WIP: ENH: Migrate from RST to Myst Markdown

Author: thewtex

CMakeLists.txt

@@ -240,7 +240,7 @@ if(BUILD_DOCUMENTATION)
   add_custom_target(copy_sources ALL
     COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/src" "${ITKSphinxExamples_BINARY_DIR}/src"
     COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Documentation" "${ITKSphinxExamples_BINARY_DIR}/Documentation"
-    COMMAND ${CMAKE_COMMAND} -E copy "${ITKSphinxExamples_SOURCE_DIR}/index.rst" "${ITKSphinxExamples_BINARY_DIR}/index.rst"
+    COMMAND ${CMAKE_COMMAND} -E copy "${ITKSphinxExamples_SOURCE_DIR}/index.md" "${ITKSphinxExamples_BINARY_DIR}/index.md"
     COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Formatting"
     "${ITKSphinxExamples_BINARY_DIR}/Formatting"
     COMMAND ${CMAKE_COMMAND} -E copy_directory "${ITKSphinxExamples_SOURCE_DIR}/Utilities"

Documentation/Build/index.md

@@ -0,0 +1,279 @@
+# Build, Run, Visualize
+
+(run-python-examples)=
+
+The Python examples do not need to be built. First, install Python from
+[python.org](https://www.python.org/), [Anaconda](https://www.anaconda.com/distribution), or a system package manager like
+Ubuntu Linux [apt](https://help.ubuntu.com/lts/serverguide/apt.html)
+or macOS [Homebrew](https://brew.sh/).
+
+Next, install the *itk* package:
+
+```
+python -m pip install --upgrade pip
+python -m pip install itk
+```
+
+:::{figure} DownloadExampleHighlighted.png
+:align: center
+:alt: Download an example
+
+Download [an example](https://itk.org/ITKExamples/src/Filtering/BinaryMathematicalMorphology/DilateABinaryImage/Documentation.html)
+by clicking the *Download* button.
+:::
+
+Download the *\<ExampleName>.zip* file from the link on the top
+of an example's webpage.  Unpack the example. For example,
+
+```
+unzip ExampleName.zip
+```
+
+Finally, run the example:
+
+```
+python ExampleName/Code.py
+```
+
+(build-individual-examples)=
+
+## Build individual examples
+
+Download the *\<ExampleName>.zip* file from the link on the top
+of the example's webpage.  Unpack the example:
+
+```
+unzip ExampleName.zip
+```
+
+Set convenience variables:
+
+```
+ITK_SOURCE=ExampleName
+ITK_BUILD=ExampleName/build
+```
+
+Move to the build directory:
+
+```
+cd ${ITK_BUILD}
+```
+
+Run CMake (minimum version 3.10.2) to configure the project.
+
+- If ITK Version 5.0.0 or above not installed but compiled on your
+  system, you will need to specify the path to your ITK build:
+
+  ```
+  cmake -DITK_DIR=/home/luis/itk_build -S ${ITK_SOURCE} -B ${ITK_BUILD}
+  ```
+
+Build the project, and run the test:
+
+```
+cmake --build .
+ctest -V
+```
+
+(building-examples)=
+
+## Build all examples and the documentation
+
+Set convenience variables:
+
+```
+ITK_SOURCE=ITKEx
+ITK_BUILD=ITKEx-build
+```
+
+Clone the repository:
+
+```
+git clone --recursive https://github.com/InsightSoftwareConsortium/ITKSphinxExamples.git ${ITK_SOURCE}
+```
+
+Make a build directory:
+
+```
+mkdir -p ${ITK_BUILD}
+cd ${ITK_BUILD}
+```
+
+Run CMake (minimum version 3.10.2) to configure the project.
+
+- If ITK is not installed nor compiled, you can then make use of the superbuild functionality:
+
+  ```
+  cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE}/Superbuild/ -B ${ITK_BUILD}
+  ```
+
+- If ITK (Version 5.0.0 or above) is installed:
+
+  ```
+  cmake -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE} -B ${ITK_BUILD}
+  ```
+
+- If ITK (Version 5.0.0 or above) is not installed but compiled on your
+  system, you will need to specify the path to your ITK build:
+
+  ```
+  ITK_COMPILED_DIR=/usr/opt/itk_build
+  cmake -DITK_DIR=${ITK_COMPILED_DIR} -DBUILD_DOCUMENTATION:BOOL=ON -S ${ITK_SOURCE_DIR} -B ${ITK_BUILD_DIR}
+  ```
+
+The superbuild will download and build all required dependencies.  If you are
+building the documentation and not using superbuild functionality, then you must
+have all the required dependencies installed, which are listed in the
+*README.rst* file located at the root of the source tree.  If you just want to
+build the examples and not their documentation, set *BUILD_DOCUMENTATION* to
+*OFF* in your CMake configuration.
+
+Build the project (this will generate the documentation and all examples):
+
+```
+cmake --build .
+```
+
+Run the tests with a superbuild:
+
+```
+cd ${ITK_BUILD_DIR}/ITKEX-build
+ctest -V
+```
+
+Run the tests without a superbuild:
+
+```
+cd ${ITK_BUILD_DIR}
+ctest -V
+```
+
+## Run an example
+
+After building the examples, you can run an example by using `cd` to move to
+the example's directory.  Then, directly run the executable.
+
+Alternatively, the `ctest` command line program that comes with [CMake] can be
+used to drive the examples as unit test.  Running:
+
+```
+ctest
+```
+
+in the binary tree will run all unit tests found in the current directory and
+below.
+
+```
+ctest -R Binary
+```
+
+will run all tests whose name matches the regular expression *Binary*.
+
+```
+ctest -V
+```
+
+will run *ctest* in verbose mode, which prints out the command executed and all
+of the resulting text output.
+
+(visualize)=
+
+## Visualize the results
+
+ITK is a library limited in scope to image analysis, and it purposely does not
+attempt to perform image visualization.  Visualizing the results of analysis is
+possible with a number of third-party applications.  Note that these packages
+are specially suited for medical images, which often have anisotropic spacing
+and can span three or more dimensions.  All applications listed are open source
+and cross-platform.
+
+3DSlicer
+
+: [3DSlicer] is an open-source software platform for the analysis and
+  visualization of medical images and for research in image guided therapy.
+  The platform provides functionality for segmentation, registration and
+  three-dimensional visualization of multi-modal image data, as well as advanced
+  image analysis algorithms for diffusion tensor imaging, functional magnetic
+  resonance imaging and image-guided therapy. Standard image file formats are
+  supported, and the application integrates interface capabilities to biomedical
+  research software and image informatics frameworks.
+
+:::{figure} Slicer.png
+:align: center
+:alt: 3DSlicer
+
+[3DSlicer]
+:::
+
+ImageViewer
+
+: An [FLTK]-based [ImageViewer] was extracted from the [ITKApps] repository.  This
+  simple yet effective slice-based viewer works on 2D and 3D images and supports
+  probing of data values.
+
+:::{figure} ImageViewer.png
+:align: center
+:alt: ITKApps ImageViewer
+
+ImageViewer
+:::
+
+ITK-SNAP
+
+: [ITK-SNAP] is segmentation application, but it is also a nice general
+  resource for visualization of the results of analysis.
+
+:::{figure} ITK-SNAP.png
+:align: center
+:alt: ITK-SNAP
+
+[ITK-SNAP]
+:::
+
+MITK
+
+: [MITK] is a free open-source software system for development of interactive
+  medical image processing software.
+
+:::{figure} MITK.png
+:align: center
+:alt: MITK
+
+[MITK]
+:::
+
+Paraview
+
+: [Paraview] is a full-featured scientific visualizion GUI written with [Qt]/[VTK].
+  It has extensive parallel processing capabilities.
+
+:::{figure} Paraview.png
+:align: center
+:alt: Paraview
+
+[Paraview]
+:::
+
+VV
+
+: [VV] is an image viewer designed for fast and simple visualization of
+  spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images.
+
+:::{figure} VV.png
+:align: center
+:alt: VV
+
+[VV]
+:::
+
+[3dslicer]: https://www.slicer.org/
+[cmake]: https://cmake.org/
+[fltk]: https://www.fltk.org/index.php
+[imageviewer]: https://github.com/KitwareMedical/ImageViewer
+[itk-snap]: http://www.itksnap.org/pmwiki/pmwiki.php
+[itkapps]: https://github.com/InsightSoftwareConsortium/ITKApps
+[mitk]: https://www.mitk.org/wiki/MITK
+[paraview]: https://www.paraview.org/
+[qt]: https://www.qt.io/developers/
+[vtk]: https://vtk.org/
+[vv]: https://www.creatis.insa-lyon.fr/rio/vv