Common Conventions

This document contains common conventions that SimpleITK filters, and objects follow. It is intended to describe the interfaces that users should use and developers should implement. If a method or class does not specify different behavior or default values then those described here, it should be assumed that it follows the following conventions.

Dimensional Vectors

Dimensional Vectors must contain at least the number of elements as the dimensions of the image, elements beyond the image’s dimension will be truncated.

The SimpleITK image class can contain 2 or 3 dimensional images. In ITK proper, certain types such as indexes, points, and sizes are templated over the image dimensions. In SimpleITK we utilize the variable length std::vector for these types, so that non-templated calls can wrap ITK’s templated image class. These types are called Dimensional Vectors. If a dimensional vector’s length is less that the dimension of the image, an exception will be generated when converted to the ITK type. If there are extra elements in the dimensional vector these values will be ignored.

Image Access

Image access is in x,y,z order, GetPixel(x,y,z) or image[x,y,z], with zero based indexing.

Mask Image Types and Default Values

The default mask image type is a scalar image of sitkUInt8 or uint8_t pixels. The default values are 0 and 1, with 1s representing the mask.

These defaults are for filter which create masks such as thresholding, and certain other segmentation filters. Additionally, these are the defaults for the binary morphology filters, so that they can easily be applied after segmentation. This choice makes many mask manipulations easier. For example, “masking” an image (scalar or vector) is simply a matter of multiplying by a mask an image. Additionally, the set of {0, 1} pixels is closed under the logical Boolean operators.

Order of Procedural Parameters

The order of the procedural parameters should be with the most frequently modified parameters at the beginning of the parameter list. While the last parameter, may be ones that the user does not need to set or are infrequently used.

Matrices as Parameters

Matrices are represented as a single dimensional vector with the entries in row major order. The vector [1, 2, 3, 4, 5, 6] represents the matrix

\begin{bmatrix} 1 & 2 & 3 \\
        4 & 5 & 6
\end{bmatrix}

Image Regions as Index and Size

The itk::ImageRegion is a frequently used class in ITK to define a sub-image area. It is defined by itk::Index and itk::Size of signed and unsigned integer types respectfully. In SimpleITK, the index and size elements are usually separated into two arguments with separate Set and Get methods.

When specified as a single argument value, it is a 1 dimensional array with the index values followed by the size values i.e. [idx_x, idx_y, idx_z, size_x, size_y, size_z].

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 only supports images with sitkFloat32 and sitkFloat64 pixel types.

Casting an image’s pixel type into another is done with the SimpleITK Cast() function.