Medical Imaging Interaction Toolkit  2018.4.99-a3d2e8fb
Medical Imaging Interaction Toolkit
mitk::LabelSetImage Class Reference

LabelSetImage class for handling labels and layers in a segmentation session. More...

#include <mitkLabelSetImage.h>

Inheritance diagram for mitk::LabelSetImage:
Collaboration diagram for mitk::LabelSetImage:

Public Types

typedef mitk::Label::PixelType PixelType
 
- Public Types inherited from mitk::Image
enum  ImportMemoryManagementType { CopyMemory, ManageMemory, ReferenceMemory, DontManageMemory }
 
typedef Image Self
 
typedef SlicedData Superclass
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef itk::SmartPointer< ImageDataItemImageDataItemPointer
 
typedef itk::Statistics::Histogram< double > HistogramType
 
typedef mitk::ImageStatisticsHolderStatisticsHolderPointer
 
typedef std::vector< ImageDataItemPointerImageDataItemPointerArray
 Vector container of SmartPointers to ImageDataItems; Class is only for internal usage to allow convenient access to all slices over iterators; See documentation of ImageDataItem for details. More...
 
- Public Types inherited from mitk::SlicedData
typedef SlicedData Self
 
typedef BaseData Superclass
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef itk::ImageRegion< RegionDimension > RegionType
 
typedef itk::Index< RegionDimension > IndexType
 
typedef IndexType::IndexValueType IndexValueType
 
typedef itk::Offset< RegionDimension > OffsetType
 
typedef OffsetType::OffsetValueType OffsetValueType
 
typedef itk::Size< RegionDimension > SizeType
 
typedef SizeType::SizeValueType SizeValueType
 
- Public Types inherited from mitk::BaseData
typedef BaseData Self
 
typedef itk::DataObject Superclass
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
- Public Types inherited from mitk::Identifiable
using UIDType = std::string
 

Public Member Functions

 mitkClassMacro (LabelSetImage, Image)
 
void Initialize (const mitk::Image *image) override
 
void Concatenate (mitk::LabelSetImage *image)
 
void ClearBuffer ()
 
void MergeLabel (PixelType pixelValue, PixelType sourcePixelValue, unsigned int layer=0)
 Merges the mitk::Label with a given target value with the active label. More...
 
void MergeLabels (PixelType pixelValue, std::vector< PixelType > &vectorOfSourcePixelValues, unsigned int layer=0)
 Merges a list of mitk::Labels with the mitk::Label that has a specific value. More...
 
void UpdateCenterOfMass (PixelType pixelValue, unsigned int layer=0)
 
void RemoveLabels (std::vector< PixelType > &VectorOfLabelPixelValues, unsigned int layer=0)
 Removes labels from the mitk::LabelSet of given layer. Calls mitk::LabelSetImage::EraseLabels() which also removes the labels from within the image. More...
 
void EraseLabel (PixelType pixelValue, unsigned int layer=0)
 Erases the label with the given value in the given layer from the underlying image. The label itself will not be erased from the respective mitk::LabelSet. In order to remove the label itself use mitk::LabelSetImage::RemoveLabels() More...
 
void EraseLabels (std::vector< PixelType > &VectorOfLabelPixelValues, unsigned int layer=0)
 Similar to mitk::LabelSetImage::EraseLabel() this funtion erase a list of labels from the image. More...
 
bool ExistLabel (PixelType pixelValue) const
 Returns true if the value exists in one of the labelsets. More...
 
bool ExistLabel (PixelType pixelValue, unsigned int layer) const
 Checks if a label exists in a certain layer. More...
 
bool ExistLabelSet (unsigned int layer) const
 Returns true if the labelset exists. More...
 
mitk::LabelGetActiveLabel (unsigned int layer=0)
 Returns the active label of a specific layer. More...
 
mitk::LabelGetLabel (PixelType pixelValue, unsigned int layer=0) const
 Returns the mitk::Label with the given pixelValue and for the given layer. More...
 
mitk::LabelSetGetActiveLabelSet ()
 Returns the currently active mitk::LabelSet. More...
 
mitk::LabelSetGetLabelSet (unsigned int layer=0)
 Gets the mitk::LabelSet for the given layer. More...
 
const mitk::LabelSetGetLabelSet (unsigned int layer=0) const
 
unsigned int GetActiveLayer () const
 Gets the ID of the currently active layer. More...
 
unsigned int GetNumberOfLabels (unsigned int layer=0) const
 Get the number of all existing mitk::Labels for a given layer. More...
 
unsigned int GetTotalNumberOfLabels () const
 Returns the number of all labels summed up across all layers. More...
 
mitk::Image::Pointer CreateLabelMask (PixelType index, bool useActiveLayer=true, unsigned int layer=0)
 
void InitializeByLabeledImage (mitk::Image::Pointer image)
 Initialize a new mitk::LabelSetImage by an given image. For all distinct pixel values of the parameter image new labels will be created. If the number of distinct pixel values exceeds mitk::Label::MAX_LABEL_VALUE a new layer will be created. More...
 
void MaskStamp (mitk::Image *mask, bool forceOverwrite)
 
void SetActiveLayer (unsigned int layer)
 
unsigned int GetNumberOfLayers () const
 
unsigned int AddLayer (mitk::LabelSet::Pointer layer=nullptr)
 Adds a new layer to the LabelSetImage. The new layer will be set as the active one. More...
 
unsigned int AddLayer (mitk::Image::Pointer layerImage, mitk::LabelSet::Pointer lset=nullptr)
 Add a layer based on a provided mitk::Image. More...
 
void AddLabelSetToLayer (const unsigned int layerIdx, const mitk::LabelSet::Pointer labelSet)
 Add a LabelSet to an existing layer. More...
 
void RemoveLayer ()
 Removes the active layer and the respective mitk::LabelSet and image information. The new active layer is the one below, if exists. More...
 
mitk::ImageGetLayerImage (unsigned int layer)
 
const mitk::ImageGetLayerImage (unsigned int layer) const
 
void OnLabelSetModified ()
 
void SetExteriorLabel (mitk::Label *label)
 Sets the label which is used as default exterior label when creating a new layer. More...
 
mitk::LabelGetExteriorLabel ()
 Gets the mitk::Label which is used as default exterior label. More...
 
const mitk::LabelGetExteriorLabel () const
 
- Public Member Functions inherited from mitk::Image
virtual std::vector< std::string > GetClassHierarchy () const override
 
virtual const char * GetClassName () const
 
Pointer Clone () const
 
const mitk::PixelType GetPixelType (int n=0) const
 Returns the PixelType of channel n. More...
 
unsigned int GetDimension () const
 Get dimension of the image. More...
 
unsigned int GetDimension (int i) const
 Get the size of dimension i (e.g., i=0 results in the number of pixels in x-direction). More...
 
virtual void * GetData ()
 Get the data vector of the complete image, i.e., of all channels linked together. More...
 
double GetPixelValueByIndex (const itk::Index< 3 > &position, unsigned int timestep=0, unsigned int component=0)
 Get the pixel value at one specific index position. More...
 
double GetPixelValueByWorldCoordinate (const mitk::Point3D &position, unsigned int timestep=0, unsigned int component=0)
 Get the pixel value at one specific world position. More...
 
virtual vtkImageData * GetVtkImageData (int t=0, int n=0)
 Get a volume at a specific time t of channel n as a vtkImageData. More...
 
virtual const vtkImageData * GetVtkImageData (int t=0, int n=0) const
 
bool IsSliceSet (int s=0, int t=0, int n=0) const override
 Get the complete image, i.e., all channels linked together, as a mitkIpPicDescriptor. More...
 
bool IsVolumeSet (int t=0, int n=0) const override
 Check whether volume at time t in channel n is set. More...
 
bool IsChannelSet (int n=0) const override
 Check whether the channel n is set. More...
 
virtual bool SetSlice (const void *data, int s=0, int t=0, int n=0)
 Set data as slice s at time t in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a slice (at least is not smaller than a slice), since there is no chance to check this. More...
 
virtual bool SetVolume (const void *data, int t=0, int n=0)
 Set data as volume at time t in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a volume (at least is not smaller than a volume), since there is no chance to check this. More...
 
virtual bool SetChannel (const void *data, int n=0)
 Set data in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a channel (at least is not smaller than a channel), since there is no chance to check this. More...
 
virtual bool SetImportSlice (void *data, int s=0, int t=0, int n=0, ImportMemoryManagementType importMemoryManagement=CopyMemory)
 Set data as slice s at time t in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a slice (at least is not smaller than a slice), since there is no chance to check this. More...
 
virtual bool SetImportVolume (void *data, int t=0, int n=0, ImportMemoryManagementType importMemoryManagement=CopyMemory)
 Set data as volume at time t in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a volume (at least is not smaller than a volume), since there is no chance to check this. More...
 
virtual bool SetImportVolume (const void *const_data, int t=0, int n=0)
 
virtual bool SetImportChannel (void *data, int n=0, ImportMemoryManagementType importMemoryManagement=CopyMemory)
 Set data in channel n. It is in the responsibility of the caller to ensure that the data vector data is really a channel (at least is not smaller than a channel), since there is no chance to check this. More...
 
virtual void Initialize (const mitk::PixelType &type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels=1)
 
virtual void Initialize (const mitk::PixelType &type, const mitk::BaseGeometry &geometry, unsigned int channels=1, int tDim=1)
 
virtual void Initialize (const mitk::PixelType &, const mitk::TimeSlicedGeometry *, unsigned int, int)
 
virtual void Initialize (const mitk::PixelType &type, const mitk::TimeGeometry &geometry, unsigned int channels=1, int tDim=-1)
 Initialize new (or re-initialize) image information by a TimeGeometry. More...
 
virtual void Initialize (const mitk::PixelType &type, int sDim, const mitk::PlaneGeometry &geometry2d, bool flipped, unsigned int channels=1, int tDim=1)
 
virtual void Initialize (const mitk::PixelType &type, int sDim, const mitk::PlaneGeometry &geometry2d, unsigned int channels=1, int tDim=1)
 
virtual void Initialize (const mitk::ImageDescriptor::Pointer inDesc)
 
virtual void Initialize (vtkImageData *vtkimagedata, int channels=1, int tDim=-1, int sDim=-1, int pDim=-1)
 
template<typename itkImageType >
void InitializeByItk (const itkImageType *itkimage, int channels=1, int tDim=-1, int sDim=-1)
 
virtual bool IsValidSlice (int s=0, int t=0, int n=0) const
 Check whether slice s at time t in channel n is valid, i.e., is (or can be) inside of the image. More...
 
virtual bool IsValidVolume (int t=0, int n=0) const
 Check whether volume at time t in channel n is valid, i.e., is (or can be) inside of the image. More...
 
virtual bool IsValidChannel (int n=0) const
 Check whether the channel n is valid, i.e., is (or can be) inside of the image. More...
 
bool IsRotated () const
 Returns true if an image is rotated, i.e. its geometry's transformation matrix has nonzero elements besides the diagonal. Non-diagonal elements are checked if larger then 1/1000 of the matrix' trace. More...
 
unsigned int * GetDimensions () const
 Get the sizes of all dimensions as an integer-array. More...
 
ImageDescriptor::Pointer GetImageDescriptor () const
 
ChannelDescriptor GetChannelDescriptor (int id=0) const
 
void SetGeometry (BaseGeometry *aGeometry3D) override
 Sets a geometry to an image. More...
 
virtual ImageDataItemPointer GetSliceData (int s=0, int t=0, int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
virtual ImageDataItemPointer GetVolumeData (int t=0, int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
virtual ImageDataItemPointer GetChannelData (int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
ScalarType GetScalarValueMin (int t=0) const
 (DEPRECATED) Get the minimum for scalar images More...
 
ScalarType GetScalarValueMax (int t=0) const
 (DEPRECATED) Get the maximum for scalar images More...
 
ScalarType GetScalarValue2ndMin (int t=0) const
 (DEPRECATED) Get the second smallest value for scalar images More...
 
ScalarType GetScalarValueMinNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the smallest value for scalar images, but do not recompute it first More...
 
ScalarType GetScalarValue2ndMinNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the second smallest value for scalar images, but do not recompute it first More...
 
ScalarType GetScalarValue2ndMax (int t=0) const
 (DEPRECATED) Get the second largest value for scalar images More...
 
ScalarType GetScalarValueMaxNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the largest value for scalar images, but do not recompute it first More...
 
ScalarType GetScalarValue2ndMaxNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the second largest value for scalar images, but do not recompute it first More...
 
ScalarType GetCountOfMinValuedVoxels (int t=0) const
 (DEPRECATED) Get the count of voxels with the smallest scalar value in the dataset More...
 
ScalarType GetCountOfMaxValuedVoxels (int t=0) const
 (DEPRECATED) Get the count of voxels with the largest scalar value in the dataset More...
 
unsigned int GetCountOfMaxValuedVoxelsNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the count of voxels with the largest scalar value in the dataset More...
 
unsigned int GetCountOfMinValuedVoxelsNoRecompute (unsigned int t=0) const
 (DEPRECATED) Get the count of voxels with the smallest scalar value in the dataset More...
 
StatisticsHolderPointer GetStatistics () const
 Returns a pointer to the ImageStatisticsHolder object that holds all statistics information for the image. More...
 
- Public Member Functions inherited from mitk::SlicedData
 itkStaticConstMacro (RegionDimension, unsigned int, 5)
 
void UpdateOutputInformation () override
 
void PrepareForNewData () override
 
void SetRequestedRegionToLargestPossibleRegion () override
 
bool RequestedRegionIsOutsideOfTheBufferedRegion () override
 
bool VerifyRequestedRegion () override
 Verify that the RequestedRegion is within the LargestPossibleRegion. More...
 
void SetRequestedRegion (const itk::DataObject *data) override
 
virtual void SetRequestedRegion (SlicedData::RegionType *region)
 
void SetLargestPossibleRegion (SlicedData::RegionType *region)
 Sets the largest possible region. The largest possible region is the entire region occupied by the data object. Note that the largest possible region should always be bigger then the requested region of a certain operation. More...
 
const RegionTypeGetLargestPossibleRegion () const
 
virtual const RegionTypeGetRequestedRegion () const
 
void CopyInformation (const itk::DataObject *data) override
 
unsigned int GetNumberOfChannels () const
 Get the number of channels. More...
 
SlicedGeometry3DGetSlicedGeometry (unsigned int t=0) const
 Convenience access method for the geometry, which is of type SlicedGeometry3D (or a sub-class of it). More...
 
const SlicedGeometry3DGetUpdatedSlicedGeometry (unsigned int t=0)
 Convenience access method for the geometry, which is of type SlicedGeometry3D (or a sub-class of it). More...
 
void SetGeometry (BaseGeometry *aGeometry3D) override
 Set the BaseGeometry of the data, which will be referenced (not copied!). It has to be a sub-class of SlicedGeometry3D. More...
 
void SetOrigin (const Point3D &origin) override
 Convenience method for setting the origin of the SlicedGeometry3D instances of all time steps. More...
 
virtual void SetSpacing (const ScalarType aSpacing[])
 Convenience method for setting the spacing of the SlicedGeometry3D instances of all time steps. More...
 
virtual void SetSpacing (mitk::Vector3D aSpacing)
 Convenience method for setting the spacing of the SlicedGeometry3D instances of all time steps. More...
 
- Public Member Functions inherited from mitk::BaseData
BaseProperty::ConstPointer GetConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) const override
 Get property by its key. More...
 
std::vector< std::string > GetPropertyKeys (const std::string &contextName="", bool includeDefaultContext=false) const override
 Query keys of existing properties. More...
 
std::vector< std::string > GetPropertyContextNames () const override
 Query names of existing contexts. More...
 
BasePropertyGetNonConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) override
 Get property by its key. More...
 
void SetProperty (const std::string &propertyKey, BaseProperty *property, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
 Add new or change existent property. More...
 
void RemoveProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
 Removes a property. If the property does not exist, nothing will be done. More...
 
const mitk::TimeGeometryGetTimeGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
const mitk::TimeGeometryGetTimeSlicedGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
mitk::TimeGeometryGetTimeGeometry ()
 Return the TimeGeometry of the data as pointer. More...
 
const mitk::TimeGeometryGetUpdatedTimeGeometry ()
 Return the TimeGeometry of the data. More...
 
const mitk::TimeGeometryGetUpdatedTimeSliceGeometry ()
 Return the TimeGeometry of the data. More...
 
const mitk::BaseGeometryGetUpdatedGeometry (int t=0)
 Return the BaseGeometry of the data at time t. More...
 
mitk::BaseGeometryGetGeometry (int t=0) const
 Return the geometry, which is a TimeGeometry, of the data as non-const pointer. More...
 
void UpdateOutputInformation () override
 Update the information for this BaseData (the geometry in particular) so that it can be used as an output of a BaseProcess. More...
 
void CopyInformation (const itk::DataObject *data) override
 Copy information from the specified data set. More...
 
virtual bool IsInitialized () const
 Check whether the data has been initialized, i.e., at least the Geometry and other header data has been set. More...
 
virtual bool IsEmptyTimeStep (unsigned int t) const
 Check whether object contains data (at a specified time), e.g., a set of points may be empty. More...
 
virtual bool IsEmpty () const
 Check whether object contains data (at least at one point in time), e.g., a set of points may be empty. More...
 
void ExecuteOperation (Operation *operation) override
 overwrite if the Data can be called by an Interactor (StateMachine). More...
 
virtual void SetTimeGeometry (TimeGeometry *geometry)
 Set the TimeGeometry of the data, which will be referenced (not copied!). More...
 
virtual void SetClonedGeometry (const BaseGeometry *aGeometry3D)
 Set a clone of the provided Geometry as Geometry of the data. Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...
 
virtual void SetClonedTimeGeometry (const TimeGeometry *geometry)
 Set a clone of the provided TimeGeometry as TimeGeometry of the data. More...
 
virtual void SetClonedGeometry (const BaseGeometry *aGeometry3D, unsigned int time)
 Set a clone of the provided geometry as BaseGeometry of a given time step. More...
 
mitk::PropertyList::Pointer GetPropertyList () const
 Get the data's property list. More...
 
void SetPropertyList (PropertyList *propertyList)
 Set the data's property list. More...
 
mitk::BaseProperty::Pointer GetProperty (const char *propertyKey) const
 Get the property (instance of BaseProperty) with key propertyKey from the PropertyList, and set it to this, respectively;. More...
 
void SetProperty (const char *propertyKey, BaseProperty *property)
 
itk::SmartPointer< mitk::BaseDataSourceGetSource () const
 Get the process object that generated this data object. More...
 
unsigned int GetTimeSteps () const
 Get the number of time steps from the TimeGeometry As the base data has not a data vector given by itself, the number of time steps is defined over the time sliced geometry. In sub classes, a better implementation could be over the length of the data vector. More...
 
unsigned long GetMTime () const override
 Get the modified time of the last change of the contents this data object or its geometry. More...
 
void Graft (const DataObject *) override
 
- Public Member Functions inherited from mitk::OperationActor
 itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()
 
- Public Member Functions inherited from mitk::Identifiable
 Identifiable ()
 
 Identifiable (const UIDType &uid)
 
 Identifiable (const Identifiable &)=delete
 
 Identifiable (Identifiable &&) noexcept
 
virtual ~Identifiable ()
 
Identifiableoperator= (const Identifiable &)=delete
 
Identifiableoperator= (Identifiable &&other) noexcept
 
UIDType GetUID () const
 Get unique ID of an object. More...
 
- Public Member Functions inherited from mitk::IPropertyOwner
 ~IPropertyOwner () override
 
- Public Member Functions inherited from mitk::IPropertyProvider
virtual ~IPropertyProvider ()
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from mitk::Image
static const char * GetStaticNameOfClass ()
 
static Pointer New ()
 
- Static Public Member Functions inherited from mitk::SlicedData
static const char * GetStaticNameOfClass ()
 
- Static Public Member Functions inherited from mitk::BaseData
static const char * GetStaticNameOfClass ()
 

Public Attributes

Message BeforeChangeLayerEvent
 BeforeChangeLayerEvent (e.g. used for GUI integration) As soon as active labelset should be changed, the signal emits. Emitted by SetActiveLayer(int layer);. More...
 
Message AfterChangeLayerEvent
 AfterchangeLayerEvent (e.g. used for GUI integration) As soon as active labelset was changed, the signal emits. Emitted by SetActiveLayer(int layer);. More...
 

Protected Member Functions

 mitkCloneMacro (Self)
 
 LabelSetImage ()
 
 LabelSetImage (const LabelSetImage &other)
 
 ~LabelSetImage () override
 
template<typename ImageType1 , typename ImageType2 >
void ChangeLayerProcessing (ImageType1 *source, ImageType2 *target)
 
template<typename TPixel , unsigned int VImageDimension>
void LayerContainerToImageProcessing (itk::Image< TPixel, VImageDimension > *source, unsigned int layer)
 
template<typename TPixel , unsigned int VImageDimension>
void ImageToLayerContainerProcessing (itk::Image< TPixel, VImageDimension > *source, unsigned int layer) const
 
template<typename ImageType >
void CalculateCenterOfMassProcessing (ImageType *input, PixelType index, unsigned int layer)
 
template<typename ImageType >
void ClearBufferProcessing (ImageType *input)
 
template<typename ImageType >
void EraseLabelProcessing (ImageType *input, PixelType index, unsigned int layer)
 
template<typename ImageType >
void MergeLabelProcessing (ImageType *input, PixelType pixelValue, PixelType index)
 
template<typename ImageType >
void ConcatenateProcessing (ImageType *input, mitk::LabelSetImage *other)
 
template<typename ImageType >
void MaskStampProcessing (ImageType *input, mitk::Image *mask, bool forceOverwrite)
 
template<typename LabelSetImageType , typename ImageType >
void InitializeByLabeledImageProcessing (LabelSetImageType *input, ImageType *other)
 
- Protected Member Functions inherited from mitk::Image
virtual itk::LightObject::Pointer InternalClone () const override
 
int GetSliceIndex (int s=0, int t=0, int n=0) const
 
int GetVolumeIndex (int t=0, int n=0) const
 
void ComputeOffsetTable ()
 
virtual bool IsValidTimeStep (int t) const
 
void Expand (unsigned int timeSteps) override
 Expands the TimeGeometry to a number of TimeSteps. More...
 
virtual ImageDataItemPointer AllocateSliceData (int s=0, int t=0, int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
virtual ImageDataItemPointer AllocateVolumeData (int t=0, int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
virtual ImageDataItemPointer AllocateChannelData (int n=0, void *data=nullptr, ImportMemoryManagementType importMemoryManagement=CopyMemory) const
 
 Image ()
 
 Image (const Image &other)
 
 ~Image () override
 
void Clear () override
 Calls ClearData() and InitializeEmpty();. More...
 
void Initialize () override
 
void PrintSelf (std::ostream &os, itk::Indent indent) const override
 
- Protected Member Functions inherited from mitk::SlicedData
 SlicedData ()
 
 SlicedData (const SlicedData &other)
 
 ~SlicedData () override
 
- Protected Member Functions inherited from mitk::BaseData
 BaseData ()
 
 BaseData (const BaseData &other)
 
 ~BaseData () override
 
virtual void InitializeTimeGeometry (unsigned int timeSteps=1)
 Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...
 
virtual void InitializeTimeSlicedGeometry (unsigned int timeSteps=1)
 Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...
 
virtual void ClearData ()
 reset to non-initialized state, release memory More...
 
virtual void InitializeEmpty ()
 Pure virtual; Must be used in subclasses to get a data object to a valid state. Should at least create one empty object and call Superclass::InitializeTimeGeometry() to ensure an existing valid geometry. More...
 
void PrintSelf (std::ostream &os, itk::Indent indent) const override
 

Protected Attributes

std::vector< LabelSet::Pointer > m_LabelSetContainer
 
std::vector< Image::Pointerm_LayerContainer
 
int m_ActiveLayer
 
bool m_activeLayerInvalid
 
mitk::Label::Pointer m_ExteriorLabel
 
- Protected Attributes inherited from mitk::Image
ImageDataItemPointerArray m_Channels
 
ImageDataItemPointerArray m_Volumes
 
ImageDataItemPointerArray m_Slices
 
itk::SimpleFastMutexLock m_ImageDataArraysLock
 
unsigned int m_Dimension
 
unsigned int * m_Dimensions
 
ImageDescriptor::Pointer m_ImageDescriptor
 
vcl_size_t * m_OffsetTable
 
ImageDataItemPointer m_CompleteData
 
StatisticsHolderPointer m_ImageStatistics
 
- Protected Attributes inherited from mitk::SlicedData
RegionType m_LargestPossibleRegion
 
RegionType m_RequestedRegion
 
bool m_RequestedRegionInitialized
 
RegionType m_BufferedRegion
 
bool m_UseLargestPossibleRegion
 
- Protected Attributes inherited from mitk::BaseData
bool m_LastRequestedRegionWasOutsideOfTheBufferedRegion
 
unsigned int m_SourceOutputIndexDuplicate
 
bool m_Initialized
 

Additional Inherited Members

- Protected Types inherited from mitk::Image
typedef itk::MutexLockHolder< itk::SimpleFastMutexLock > MutexHolder
 

Detailed Description

LabelSetImage class for handling labels and layers in a segmentation session.

Handles operations for adding, removing, erasing and editing labels and layers.

Definition at line 29 of file mitkLabelSetImage.h.

Member Typedef Documentation

◆ PixelType

Constructor & Destructor Documentation

◆ LabelSetImage() [1/2]

mitk::LabelSetImage::LabelSetImage ( )
protected

◆ LabelSetImage() [2/2]

◆ ~LabelSetImage()

mitk::LabelSetImage::~LabelSetImage ( )
overrideprotected

Definition at line 158 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Member Function Documentation

◆ AddLabelSetToLayer()

void mitk::LabelSetImage::AddLabelSetToLayer ( const unsigned int  layerIdx,
const mitk::LabelSet::Pointer  labelSet 
)

Add a LabelSet to an existing layer.

This will replace an existing labelSet if one exists. Throws an exceptions if you are trying to add a labelSet to a non-existing layer.

If there are no labelSets for layers with an id less than layerIdx default ones will be added for them.

Parameters
layerIdxThe index of the layer the LabelSet should be added to
labelSetThe LabelSet that should be added

Definition at line 273 of file mitkLabelSetImage.cpp.

References GetExteriorLabel(), m_LabelSetContainer, m_LayerContainer, mitkThrow, and mitk::LabelSet::New().

◆ AddLayer() [1/2]

unsigned int mitk::LabelSetImage::AddLayer ( mitk::LabelSet::Pointer  layer = nullptr)

Adds a new layer to the LabelSetImage. The new layer will be set as the active one.

Parameters
layera mitk::LabelSet which will be set as new layer.
Returns
the layer ID of the new layer

Definition at line 212 of file mitkLabelSetImage.cpp.

References AccessByItk, AccessFixedDimensionByItk, mitk::Image::Clone(), mitk::Image::GetDimension(), mitk::Image::GetDimensions(), mitk::Image::GetImageDescriptor(), mitk::SlicedData::GetNumberOfChannels(), mitk::Image::GetPixelType(), mitk::BaseData::GetTimeGeometry(), mitk::Image::New(), and SetToZero().

Referenced by Initialize(), and InitializeByLabeledImageProcessing().

◆ AddLayer() [2/2]

unsigned int mitk::LabelSetImage::AddLayer ( mitk::Image::Pointer  layerImage,
mitk::LabelSet::Pointer  lset = nullptr 
)

Add a layer based on a provided mitk::Image.

Parameters
layerImageis added to the vector of label images
lseta label set that will be added to the new layer if provided
Returns
the layer ID of the new layer

Definition at line 235 of file mitkLabelSetImage.cpp.

References GetExteriorLabel(), ls, m_LabelSetContainer, m_LayerContainer, mitk::LabelSet::New(), OnLabelSetModified(), and SetActiveLayer().

◆ CalculateCenterOfMassProcessing()

template<typename ImageType >
void mitk::LabelSetImage::CalculateCenterOfMassProcessing ( ImageType input,
PixelType  index,
unsigned int  layer 
)
protected

◆ ChangeLayerProcessing()

template<typename ImageType1 , typename ImageType2 >
void mitk::LabelSetImage::ChangeLayerProcessing ( ImageType1 *  source,
ImageType2 *  target 
)
protected

◆ ClearBuffer()

void mitk::LabelSetImage::ClearBuffer ( )

Definition at line 385 of file mitkLabelSetImage.cpp.

References AccessByItk, ClearBufferProcessing(), and mitkThrow.

◆ ClearBufferProcessing()

template<typename ImageType >
void mitk::LabelSetImage::ClearBufferProcessing ( ImageType input)
protected

Definition at line 786 of file mitkLabelSetImage.cpp.

Referenced by ClearBuffer().

◆ Concatenate()

◆ ConcatenateProcessing()

template<typename ImageType >
void mitk::LabelSetImage::ConcatenateProcessing ( ImageType input,
mitk::LabelSetImage other 
)
protected

Definition at line 793 of file mitkLabelSetImage.cpp.

References mitk::CastToItkImage(), GetActiveLayer(), GetLabel(), and GetNumberOfLabels().

Referenced by Concatenate().

◆ CreateLabelMask()

mitk::Image::Pointer mitk::LabelSetImage::CreateLabelMask ( PixelType  index,
bool  useActiveLayer = true,
unsigned int  layer = 0 
)

◆ EraseLabel()

void mitk::LabelSetImage::EraseLabel ( PixelType  pixelValue,
unsigned int  layer = 0 
)

Erases the label with the given value in the given layer from the underlying image. The label itself will not be erased from the respective mitk::LabelSet. In order to remove the label itself use mitk::LabelSetImage::RemoveLabels()

Parameters
pixelValuethe label which will be remove from the image
layerthe layer in which the label should be removed

Definition at line 465 of file mitkLabelSetImage.cpp.

References AccessByItk_2, EraseLabelProcessing(), and mitkThrow.

Referenced by EraseLabels(), RemoveLabels(), and QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ EraseLabelProcessing()

template<typename ImageType >
void mitk::LabelSetImage::EraseLabelProcessing ( ImageType input,
PixelType  index,
unsigned int  layer 
)
protected

Definition at line 873 of file mitkLabelSetImage.cpp.

Referenced by EraseLabel().

◆ EraseLabels()

void mitk::LabelSetImage::EraseLabels ( std::vector< PixelType > &  VectorOfLabelPixelValues,
unsigned int  layer = 0 
)

Similar to mitk::LabelSetImage::EraseLabel() this funtion erase a list of labels from the image.

Parameters
VectorOfLabelPixelValuesthe list of labels that should be remove
layerthe layer for which the labels should be removed

Definition at line 457 of file mitkLabelSetImage.cpp.

References EraseLabel().

Referenced by QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ ExistLabel() [1/2]

bool mitk::LabelSetImage::ExistLabel ( PixelType  pixelValue) const

Returns true if the value exists in one of the labelsets.

Definition at line 398 of file mitkLabelSetImage.cpp.

References GetNumberOfLayers(), and m_LabelSetContainer.

Referenced by InitializeByLabeledImageProcessing().

◆ ExistLabel() [2/2]

bool mitk::LabelSetImage::ExistLabel ( PixelType  pixelValue,
unsigned int  layer 
) const

Checks if a label exists in a certain layer.

Parameters
pixelValuethe label value
layerthe layer in which should be searched for the label
Returns
true if the label exists otherwise false

Definition at line 406 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

◆ ExistLabelSet()

bool mitk::LabelSetImage::ExistLabelSet ( unsigned int  layer) const

Returns true if the labelset exists.

Definition at line 412 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

◆ GetActiveLabel()

mitk::Label * mitk::LabelSetImage::GetActiveLabel ( unsigned int  layer = 0)

Returns the active label of a specific layer.

Parameters
layerthe layer ID for which the active label should be returned
Returns
the active label of the specified layer

Definition at line 478 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Referenced by MaskStampProcessing(), mitk::PaintbrushTool::MouseMoved(), mitk::SetRegionTool::OnMouseReleased(), and QmitkLabelSetWidget::ResetAllTableWidgetItems().

◆ GetActiveLabelSet()

◆ GetActiveLayer()

◆ GetExteriorLabel() [1/2]

mitk::Label * mitk::LabelSetImage::GetExteriorLabel ( )

Gets the mitk::Label which is used as default exterior label.

Returns
the exterior mitk::Label

Definition at line 115 of file mitkLabelSetImage.cpp.

References m_ExteriorLabel.

Referenced by AddLabelSetToLayer(), AddLayer(), and mitk::ContourModelUtils::FillSliceInSlice().

◆ GetExteriorLabel() [2/2]

const mitk::Label * mitk::LabelSetImage::GetExteriorLabel ( ) const

Definition at line 120 of file mitkLabelSetImage.cpp.

References m_ExteriorLabel.

◆ GetLabel()

mitk::Label * mitk::LabelSetImage::GetLabel ( PixelType  pixelValue,
unsigned int  layer = 0 
) const

Returns the mitk::Label with the given pixelValue and for the given layer.

Parameters
pixelValuethe pixel value of the label
layerthe layer in which the labels should be located
Returns
the mitk::Label if available otherwise nullptr

Definition at line 486 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Referenced by ConcatenateProcessing(), QmitkLabelSetWidget::GetLabelStringList(), MaskStampProcessing(), QmitkLabelSetWidget::SetDataStorage(), QmitkLabelSetWidget::SetOrganColors(), QmitkLabelSetWidget::UpdateAllTableWidgetItems(), QmitkLabelSetWidget::UpdateControls(), and QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ GetLabelSet() [1/2]

mitk::LabelSet * mitk::LabelSetImage::GetLabelSet ( unsigned int  layer = 0)

Gets the mitk::LabelSet for the given layer.

Parameters
layerthe layer for which the mitk::LabelSet should be retrieved
Returns
the respective mitk::LabelSet or nullptr if non exists for the given layer

Definition at line 494 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Referenced by CalculateCenterOfMassProcessing(), Concatenate(), mitk::DICOMSegmentationPropertyHelper::DeriveDICOMSegmentationProperties(), mitk::DICOMSegmentationIO::DoRead(), mitk::Equal(), InitializeByLabeledImageProcessing(), LabelSetImage(), MergeLabel(), MergeLabels(), RemoveLabels(), and RemoveLayer().

◆ GetLabelSet() [2/2]

const mitk::LabelSet * mitk::LabelSetImage::GetLabelSet ( unsigned int  layer = 0) const

Definition at line 502 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

◆ GetLayerImage() [1/2]

mitk::Image * mitk::LabelSetImage::GetLayerImage ( unsigned int  layer)

Definition at line 163 of file mitkLabelSetImage.cpp.

References m_LayerContainer.

Referenced by mitk::Equal(), and LabelSetImage().

◆ GetLayerImage() [2/2]

const mitk::Image * mitk::LabelSetImage::GetLayerImage ( unsigned int  layer) const

Definition at line 168 of file mitkLabelSetImage.cpp.

References m_LayerContainer.

◆ GetNumberOfLabels()

unsigned int mitk::LabelSetImage::GetNumberOfLabels ( unsigned int  layer = 0) const

Get the number of all existing mitk::Labels for a given layer.

Parameters
layerthe layer ID for which the active mitk::Labels should be retrieved
Returns
the number of all existing mitk::Labels for the given layer

Definition at line 530 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Referenced by ConcatenateProcessing(), InitializeByLabeledImageProcessing(), and QmitkLabelSetWidget::ResetAllTableWidgetItems().

◆ GetNumberOfLayers()

◆ GetTotalNumberOfLabels()

unsigned int mitk::LabelSetImage::GetTotalNumberOfLabels ( ) const

Returns the number of all labels summed up across all layers.

Returns
the overall number of labels across all layers

Definition at line 535 of file mitkLabelSetImage.cpp.

References m_LabelSetContainer.

Referenced by mitk::Equal().

◆ ImageToLayerContainerProcessing()

template<typename TPixel , unsigned int VImageDimension>
void mitk::LabelSetImage::ImageToLayerContainerProcessing ( itk::Image< TPixel, VImageDimension > *  source,
unsigned int  layer 
) const
protected

Definition at line 847 of file mitkLabelSetImage.cpp.

References m_LayerContainer.

Referenced by SetActiveLayer().

◆ Initialize()

void mitk::LabelSetImage::Initialize ( const mitk::Image image)
overridevirtual

initialize new (or re-initialize) image information by another mitk-image. Only the header is used, not the data vector!

Reimplemented from mitk::Image.

Definition at line 125 of file mitkLabelSetImage.cpp.

References AccessByItk, AccessFixedDimensionByItk, AddLayer(), mitk::TimeGeometry::Clone(), mitk::DICOMQIPropertyHelper::DeriveDICOMSourceProperties(), mitk::Image::GetDimension(), mitk::Image::GetDimensions(), mitk::BaseData::GetTimeGeometry(), mitk::BaseData::SetTimeGeometry(), and SetToZero().

◆ InitializeByLabeledImage()

void mitk::LabelSetImage::InitializeByLabeledImage ( mitk::Image::Pointer  image)

Initialize a new mitk::LabelSetImage by an given image. For all distinct pixel values of the parameter image new labels will be created. If the number of distinct pixel values exceeds mitk::Label::MAX_LABEL_VALUE a new layer will be created.

Parameters
imagethe image which is used for initialization

Definition at line 619 of file mitkLabelSetImage.cpp.

References AccessTwoImagesFixedDimensionByItk, mitk::ImageWriteAccessor::GetData(), mitk::Image::Initialize(), InitializeByLabeledImageProcessing(), mitkThrow, and mitk::BaseData::SetTimeGeometry().

◆ InitializeByLabeledImageProcessing()

template<typename LabelSetImageType , typename ImageType >
void mitk::LabelSetImage::InitializeByLabeledImageProcessing ( LabelSetImageType *  input,
ImageType other 
)
protected

◆ LayerContainerToImageProcessing()

template<typename TPixel , unsigned int VImageDimension>
void mitk::LabelSetImage::LayerContainerToImageProcessing ( itk::Image< TPixel, VImageDimension > *  source,
unsigned int  layer 
)
protected

Definition at line 822 of file mitkLabelSetImage.cpp.

References m_LayerContainer.

Referenced by SetActiveLayer().

◆ MaskStamp()

void mitk::LabelSetImage::MaskStamp ( mitk::Image mask,
bool  forceOverwrite 
)

◆ MaskStampProcessing()

template<typename ImageType >
void mitk::LabelSetImage::MaskStampProcessing ( ImageType input,
mitk::Image mask,
bool  forceOverwrite 
)
protected

◆ MergeLabel()

void mitk::LabelSetImage::MergeLabel ( PixelType  pixelValue,
PixelType  sourcePixelValue,
unsigned int  layer = 0 
)

Merges the mitk::Label with a given target value with the active label.

Parameters
pixelValuethe value of the label that should be the new merged label
sourcePixelValuethe value of the label that should be merged into the specified one
layerthe layer in which the merge should be performed

Definition at line 417 of file mitkLabelSetImage.cpp.

References AccessByItk_2, GetLabelSet(), MergeLabelProcessing(), mitkThrow, and mitk::LabelSet::SetActiveLabel().

Referenced by QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ MergeLabelProcessing()

template<typename ImageType >
void mitk::LabelSetImage::MergeLabelProcessing ( ImageType input,
PixelType  pixelValue,
PixelType  index 
)
protected

Definition at line 893 of file mitkLabelSetImage.cpp.

Referenced by MergeLabel(), and MergeLabels().

◆ MergeLabels()

void mitk::LabelSetImage::MergeLabels ( PixelType  pixelValue,
std::vector< PixelType > &  vectorOfSourcePixelValues,
unsigned int  layer = 0 
)

Merges a list of mitk::Labels with the mitk::Label that has a specific value.

Parameters
pixelValuethe value of the label that should be the new merged label
vectorOfSourcePixelValuesthe list of label values that should be merge into the specified one
layerthe layer in which the merge should be performed

Definition at line 431 of file mitkLabelSetImage.cpp.

References AccessByItk_2, GetLabelSet(), MergeLabelProcessing(), mitkThrow, and mitk::LabelSet::SetActiveLabel().

Referenced by QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ mitkClassMacro()

mitk::LabelSetImage::mitkClassMacro ( LabelSetImage  ,
Image   
)

◆ mitkCloneMacro()

mitk::LabelSetImage::mitkCloneMacro ( Self  )
protected

◆ New()

◆ OnLabelSetModified()

void mitk::LabelSetImage::OnLabelSetModified ( )

Definition at line 105 of file mitkLabelSetImage.cpp.

Referenced by AddLayer(), and LabelSetImage().

◆ RemoveLabels()

void mitk::LabelSetImage::RemoveLabels ( std::vector< PixelType > &  VectorOfLabelPixelValues,
unsigned int  layer = 0 
)

Removes labels from the mitk::LabelSet of given layer. Calls mitk::LabelSetImage::EraseLabels() which also removes the labels from within the image.

Parameters
VectorOfLabelPixelValuesa list of labels to be removed
layerthe layer in which the labels should be removed

Definition at line 448 of file mitkLabelSetImage.cpp.

References EraseLabel(), GetLabelSet(), and mitk::LabelSet::RemoveLabel().

Referenced by QmitkLabelSetWidget::~QmitkLabelSetWidget().

◆ RemoveLayer()

void mitk::LabelSetImage::RemoveLayer ( )

Removes the active layer and the respective mitk::LabelSet and image information. The new active layer is the one below, if exists.

Definition at line 183 of file mitkLabelSetImage.cpp.

References GetActiveLayer(), GetLabelSet(), m_activeLayerInvalid, m_LabelSetContainer, m_LayerContainer, and SetActiveLayer().

◆ SetActiveLayer()

◆ SetExteriorLabel()

void mitk::LabelSetImage::SetExteriorLabel ( mitk::Label label)

Sets the label which is used as default exterior label when creating a new layer.

Parameters
labelthe label which will be used as new exterior label

Definition at line 110 of file mitkLabelSetImage.cpp.

References m_ExteriorLabel.

◆ UpdateCenterOfMass()

void mitk::LabelSetImage::UpdateCenterOfMass ( PixelType  pixelValue,
unsigned int  layer = 0 
)

Member Data Documentation

◆ AfterChangeLayerEvent

Message mitk::LabelSetImage::AfterChangeLayerEvent

AfterchangeLayerEvent (e.g. used for GUI integration) As soon as active labelset was changed, the signal emits. Emitted by SetActiveLayer(int layer);.

Definition at line 49 of file mitkLabelSetImage.h.

Referenced by SetActiveLayer().

◆ BeforeChangeLayerEvent

Message mitk::LabelSetImage::BeforeChangeLayerEvent

BeforeChangeLayerEvent (e.g. used for GUI integration) As soon as active labelset should be changed, the signal emits. Emitted by SetActiveLayer(int layer);.

Definition at line 42 of file mitkLabelSetImage.h.

Referenced by SetActiveLayer().

◆ m_ActiveLayer

int mitk::LabelSetImage::m_ActiveLayer
protected

Definition at line 309 of file mitkLabelSetImage.h.

Referenced by GetActiveLayer(), and SetActiveLayer().

◆ m_activeLayerInvalid

bool mitk::LabelSetImage::m_activeLayerInvalid
protected

Definition at line 311 of file mitkLabelSetImage.h.

Referenced by RemoveLayer(), and SetActiveLayer().

◆ m_ExteriorLabel

mitk::Label::Pointer mitk::LabelSetImage::m_ExteriorLabel
protected

Definition at line 313 of file mitkLabelSetImage.h.

Referenced by GetExteriorLabel(), LabelSetImage(), and SetExteriorLabel().

◆ m_LabelSetContainer

◆ m_LayerContainer

std::vector<Image::Pointer> mitk::LabelSetImage::m_LayerContainer
protected

The documentation for this class was generated from the following files: