into an [`itk::Image`](https://itk.org/Doxygen/html/classitk_1_1Image.html).
+[`vtkImageData`](https://vtk.org/doc/nightly/html/classvtkImageData.html) into an [`itk::Image`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1Image.html).
 
 Supported VTK file formats can be found in https://docs.vtk.org/en/latest/supported_data_formats.html.
 
@@ -93,13 +93,13 @@ formats:
 | File Format | Read/Write | Import |
 | ----------- | ---------- | ------ |
 | [BYU](http://www.eg-models.de/formats/Format_Byu.html) |
- [`itk::BYUMeshIO`](https://itk.org/Doxygen/html/classitk_1_1BYUMeshIO.html) | |
-| [FreeSurfer surface, binary and ASCII](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm) | [`itk::FreeSurferBinaryMeshIO`](https://itk.org/Doxygen/html/classitk_1_1FreeSurferBinaryMeshIO.html), [`itk::FreeSurferAsciiMeshIO`](https://itk.org/Doxygen/html/classitk_1_1FreeSurferAsciiMeshIO.html) | |
-| [OFF](https://en.wikipedia.org/wiki/OFF_%28file_format%29) | [`ìtk::OFFMeshIO`](https://itk.org/Doxygen/html/classitk_1_1OFFMeshIO.html) | |
+ [`itk::BYUMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1BYUMeshIO.html) | |
+| [FreeSurfer surface, binary and ASCII](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm) | [`itk::FreeSurferBinaryMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1FreeSurferBinaryMeshIO.html), [`itk::FreeSurferAsciiMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1FreeSurferAsciiMeshIO.html) | |
+| [OFF](https://en.wikipedia.org/wiki/OFF_%28file_format%29) | [`ìtk::OFFMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1OFFMeshIO.html) | |
 | [STL](https://en.wikipedia.org/wiki/STL_%28file_format%29) | | |
 | [SWC Neuron Morphology](https://swc-specification.readthedocs.io/en/latest/) | | |
-| [OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file) | [`ìtk::OBJMeshIO`](https://itk.org/Doxygen/html/classitk_1_1OBJMeshIO.html) | |
-| [VTK legacy file format for vtkPolyData](https://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf) | [`itk::VTKPolyDataMeshIO`](https://itk.org/Doxygen/html/classitk_1_1VTKPolyDataMeshIO.html) | |
+| [OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file) | [`ìtk::OBJMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1OBJMeshIO.html) | |
+| [VTK legacy file format for vtkPolyData](https://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf) | [`itk::VTKPolyDataMeshIO`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1VTKPolyDataMeshIO.html) | |
 
 More information on supported mesh and point set file formats is available on the
 [ITK-Wasm Mesh and Point Set File Formats](https://wasm.itk.org/en/latest/introduction/file_formats/meshes.html)
@@ -111,9 +111,9 @@ ITK supports reading and writing the following transform file formats:
 
 | File Format | Read/Write | Import |
 | ----------- | ---------- | ------ |
-| InsightLegacy | [`itk::TxtTransformIOTemplate`](https://itk.org/Doxygen/html/classitk_1_1TxtTransformIOTemplate.html) | |
-| ITK HDF5 | [`itk::HDF5TransformIOTemplate`](https://itk.org/Doxygen/html/classitk_1_1HDF5TransformIOTemplate.html) | |
-| MATLAB | [`itk::MatlabTransformIOTemplate`](https://itk.org/Doxygen/html/classitk_1_1MatlabTransformIOTemplate.html) | |
+| InsightLegacy | [`itk::TxtTransformIOTemplate`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1TxtTransformIOTemplate.html) | |
+| ITK HDF5 | [`itk::HDF5TransformIOTemplate`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1HDF5TransformIOTemplate.html) | |
+| MATLAB | [`itk::MatlabTransformIOTemplate`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MatlabTransformIOTemplate.html) | |
 | MINC (Medical Image NetCDF) | `itk::MINCTransformIOTemplate` | |
 
 #### DICOM data
@@ -127,7 +127,7 @@ in case of desperation.
 1. Use the [itk-wasm dicom](https://itk-wasm-dicom-docs.on.fleek.co/#/),
    package, which is available from [here](https://itk-wasm-dicom-python-docs.on.fleek.co/).
    It has the broadest support and is the easiest to use.
-1. Use the [`itk::ImageSeriesReader`](https://itk.org/Doxygen/html/classitk_1_1ImageSeriesReader.html) in combination with the
+1. Use the [`itk::ImageSeriesReader`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageSeriesReader.html) in combination with the
    `DicomSeriesFileNames`. For a full example on how to do this,
    please look at the [`DicomSeriesReadImageWrite2.cxx`](https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/IO/DicomSeriesReadImageWrite2.cxx)
    code.
@@ -520,8 +520,8 @@ overview](http://www.itk.org/CourseWare/Training/RegistrationMethodsOverview.pdf
 
 ### Why can't I read any image files? or Why am I getting the exception message: `There are no registered IO factories.`?
 
-When trying to read or write a file using the [`itk::ImageFileReader`](https://itk.org/Doxygen/html/classitk_1_1ImageFileReader.html)
-or the [`itk::ImageFileWriter`](https://itk.org/Doxygen/html/classitk_1_1ImageFileWriter.html) I got an exception with the following message:
+When trying to read or write a file using the [`itk::ImageFileReader`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageFileReader.html)
+or the [`itk::ImageFileWriter`](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1ImageFileWriter.html) I got an exception with the following message:
 
 ```{bash}
 itk::ImageFileReaderException (00F7F494)

Documentation/docs/migration_guides/itk_5_migration_guide.md

@@ -69,8 +69,8 @@ Availability of the C++11 standard allows use of many Standard Library
 features. These were previously implemented as portable ITK classes.
 The standard library classes are preferred over ITK's implementations.
 The most notable examples of this are:
- * [atomic integers](https://itk.org/Doxygen413/html/classitk_1_1AtomicInt.html) should be replaced by `std::atomic`.
- * [mutex locks](https://itk.org/Doxygen413/html/classitk_1_1MutexLock.html)
+ * [atomic integers](https://docs.itk.org/projects/doxygen/en/v4.13.0/classitk_1_1AtomicInt.html) should be replaced by `std::atomic`.
+ * [mutex locks](https://docs.itk.org/projects/doxygen/en/v4.13.0/classitk_1_1MutexLock.html)
 and related classes should be replaced by the similarly named classes from STL's
 [`<mutex>`](https://en.cppreference.com/w/cpp/header/mutex) header.
  * `itksys::hash_map` should be replaced by [std::unordered_map](https://en.cppreference.com/w/cpp/container/unordered_map).
@@ -368,7 +368,7 @@ It should be replaced by [itk::SimpleFilterWatcher](../../../Modules/Core/Common
 `itksys::hash_map` has been removed. It should be replaced by `std::unordered_map`.
 
 `WatershedImageFilter` produces slightly different results due to changes of `hash_map`.
-Generally, [MorphologicalWatersheds](https://itk.org/Doxygen/html/classitk_1_1MorphologicalWatershedImageFilter.html)
+Generally, [MorphologicalWatersheds](https://docs.itk.org/projects/doxygen/en/stable/classitk_1_1MorphologicalWatershedImageFilter.html)
 produce more stable results and should be preferred to regular watersheds.
 
 Since `itk::ProgressReporter` does not work well with the new threading model,

Documentation/docs/releases/2.0.md

@@ -16,7 +16,7 @@ formats are:
 -   ACR-NEMA version 1 and 2
 -   Dicom version 3.0 (including various encodings of jpeg, RLE)
 
-Class Reference : [GDCMImageIO](https://www.itk.org/Doxygen/html/classitk_1_1GDCMImageIO.html), [GDCMSeriesFileNames](https://www.itk.org/Doxygen/html/classitk_1_1GDCMSeriesFileNames.html)\
+Class Reference : [GDCMImageIO](https://docs.itk.org/projects/doxygen/en/v2.2.0/classitk_1_1GDCMImageIO.html), [GDCMSeriesFileNames](https://docs.itk.org/projects/doxygen/en/v2.2.0/classitk_1_1GDCMSeriesFileNames.html)\
 Examples : (None)
 
 ## New itkVesselTubeSpatialObject with metaIO file format to support vessel representation

Documentation/docs/releases/4.6.md

@@ -11,7 +11,7 @@ the Sphinx repository and the Wiki, which can now also be build as
 Remote modules. The Software Guide was split into two books and
 configure and build instructions were revised.
 
-\[1\] <https://www.itk.org/Doxygen/html/modules.html>
+\[1\] <https://docs.itk.org/projects/doxygen/en/v4.6.0/modules.html>
 
 New Features
 

Documentation/docs/releases/5.0.md

@@ -61,7 +61,7 @@ Additionally, a major upgrade of the ITK Spatial Object framework, which provide
 
 **Ranges**
 
-ITK 5.0 has a new [Experimental namespace](https://itk.org/Doxygen/html/namespaceitk_1_1Experimental.html). This namespace includes three _range_ class templates, `ShapedImageNeighborhoodRange`, `IndexRange`, and `ImageBufferRange`, to iterate efficiently over a neighborhood of pixels, the indices of an image region, and the pixels of an image buffer, respectively. These ranges can be used in a C++11 range-base for-loop. Their `begin()` and `end()` can be passed directly to an `std` algorithm.
+ITK 5.0 has a new [Experimental namespace](https://docs.itk.org/projects/doxygen/en/stable/namespaceitk_1_1Experimental.html). This namespace includes three _range_ class templates, `ShapedImageNeighborhoodRange`, `IndexRange`, and `ImageBufferRange`, to iterate efficiently over a neighborhood of pixels, the indices of an image region, and the pixels of an image buffer, respectively. These ranges can be used in a C++11 range-base for-loop. Their `begin()` and `end()` can be passed directly to an `std` algorithm.
 
 **New Features**