Medical Imaging Interaction Toolkit
2021.02.9900f000b3
Medical Imaging Interaction Toolkit

Geometries are used to describe the geometrical properties of data objects in space and time. To use the geometry classes in the right way you have to understand the three different coordinate types present in MITK:
Like ITK, MITK differenciate between points and vectors. A point defines a position in a coordinate system while a vector is the distance between two points. Therefore points and vectors behave different if a coordinate transformation is applied. An offest in a coordinate transformation will affect a transformed point but not a vector.
An Example:
If two systems are given, which differ by a offset of (1,0,0). The point A(2,2,2) in system one will correspont to point A'(3,2,2) in the second system. But a vector a(2,2,2) will correspond to the vector a'(2,2,2).
As the superclass of all MITK geometries mitk::BaseGeometry holds:
isImageGeometry
, which indicates whether the coordinates are centerbased or not! See also: Introduction to Geometries and Putting it together for an Image . IMPORTANT: Putting it together for an Image.Every data object (sub)class of BaseData has a mitk::TimeGeometry which is accessed by mitk::BaseData::GetTimeGeometry(). This mitk::TimeGeometry holds one or more mitk::BaseGeometry objects which describes the object at specific time points, e.g. provides conversion between world and index coordinates and contains bounding boxes covering the area in which the data are placed. There is the possibility of using different implementations of the abstract mitk::TimeGeometry class which may differ in how the time steps are saved and the times are calculated.
There are two ways to represent a time, either by a mitk::TimePointType or a mitk::TimeStepType. The first is similar to the continous index coordinates and defines a Time Point in milliseconds from timepoint zero. The second type is similar to index coordinates. These are discrete values which specify the number of the current time step going from 0 to GetNumberOfTimeSteps(). The conversion between a time point and a time step is done by calling the method mitk::TimeGeometry::TimeStepToTimePoint() or mitk::TimeGeometry::TimePointToTimeStep(). Note that the duration of a time step may differ from object to object, so in general it is better to calculate the corresponding time steps by using time points. Also the distance of the time steps does not need to be equidistant over time, it depends on the used mitk::TimeGeometry implementation.
Each mitk::TimeGeometry has a bounding box covering the whole area in which the corresponding object is situated during all time steps. This bounding box may be accessed by calling mitk::TimeGeometry::GetBoundingBoxInWorld() and is always in world coordinates. The bounding box is calculated from all time steps, to manually start this calculation process call mitk::TimeGeometry::Update(). The bounding box is not updated if the getter is called.
The mitk::TimeGeometry does not provide a transformation of world coordinates into image coordinates since each time step may has a different transformation. If a conversion between image and world is needed, the mitk::BaseGeometry for a specific time step or time point must be fetched either by mitk::TimeGeometry::GetGeometryForTimeStep() or mitk::TimeGeometry::GetGeometryForTimePoint() and then the conversion is calculated by using this geometry.
The mitk::TimeGeometry class is an abstract class therefore it is not possible to instantiate it. Instead a derived class must be used. Currently the only class that can be chosen is mitk::ProportionalTimeGeometry which assumes that the time steps are ordered equidistant. To initialize an object with given geometries call mitk::ProportionalTimeGeometry::Initialize() with an existing BaseGeometry and the number of time steps. The given geometries will be copied and not referenced!
Also, the mitk::BaseGeometry is an abstract class and derived classes must be used. The most simple implementation, i.e. the one to one implementation of the BaseGeometry class, is the class mitk::Geometry3D.
mitk::SlicedGeometry3D is a subclass of mitk::BaseGeometry, which describes data objects consisting of slices, e.g., objects of type Image (or mitk::SlicedData, which is the superclass of mitk::Image). Therefore, mitk::Image::GetTimeGeometry() will contain a list of mitk::SlicedGeometry3D instances. There is a special method mitk::SlicedData::GetSlicedGeometry(t) which directly returns a mitk::SlicedGeometry3D to avoid the need of casting.
The class mitk::SlicedGeometry3D contains a list of mitk::PlaneGeometry objects describing the slices in the image. We have here spatial steps from 0 to GetSlices(). mitk::SlicedGeometry3D::InitializeEvenlySpaced(PlaneGeometry *planeGeometry, unsigned int slices) initializes a stack of slices with the same thickness, one starting at the position where the previous one ends.
mitk::PlaneGeometry provides methods for working with 2D manifolds (i.e., simply spoken, an object that can be described using a 2D coordinatesystem) in 3D space. For example it allows mapping of a 3D point on the 2D manifold using mitk::PlaneGeometry::Map().
Finally there is the mitk::AbstractTransformGeometry which describes a 2D manifold in 3D space, defined by a vtkAbstractTransform. It is a abstract superclass for arbitrary user defined geometries. An example is the mitk::ThinPlateSplineCurvedGeometry.
Please read this section carefully if you are working with Images!
The definition of the position of the corners of an image is different than the one of other data objects:
As mentioned in the previous section, world coordinates of data objects (e.g. surfaces) usually specify the bottom left back corner of an object.
In contrast to that, a geometry of an mitk::Image is centerbased, which means that the world coordinates of a voxel belonging to an image points to the center of that voxel. E.g:
If the origin of e.g. a surface lies at (15,10,0) in world coordinates, the origin`s world coordinates for an image are internally calculated like the following:
If the image`s spacing is (x,y,z)=(1,1,3) then the corner coordinates are (14.5,9.5,1.5).
If your geometry describes an image, the member variable isImageGeometry
must be changed to true. This variable indicates also if your geometry is centerbased or not.
The change can be done in two ways:
setImageGeometry(true)
or imageGeometryOn()
to set the bool variable to true.isImageGeometry
set to false (default). In that case, call the function ChangeImageGeometryConsideringOriginOffset(true)
. It will adjust your origin automatically and set the bool flag to true.If you experience displaced contours, figures or other stuff, it is an indicator that you have not considered the origin offset mentioned above.
An image has a mitk::TimeGeometry, which contains one or more mitk::SlicedGeometry3D instances (one for each time step), all of which contain one or more instances of (subclasses of) mitk::PlaneGeometry.
As a reminder: Geometry instances referring to images need a slightly different definition of corners, see mitk::BaseGeometry::SetImageGeometry. This is usualy automatically called by Image.
Attention: Not automatically updated when changed hardcoded. Example: geometry>GetVtkMatrix()>Rotate
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