#include <itkContourExtractor2DImageFilter.h>

Detailed Description

template<typename TInputImage>
class itk::ContourExtractor2DImageFilter< TInputImage >

Computes a list of PolyLineParametricPath objects from the contours in a 2D image.

Uses the "marching squares" method to compute a the iso-valued contours of the input 2D image for a given intensity value. Multiple outputs may be produced because an image can have multiple contours at a given level, so it is advised to call GetNumberOfIndexedOutputs() and GetOutput(n) to retrieve all of the contours. The contour value to be extracted can be set with SetContourValue(). Image intensities will be linearly interpolated to provide sub-pixel resolution for the output contours.

The marching squares algorithm is a special case of the marching cubes algorithm (Lorensen, William and Harvey E. Cline. Marching Cubes: A High Resolution 3D Surface Construction Algorithm. Computer Graphics (SIGGRAPH 87 Proceedings) 21(4) July 1987, p. 163-170). A simple explanation is available here: http://users.polytech.unice.fr/~lingrand/MarchingCubes/algo.html

There is an ambiguous case in the marching squares algorithm: if a given 2x2-pixel square has two high-valued and two low-valued pixels, each pair diagonally adjacent. (Note that high-valued and low-valued are with respect to the contour value sought when LabelContours is false. When LabelContours is true, high-valued means the label being traced and low-valued means any other label.) In this case, the default behavior is that the low-valued pixels are connected into the same contour via an isthmus that separates the high-valued pixels into separate contours. To reverse this, call VertexConnectHighPixelsOn(). Note that when LabelContours is true, the default behavior will leave all four pixels in separate contours. In this case, VertexConnectHighPixels equal to true can instead create contours that are crossing barbells.

Outputs are not guaranteed to be closed paths: contours which intersect the image edge will be left open. All other paths will be closed. (The closedness of a path can be tested by checking whether the beginning point is the same as the end point.)

Produced paths are oriented. Following the path from beginning to end, image intensity values lower than the contour value are to the left of the path and intensity values greater than the contour value are to the right. In other words, the image gradient at a path segment is (approximately) in the direct of that segment rotated right by 90 degrees, because the image intensity values increase from left-to-right across the segment. This means that the generated contours will circle clockwise around "hills" of above-contour-value intensity, and counter-clockwise around "depressions" of below-contour-value intensity. This convention can be reversed by calling ReverseContourOrientationOn().

By default values are interpreted as intensities relative to a contour value. First calling LabelContoursOn() changes this behavior to instead interpret each value as a label. Boundaries are computed for each label separately and all are returned. The value of LabelContours affects the interpretation of VertexConnectHighPixels; see above.

By default the input image's largest possible region will be processed; call SetRequestedRegion() to process a different region, or ClearRequestedRegion() to revert to the default value. Note that the requested regions are usually set on the output; however since paths have no notion of a "region", this must be set at the filter level.

This class was contributed to the Insight Journal by Zachary Pincus. https://www.insight-journal.org/browse/publication/72

See also: Image; Path; PolyLineParametricPath

ITK Sphinx Examples:

All ITK Sphinx Examples

Extract Contours From Image

Examples: SphinxExamples/src/Filtering/Path/ExtractContoursFromImage/Code.cxx.

Definition at line 108 of file itkContourExtractor2DImageFilter.h.

Inheritance diagram for itk::ContourExtractor2DImageFilter< TInputImage >:

Collaboration diagram for itk::ContourExtractor2DImageFilter< TInputImage >:

Classes
struct	ContourData

class	ContourType

struct	VertexHash

Public Types
using	ConstPointer = SmartPointer< const Self >

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageType = TInputImage

using	InputIndexType = typename InputImageType::IndexType

using	InputOffsetType = typename InputImageType::OffsetType

using	InputPixelType = typename InputImageType::PixelType

using	InputRealType = typename NumericTraits< InputPixelType >::RealType

using	InputRegionType = typename InputImageType::RegionType

using	InputSizeType = typename InputImageType::SizeType

using	OutputPathPointer = typename OutputPathType::Pointer

using	OutputPathType = PolyLineParametricPath< 2 >

using	Pointer = SmartPointer< Self >

using	RegionConstIterator = ImageRegionConstIterator< InputImageType >

using	RegionConstRange = ImageRegionRange< const InputImageType >

using	RegionIndexRange = ImageRegionIndexRange< InputImageType::ImageDimension >

using	RegionIterator = ImageRegionIterator< InputImageType >

using	RegionRange = ImageRegionRange< InputImageType >

using	Self = ContourExtractor2DImageFilter

using	Superclass = ImageToPathFilter< InputImageType, OutputPathType >

using	VertexListConstPointer = typename VertexListType::ConstPointer

using	VertexListType = typename OutputPathType::VertexListType

using	VertexType = typename OutputPathType::VertexType

using	VertexValueType = typename VertexType::ValueType

Public Types inherited from itk::ImageToPathFilter< TInputImage, PolyLineParametricPath< 2 > >
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 = TInputImage

using	Pointer = SmartPointer< Self >

using	Self = ImageToPathFilter

using	Superclass = PathSource< PolyLineParametricPath< 2 > >

Public Types inherited from itk::PathSource< PolyLineParametricPath< 2 > >
using	ConstPointer = SmartPointer< const Self >

using	DataObjectPointer = DataObject::Pointer

using	OutputPathIndexType = typename OutputPathType::IndexType

using	OutputPathInputType = typename OutputPathType::InputType

using	OutputPathOffsetType = typename OutputPathType::OffsetType

using	OutputPathOutputType = typename OutputPathType::OutputType

using	OutputPathPointer = typename OutputPathType::Pointer

using	OutputPathType = PolyLineParametricPath< 2 >

using	Pointer = SmartPointer< Self >

using	Self = PathSource

using	Superclass = ProcessObject

using	DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

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
void	ClearRequestedRegion ()

const char *	GetNameOfClass () const override

virtual const InputRegionType &	GetRequestedRegion () const

void	SetRequestedRegion (const InputRegionType region)


virtual void	SetReverseContourOrientation (bool _arg)

virtual const bool &	GetReverseContourOrientation () const

virtual void	ReverseContourOrientationOn ()


virtual void	SetVertexConnectHighPixels (bool _arg)

virtual const bool &	GetVertexConnectHighPixels () const

virtual void	VertexConnectHighPixelsOn ()


virtual void	SetLabelContours (bool _arg)

virtual const bool &	GetLabelContours () const

virtual void	LabelContoursOn ()


virtual void	SetContourValue (InputRealType _arg)

virtual const InputRealType &	GetContourValue () const

Public Member Functions inherited from itk::ImageToPathFilter< TInputImage, PolyLineParametricPath< 2 > >
const InputImageType *	GetInput ()

const InputImageType *	GetInput (unsigned int idx)

const char *	GetNameOfClass () const override

virtual void	SetInput (const InputImageType *input)

virtual void	SetInput (unsigned int, const TInputImage *image)

Public Member Functions inherited from itk::PathSource< PolyLineParametricPath< 2 > >
const char *	GetNameOfClass () const override

OutputPathType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, OutputPathType *graft)

virtual void	GraftOutput (OutputPathType *graft)

OutputPathType *	GetOutput ()

DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) override

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

virtual float	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

void	IncrementProgress (float increment)

virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

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 val)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () 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 noexcept override

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
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::PathSource< PolyLineParametricPath< 2 > >
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 val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Static Public Attributes
static constexpr unsigned int	InputImageDimension { TInputImage::ImageDimension }

Static Public Attributes inherited from itk::ImageToPathFilter< TInputImage, PolyLineParametricPath< 2 > >
static constexpr unsigned int	InputImageDimension

Protected Member Functions
	ContourExtractor2DImageFilter ()

void	GenerateData () override

void	GenerateInputRequestedRegion () override

void	PrintSelf (std::ostream &os, Indent indent) const override

	~ContourExtractor2DImageFilter () override=default

Protected Member Functions inherited from itk::ImageToPathFilter< TInputImage, PolyLineParametricPath< 2 > >
	ImageToPathFilter ()

void	PrintSelf (std::ostream &os, Indent indent) const override

	~ImageToPathFilter () override=default

Protected Member Functions inherited from itk::PathSource< PolyLineParametricPath< 2 > >
	PathSource ()

void	PrintSelf (std::ostream &os, Indent indent) const override

	~PathSource () override=default

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)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (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

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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 idx, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &name, DataObject *output)

virtual void	SetPrimaryInput (DataObject *object)

virtual void	SetPrimaryOutput (DataObject *object)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyInputInformation () ITKv5_CONST

virtual void	VerifyPreconditions () ITKv5_CONST

	~ProcessObject () override

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () const

DataObject *	GetOutput (DataObjectPointerArraySizeType i)

const DataObject *	GetOutput (DataObjectPointerArraySizeType i) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

virtual bool	GetThreaderUpdateProgress () const

virtual void	ThreaderUpdateProgressOn ()

virtual void	SetThreaderUpdateProgress (bool arg)

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~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 ()

Private Types
using	ContourConstIterator = typename ContourType::const_iterator

using	ContourContainerConstIterator = typename ContourContainerType::const_iterator

using	ContourContainerIterator = typename ContourContainerType::iterator

using	ContourContainerType = std::list< ContourType >

using	LabelsConstIterator = typename LabelsContainer::const_iterator

using	LabelsContainer = std::vector< InputPixelType >

using	LabelsIterator = typename LabelsContainer::iterator

using	VertexToContourContainerIteratorMap = std::unordered_map< VertexType, ContourContainerIterator, VertexHash >

using	VertexToContourContainerIteratorMapConstIterator = typename VertexToContourContainerIteratorMap::const_iterator

using	VertexToContourContainerIteratorMapIterator = typename VertexToContourContainerIteratorMap::iterator

using	VertexToContourContainerIteratorMapKeyValuePair = typename VertexToContourContainerIteratorMap::value_type

Private Member Functions
void	AddSegment (const VertexType from, const VertexType to, ContourData &contourData)

void	CreateSingleContour (InputPixelType label, const InputImageType *input, const InputRegionType extendedRegion, SizeValueType totalNumberOfPixels, ContourContainerType &contoursOutput)

void	FillOutputs (const std::vector< InputPixelType > &allLabels, std::unordered_map< InputPixelType, ContourContainerType > &labelsContoursOutput)

void	GenerateDataForLabels ()

VertexType	InterpolateContourPosition (InputPixelType fromValue, InputPixelType toValue, InputIndexType fromIndex, InputOffsetType toOffset)

Private Attributes
InputRealType	m_ContourValue {}

bool	m_LabelContours {}

InputRegionType	m_RequestedRegion {}

bool	m_ReverseContourOrientation {}

InputPixelType	m_UnusedLabel {}

bool	m_UseCustomRegion {}

bool	m_VertexConnectHighPixels {}

Additional Inherited Members
Static Protected Member Functions inherited from itk::ProcessObject
static constexpr float	progressFixedToFloat (uint32_t fixed)

static uint32_t	progressFloatToFixed (float f)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime {}

bool	m_Updating {}

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}