Medical Imaging Interaction Toolkit  2018.4.99-31d1c60d
Medical Imaging Interaction Toolkit
MITK Image

Introduction to MITK Image

The MITK Image obviously is a very central class to MITK and one of those you are most likely to work with. This section will get you up and running with the basics. Consider this document a prerequisite for the Pipelining Introduction and the Geometry Overview.

mitkimagehierarchy.png

Image is a direct descendant of SlicedData which itself inherits from BaseData. In MITK, BaseData is the common DataType from which all other Datatypes stem. SlicedData specifies this class to contain image slices, a typical example being a CT scan, and introduces properties and methods necessary to give the data a well defined geometry. Image further specializes the concept to allow for multiple channels, volumes and slices as well as additional information like image properties.

For the sake of this introduction, we will have a look at three different aspects:

  1. SlicedData and Geometry
  2. ImageData
  3. Image Properties

SlicedData and Geometry

The mother class of Image introduces a fundamental aspect: Image geometry. It defines the image's spatial context: Dimension and orientation. A more in depth introduction is given here: Geometry Overview

ImageData

Objects of the class Image store the actual image data. It is important to discern four different concepts:

  1. Channels, which can be of a specific data type e.g. an intensity image or a vector field. Each channel consists of one or more...
  2. Volumes, which contain data of a certain type. A volume is represented by ImageDataItems that define volume properties. Inside of a channel, each volume must be of the same type (float, int, etc.). Each volume consists of several...
  3. Slices, which each contain a two-dimensional image slice.

There is also the pointer m_CompleteData that references all of the data (i.e. all volumes) as a singular array. This member is helpful, when one wants to copy image data from one image to another.

mitkimagememory.png

Image Properties

Lastly, we'll talk about properties. Properties are a set of additional information mainly used to save DICOM information. The functionality is introduced very early in the image's lineage, in BaseData. The system works quite similar to a hashmap by using property keys and properties. For further reference, see BaseData::GetProperty() or, for a simple example implementation, USImage::GetMetadata().

Access image data

Since many modules and plugins in MITK work with the same images, it can be difficult to comprehend and control all ongoing image accesses. Thus, we decided to introduce the concept of image accessors. They are responsible for organisation of image access and for keeping data consistent. Every Image manages its image accessors and thus is responsible for them. In the following subsections, image accessors are explained and their use is depicted. Code examples are added to make understanding easier.

Image accessors

Image accessors provide an image access, which is

  1. controlled and surveilled: at all time it is known how many instances have access to a specific image part.
  2. consistent and thread-safe: a lock-mechanism allows a concurrent read access on image parts and guarantees a consistent data state during access.
  3. restricted to an image part: it is possible to restrict access to a specific image part (e.g. volume or slice), which is represented in an ImageDataItem.
  4. simple and comfortable through pixel index: get- and set-methods are provided to access pixel values easily (see next section).

The existing instantiable image accessor classes are: mitk::ImageReadAccessor, mitk::ImageWriteAccessor and mitk::ImageVtkAccessor. They all inherit from mitk::ImageAccessorBase, which mainly contains the lock functionality and a representation of the specified image area. The classes mitk::ImageReadAccessor and mitk::ImageWriteAccessor provide access to an mitk::Image or mitk::ImageDataItem and supply a (const) void* pointer, while mitk::ImageVtkAccessor supports Vtk image access in a legacy mode (you should not instantiate it).

mitkimageaccessorhierarchy.png

How to get access

Although the concept of image accessors is extensive, the use of image accessors is simple. Requesting an image access consists only of creating an instance of an image accessor. The constructor of an image accessor requires a pointer to the mitk::Image class and optionally an image part (e.g. mitk::ImageDataItem), which restricts the access of an image accessor to a specific image sector (e.g. Volume, Slice). Since the constructor can throw a mitk::Exception, it is necessary to order an image accessor within a try block. Possible exceptions are invalid images, wrong dimensions, etc. which cannot be accepted.

If only a pointer to image data is needed, following code example shows how to get a const or non-const pointer. mitk::ImageReadAccessor only provides a const void* pointer while mitk::ImageWriteAccessor provides a void* pointer to image data.

// we assume you already have an mitk::Image::Pointer image

try
{
  mitk::ImageReadAccessor readAccess(image, image->GetVolumeData(0));
  const void* cPointer = readAccess.GetData();

  mitk::ImageWriteAccessor writeAccess(image);
  void* vPointer = writeAccess.GetData();
}
catch(mitk::Exception& e)
{
  // deal with the situation not to have access
}

Please note that an explicit call of Modified() method is needed after the write access is done. The accessor makes no such call on default.

A more convenient way to access image data is provided by the classes mitk::ImagePixelReadAccessor and mitk::ImagePixelWriteAccessor. They are equipped with set- and get-methods, which allow an index-based access. Both classes are templated and need to know about pixel type and image dimension at compile time. That means, both parameters need to be defined with arrow brackets when calling the constructor.

// we assume you already have an mitk::Image::Pointer image

try
{
  itk::Index<2> idx = {{ 12, 34 }};

  mitk::ImagePixelReadAccessor<short,2> readAccess(image, image->GetSliceData(2));
  short value = readAccess.GetPixelByIndex(idx);

  mitk::ImagePixelWriteAccessor<short,2> writeAccess(image, image->GetSliceData(4));
  writeAccess.SetPixelByIndex(idx, 42);
}
catch(mitk::Exception& e)
{
  // deal with the situation not to have access
}

Additional properties

It is possible to commit options to the constructor affecting the behavior of an image accessor. Properties have to be specified using enum flags (e.g. mitk::ImageAccessorBase::ExceptionIfLocked) and can be unified by bitwise operations. The flag ExceptionIfLocked causes an exception if the requested image part is locked. Usually the requesting image accessor waits for the locking image accessor.

try
{
  mitk::ImageReadAccessor imageAccess(image, image->GetSliceData(2), mitk::ImageAccessorBase::ExceptionIfLocked);
  const void* pointer = imageAccess.GetData();
}
catch(mitk::MemoryIsLockedException& e) {
  // do something else
}
catch(mitk::Exception& e) {
  // deal with the situation not to have access
}

Working with MITK Image

Cloning a MITK Image

In order to clone an image, you can simply call the inherited method Clone(). It returns an itk::SmartPointer and works also with const image pointers.

mitk::Image::Pointer testMethod(const mitk::Image* image)
{
  mitk::Image::Pointer nIm = image->Clone();
  return nIm;
}

Cloning can also be done manually by copying the Geometry, the visual Data and further properties separately. The simplest way to achieve this is to first call Image::Initialize(const Image * image). This will copy the geometry information, but not the data or the properties. Afterwards, copy the image's data (e.g. with SetVolume) and, if necessary, it's properties with SetPropertyList(image->GetPropertyList()).

Inheriting from MITK Image

In general, one should try to avoid inheriting from mitk Image. The simple reason for this is that your derived class will not cleanly work together with the Filters already implemented (See the chapter on Pipelining for Details). If however, mitk Image does not offer the functionality you require it is possible to do so. See the documentation for various examples of classes that inherit from image.