SimpleITK
1.0.1
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Derived class implementing a specific patch-based denoising algorithm, as detailed below. More...
#include <sitkPatchBasedDenoisingImageFilter.h>
Public Types | |
enum | NoiseModelType { NOMODEL, GAUSSIAN, RICIAN, POISSON } |
typedef BasicPixelIDTypeList | PixelIDTypeList |
typedef PatchBasedDenoisingImageFilter | Self |
Public Types inherited from itk::simple::ImageFilter< 1 > | |
typedef ImageFilter | Self |
Public Types inherited from itk::simple::ProcessObject | |
typedef ProcessObject | Self |
Public Member Functions | |
Self & | AlwaysTreatComponentsAsEuclideanOff () |
Self & | AlwaysTreatComponentsAsEuclideanOn () |
Image | Execute (const Image &image1) |
Image | Execute (const Image &image1, double kernelBandwidthSigma, uint32_t patchRadius, uint32_t numberOfIterations, uint32_t numberOfSamplePatches, double sampleVariance, PatchBasedDenoisingImageFilter::NoiseModelType noiseModel, double noiseSigma, double noiseModelFidelityWeight, bool alwaysTreatComponentsAsEuclidean, bool kernelBandwidthEstimation, double kernelBandwidthMultiplicationFactor, uint32_t kernelBandwidthUpdateFrequency, double kernelBandwidthFractionPixelsForEstimation) |
bool | GetAlwaysTreatComponentsAsEuclidean () const |
bool | GetKernelBandwidthEstimation () const |
double | GetKernelBandwidthFractionPixelsForEstimation () const |
double | GetKernelBandwidthMultiplicationFactor () const |
double | GetKernelBandwidthSigma () const |
uint32_t | GetKernelBandwidthUpdateFrequency () const |
std::string | GetName () const |
NoiseModelType | GetNoiseModel () const |
double | GetNoiseModelFidelityWeight () const |
double | GetNoiseSigma () const |
uint32_t | GetNumberOfIterations () const |
uint32_t | GetNumberOfSamplePatches () const |
uint32_t | GetPatchRadius () const |
double | GetSampleVariance () const |
Self & | KernelBandwidthEstimationOff () |
Self & | KernelBandwidthEstimationOn () |
PatchBasedDenoisingImageFilter () | |
Self & | SetAlwaysTreatComponentsAsEuclidean (bool AlwaysTreatComponentsAsEuclidean) |
Self & | SetKernelBandwidthEstimation (bool KernelBandwidthEstimation) |
Self & | SetKernelBandwidthFractionPixelsForEstimation (double KernelBandwidthFractionPixelsForEstimation) |
Self & | SetKernelBandwidthMultiplicationFactor (double KernelBandwidthMultiplicationFactor) |
Self & | SetKernelBandwidthSigma (double KernelBandwidthSigma) |
Self & | SetKernelBandwidthUpdateFrequency (uint32_t KernelBandwidthUpdateFrequency) |
Self & | SetNoiseModel (NoiseModelType NoiseModel) |
Self & | SetNoiseModelFidelityWeight (double NoiseModelFidelityWeight) |
Self & | SetNoiseSigma (double NoiseSigma) |
Self & | SetNumberOfIterations (uint32_t NumberOfIterations) |
Self & | SetNumberOfSamplePatches (uint32_t NumberOfSamplePatches) |
Self & | SetPatchRadius (uint32_t PatchRadius) |
Self & | SetSampleVariance (double SampleVariance) |
std::string | ToString () const |
~PatchBasedDenoisingImageFilter () | |
Public Member Functions inherited from itk::simple::ImageFilter< 1 > | |
ImageFilter () | |
virtual | ~ImageFilter ()=0 |
Public Member Functions inherited from itk::simple::ProcessObject | |
virtual void | Abort () |
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 |
Private Types | |
typedef Image(Self::* | MemberFunctionType) (const Image &image1) |
Private Member Functions | |
template<class TImageType > | |
Image | ExecuteInternal (const Image &image1) |
Private Attributes | |
bool | m_AlwaysTreatComponentsAsEuclidean |
bool | m_KernelBandwidthEstimation |
double | m_KernelBandwidthFractionPixelsForEstimation |
double | m_KernelBandwidthMultiplicationFactor |
double | m_KernelBandwidthSigma |
uint32_t | m_KernelBandwidthUpdateFrequency |
nsstd::auto_ptr< detail::MemberFunctionFactory< MemberFunctionType > > | m_MemberFactory |
NoiseModelType | m_NoiseModel |
double | m_NoiseModelFidelityWeight |
double | m_NoiseSigma |
uint32_t | m_NumberOfIterations |
uint32_t | m_NumberOfSamplePatches |
uint32_t | m_PatchRadius |
double | m_SampleVariance |
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 void | SetGlobalDefaultNumberOfThreads (unsigned int n) |
static unsigned int | GetGlobalDefaultNumberOfThreads () |
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... | |
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) throw () |
virtual void | PreUpdate (itk::ProcessObject *p) |
virtual void | RemoveITKObserver (EventCommand &e) |
Protected Member Functions inherited from itk::simple::NonCopyable | |
NonCopyable () | |
Static Protected Member Functions inherited from itk::simple::ImageFilter< 1 > | |
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 TImageType > | |
static Image | CastITKToImage (TImageType *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) |
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) |
Derived class implementing a specific patch-based denoising algorithm, as detailed below.
This class is derived from the base class PatchBasedDenoisingBaseImageFilter ; please refer to the documentation of the base class first. This class implements a denoising filter that uses iterative non-local, or semi-local, weighted averaging of image patches for image denoising. The intensity at each pixel 'p' gets updated as a weighted average of intensities of a chosen subset of pixels from the image.
This class implements the denoising algorithm using a Gaussian kernel function for nonparametric density estimation. The class implements a scheme to automatically estimated the kernel bandwidth parameter (namely, sigma) using leave-one-out cross validation. It implements schemes for random sampling of patches non-locally (from the entire image) as well as semi-locally (from the spatial proximity of the pixel being denoised at the specific point in time). It implements a specific scheme for defining patch weights (mask) as described in Awate and Whitaker 2005 IEEE CVPR and 2006 IEEE TPAMI.
Definition at line 46 of file sitkPatchBasedDenoisingImageFilter.h.
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Setup for member function dispatching
Definition at line 235 of file sitkPatchBasedDenoisingImageFilter.h.
Define the pixels types supported by this filter
Definition at line 58 of file sitkPatchBasedDenoisingImageFilter.h.
Definition at line 48 of file sitkPatchBasedDenoisingImageFilter.h.
Enumerator | |
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NOMODEL | |
GAUSSIAN | |
RICIAN | |
POISSON |
Definition at line 118 of file sitkPatchBasedDenoisingImageFilter.h.
itk::simple::PatchBasedDenoisingImageFilter::PatchBasedDenoisingImageFilter | ( | ) |
Default Constructor that takes no arguments and initializes default parameters
itk::simple::PatchBasedDenoisingImageFilter::~PatchBasedDenoisingImageFilter | ( | ) |
Destructor
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Definition at line 161 of file sitkPatchBasedDenoisingImageFilter.h.
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Set the value of AlwaysTreatComponentsAsEuclidean to true or false respectfully.
Definition at line 160 of file sitkPatchBasedDenoisingImageFilter.h.
Execute the filter on the input image
Image itk::simple::PatchBasedDenoisingImageFilter::Execute | ( | const Image & | image1, |
double | kernelBandwidthSigma, | ||
uint32_t | patchRadius, | ||
uint32_t | numberOfIterations, | ||
uint32_t | numberOfSamplePatches, | ||
double | sampleVariance, | ||
PatchBasedDenoisingImageFilter::NoiseModelType | noiseModel, | ||
double | noiseSigma, | ||
double | noiseModelFidelityWeight, | ||
bool | alwaysTreatComponentsAsEuclidean, | ||
bool | kernelBandwidthEstimation, | ||
double | kernelBandwidthMultiplicationFactor, | ||
uint32_t | kernelBandwidthUpdateFrequency, | ||
double | kernelBandwidthFractionPixelsForEstimation | ||
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Execute the filter on the input image with the given parameters
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Set/Get flag indicating whether all components should always be treated as if they are in euclidean space regardless of pixel type. Defaults to false.
Definition at line 167 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get flag indicating whether kernel-bandwidth should be estimated automatically from the image data. Defaults to true.
Definition at line 183 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the fraction of the image to use for kernel bandwidth sigma estimation. To reduce the computational burden for computing sigma, a small random fraction of the image pixels can be used.
Definition at line 215 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the kernel bandwidth sigma multiplication factor used to modify the automatically-estimated kernel bandwidth sigma. At times, it may be desirable to modify the value of the automatically-estimated sigma. Typically, this number isn't very far from 1. Note: This is used only when KernelBandwidthEstimation is True/On.
Definition at line 193 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get initial kernel bandwidth estimate. To prevent the class from automatically modifying this estimate, set KernelBandwidthEstimation to false in the base class.
Definition at line 70 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the update frequency for the kernel bandwidth estimation. An optimal bandwidth will be re-estimated based on the denoised image after every 'n' iterations. Must be a positive integer. Defaults to 3, i.e. bandwidth updated after every 3 denoising iteration.
Definition at line 205 of file sitkPatchBasedDenoisingImageFilter.h.
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Name of this class
Implements itk::simple::ProcessObject.
Definition at line 217 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the noise model type. Defaults to GAUSSIAN. To use the noise model during denoising, FidelityWeight must be positive.
Definition at line 130 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the weight on the fidelity term (penalizes deviations from the noisy data). This option is used when a noise model is specified. This weight controls the balance between the smoothing and the closeness to the noisy data.
Definition at line 151 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 139 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the number of denoising iterations to perform. Must be a positive integer. Defaults to 1.
Definition at line 94 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 104 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the patch radius specified in physical coordinates. Patch radius is preferably set to an even number. Currently, only isotropic patches in physical space are allowed; patches can be anisotropic in voxel space.
Definition at line 82 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the variance of the domain where patches are sampled.
Definition at line 116 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 177 of file sitkPatchBasedDenoisingImageFilter.h.
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Set the value of KernelBandwidthEstimation to true or false respectfully.
Definition at line 176 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get flag indicating whether all components should always be treated as if they are in euclidean space regardless of pixel type. Defaults to false.
Definition at line 157 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get flag indicating whether kernel-bandwidth should be estimated automatically from the image data. Defaults to true.
Definition at line 173 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the fraction of the image to use for kernel bandwidth sigma estimation. To reduce the computational burden for computing sigma, a small random fraction of the image pixels can be used.
Definition at line 210 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the kernel bandwidth sigma multiplication factor used to modify the automatically-estimated kernel bandwidth sigma. At times, it may be desirable to modify the value of the automatically-estimated sigma. Typically, this number isn't very far from 1. Note: This is used only when KernelBandwidthEstimation is True/On.
Definition at line 188 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get initial kernel bandwidth estimate. To prevent the class from automatically modifying this estimate, set KernelBandwidthEstimation to false in the base class.
Definition at line 65 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the update frequency for the kernel bandwidth estimation. An optimal bandwidth will be re-estimated based on the denoised image after every 'n' iterations. Must be a positive integer. Defaults to 3, i.e. bandwidth updated after every 3 denoising iteration.
Definition at line 199 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the noise model type. Defaults to GAUSSIAN. To use the noise model during denoising, FidelityWeight must be positive.
Definition at line 124 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the weight on the fidelity term (penalizes deviations from the noisy data). This option is used when a noise model is specified. This weight controls the balance between the smoothing and the closeness to the noisy data.
Definition at line 145 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the noise sigma. Used by the noise model where appropriate, defaults to 5% of the image intensity range
Definition at line 135 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the number of denoising iterations to perform. Must be a positive integer. Defaults to 1.
Definition at line 88 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the number of patches to sample for each pixel.
Definition at line 100 of file sitkPatchBasedDenoisingImageFilter.h.
Set/Get the patch radius specified in physical coordinates. Patch radius is preferably set to an even number. Currently, only isotropic patches in physical space are allowed; patches can be anisotropic in voxel space.
Definition at line 76 of file sitkPatchBasedDenoisingImageFilter.h.
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Set/Get the variance of the domain where patches are sampled.
Definition at line 110 of file sitkPatchBasedDenoisingImageFilter.h.
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Print ourselves out
Reimplemented from itk::simple::ProcessObject.
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Definition at line 240 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 255 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 256 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 259 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 257 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 246 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 258 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 242 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 252 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 254 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 253 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 249 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 250 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 247 of file sitkPatchBasedDenoisingImageFilter.h.
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Definition at line 251 of file sitkPatchBasedDenoisingImageFilter.h.