How to write a new example#
In this section we describe how to write an example by walking through the sections of an example’s reStructuredText file. The mechanics of submitting an example via Git are covered in other sections.
All lines should be wrapped to 80 characters or less. This improves readability in text editors. It is generally ITK’s policy to format code lines without wrapping up to 200 characters, but the 80 character limit keeps code readable in the PDF output.
Please remove all trailing whitespace. Use two newlines between section headings.
Follow ITK conventions for coding; do not use TABs, and use two spacing for indentation.
The characters used to define reStructuredText sections are as follows:
Title ===== Section ------- Subsection ..........
The examples live inside the src directory of the repository. They are organized by the dominant class demonstrated in the example. There are two directories of organization which mirror the directory layout in ITKv4, Group followed by Module. Therefore, place the example in the directory corresponding to the Module of one of the prominant classes used in the example.
For instance, an examples that demonstrates the BinaryDilateImageFilter would be placed in the src/Filtering/BinaryMathematicalMorphology/ directory.
Note that when adding new examples, both CMakeLists.txt and index.rst files for the tree should be updated (to enforce the examples to be compiled, tested and to appear in the sphinx documentation). For this reason, we recommend to use the provided python script CreateNewExample.py see Create a new example
The ITK Sphinx Examples are intended to be a set of cookbook recipes that concisely demonstrate how to achieve a single objective. In general, they are intended to provide an answer to the question, “How do I …?” The title for an example can be derived by placing the example in the question format; we call this the Trebek Title Method.
For instance, an example that answers the question, “How do I dilate a binary image?” would be called Dilate a binary image. This determines the title in the reStructuredText file:
Dilate a binary image =====================
and it also determines the name of the directory, file, and test associated with the example. These names come from a CamelCase conversion of the title. For instance, in this case, the corresponding CamelCase title is DilateABinaryImage. All files for the examples are placed in a directory called DilateABinaryImage, the C++ code is placed in DilateABinaryImage.cxx, Python code in DilateABinaryImage.py, reStructuredText documentation in DilateABinaryImage.rst, and the test will be named DilateABinaryImageTest.
Index entries follow the title entry. They are entered with the Sphinx index directive; see that documentation for more information on how to specify index entries. Important classes for the example or terms associated with the example should be single entries. Term index entries should be lower case to distinguish them from classes or methods in the index. Terms with sub-terms or classes with important methods demonstrated should be used as pair entries. Use seealso instead of see to add a see also entry. For instance, with our dilate a binary image example:
.. index:: single: BinaryBallStructuringElement single: BinaryDilateImageFilter pair: mathematical morphology; dilation pair: BinaryBallStructuringElement; SetRadius .. seealso:: dilation; erosion
This section contains a short summary of the example.
This section sources the relevant code for inclusion in the documentation with syntax highlighting care of Pygments. The literalinclude directive performs this function. This ensures that all the code that is documented is also tested. Each program should be included in a subsection corresponding to its language; one of C++, Python, or Java. For instance:
C++ ... .. literalinclude:: DilateABinaryImage.cxx
Follow ITK style guidelines when writing code. Keep the example as simple as possible, and follow the best practices layed out in the rest of the examples. Do basic argument checking and parsing. Wrap Update() calls in a try / catch for C++ code, etc.
Include images or text output here that results from the example.
If there was an input image, display it for reference. The images displayed here should be rendered in the PNG format for display either by directly outputing to PNG format or by rendering with your favorite visualization application and saving a screenshot. Display the image with the figure directive. Provide alt text with the :alt: option and a brief descriptive caption. For instance:
.. figure:: DilateABinaryImageOutputBaseline.png :scale: 50% :alt: Dilated output. Dilated output.
Text output should be placed in a literal block by inserting two colons followed by indentation. For instance:
:: Registration done ! Number of iterations = 27 Translation along X = 25.0966 Translation along Y = 22.3275 Optimal metric value = 4597.96
For data structures rendered as a PolyData, such as meshes, a screenshot of the input and output rendering is insightful and motivating. The screenshot can be rendered with your favorite visualization, then included like the image renderings per above.
As a supplement to the renderings, an interactive 3D WebGL can be included in HTML output. This can be produced with the –webgl flag to the VTK Python script in the repository at Utilities/Visualization/VTKPolyData.py. In recent releases of Paraview, it can be produced by clicking File, Export Scene, WEBGL files. In the reStructuredText file, add:
.. raw:: html <div class="figure"> <iframe src="InputMesh.html" width="200" height="225" seamless></iframe> <p class="caption">Interactive input mesh</p> </div>
At the end of the example, provide quick reference and a link to the doxygen
documentation for the important classes or structs used in the example. To do this, use
breathelink directive for C++ classes or
breathelinkstruct directive for C++ structs, as follows:
.. breathelink:: itk::BinaryDilateImageFilter .. breathelinkstruct:: itk::Index
breathelinkstruct are custom directives which make the use of: