ITK  5.0.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Friends | List of all members
itk::MorphologicalContourInterpolator< TImage > Class Template Reference

#include <itkMorphologicalContourInterpolator.h>

+ Inheritance diagram for itk::MorphologicalContourInterpolator< TImage >:
+ Collaboration diagram for itk::MorphologicalContourInterpolator< TImage >:

Detailed Description

template<typename TImage>
class itk::MorphologicalContourInterpolator< TImage >

Interpolates contours between slices. Based on a paper by Albu et al.

Inputs and Outputs
This is an image-to-image filter. The dimensionality is 3D or higher. Input contains an image with some slices segmented, usually manually. The output has all in-between slices also segmented.
Parameters
Slices are detected at positions where a pixel exists with same labeled neighbors in slice and only clear (0) neighbors perpendicular to the slice. If default behaviour is unwanted, contour indices can be set by enabling UseCustomSlicePositions and calling SetLabeledSliceIndices.

Filter can be restricted to run along only one axis, and/or to interpolate just one label.

Since optimal alignment between slices would require exhaustive search, the default is to use heuristic (breadth first search starting from centroid).

There is also an alternative algorithm based on distance transform approach. It is slightly faster, but it can jump across a twisty shape (not geodesic).

Reference: Albu AB, Beugeling T, Laurendeau D. "A morphology-based approach for interslice interpolation of anatomical slices from volumetric images." IEEE Trans Biomed Eng. 2008 Aug;55(8):2022-38. DOI:10.1109/TBME.2008.921158

Acknowledgement: This work is supported by NIH grant R01 EB014346, "Continued development and maintenance of the ITK-SNAP 3D image segmentation software."

Definition at line 65 of file itkMorphologicalContourInterpolator.h.

Public Types

using LabeledSlicesType = itksys::hash_map< typename TImage::PixelType, SliceSetType >
 
using Pointer = SmartPointer< Self >
 
using Self = MorphologicalContourInterpolator
 
using SliceIndicesType = std::vector< LabeledSlicesType >
 
using SliceSetType = std::set< typename TImage::IndexValueType >
 
using SliceType = Image< typename TImage::PixelType, TImage::ImageDimension-1 >
 
using Superclass = ImageToImageFilter< TImage, TImage >
 
- Public Types inherited from itk::ImageToImageFilter< TImage, TImage >
using ConstPointer = SmartPointer< const Self >
 
using InputImageConstPointer = typename InputImageType::ConstPointer
 
using InputImagePixelType = typename InputImageType::PixelType
 
using InputImagePointer = typename InputImageType::Pointer
 
using InputImageRegionType = typename InputImageType::RegionType
 
using InputImageType = TImage
 
using OutputImagePixelType = typename Superclass::OutputImagePixelType
 
using OutputImageRegionType = typename Superclass::OutputImageRegionType
 
using Pointer = SmartPointer< Self >
 
using Self = ImageToImageFilter
 
using Superclass = ImageSource< TImage >
 
- Public Types inherited from itk::ImageSource< TImage >
using ConstPointer = SmartPointer< const Self >
 
using DataObjectIdentifierType = Superclass::DataObjectIdentifierType
 
using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType
 
using OutputImagePixelType = typename OutputImageType::PixelType
 
using OutputImagePointer = typename OutputImageType::Pointer
 
using OutputImageRegionType = typename OutputImageType::RegionType
 
using OutputImageType = TImage
 
using Pointer = SmartPointer< Self >
 
using Self = ImageSource
 
using Superclass = ProcessObject
 
- Public Types inherited from itk::ProcessObject
using ConstPointer = SmartPointer< const Self >
 
using DataObjectIdentifierType = DataObject::DataObjectIdentifierType
 
using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArray = std::vector< DataObjectPointer >
 
using DataObjectPointerArraySizeType = DataObjectPointerArray::size_type
 
using MultiThreaderType = MultiThreaderBase
 
using NameArray = std::vector< DataObjectIdentifierType >
 
using Pointer = SmartPointer< Self >
 
using Self = ProcessObject
 
using Superclass = Object
 
- Public Types inherited from itk::Object
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = Object
 
using Superclass = LightObject
 
- Public Types inherited from itk::LightObject
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = LightObject
 

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother () const
 
void DetermineSliceOrientations ()
 
virtual int GetAxis ()
 
virtual int GetAxis () const
 
virtual bool GetHeuristicAlignment ()
 
virtual bool GetHeuristicAlignment () const
 
virtual TImage::PixelType GetLabel ()
 
virtual TImage::PixelType GetLabel () const
 
SliceSetType GetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label)
 
SliceIndicesType GetLabeledSliceIndices ()
 
virtual const char * GetNameOfClass () const
 
virtual bool GetUseBallStructuringElement ()
 
virtual bool GetUseBallStructuringElement () const
 
virtual bool GetUseCustomSlicePositions ()
 
virtual bool GetUseCustomSlicePositions () const
 
virtual bool GetUseDistanceTransform ()
 
virtual bool GetUseDistanceTransform () const
 
virtual void SetAxis (int _arg)
 
virtual void SetHeuristicAlignment (bool _arg)
 
virtual void SetLabel (typename TImage::PixelType _arg)
 
virtual void SetUseCustomSlicePositions (bool _arg)
 
virtual void SetUseDistanceTransform (bool _arg)
 
void SetUseBallStructuringElement (bool useBall)
 
void ClearLabeledSliceIndices ()
 
void SetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label, const std::vector< typename TImage::IndexValueType > &indices)
 
void SetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label, const SliceSetType &indices)
 
- Public Member Functions inherited from itk::ImageToImageFilter< TImage, TImage >
const InputImageTypeGetInput () const
 
const InputImageTypeGetInput (unsigned int idx) const
 
void PopBackInput () override
 
void PopFrontInput () override
 
virtual void PushBackInput (const InputImageType *image)
 
virtual void PushFrontInput (const InputImageType *image)
 
virtual void SetInput (const InputImageType *image)
 
virtual void SetInput (unsigned int, const TImage *image)
 
virtual void SetCoordinateTolerance (double _arg)
 
virtual double GetCoordinateTolerance () const
 
virtual void SetDirectionTolerance (double _arg)
 
virtual double GetDirectionTolerance () const
 
- Public Member Functions inherited from itk::ImageSource< TImage >
OutputImageTypeGetOutput (unsigned int idx)
 
OutputImageTypeGetOutput ()
 
const OutputImageTypeGetOutput () const
 
virtual void GraftOutput (DataObject *output)
 
virtual void GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
 
virtual void GraftNthOutput (unsigned int idx, DataObject *output)
 
ProcessObject::DataObjectPointer MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
 
ProcessObject::DataObjectPointer MakeOutput (const ProcessObject::DataObjectIdentifierType &) override
 
- Public Member Functions inherited from itk::ProcessObject
virtual void AbortGenerateDataOff ()
 
virtual void AbortGenerateDataOn ()
 
virtual void EnlargeOutputRequestedRegion (DataObject *)
 
virtual const bool & GetAbortGenerateData () const
 
DataObjectPointerArray GetIndexedInputs ()
 
DataObjectPointerArray GetIndexedOutputs ()
 
NameArray GetInputNames () const
 
DataObjectPointerArray GetInputs ()
 
MultiThreaderTypeGetMultiThreader () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedInputs () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedOutputs () const
 
DataObjectPointerArraySizeType GetNumberOfInputs () const
 
DataObjectPointerArraySizeType GetNumberOfOutputs () const
 
virtual
DataObjectPointerArraySizeType 
GetNumberOfValidRequiredInputs () const
 
NameArray GetOutputNames () const
 
DataObjectPointerArray GetOutputs ()
 
virtual const float & GetProgress () const
 
NameArray GetRequiredInputNames () const
 
bool HasInput (const DataObjectIdentifierType &key) const
 
bool HasOutput (const DataObjectIdentifierType &key) const
 
virtual void PrepareOutputs ()
 
virtual void PropagateRequestedRegion (DataObject *output)
 
virtual void ResetPipeline ()
 
virtual void SetAbortGenerateData (bool _arg)
 
void SetMultiThreader (MultiThreaderType *threader)
 
virtual void Update ()
 
virtual void UpdateLargestPossibleRegion ()
 
virtual void UpdateOutputData (DataObject *output)
 
virtual void UpdateOutputInformation ()
 
void UpdateProgress (float progress)
 
virtual void SetReleaseDataFlag (bool flag)
 
virtual bool GetReleaseDataFlag () const
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)
 
virtual const bool & GetReleaseDataBeforeUpdateFlag () const
 
virtual void ReleaseDataBeforeUpdateFlagOn ()
 
virtual void ReleaseDataBeforeUpdateFlagOff ()
 
virtual void SetNumberOfWorkUnits (ThreadIdType _arg)
 
virtual const ThreadIdTypeGetNumberOfWorkUnits () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetReferenceCount (int) override
 
void UnRegister () const noexceptoverride
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetMetaDataDictionary (MetaDataDictionary &&rrhs)
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkCloneMacro (Self)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool flag)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Protected Types

using BinarizerType = BinaryThresholdImageFilter< SliceType, BoolSliceType >
 
using BoolImageType = Image< bool, TImage::ImageDimension >
 
using BoolSliceType = Image< bool, TImage::ImageDimension-1 >
 
using BoundingBoxesType = itksys::hash_map< typename TImage::PixelType, typename TImage::RegionType >
 
using ConnectedComponentsType = ConnectedComponentImageFilter< BoolSliceType, SliceType >
 
using FloatSliceType = Image< float, TImage::ImageDimension-1 >
 
using PixelList = std::vector< typename TImage::PixelType >
 
using RoiType = ExtractImageFilter< TImage, SliceType >
 
- Protected Types inherited from itk::ImageToImageFilter< TImage, TImage >
using InputToOutputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::OutputImageDimension, Self::InputImageDimension >
 
using OutputToInputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::InputImageDimension, Self::OutputImageDimension >
 

Protected Member Functions

SliceType::IndexType Align (typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds)
 
void AllocateOutputs () override
 
SliceType::RegionType BoundingBox (itk::SmartPointer< SliceType > image)
 
IdentifierType CardinalSymmetricDifference (typename BoolSliceType::Pointer &shape1, typename BoolSliceType::Pointer &shape2)
 
SliceType::IndexType Centroid (typename SliceType::Pointer &conn, const PixelList &regionIds)
 
BoolSliceType::Pointer Dilate1 (typename BoolSliceType::Pointer &seed, typename BoolSliceType::Pointer &mask)
 
template<typename T2 >
void ExpandRegion (typename T2::RegionType &region, const typename T2::IndexType &index)
 
void Extrapolate (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId)
 
BoolSliceType::Pointer FindMedianImageDilations (typename BoolSliceType::Pointer &intersection, typename BoolSliceType::Pointer &iMask, typename BoolSliceType::Pointer &jMask)
 
BoolSliceType::Pointer FindMedianImageDistances (typename BoolSliceType::Pointer &intersection, typename BoolSliceType::Pointer &iMask, typename BoolSliceType::Pointer &jMask)
 
void GenerateData () override
 
std::vector< typename
BoolSliceType::Pointer
GenerateDilationSequence (typename BoolSliceType::Pointer &begin, typename BoolSliceType::Pointer &end)
 
bool ImagesEqual (typename BoolSliceType::Pointer &a, typename BoolSliceType::Pointer &b)
 
void Interpolate1to1 (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, typename TImage::PixelType jRegionId, const typename SliceType::IndexType &translation, bool recursive)
 
void Interpolate1toN (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds, const typename SliceType::IndexType &translation)
 
void InterpolateAlong (int axis, TImage *out, float startProgress, float endProgress)
 
void InterpolateBetweenTwo (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iconn, typename SliceType::Pointer &jconn)
 
IdentifierType Intersection (typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds, const typename SliceType::IndexType &translation)
 
void IntersectionRegions (const typename SliceType::IndexType &translation, typename SliceType::RegionType &iRegion, typename SliceType::RegionType &jRegion)
 
FloatSliceType::Pointer MaurerDM (typename BoolSliceType::Pointer &inImage)
 
 MorphologicalContourInterpolator ()
 
SliceType::Pointer RegionedConnectedComponents (const typename TImage::RegionType &region, typename TImage::PixelType label, IdentifierType &objectCount)
 
SliceType::Pointer TranslateImage (typename SliceType::Pointer &image, const typename SliceType::IndexType &translation, typename SliceType::RegionType newRegion)
 
 ~MorphologicalContourInterpolator () override
 
- Protected Member Functions inherited from itk::ImageToImageFilter< TImage, TImage >
virtual void CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
 
virtual void CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
 
void GenerateInputRequestedRegion () override
 
 ImageToImageFilter ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
void VerifyInputInformation () ITKv5_CONST override
 
 ~ImageToImageFilter () override
 
void PushBackInput (const DataObject *input) override
 
void PushFrontInput (const DataObject *input) override
 
- Protected Member Functions inherited from itk::ImageSource< TImage >
virtual void AfterThreadedGenerateData ()
 
virtual void BeforeThreadedGenerateData ()
 
void ClassicMultiThread (ThreadFunctionType callbackFunction)
 
void GenerateData () override
 
virtual const
ImageRegionSplitterBase
GetImageRegionSplitter () const
 
 ImageSource ()
 
virtual unsigned int SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)
 
 ~ImageSource () override=default
 
virtual void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
 
virtual void DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)
 
virtual bool GetDynamicMultiThreading () const
 
virtual void SetDynamicMultiThreading (bool _arg)
 
virtual void DynamicMultiThreadingOn ()
 
virtual void DynamicMultiThreadingOff ()
 
- Protected Member Functions inherited from itk::ProcessObject
virtual void AddInput (DataObject *input)
 
void AddOptionalInputName (const DataObjectIdentifierType &)
 
void AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
virtual void AddOutput (DataObject *output)
 
bool AddRequiredInputName (const DataObjectIdentifierType &)
 
bool AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
virtual void CacheInputReleaseDataFlags ()
 
virtual void GenerateOutputInformation ()
 
virtual void GenerateOutputRequestedRegion (DataObject *output)
 
DataObjectGetInput (const DataObjectIdentifierType &key)
 
const DataObjectGetInput (const DataObjectIdentifierType &key) const
 
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredInputs () const
 
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredOutputs () const
 
bool IsIndexedInputName (const DataObjectIdentifierType &) const
 
bool IsIndexedOutputName (const DataObjectIdentifierType &) const
 
bool IsRequiredInputName (const DataObjectIdentifierType &) const
 
DataObjectPointerArraySizeType MakeIndexFromInputName (const DataObjectIdentifierType &name) const
 
DataObjectPointerArraySizeType MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
 
DataObjectIdentifierType MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
 
DataObjectIdentifierType MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
 
 ProcessObject ()
 
virtual void PropagateResetPipeline ()
 
virtual void ReleaseInputs ()
 
virtual void RemoveInput (const DataObjectIdentifierType &key)
 
virtual void RemoveInput (DataObjectPointerArraySizeType)
 
virtual void RemoveOutput (const DataObjectIdentifierType &key)
 
virtual void RemoveOutput (DataObjectPointerArraySizeType idx)
 
bool RemoveRequiredInputName (const DataObjectIdentifierType &)
 
virtual void RestoreInputReleaseDataFlags ()
 
virtual void SetInput (const DataObjectIdentifierType &key, DataObject *input)
 
virtual void SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
 
virtual void SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
 
void SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
 
void SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
 
virtual void SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
 
virtual void SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
 
virtual void SetOutput (const DataObjectIdentifierType &key, DataObject *output)
 
virtual void SetPrimaryInput (DataObject *input)
 
virtual void SetPrimaryOutput (DataObject *output)
 
void SetRequiredInputNames (const NameArray &)
 
virtual void VerifyPreconditions () ITKv5_CONST
 
 ~ProcessObject () override
 
DataObjectGetInput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetInput (DataObjectPointerArraySizeType idx) const
 
DataObjectGetPrimaryInput ()
 
const DataObjectGetPrimaryInput () const
 
virtual void SetPrimaryInputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryInputName () const
 
DataObjectGetOutput (const DataObjectIdentifierType &key)
 
const DataObjectGetOutput (const DataObjectIdentifierType &key) const
 
virtual void SetPrimaryOutputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryOutputName () const
 
DataObjectGetOutput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetOutput (DataObjectPointerArraySizeType idx) const
 
DataObjectGetPrimaryOutput ()
 
const DataObjectGetPrimaryOutput () const
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
 ~Object () override
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Protected Attributes

int m_Axis
 
BinarizerType::Pointer m_Binarizer
 
BoundingBoxesType m_BoundingBoxes
 
ConnectedComponentsType::Pointer m_ConnectedComponents
 
bool m_HeuristicAlignment
 
TImage::PixelType m_Label
 
SliceIndicesType m_LabeledSlices
 
IdentifierType m_MaxAlignIters
 
IdentifierType m_MinAlignIters
 
RoiType::Pointer m_RoI
 
IdentifierType m_ThreadCount
 
bool m_UseBallStructuringElement
 
bool m_UseCustomSlicePositions
 
bool m_UseDistanceTransform
 
- Protected Attributes inherited from itk::ImageSource< TImage >
bool m_DynamicMultiThreading
 
- Protected Attributes inherited from itk::ProcessObject
TimeStamp m_OutputInformationMTime
 
bool m_Updating
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

Friends

template<typename T >
class MorphologicalContourInterpolatorParallelInvoker
 

Additional Inherited Members

- Static Public Attributes inherited from itk::ImageToImageFilter< TImage, TImage >
static constexpr unsigned int InputImageDimension
 
static constexpr unsigned int OutputImageDimension
 
- Static Public Attributes inherited from itk::ImageSource< TImage >
static constexpr unsigned int OutputImageDimension
 
- Static Protected Member Functions inherited from itk::ImageSource< TImage >
static const
ImageRegionSplitterBase
GetGlobalDefaultSplitter ()
 
static
ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION 
ThreaderCallback (void *arg)
 

Member Typedef Documentation

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::BinarizerType = BinaryThresholdImageFilter< SliceType, BoolSliceType >
protected

Definition at line 398 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::BoolImageType = Image< bool, TImage::ImageDimension >
protected

Derived image type alias.

Definition at line 239 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::BoolSliceType = Image< bool, TImage::ImageDimension - 1 >
protected

Definition at line 241 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::BoundingBoxesType = itksys::hash_map< typename TImage::PixelType, typename TImage::RegionType >
protected

Definition at line 371 of file itkMorphologicalContourInterpolator.h.

Definition at line 401 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::FloatSliceType = Image< float, TImage::ImageDimension - 1 >
protected

Definition at line 240 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::LabeledSlicesType = itksys::hash_map< typename TImage::PixelType, SliceSetType >

Definition at line 214 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::PixelList = std::vector< typename TImage::PixelType >
protected

Definition at line 315 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::Pointer = SmartPointer< Self >

Definition at line 77 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::RoiType = ExtractImageFilter< TImage, SliceType >
protected

Definition at line 395 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::Self = MorphologicalContourInterpolator

Standard class type alias.

Definition at line 75 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::SliceIndicesType = std::vector< LabeledSlicesType >

Definition at line 215 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::SliceSetType = std::set< typename TImage::IndexValueType >

An std::set of slice indices which need to be interpolated.

Definition at line 170 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::SliceType = Image< typename TImage::PixelType, TImage::ImageDimension - 1 >

Definition at line 78 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
using itk::MorphologicalContourInterpolator< TImage >::Superclass = ImageToImageFilter< TImage, TImage >

Definition at line 76 of file itkMorphologicalContourInterpolator.h.

Constructor & Destructor Documentation

template<typename TImage >
itk::MorphologicalContourInterpolator< TImage >::MorphologicalContourInterpolator ( )
protected
template<typename TImage >
itk::MorphologicalContourInterpolator< TImage >::~MorphologicalContourInterpolator ( )
inlineoverrideprotected

Definition at line 226 of file itkMorphologicalContourInterpolator.h.

Member Function Documentation

template<typename TImage >
SliceType::IndexType itk::MorphologicalContourInterpolator< TImage >::Align ( typename SliceType::Pointer iConn,
typename TImage::PixelType  iRegionId,
typename SliceType::Pointer jConn,
const PixelList jRegionIds 
)
protected

How much j needs to be translated to best align with i

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::AllocateOutputs ( )
overrideprotectedvirtual

Copied from ImageSource and changed to allocate a cleared buffer.

Reimplemented from itk::ImageSource< TImage >.

template<typename TImage >
SliceType::RegionType itk::MorphologicalContourInterpolator< TImage >::BoundingBox ( itk::SmartPointer< SliceType image)
protected

Calculates a bounding box of non-zero pixels.

template<typename TImage >
IdentifierType itk::MorphologicalContourInterpolator< TImage >::CardinalSymmetricDifference ( typename BoolSliceType::Pointer shape1,
typename BoolSliceType::Pointer shape2 
)
protected

The returns cardingal of the symmetric distance between images. The images must cover the same region.

template<typename TImage >
SliceType::IndexType itk::MorphologicalContourInterpolator< TImage >::Centroid ( typename SliceType::Pointer conn,
const PixelList regionIds 
)
protected

Returns the centroid of given regions

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::ClearLabeledSliceIndices ( )
inline

Clears all custom slice positions.

Definition at line 174 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >
virtual::itk::LightObject::Pointer itk::MorphologicalContourInterpolator< TImage >::CreateAnother ( ) const
virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::DetermineSliceOrientations ( )

If there is a pixel whose all 4-way neighbors belong the the same label except along one axis, and along that axis its neighbors are 0 (background), then that axis should be interpolated along. Interpolation is possible along more than one axis. Updates LabeledSliceIndices.

template<typename TImage >
BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::Dilate1 ( typename BoolSliceType::Pointer seed,
typename BoolSliceType::Pointer mask 
)
protected

Seed and mask must cover the same region (size and index the same).

template<typename TImage >
template<typename T2 >
void itk::MorphologicalContourInterpolator< TImage >::ExpandRegion ( typename T2::RegionType &  region,
const typename T2::IndexType &  index 
)
protected

Expands a region to incorporate the provided index. Assumes both a valid region and a valid index. It can be invoked with 2D or 3D region, hence the additional template parameter.

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::Extrapolate ( int  axis,
TImage *  out,
typename TImage::PixelType  label,
typename TImage::IndexValueType  i,
typename TImage::IndexValueType  j,
typename SliceType::Pointer iConn,
typename TImage::PixelType  iRegionId 
)
protected

Slice i has a region, slice j does not

template<typename TImage >
BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::FindMedianImageDilations ( typename BoolSliceType::Pointer intersection,
typename BoolSliceType::Pointer iMask,
typename BoolSliceType::Pointer jMask 
)
protected

Finds an interpolating mask for these two aligned masks

template<typename TImage >
BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::FindMedianImageDistances ( typename BoolSliceType::Pointer intersection,
typename BoolSliceType::Pointer iMask,
typename BoolSliceType::Pointer jMask 
)
protected

Finds an interpolating mask for these two aligned masks

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::GenerateData ( )
overrideprotectedvirtual

Does the real work.

Reimplemented from itk::ProcessObject.

template<typename TImage >
std::vector< typename BoolSliceType::Pointer > itk::MorphologicalContourInterpolator< TImage >::GenerateDilationSequence ( typename BoolSliceType::Pointer begin,
typename BoolSliceType::Pointer end 
)
protected

A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same)

template<typename TImage >
virtual int itk::MorphologicalContourInterpolator< TImage >::GetAxis ( )
virtual

Axis of interpolation. -1 means interpolation along all axes (default).

template<typename TImage >
virtual int itk::MorphologicalContourInterpolator< TImage >::GetAxis ( ) const
virtual

Axis of interpolation. -1 means interpolation along all axes (default).

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetHeuristicAlignment ( )
virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetHeuristicAlignment ( ) const
virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >
virtual TImage::PixelType itk::MorphologicalContourInterpolator< TImage >::GetLabel ( )
virtual

Which label is interpolated. 0 means all labels (default).

template<typename TImage >
virtual TImage::PixelType itk::MorphologicalContourInterpolator< TImage >::GetLabel ( ) const
virtual

Which label is interpolated. 0 means all labels (default).

template<typename TImage >
SliceSetType itk::MorphologicalContourInterpolator< TImage >::GetLabeledSliceIndices ( unsigned int  axis,
typename TImage::PixelType  label 
)
inline

Slice indices between which interpolation is done.

Definition at line 208 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices.

template<typename TImage >
SliceIndicesType itk::MorphologicalContourInterpolator< TImage >::GetLabeledSliceIndices ( )
inline

Slice indices between which interpolation is done.

Definition at line 219 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices.

template<typename TImage >
virtual const char* itk::MorphologicalContourInterpolator< TImage >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageToImageFilter< TImage, TImage >.

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseBallStructuringElement ( )
virtual

Use ball instead of default cross structuring element for repeated dilations.

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseBallStructuringElement ( ) const
virtual

Use ball instead of default cross structuring element for repeated dilations.

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseCustomSlicePositions ( )
virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseCustomSlicePositions ( ) const
virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseDistanceTransform ( )
virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >
virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseDistanceTransform ( ) const
virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >
bool itk::MorphologicalContourInterpolator< TImage >::ImagesEqual ( typename BoolSliceType::Pointer a,
typename BoolSliceType::Pointer b 
)
protected

Are these two slices equal?

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::Interpolate1to1 ( int  axis,
TImage *  out,
typename TImage::PixelType  label,
typename TImage::IndexValueType  i,
typename TImage::IndexValueType  j,
typename SliceType::Pointer iConn,
typename TImage::PixelType  iRegionId,
typename SliceType::Pointer jConn,
typename TImage::PixelType  jRegionId,
const typename SliceType::IndexType translation,
bool  recursive 
)
protected

Build transition sequence and pick the median

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::Interpolate1toN ( int  axis,
TImage *  out,
typename TImage::PixelType  label,
typename TImage::IndexValueType  i,
typename TImage::IndexValueType  j,
typename SliceType::Pointer iConn,
typename TImage::PixelType  iRegionId,
typename SliceType::Pointer jConn,
const PixelList jRegionIds,
const typename SliceType::IndexType translation 
)
protected

Splits the bigger region and does N 1-to-1 interpolations

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::InterpolateAlong ( int  axis,
TImage *  out,
float  startProgress,
float  endProgress 
)
protected

If interpolation is done along more than one axis, the interpolations are merged using a modified "or" rule: -if all interpolated images have 0 for a given pixel, the output is 0 -if just one image has a non-zero label, then that label is chosen -if more than one image has a non-zero label, last written label is chosen

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::InterpolateBetweenTwo ( int  axis,
TImage *  out,
typename TImage::PixelType  label,
typename TImage::IndexValueType  i,
typename TImage::IndexValueType  j,
typename SliceType::Pointer iconn,
typename SliceType::Pointer jconn 
)
protected

Determines correspondances between two slices and calls apropriate methods.

template<typename TImage >
IdentifierType itk::MorphologicalContourInterpolator< TImage >::Intersection ( typename SliceType::Pointer iConn,
typename TImage::PixelType  iRegionId,
typename SliceType::Pointer jConn,
const PixelList jRegionIds,
const typename SliceType::IndexType translation 
)
protected

Returns number of intersecting pixels

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::IntersectionRegions ( const typename SliceType::IndexType translation,
typename SliceType::RegionType iRegion,
typename SliceType::RegionType jRegion 
)
protected

Calculates maximum intersection region for both slices given a translation. Both inputs are modified so that jRegion is a translated version of iRegion.

template<typename TImage >
FloatSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::MaurerDM ( typename BoolSliceType::Pointer inImage)
protected

Creates a signed distance field image.

template<typename TImage >
static Pointer itk::MorphologicalContourInterpolator< TImage >::New ( )
static

Method for creation through the object factory.

template<typename TImage >
SliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::RegionedConnectedComponents ( const typename TImage::RegionType &  region,
typename TImage::PixelType  label,
IdentifierType objectCount 
)
protected

Connected components of a specified region.

template<typename TImage >
virtual void itk::MorphologicalContourInterpolator< TImage >::SetAxis ( int  _arg)
virtual

Interpolate only along this axis. Interpolates along all axes if set to -1 (default).

template<typename TImage >
virtual void itk::MorphologicalContourInterpolator< TImage >::SetHeuristicAlignment ( bool  _arg)
virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >
virtual void itk::MorphologicalContourInterpolator< TImage >::SetLabel ( typename TImage::PixelType  _arg)
virtual

Interpolate only this label. Interpolates all labels if set to 0 (default).

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::SetLabeledSliceIndices ( unsigned int  axis,
typename TImage::PixelType  label,
const std::vector< typename TImage::IndexValueType > &  indices 
)
inline

If default slice detection is not wanted, slice indices between which interpolation is done can be set using this method.

Definition at line 185 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::SetLabeledSliceIndices ( unsigned int  axis,
typename TImage::PixelType  label,
const SliceSetType indices 
)
inline

If default slice detection is not wanted, slice indices between which interpolation is done can be set using this method.

Definition at line 199 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >
void itk::MorphologicalContourInterpolator< TImage >::SetUseBallStructuringElement ( bool  useBall)
inline
template<typename TImage >
virtual void itk::MorphologicalContourInterpolator< TImage >::SetUseCustomSlicePositions ( bool  _arg)
virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >
virtual void itk::MorphologicalContourInterpolator< TImage >::SetUseDistanceTransform ( bool  _arg)
virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >
SliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::TranslateImage ( typename SliceType::Pointer image,
const typename SliceType::IndexType translation,
typename SliceType::RegionType  newRegion 
)
protected

Crates a translated copy of part of the image which fits in the newRegion.

Friends And Related Function Documentation

template<typename TImage >
template<typename T >
friend class MorphologicalContourInterpolatorParallelInvoker
friend

Definition at line 69 of file itkMorphologicalContourInterpolator.h.

Member Data Documentation

template<typename TImage >
int itk::MorphologicalContourInterpolator< TImage >::m_Axis
protected

Definition at line 228 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
BinarizerType::Pointer itk::MorphologicalContourInterpolator< TImage >::m_Binarizer
protected

Definition at line 399 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
BoundingBoxesType itk::MorphologicalContourInterpolator< TImage >::m_BoundingBoxes
protected

Definition at line 372 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
ConnectedComponentsType::Pointer itk::MorphologicalContourInterpolator< TImage >::m_ConnectedComponents
protected
template<typename TImage >
bool itk::MorphologicalContourInterpolator< TImage >::m_HeuristicAlignment
protected

Definition at line 229 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
TImage::PixelType itk::MorphologicalContourInterpolator< TImage >::m_Label
protected

Definition at line 227 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
SliceIndicesType itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices
protected
template<typename TImage >
IdentifierType itk::MorphologicalContourInterpolator< TImage >::m_MaxAlignIters
protected

Definition at line 234 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
IdentifierType itk::MorphologicalContourInterpolator< TImage >::m_MinAlignIters
protected

Definition at line 233 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
RoiType::Pointer itk::MorphologicalContourInterpolator< TImage >::m_RoI
protected

Definition at line 396 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
IdentifierType itk::MorphologicalContourInterpolator< TImage >::m_ThreadCount
protected

Definition at line 235 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
bool itk::MorphologicalContourInterpolator< TImage >::m_UseBallStructuringElement
protected
template<typename TImage >
bool itk::MorphologicalContourInterpolator< TImage >::m_UseCustomSlicePositions
protected

Definition at line 232 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >
bool itk::MorphologicalContourInterpolator< TImage >::m_UseDistanceTransform
protected

Definition at line 230 of file itkMorphologicalContourInterpolator.h.


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