Update Doxygen URL to simpleitk.org

Examples/DemonsRegistration1/Documentation.rst

@@ -8,7 +8,7 @@ Overview
 --------
 
 This example illustrates how to use the `classic Demons registration algorithm
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1DemonsRegistrationFilter.html>`_.
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1DemonsRegistrationFilter.html>`_.
 The user supplied parameters for the algorithm are the number of iterations and
 the standard deviations for the Gaussian smoothing of the total displacement
 field. Additional methods which control regularization, total field smoothing

Examples/DemonsRegistration2/Documentation.rst

@@ -8,7 +8,7 @@ Overview
 --------
 
 This example illustrates how to use the `fast symmetric forces Demons algorithm
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1FastSymmetricForcesDemonsRegistrationFilter.html>`_.
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1FastSymmetricForcesDemonsRegistrationFilter.html>`_.
 As the name implies, unlike the classical algorithm, the forces are symmetric.
 
 The underlying assumption of the demons framework is that the intensities of

Examples/DicomImagePrintTags/Documentation.rst

@@ -6,7 +6,7 @@ Read Image Meta-Data Dictionary and Print
 Overview
 --------
 
-This example illustrates how to read only an image's information and meta-data dictionary without loading the pixel content via the `ImageFileReader <https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageFileReader.html>`_.
+This example illustrates how to read only an image's information and meta-data dictionary without loading the pixel content via the `ImageFileReader <https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageFileReader.html>`_.
 
 Reading an entire image potentially is memory and time intensive operation when the image is large or many files must be read. The image information and meta-data dictionary can be read without the bulk data by using the ImageFilerReader's object oriented interface, with use of the ImageFileReader::ReadImageInformation method.
 

Examples/FastMarchingSegmentation/Documentation.rst

@@ -14,20 +14,20 @@ growing segmentation which is controlled by a speed image.
 A good propagation speed image for segmentation is close to zero
 near object boundaries and relatively high in between. In this example,
 an input feature image is smoothed with an `anisotropic
-diffusion <https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1CurvatureAnisotropicDiffusionImageFilter.html>`_
+diffusion <https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1CurvatureAnisotropicDiffusionImageFilter.html>`_
 method, then the gradient magnitude is used to produce an edge
 image. A Gaussian with a parameterized *sigma* is used during the
 gradient computation to enable the level-set to slow down near
 edges. The `Sigmoid filter
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1SigmoidImageFilter.html>`_
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1SigmoidImageFilter.html>`_
 performs a linear transform on the gradient magnitude so that
 boundaries are near zero and homogeneous regions are close to one. The
 values for *alpha* and *beta* are provided in the testing code. The heuristics used to
 estimate good values are dependent on the minimum value along a boundary
 and the mean value of the gradient in the object's region.
 
 Lastly the `fast marching filter
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1FastMarchingImageFilter.html>`_
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1FastMarchingImageFilter.html>`_
 is configured with an initial trial point and starting value. Each
 trial point consists of a tuple for an image index including an optional
 unsigned starting seed value at the trial point. The trial points are

Examples/FilterProgressReporting/Documentation.rst

@@ -18,7 +18,7 @@ Events
 ------
 
 Events are a simple enumerated type in SimpleITK, represented by
-the `EventEnum type <https://itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#aa7399868984d99493c5a307cce373ace>`_.
+the `EventEnum type <https://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#aa7399868984d99493c5a307cce373ace>`_.
 More information about each event type can be found in the documentation
 for the enum. All SimpleITK filters, including the reading
 and writing ones, are derived from the ProcessObject class which has

Examples/ImageIOSelection/Documentation.rst

@@ -8,8 +8,8 @@ Overview
 
 This example illustrates how to explicitly select a specific IO for image reading.
 
-When using the default settings for the `ImageFileReader class <https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageFileReader.html>`_ or
-the `ReadImage <https://itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#ae3b678b5b043c5a8c93aa616d5ee574c>`_ function
+When using the default settings for the `ImageFileReader class <https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageFileReader.html>`_ or
+the `ReadImage <https://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#ae3b678b5b043c5a8c93aa616d5ee574c>`_ function
 you have minimal control over the reading. That is, the specific IO mechanism is
 determined automatically based on the file type and the file is read into
 memory.

Examples/ImageRegistrationMethodBSpline3/Documentation.rst

@@ -11,15 +11,15 @@ Overview
 This example performs registration of multi-modality images with a multi-resolution BSpline approach.
 
 A `BSplineTransform
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1BSplineTransform.html>`_
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1BSplineTransform.html>`_
 usually has a large number of parameters which increases the
 complexity and duration of optimizing the deformation. The
 multi-resolution BSpline approach initially performs the registration
 at a lower resolution with fewer parameters at the first level and
 then adapts or resamples the BSpline control points to a higher
 resolution at subsequent levels. This transformation adaption is done
 concurrently with the `ImageRegistrationMethod's
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html>`_
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageRegistrationMethod.html>`_
 multi-level feature. This enables the setting of the shrink factor,
 smoothing sigmas, sampling percentage and BSpline resolution to vary
 per level to efficiently solve a diverse set of registration

Examples/ImageViewing/Documentation.rst

@@ -24,9 +24,9 @@ location and then launches the viewer. Potential issues with this approach:
 
 To control viewing you have two options:
 
-  1. Procedural approach. Use the `Show <https://itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a86cb9e226d455efca3ba034dc2154605>`_
+  1. Procedural approach. Use the `Show <https://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#a86cb9e226d455efca3ba034dc2154605>`_
      function, with control primarily done via environment variable settings.
-  2. Object oriented approach. Use the `ImageViewer <https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageViewer.html>`_
+  2. Object oriented approach. Use the `ImageViewer <https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageViewer.html>`_
      class, with control via the object's interface.
 
 One can either set the viewing application, if you just want to change the

Examples/N4BiasFieldCorrection/Documentation.rst

@@ -14,7 +14,7 @@ classification.
 
 This example demonstrates how to use the SimpleITK
 `N4BiasFieldCorrectionImageFilter
-<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1N4BiasFieldCorrectionImageFilter.html>`_
+<https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1N4BiasFieldCorrectionImageFilter.html>`_
 class. This filter has one required input image which is affected by a
 bias field we wish to correct. The primary input is required to have a
 "real" pixel type of either `sitkFloat32` or

Readme.md

@@ -57,7 +57,7 @@ B. C. Lowekamp, D. T. Chen, L. Ibáñez, D. Blezek, "The Design of SimpleITK", *
 Documentation
 -------------
 With massive libraries like SimpleITK, good documentation is a must. The documentation for SimpleITK is split up into multiple levels:
-1. [API Documentation](https://itk.org/SimpleITKDoxygen/html/) - This contains class and function documentation. The descriptions for functions and classes are primarily borrowed from the original ITK C++ classes.
+1. [API Documentation](https://simpleitk.org/doxygen/latest/html/) - This contains class and function documentation. The descriptions for functions and classes are primarily borrowed from the original ITK C++ classes.
 2. [SimpleITK Documentation](http://simpleitk.readthedocs.io/en/master/) - This site contains high-level guides (fundamental SimpleITK concepts, common conventions, etc.), details with respect to the toolkit's binary distributions, instructions for building the toolkit, as well as SimpleITK examples in all supported programming languages. [This site replaced the
 [SimpleITK Wiki](https://itk.org/Wiki/SimpleITK)  which is mostly of interest for historical reasons.]
 3. [Juypyter Notebook Repository](http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/) - This repository contains a collection of Jupyter Notebooks illustrating the use of SimpleITK for educational and research activities. The notebooks demonstrate the use of SimpleITK for interactive image analysis using the Python and R programming languages. Recommended reading, if you are starting with SimpleITK.

Utilities/JSON/JSONGenerateSphinxFiltersDoc.py

@@ -28,7 +28,7 @@
 
    * - Filter Name\n     - Brief Description''')
 
-entryFormat = "\n   * - `{0} <https://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1{1}.html>`_\n     - {2}"
+entryFormat = "\n   * - `{0} <https://www.simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1{1}.html>`_\n     - {2}"
 json_list = []
 for fname in sys.argv[1:]:
     with open( fname, "r" ) as fp:

Wrapping/Python/Packaging/setup.py.in

@@ -78,7 +78,7 @@ setup(
     packages= ['SimpleITK'],
     package_dir = {'SimpleITK':r'@SimpleITK_PYTHON_PACKAGE_DIR@'},
     data_files = [("", doc_files)],
-    download_url = r'https://www.itk.org/SimpleITKDoxygen/html/PyDownloadPage.html',
+    download_url = r'https://www.simpleitk.org/doxygen/latest/html/PyDownloadPage.html',
     platforms = [],
     description = r'SimpleITK is a simplified interface to the Insight Toolkit (ITK) for image registration and segmentation',
     long_description  = 'SimpleITK provides an abstraction layer to ITK that enables developers \

Wrapping/R/Packaging/SimpleITK/man/SimpleITK_Image-class.Rd

@@ -103,5 +103,5 @@ Arrays can be converted to images using \code{as.image}.
 }
 }
 \references{
-\url{https://itk.org/SimpleITKDoxygen/html/index.html}
+\url{https://simpleitk.org/doxygen/latest/html/index.html}
 }

Wrapping/R/Packaging/SimpleITK/vignettes/SimpleITK_tutorial.Rnw

@@ -254,7 +254,7 @@ Testing.
 Beware of images from saved workspaces. External references, which is how images are represented, are not preserved when objects are saved to disk. Thus, attempting to use images from a saved workspace will result in ungraceful crashes.
 
 \section{Building and Installing}
-Fetch SimpleITK from the git repository. Visit \url{https://www.itk.org/SimpleITKDoxygen/html/Wrapping.html} for the latest instructions on building and installing.
+Fetch SimpleITK from the git repository. Visit \url{https://www.simpleitk.org/doxygen/latest/html/Wrapping.html} for the latest instructions on building and installing.
 \section{Development}
 
 \end{document}

docs/source/conventions.rst

@@ -15,7 +15,7 @@ The SimpleITK image class can contain 2 or 3 dimensional images. In ITK proper,
 Image Access
 ............
 
-`Image <http://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html>`_ access is in x,y,z order, ``GetPixel(x,y,z)`` or ``image[x,y,z]``, with zero based indexing.
+`Image <http://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1Image.html>`_ access is in x,y,z order, ``GetPixel(x,y,z)`` or ``image[x,y,z]``, with zero based indexing.
 
 .. _lbl_conventions_mask_image:
 
@@ -58,6 +58,6 @@ Images As Parameters
 
 The dimensionality (2D or 3D) and pixel type (``sitkUInt8``, ``sitkFloat64``...) of images is required to be the same for most methods that receive multiple images as input.
 
-The `ImageRegistrationMethod <http://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html>`_ only supports images with ``sitkFloat32`` and ``sitkFloat64`` pixel types.
+The `ImageRegistrationMethod <http://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ImageRegistrationMethod.html>`_ only supports images with ``sitkFloat32`` and ``sitkFloat64`` pixel types.
 
-Casting an image's pixel type into another is done with the SimpleITK `Cast() <http://itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#af8c9d7cc96a299a05890e9c3db911885>`_ function.
+Casting an image's pixel type into another is done with the SimpleITK `Cast() <http://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#af8c9d7cc96a299a05890e9c3db911885>`_ function.

docs/source/faq.rst

@@ -67,7 +67,7 @@ There are nearly **300 ITK image filters** wrapped
 in SimpleITK. We have a
 :ref:`list of filters <lbl_filter>` accompanied by a brief
 description. Additionally the
-`Doxygen <https://www.itk.org/SimpleITKDoxygen/html/classes.html>`__ can
+`Doxygen <https://www.simpleitk.org/doxygen/latest/html/classes.html>`__ can
 be examined to determine the availability of a filter.
 
 What image file formats can SimpleITK read?
@@ -137,7 +137,7 @@ Can I use another image file viewer beside ImageJ?
 --------------------------------------------------
 
 By default when the `Show
-function <https://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a7bacfc4685cff93e46d7401865f9579e>`__
+function <https://www.simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#a7bacfc4685cff93e46d7401865f9579e>`__
 is called, SimpleITK writes out a temporary image in Nifti format then
 launches `ImageJ <http://rsbweb.nih.gov/ij/index.html>`__. The user can
 override the file format of the temporary file and/or the application
@@ -174,7 +174,7 @@ images, there are the **SITK\_SHOW\_COLOR\_COMMAND** and
 
 More details on the Show function, including use of the "%a" and "%f"
 tokens, is at the `Show function Doxygen
-page <https://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a7bacfc4685cff93e46d7401865f9579e>`__.
+page <https://www.simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#a7bacfc4685cff93e46d7401865f9579e>`__.
 
 How can I use 3D Slicer to view my images?
 ------------------------------------------