ANIMA  4.0
Classes | Public Types | Public Member Functions | Protected Types | Protected Member Functions | Static Protected Member Functions | List of all members
anima::BaseTractographyImageFilter Class Referenceabstract

#include <animaBaseTractographyImageFilter.h>

+ Inheritance diagram for anima::BaseTractographyImageFilter:
+ Collaboration diagram for anima::BaseTractographyImageFilter:

Classes

struct  trackerArguments
 

Public Types

typedef itk::SmartPointer< const Self > ConstPointer
 
typedef itk::ContinuousIndex< double, 3 > ContinuousIndexType
 
typedef std::vector< std::pair< FiberProgressType, FiberType > > FiberProcessVectorType
 
enum  FiberProgressType {
  Forward,
  Backward,
  Both
}
 
typedef std::vector< PointType > FiberType
 
typedef MaskImageType::IndexType IndexType
 
typedef MaskImageType::Pointer MaskImagePointer
 
typedef itk::Image< unsigned short, 3 > MaskImageType
 
typedef ModelImageType::Pointer ModelImagePointer
 
typedef itk::VectorImage< double, 3 > ModelImageType
 
typedef itk::SmartPointer< Self > Pointer
 
typedef MaskImageType::PointType PointType
 
typedef ModelImageType::RegionType RegionType
 
typedef BaseTractographyImageFilter Self
 
typedef itk::ProcessObject Superclass
 
typedef ModelImageType::PixelType VectorType
 

Public Member Functions

void createVTKOutput (std::vector< std::vector< PointType > > &filteredFibers)
 
ModelImageType * GetInputImage ()
 
virtual const char * GetNameOfClass () const
 
vtkPolyData * GetOutput ()
 
void SetComputeLocalColors (bool flag)
 
void SetCutMask (MaskImageType *mask)
 
void SetFilteringMask (MaskImageType *mask)
 
void SetForbiddenMask (MaskImageType *mask)
 
virtual void SetInputImage (ModelImageType *input)
 
void SetMaxFiberAngle (double num)
 
void SetMaxLengthFiber (double num)
 
void SetMinLengthFiber (double num)
 
void SetNumberOfFibersPerPixel (unsigned int num)
 
void SetSeedingMask (MaskImageType *mask)
 
void SetStepProgression (double num)
 
void Update () ITK_OVERRIDE
 

Protected Types

typedef itk::ImageBase< ModelImageType::ImageDimension > ImageBaseType
 

Protected Member Functions

 BaseTractographyImageFilter ()
 
bool CheckIndexInImageBounds (IndexType &index, ImageBaseType *testImage)
 
virtual bool CheckIndexInImageBounds (ContinuousIndexType &index)=0
 
virtual bool CheckModelCompatibility (VectorType &modelValue, itk::ThreadIdType threadId)=0
 
virtual void ComputeAdditionalScalarMaps ()
 
FiberProcessVectorType ComputeFiber (FiberType &fiber, FiberProgressType ways, itk::ThreadIdType threadId)
 
std::vector< FiberType > FilterOutputFibers (std::vector< FiberType > &fibers)
 
virtual PointType GetModelPrincipalDirection (VectorType &modelValue, bool is2d, itk::ThreadIdType threadId)=0
 
virtual void GetModelValue (ContinuousIndexType &index, VectorType &modelValue)=0
 Computes value of model from data. May use SNR and previous model value to perform smart interpolation. Replaces SNR and modelValue by the outputs. More...
 
virtual PointType GetNextDirection (PointType &previousDirection, VectorType &modelValue, bool is2d, itk::ThreadIdType threadId)=0
 
bool isZero (VectorType &value)
 
virtual void PrepareTractography ()
 
void ThreadedTrackComputer (unsigned int numThread, std::vector< FiberType > &resultFibers, unsigned int startSeedIndex, unsigned int endSeedIndex)
 
void ThreadTrack (unsigned int numThread, std::vector< FiberType > &resultFibers)
 
virtual ~BaseTractographyImageFilter ()
 

Static Protected Member Functions

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION ThreadTracker (void *arg)
 

Detailed Description

Definition at line 20 of file animaBaseTractographyImageFilter.h.

Member Typedef Documentation

◆ ConstPointer

typedef itk::SmartPointer<const Self> anima::BaseTractographyImageFilter::ConstPointer

Definition at line 28 of file animaBaseTractographyImageFilter.h.

◆ ContinuousIndexType

typedef itk::ContinuousIndex<double, 3> anima::BaseTractographyImageFilter::ContinuousIndexType

Definition at line 42 of file animaBaseTractographyImageFilter.h.

◆ FiberProcessVectorType

typedef std::vector<std::pair < FiberProgressType, FiberType > > anima::BaseTractographyImageFilter::FiberProcessVectorType

Definition at line 50 of file animaBaseTractographyImageFilter.h.

◆ FiberType

typedef std::vector<PointType> anima::BaseTractographyImageFilter::FiberType

Definition at line 49 of file animaBaseTractographyImageFilter.h.

◆ ImageBaseType

typedef itk::ImageBase<ModelImageType::ImageDimension> anima::BaseTractographyImageFilter::ImageBaseType
protected

Definition at line 95 of file animaBaseTractographyImageFilter.h.

◆ IndexType

typedef MaskImageType::IndexType anima::BaseTractographyImageFilter::IndexType

Definition at line 47 of file animaBaseTractographyImageFilter.h.

◆ MaskImagePointer

typedef MaskImageType::Pointer anima::BaseTractographyImageFilter::MaskImagePointer

Definition at line 45 of file animaBaseTractographyImageFilter.h.

◆ MaskImageType

typedef itk::Image<unsigned short, 3> anima::BaseTractographyImageFilter::MaskImageType

Definition at line 44 of file animaBaseTractographyImageFilter.h.

◆ ModelImagePointer

typedef ModelImageType::Pointer anima::BaseTractographyImageFilter::ModelImagePointer

Definition at line 39 of file animaBaseTractographyImageFilter.h.

◆ ModelImageType

typedef itk::VectorImage<double, 3> anima::BaseTractographyImageFilter::ModelImageType

Definition at line 38 of file animaBaseTractographyImageFilter.h.

◆ Pointer

typedef itk::SmartPointer<Self> anima::BaseTractographyImageFilter::Pointer

Definition at line 27 of file animaBaseTractographyImageFilter.h.

◆ PointType

typedef MaskImageType::PointType anima::BaseTractographyImageFilter::PointType

Definition at line 46 of file animaBaseTractographyImageFilter.h.

◆ RegionType

typedef ModelImageType::RegionType anima::BaseTractographyImageFilter::RegionType

Definition at line 41 of file animaBaseTractographyImageFilter.h.

◆ Self

typedef BaseTractographyImageFilter anima::BaseTractographyImageFilter::Self

SmartPointer typedef support

Definition at line 24 of file animaBaseTractographyImageFilter.h.

◆ Superclass

typedef itk::ProcessObject anima::BaseTractographyImageFilter::Superclass

Definition at line 25 of file animaBaseTractographyImageFilter.h.

◆ VectorType

typedef ModelImageType::PixelType anima::BaseTractographyImageFilter::VectorType

Definition at line 40 of file animaBaseTractographyImageFilter.h.

Member Enumeration Documentation

◆ FiberProgressType

enum anima::BaseTractographyImageFilter::FiberProgressType
Enumerator
Forward 
Backward 
Both 

Definition at line 32 of file animaBaseTractographyImageFilter.h.

Constructor & Destructor Documentation

◆ BaseTractographyImageFilter()

anima::BaseTractographyImageFilter::BaseTractographyImageFilter ( )
protected

Definition at line 15 of file animaBaseTractographyImageFilter.cxx.

◆ ~BaseTractographyImageFilter()

anima::BaseTractographyImageFilter::~BaseTractographyImageFilter ( )
protectedvirtual

Definition at line 29 of file animaBaseTractographyImageFilter.cxx.

Member Function Documentation

◆ CheckIndexInImageBounds() [1/2]

bool anima::BaseTractographyImageFilter::CheckIndexInImageBounds ( IndexType &  index,
ImageBaseType *  testImage 
)
protected

Definition at line 565 of file animaBaseTractographyImageFilter.cxx.

Referenced by ComputeFiber().

◆ CheckIndexInImageBounds() [2/2]

virtual bool anima::BaseTractographyImageFilter::CheckIndexInImageBounds ( ContinuousIndexType &  index)
protectedpure virtual

Implemented in anima::dtiTractographyImageFilter.

◆ CheckModelCompatibility()

virtual bool anima::BaseTractographyImageFilter::CheckModelCompatibility ( VectorType &  modelValue,
itk::ThreadIdType  threadId 
)
protectedpure virtual

Implemented in anima::dtiTractographyImageFilter.

Referenced by ComputeFiber().

◆ ComputeAdditionalScalarMaps()

virtual void anima::BaseTractographyImageFilter::ComputeAdditionalScalarMaps ( )
inlineprotectedvirtual

Reimplemented in anima::dtiTractographyImageFilter.

Definition at line 105 of file animaBaseTractographyImageFilter.h.

Referenced by createVTKOutput().

◆ ComputeFiber()

BaseTractographyImageFilter::FiberProcessVectorType anima::BaseTractographyImageFilter::ComputeFiber ( BaseTractographyImageFilter::FiberType &  fiber,
BaseTractographyImageFilter::FiberProgressType  ways,
itk::ThreadIdType  threadId 
)
protected

Definition at line 315 of file animaBaseTractographyImageFilter.cxx.

References Backward, Both, CheckIndexInImageBounds(), CheckModelCompatibility(), anima::ComputeOrientationAngle(), anima::ComputeScalarProduct(), Forward, GetModelPrincipalDirection(), GetModelValue(), GetNextDirection(), isZero(), and anima::Revert().

Referenced by ThreadedTrackComputer().

◆ createVTKOutput()

void anima::BaseTractographyImageFilter::createVTKOutput ( std::vector< std::vector< PointType > > &  filteredFibers)

Definition at line 287 of file animaBaseTractographyImageFilter.cxx.

References ComputeAdditionalScalarMaps().

Referenced by Update().

◆ FilterOutputFibers()

std::vector< std::vector< BaseTractographyImageFilter::PointType > > anima::BaseTractographyImageFilter::FilterOutputFibers ( std::vector< FiberType > &  fibers)
protected

Definition at line 236 of file animaBaseTractographyImageFilter.cxx.

Referenced by Update().

◆ GetInputImage()

ModelImageType* anima::BaseTractographyImageFilter::GetInputImage ( )
inline

Definition at line 58 of file animaBaseTractographyImageFilter.h.

Referenced by anima::dtiTractographyImageFilter::ComputeAdditionalScalarMaps(), and anima::dtiTractographyImageFilter::SetInputImage().

◆ GetModelPrincipalDirection()

virtual PointType anima::BaseTractographyImageFilter::GetModelPrincipalDirection ( VectorType &  modelValue,
bool  is2d,
itk::ThreadIdType  threadId 
)
protectedpure virtual

Implemented in anima::dtiTractographyImageFilter.

Referenced by ComputeFiber().

◆ GetModelValue()

virtual void anima::BaseTractographyImageFilter::GetModelValue ( ContinuousIndexType &  index,
VectorType &  modelValue 
)
protectedpure virtual

Computes value of model from data. May use SNR and previous model value to perform smart interpolation. Replaces SNR and modelValue by the outputs.

Implemented in anima::dtiTractographyImageFilter.

Referenced by ComputeFiber().

◆ GetNameOfClass()

virtual const char* anima::BaseTractographyImageFilter::GetNameOfClass ( ) const
virtual

Reimplemented in anima::dtiTractographyImageFilter.

◆ GetNextDirection()

virtual PointType anima::BaseTractographyImageFilter::GetNextDirection ( PointType &  previousDirection,
VectorType &  modelValue,
bool  is2d,
itk::ThreadIdType  threadId 
)
protectedpure virtual

Implemented in anima::dtiTractographyImageFilter.

Referenced by ComputeFiber().

◆ GetOutput()

vtkPolyData* anima::BaseTractographyImageFilter::GetOutput ( )
inline

Definition at line 77 of file animaBaseTractographyImageFilter.h.

Referenced by anima::dtiTractographyImageFilter::ComputeAdditionalScalarMaps().

◆ isZero()

bool anima::BaseTractographyImageFilter::isZero ( VectorType &  value)
protected

Definition at line 578 of file animaBaseTractographyImageFilter.cxx.

Referenced by ComputeFiber().

◆ PrepareTractography()

void anima::BaseTractographyImageFilter::PrepareTractography ( )
protectedvirtual

Definition at line 76 of file animaBaseTractographyImageFilter.cxx.

References Both.

Referenced by Update().

◆ SetComputeLocalColors()

void anima::BaseTractographyImageFilter::SetComputeLocalColors ( bool  flag)
inline

Definition at line 75 of file animaBaseTractographyImageFilter.h.

◆ SetCutMask()

void anima::BaseTractographyImageFilter::SetCutMask ( MaskImageType *  mask)
inline

Definition at line 63 of file animaBaseTractographyImageFilter.h.

◆ SetFilteringMask()

void anima::BaseTractographyImageFilter::SetFilteringMask ( MaskImageType *  mask)
inline

Definition at line 61 of file animaBaseTractographyImageFilter.h.

◆ SetForbiddenMask()

void anima::BaseTractographyImageFilter::SetForbiddenMask ( MaskImageType *  mask)
inline

Definition at line 62 of file animaBaseTractographyImageFilter.h.

◆ SetInputImage()

virtual void anima::BaseTractographyImageFilter::SetInputImage ( ModelImageType *  input)
inlinevirtual

Reimplemented in anima::dtiTractographyImageFilter.

Definition at line 57 of file animaBaseTractographyImageFilter.h.

Referenced by anima::dtiTractographyImageFilter::SetInputImage().

◆ SetMaxFiberAngle()

void anima::BaseTractographyImageFilter::SetMaxFiberAngle ( double  num)
inline

Definition at line 69 of file animaBaseTractographyImageFilter.h.

◆ SetMaxLengthFiber()

void anima::BaseTractographyImageFilter::SetMaxLengthFiber ( double  num)
inline

Definition at line 71 of file animaBaseTractographyImageFilter.h.

◆ SetMinLengthFiber()

void anima::BaseTractographyImageFilter::SetMinLengthFiber ( double  num)
inline

Definition at line 70 of file animaBaseTractographyImageFilter.h.

◆ SetNumberOfFibersPerPixel()

void anima::BaseTractographyImageFilter::SetNumberOfFibersPerPixel ( unsigned int  num)
inline

Definition at line 65 of file animaBaseTractographyImageFilter.h.

◆ SetSeedingMask()

void anima::BaseTractographyImageFilter::SetSeedingMask ( MaskImageType *  mask)
inline

Definition at line 60 of file animaBaseTractographyImageFilter.h.

◆ SetStepProgression()

void anima::BaseTractographyImageFilter::SetStepProgression ( double  num)
inline

Definition at line 67 of file animaBaseTractographyImageFilter.h.

◆ ThreadedTrackComputer()

void anima::BaseTractographyImageFilter::ThreadedTrackComputer ( unsigned int  numThread,
std::vector< FiberType > &  resultFibers,
unsigned int  startSeedIndex,
unsigned int  endSeedIndex 
)
protected

Definition at line 221 of file animaBaseTractographyImageFilter.cxx.

References ComputeFiber().

Referenced by ThreadTrack().

◆ ThreadTrack()

void anima::BaseTractographyImageFilter::ThreadTrack ( unsigned int  numThread,
std::vector< FiberType > &  resultFibers 
)
protected

Definition at line 184 of file animaBaseTractographyImageFilter.cxx.

References ThreadedTrackComputer().

Referenced by ThreadTracker().

◆ ThreadTracker()

ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION anima::BaseTractographyImageFilter::ThreadTracker ( void *  arg)
staticprotected

Definition at line 173 of file animaBaseTractographyImageFilter.cxx.

References anima::BaseTractographyImageFilter::trackerArguments::resultFibersFromThreads, ThreadTrack(), and anima::BaseTractographyImageFilter::trackerArguments::trackerPtr.

Referenced by Update().

◆ Update()

void anima::BaseTractographyImageFilter::Update ( )

Definition at line 35 of file animaBaseTractographyImageFilter.cxx.

References createVTKOutput(), FilterOutputFibers(), PrepareTractography(), anima::BaseTractographyImageFilter::trackerArguments::resultFibersFromThreads, ThreadTracker(), and anima::BaseTractographyImageFilter::trackerArguments::trackerPtr.

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