SimpleITK
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Solve an Eikonal equation using Fast Marching. More...
#include <sitkFastMarchingImageFilter.h>
Solve an Eikonal equation using Fast Marching.
Fast marching solves an Eikonal equation where the speed is always non-negative and depends on the position only. Starting from an initial position on the front, fast marching systematically moves the front forward one grid point at a time.
Updates are performed using an entropy satisfy scheme where only "upwind" neighborhoods are used. This implementation of Fast Marching uses a std::priority_queue to locate the next proper grid position to update.
Fast Marching sweeps through N grid points in (N log N) steps to obtain the arrival time value as the front propagates through the grid.
Implementation of this class is based on Chapter 8 of "Level Set Methods and Fast Marching Methods", J.A. Sethian, Cambridge Press, Second edition, 1999.
This class is templated over the level set image type and the speed image type. The initial front is specified by two containers: one containing the known points and one containing the trial points. Alive points are those that are already part of the object, and trial points are considered for inclusion. In order for the filter to evolve, at least some trial points must be specified. These can for instance be specified as the layer of pixels around the alive points.
The speed function can be specified as a speed image or a speed constant. The speed image is set using the method SetInput() . If the speed image is nullptr, a constant speed function is used and is specified using method the SetSpeedConstant() .
If the speed function is constant and of value one, fast marching results in an approximate distance function from the initial alive points. FastMarchingImageFilter is used in the ReinitializeLevelSetImageFilter object to create a signed distance function from the zero level set.
The algorithm can be terminated early by setting an appropriate stopping value. The algorithm terminates when the current arrival time being processed is greater than the stopping value.
There are two ways to specify the output image information ( LargestPossibleRegion, Spacing, Origin): (a) it is copied directly from the input speed image or (b) it is specified by the user. Default values are used if the user does not specify all the information.
The output information is computed as follows. If the speed image is nullptr or if the OverrideOutputInformation is set to true, the output information is set from user specified parameters. These parameters can be specified using methods SetOutputRegion() , SetOutputSpacing() , SetOutputDirection() , and SetOutputOrigin() . Else if the speed image is not nullptr, the output information is copied from the input speed image.
For an alternative implementation, see itk::FastMarchingImageFilter .
Possible Improvements: In the current implementation, std::priority_queue only allows taking nodes out from the front and putting nodes in from the back. To update a value already on the heap, a new node is added to the heap. The defunct old node is left on the heap. When it is removed from the top, it will be recognized as invalid and not used. Future implementations can implement the heap in a different way allowing the values to be updated. This will generally require some sift-up and sift-down functions and an image of back-pointers going from the image to heap in order to locate the node which is to be updated.
Definition at line 68 of file sitkFastMarchingImageFilter.h.
Public Types | |
using | PixelIDTypeList = BasicPixelIDTypeList |
using | Self = FastMarchingImageFilter |
Public Types inherited from itk::simple::ImageFilter | |
using | Self = ImageFilter |
Public Types inherited from itk::simple::ProcessObject | |
using | Self = ProcessObject |
Public Member Functions | |
Self & | AddTrialPoint (std::vector< unsigned int > point) |
Add TrialPoints point. More... | |
Self & | ClearTrialPoints () |
Remove all TrialPoints points. More... | |
Image | Execute (const Image &image1) |
FastMarchingImageFilter () | |
std::vector< double > | GetInitialTrialValues () const |
std::string | GetName () const |
double | GetNormalizationFactor () const |
double | GetStoppingValue () const |
std::vector< std::vector< unsigned int > > | GetTrialPoints () const |
Self & | SetInitialTrialValues (std::vector< double > InitialTrialValues) |
Set the initial seed values for corresponding trial points. More... | |
Self & | SetNormalizationFactor (double NormalizationFactor) |
Self & | SetStoppingValue (double StoppingValue) |
Self & | SetTrialPoints (std::vector< std::vector< unsigned int > > TrialPoints) |
std::string | ToString () const |
virtual | ~FastMarchingImageFilter () |
Public Member Functions inherited from itk::simple::ImageFilter | |
ImageFilter () | |
virtual | ~ImageFilter ()=0 |
Public Member Functions inherited from itk::simple::ProcessObject | |
virtual void | Abort () |
virtual int | AddCommand (itk::simple::EventEnum event, const std::function< void()> &func) |
Directly add a callback to observe an event. More... | |
virtual int | AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd) |
Add a Command Object to observer the event. More... | |
virtual float | GetProgress () const |
An Active Measurement of the progress of execution. More... | |
virtual bool | HasCommand (itk::simple::EventEnum event) const |
Query of this object has any registered commands for event. More... | |
ProcessObject () | |
virtual void | RemoveAllCommands () |
Remove all registered commands. More... | |
virtual | ~ProcessObject () |
virtual void | DebugOn () |
virtual void | DebugOff () |
virtual bool | GetDebug () const |
virtual void | SetDebug (bool debugFlag) |
virtual void | SetNumberOfThreads (unsigned int n) |
virtual unsigned int | GetNumberOfThreads () const |
virtual void | SetNumberOfWorkUnits (unsigned int n) |
virtual unsigned int | GetNumberOfWorkUnits () const |
Private Types | |
using | MemberFunctionType = Image(Self::*)(const Image &image1) |
Private Member Functions | |
template<class TImageType > | |
Image | ExecuteInternal (const Image &image1) |
Private Attributes | |
std::vector< double > | m_InitialTrialValues {std::vector<double>()} |
std::unique_ptr< detail::MemberFunctionFactory< MemberFunctionType > > | m_MemberFactory |
double | m_NormalizationFactor {1.0} |
double | m_StoppingValue {std::numeric_limits<double>::max()/2.0} |
std::vector< std::vector< unsigned int > > | m_TrialPoints {std::vector< std::vector<unsigned int > >()} |
Friends | |
struct | detail::MemberFunctionAddressor< MemberFunctionType > |
Additional Inherited Members | |
Static Public Member Functions inherited from itk::simple::ProcessObject | |
static bool | GetGlobalDefaultDebug () |
static void | GlobalDefaultDebugOff () |
static void | GlobalDefaultDebugOn () |
static void | SetGlobalDefaultDebug (bool debugFlag) |
static void | GlobalWarningDisplayOn () |
static void | GlobalWarningDisplayOff () |
static void | SetGlobalWarningDisplay (bool flag) |
static bool | GetGlobalWarningDisplay () |
static double | GetGlobalDefaultCoordinateTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultCoordinateTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
static double | GetGlobalDefaultDirectionTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultDirectionTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
static bool | SetGlobalDefaultThreader (const std::string &threader) |
Set/Get the default threader used for process objects. More... | |
static std::string | GetGlobalDefaultThreader () |
Set/Get the default threader used for process objects. More... | |
static void | SetGlobalDefaultNumberOfThreads (unsigned int n) |
static unsigned int | GetGlobalDefaultNumberOfThreads () |
Set/Get the default threader used for process objects. More... | |
Protected Member Functions inherited from itk::simple::ImageFilter | |
void | CheckImageMatchingDimension (const Image &image1, const Image &image2, const std::string &image2Name) |
void | CheckImageMatchingPixelType (const Image &image1, const Image &image2, const std::string &image2Name) |
void | CheckImageMatchingSize (const Image &image1, const Image &image2, const std::string &image2Name) |
Protected Member Functions inherited from itk::simple::ProcessObject | |
virtual unsigned long | AddITKObserver (const itk::EventObject &, itk::Command *) |
virtual itk::ProcessObject * | GetActiveProcess () |
virtual void | OnActiveProcessDelete () |
virtual void | onCommandDelete (const itk::simple::Command *cmd) noexcept |
virtual void | PreUpdate (itk::ProcessObject *p) |
virtual void | RemoveITKObserver (EventCommand &e) |
Protected Member Functions inherited from itk::simple::NonCopyable | |
NonCopyable ()=default | |
NonCopyable (const NonCopyable &)=delete | |
NonCopyable & | operator= (const NonCopyable &)=delete |
Static Protected Member Functions inherited from itk::simple::ImageFilter | |
template<class TImageType > | |
static void | FixNonZeroIndex (TImageType *img) |
Static Protected Member Functions inherited from itk::simple::ProcessObject | |
template<class TImageType > | |
static TImageType::ConstPointer | CastImageToITK (const Image &img) |
template<class TPixelType , unsigned int VImageDimension, unsigned int VLength, template< typename, unsigned int > class TVector> | |
static Image | CastITKToImage (itk::Image< TVector< TPixelType, VLength >, VImageDimension > *img) |
template<unsigned int VImageDimension, unsigned int VLength, template< unsigned int > class TVector> | |
static Image | CastITKToImage (itk::Image< TVector< VLength >, VImageDimension > *img) |
template<class TImageType > | |
static Image | CastITKToImage (TImageType *img) |
static const itk::EventObject & | GetITKEventObject (EventEnum e) |
template<typename T > | |
static std::ostream & | ToStringHelper (std::ostream &os, const T &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const signed char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const unsigned char &v) |
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Setup for member function dispatching
Definition at line 142 of file sitkFastMarchingImageFilter.h.
Define the pixels types supported by this filter
Definition at line 80 of file sitkFastMarchingImageFilter.h.
Definition at line 70 of file sitkFastMarchingImageFilter.h.
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Destructor
itk::simple::FastMarchingImageFilter::FastMarchingImageFilter | ( | ) |
Default Constructor that takes no arguments and initializes default parameters
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Add TrialPoints point.
Definition at line 93 of file sitkFastMarchingImageFilter.h.
References itk::point().
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Remove all TrialPoints points.
Definition at line 95 of file sitkFastMarchingImageFilter.h.
Execute the filter on the input image
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Definition at line 125 of file sitkFastMarchingImageFilter.h.
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Name of this class
Implements itk::simple::ProcessObject.
Definition at line 128 of file sitkFastMarchingImageFilter.h.
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Set/Get the Normalization Factor for the Speed Image . The values in the Speed Image is divided by this factor. This allows the use of images with integer pixel types to represent the speed.
Definition at line 106 of file sitkFastMarchingImageFilter.h.
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Get the Fast Marching algorithm Stopping Value.
Definition at line 116 of file sitkFastMarchingImageFilter.h.
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Get the container of Trial Points representing the initial front.
Definition at line 91 of file sitkFastMarchingImageFilter.h.
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Set the initial seed values for corresponding trial points.
Definition at line 121 of file sitkFastMarchingImageFilter.h.
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Set/Get the Normalization Factor for the Speed Image . The values in the Speed Image is divided by this factor. This allows the use of images with integer pixel types to represent the speed.
Definition at line 101 of file sitkFastMarchingImageFilter.h.
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Set the Fast Marching algorithm Stopping Value. The Fast Marching algorithm is terminated when the value of the smallest trial point is greater than the stopping value.
Definition at line 111 of file sitkFastMarchingImageFilter.h.
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Set the container of Trial Points representing the initial front. Trial points are represented as a VectorContainer of LevelSetNodes.
Definition at line 86 of file sitkFastMarchingImageFilter.h.
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Print ourselves out
Reimplemented from itk::simple::ProcessObject.
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Definition at line 146 of file sitkFastMarchingImageFilter.h.
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Definition at line 157 of file sitkFastMarchingImageFilter.h.
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Definition at line 148 of file sitkFastMarchingImageFilter.h.
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Definition at line 153 of file sitkFastMarchingImageFilter.h.
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Definition at line 155 of file sitkFastMarchingImageFilter.h.
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Definition at line 151 of file sitkFastMarchingImageFilter.h.