NifTK
16.4.1 - 0798f20
CMIC's Translational Medical Imaging Platform
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2D image filter class to compute basic image features (BIFs) on an image. More...
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struct | BasicImageFeaturesThreadStruct |
Public Member Functions | |
virtual const char * | GetClassName () const |
itkStaticConstMacro (ImageDimension, unsigned int, TInputImage::ImageDimension) | |
void | SetDebug (bool b) |
Set the debugging output. More... | |
void | DebugOn () |
Set debugging output on. More... | |
void | DebugOff () |
Set debugging output off. More... | |
void | SetVerbose (bool b) |
Set the verbose output. More... | |
void | VerboseOn () |
Set verbose output on. More... | |
void | VerboseOff () |
Set verbose output off. More... | |
void | SetSigma (RealType sigma) |
virtual void | GenerateInputRequestedRegion () throw ( InvalidRequestedRegionError ) |
void | SetNormalizeAcrossScale (bool normalizeInScaleSpace) |
virtual bool | GetNormalizeAcrossScale () const |
void | CalculateOrientatedBIFs (void) |
Turn on calculation of orientated BIFs. More... | |
void | SecondOrderOnly (void) |
Ignore slopes, so classify only as second order. More... | |
virtual void | SetEpsilon (InternalRealType _arg) |
Set the noise suppression parameter. More... | |
virtual InternalRealType | GetEpsilon () |
Get the noise suppression parameter. More... | |
virtual void | SetNumberOfOrientations (unsigned int _arg) |
Set the number of orientations to quantise into. More... | |
virtual unsigned int | GetNumberOfOrientations () |
Get the number of orientations to quantise into. More... | |
void | SetOrigin (OriginType o) |
Set the origin for oriented BIFs. More... | |
virtual OriginType | GetOrigin () |
Get the origin for oriented BIFs. More... | |
void | SetFlipHorizontally (void) |
Set the coefficient to flip the orientation horizontally. More... | |
void | SetFlipVertically (void) |
Set the coefficient to flip the orientation vertically. More... | |
void | SetLocalOrientation (RealImagePointer OrientationInX, RealImagePointer OrientationInY) |
Set the local reference orientation images. More... | |
virtual void | SetOrientationInY (RealImageType *_arg) |
Set the local reference orientation image in 'y'. More... | |
virtual void | SetMask (MaskImageType *_arg) |
Set an optional mask image. More... | |
virtual RealImageType * | GetS00 () |
virtual RealImageType * | GetS10 () |
Get a pointer to the zero order smoothed image. More... | |
virtual RealImageType * | GetS01 () |
Get a pointer to the first derivative in 'x'. More... | |
virtual RealImageType * | GetS11 () |
Get a pointer to the first derivative in 'y'. More... | |
virtual RealImageType * | GetS20 () |
Get a pointer to the second derivative in 'xy'. More... | |
virtual RealImageType * | GetS02 () |
Get a pointer to the second derivative in 'xx'. More... | |
virtual RealImageType * | GetResponseFlat () |
Get a pointer to the second derivative in 'yy'. More... | |
virtual RealImageType * | GetResponseSlope () |
Get a pointer to the flatness response. More... | |
virtual RealImageType * | GetResponseDarkBlob () |
Get a pointer to the slope-like response. More... | |
virtual RealImageType * | GetResponseLightBlob () |
Get a pointer to the dark blob response. More... | |
virtual RealImageType * | GetResponseDarkLine () |
Get a pointer to the light blob response. More... | |
virtual RealImageType * | GetResponseLightLine () |
Get a pointer to the dark line response. More... | |
virtual RealImageType * | GetResponseSaddle () |
Get a pointer to the light line response. More... | |
virtual RealImageType * | GetOrientation () |
Get a pointer to the saddle like response. More... | |
void | WriteDerivativeToFile (int n, std::string filename) |
Get a pointer to the structure orientation. More... | |
void | WriteFilterResponseToFile (int n, std::string filename) |
Write one of the response images to a file ( 0 < n < 7 ) More... | |
void | SetSingleThreadedExecution (void) |
For debugging purposes, set single threaded execution. More... | |
Static Public Member Functions | |
static Pointer | New () |
Protected Member Functions | |
BasicImageFeaturesImageFilter () | |
virtual | ~BasicImageFeaturesImageFilter () |
void | PrintSelf (std::ostream &os, Indent indent) const |
RealImagePointer | GetDerivative (DerivativeFilterOrderEnumTypeX xOrder, DerivativeFilterOrderEnumTypeY yOrder) |
virtual void | BeforeThreadedGenerateData (void) |
virtual void | AfterThreadedGenerateData (void) |
void | GenerateData () |
void | ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) |
void | EnlargeOutputRequestedRegion (DataObject *output) |
Protected Attributes | |
bool | m_FlagMultiThreadedExecution |
Flag to turn multithreading on or off. More... | |
bool | m_FlagCalculateOrientatedBIFs |
Flag to calculate orientated BIFs. More... | |
bool | m_FlagLocalOrientationSet |
Flag to calculate orientated BIFs using local orientation images. More... | |
unsigned int | m_NumberOfOrientations |
bool | m_NormalizeAcrossScale |
bool | m_FlagSecondOrderOnly |
Only report linear structures. More... | |
InternalRealType | m_Epsilon |
Noise suppression parameter. More... | |
InternalRealType | m_Sigma |
Scale. More... | |
bool | m_FlagOriginSet |
Flag indicating whether the orgin has been set. More... | |
OriginType | m_Origin |
The origin to use for oriented BIFs. More... | |
RealType | flipHorizontally |
Coefficient to flip the orientation horizontally. More... | |
RealType | flipVertically |
Coefficient to flip the orientation vertically. More... | |
RealImagePointer | m_OrientationInX |
Set the local reference orientation image in 'x'. More... | |
RealImagePointer | m_OrientationInY |
Set the local reference orientation image in 'y'. More... | |
MaskImagePointer | m_Mask |
Optional mask image. More... | |
MaskFilterPointer | m_MaskFilter |
RealImagePointer | m_S00 |
Zero order smoothed image. More... | |
RealImagePointer | m_S10 |
First derivative in 'x'. More... | |
RealImagePointer | m_S01 |
First derivative in 'y'. More... | |
RealImagePointer | m_S11 |
Second derivative in 'xy'. More... | |
RealImagePointer | m_S20 |
Second derivative in 'xx'. More... | |
RealImagePointer | m_S02 |
Second derivative in 'yy'. More... | |
RealImagePointer | m_ResponseFlat |
Flat region response. More... | |
RealImagePointer | m_ResponseSlope |
Slope-like region response. More... | |
RealImagePointer | m_ResponseDarkBlob |
DarkBlob region response. More... | |
RealImagePointer | m_ResponseLightBlob |
LightBlob region response. More... | |
RealImagePointer | m_ResponseDarkLine |
DarkLine region response. More... | |
RealImagePointer | m_ResponseLightLine |
LightLine region response. More... | |
RealImagePointer | m_ResponseSaddle |
Saddle region response. More... | |
RealImagePointer | m_Orientation |
Orientation of the structure. More... | |
2D image filter class to compute basic image features (BIFs) on an image.
The categories are: 0 = flat 1 = slope 2 = minimum 3 = maximum 4 = light line 5 = dark line 6 = saddle
typedef SmartPointer< const Self > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::ConstPointer |
typedef DerivativeFilterTypeX::OrderEnumType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterOrderEnumTypeX |
Pointer to a derivative filter.
typedef DerivativeFilterTypeY::OrderEnumType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterOrderEnumTypeY |
typedef DerivativeFilterTypeX::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterPointerX |
Pointer to a derivative filtr. e
typedef DerivativeFilterTypeY::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterPointerY |
typedef LewisGriffinRecursiveGaussianImageFilter< InputImageType, RealImageType > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterTypeX |
Derivative filter type, it will be the first in the pipeline
typedef LewisGriffinRecursiveGaussianImageFilter< RealImageType, RealImageType > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::DerivativeFilterTypeY |
typedef InputImageType::ConstPointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImageConstPointer |
typedef InputImageType::PixelType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImagePixelType |
typedef InputImageType::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImagePointer |
typedef InputImageType::PointType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImagePointType |
typedef InputImageType::RegionType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImageRegionType |
typedef InputImageType::SpacingType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImageSpacingType |
typedef TInputImage itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InputImageType |
Type of the input image
typedef float itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::InternalRealType |
Define the image type for internal computations RealType is usually 'double' in NumericTraits. Here we prefer float in order to save memory.
typedef MaskFilterType::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::MaskFilterPointer |
typedef itk::MaskImageFilter< OutputImageType, MaskImageType, OutputImageType > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::MaskFilterType |
typedef MaskImageType::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::MaskImagePointer |
typedef itk::Image<MaskPixelType, ImageDimension> itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::MaskImageType |
typedef unsigned char itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::MaskPixelType |
Optional mask image
typedef OutputImagePointType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OriginType |
typedef OutputImageType::IndexType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImageIndexType |
typedef OutputImageType::PixelType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImagePixelType |
typedef OutputImageType::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImagePointer |
typedef OutputImageType::PointType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImagePointType |
typedef OutputImageType::RegionType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImageRegionType |
typedef TOutputImage itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::OutputImageType |
Type of the output image
typedef SmartPointer< Self > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::Pointer |
typedef RealImageType::Pointer itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::RealImagePointer |
typedef Image< InternalRealType, TInputImage::ImageDimension > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::RealImageType |
typedef NumericTraits<InputImagePixelType>::RealType itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::RealType |
typedef BasicImageFeaturesImageFilter itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::Self |
Standard class typedefs.
typedef ImageToImageFilter< TInputImage,TOutputImage > itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::Superclass |
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If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.
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If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.
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Turn on calculation of orientated BIFs.
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Set debugging output off.
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Set debugging output on.
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Single threaded execution, for debugging purposes ( call SetSingleThreadedExecution() )
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BasicImageFeaturesImageFilter needs all of the input to produce an output. Therefore, GradientRecursiveGaussianImageFilter needs to provide an implementation for GenerateInputRequestedRegion in order to inform the pipeline execution model.
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Run-time type information (and related methods).
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Get the noise suppression parameter.
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Get the number of orientations to quantise into.
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Get a pointer to the saddle like response.
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Get the origin for oriented BIFs.
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Get a pointer to the slope-like response.
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Get a pointer to the light blob response.
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Get a pointer to the second derivative in 'yy'.
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Get a pointer to the dark blob response.
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Get a pointer to the dark line response.
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Get a pointer to the light line response.
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Get a pointer to the flatness response.
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Get a pointer to the first derivative in 'x'.
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Get a pointer to the second derivative in 'xx'.
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Get a pointer to the zero order smoothed image.
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Get a pointer to the first derivative in 'y'.
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Get a pointer to the second derivative in 'xy'.
itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::itkStaticConstMacro | ( | ImageDimension | , |
unsigned | int, | ||
TInputImage::ImageDimension | |||
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Image dimension.
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Method for creation through the object factory.
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Ignore slopes, so classify only as second order.
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Set the debugging output.
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Set the noise suppression parameter.
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Set the coefficient to flip the orientation horizontally.
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Set the coefficient to flip the orientation vertically.
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Set the local reference orientation images.
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Set an optional mask image.
void itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::SetNormalizeAcrossScale | ( | bool | normalizeInScaleSpace | ) |
Define which normalization factor will be used for the Gaussian
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Set the number of orientations to quantise into.
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Set the local reference orientation image in 'y'.
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Set the origin for oriented BIFs.
void itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::SetSigma | ( | RealType | sigma | ) |
Set Sigma value.
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For debugging purposes, set single threaded execution.
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Set the verbose output.
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BasicImageFeaturesImageFilter can be implemented as a multithreaded filter. Therefore, this implementation provides a ThreadedGenerateData() routine which is called for each processing thread. The output image data is allocated automatically by the superclass prior to calling ThreadedGenerateData(). ThreadedGenerateData can only write to the portion of the output image specified by the parameter "outputRegionForThread"
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Set verbose output off.
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Set verbose output on.
void itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::WriteDerivativeToFile | ( | int | n, |
std::string | filename | ||
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Get a pointer to the structure orientation.
Write one of the derivatives to a file ( 0 < n < 6 )
void itk::BasicImageFeaturesImageFilter< TInputImage, TOutputImage >::WriteFilterResponseToFile | ( | int | n, |
std::string | filename | ||
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Write one of the response images to a file ( 0 < n < 7 )
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Coefficient to flip the orientation horizontally.
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Coefficient to flip the orientation vertically.
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Noise suppression parameter.
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Flag to calculate orientated BIFs.
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Flag to calculate orientated BIFs using local orientation images.
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Flag to turn multithreading on or off.
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Flag indicating whether the orgin has been set.
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Only report linear structures.
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Optional mask image.
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Normalize the image across scale space
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The number of orientations to quantise into. For example the default value, 8, results in 45 degree quantisation (eight slope orientations and four line orientations).
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Orientation of the structure.
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Set the local reference orientation image in 'x'.
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Set the local reference orientation image in 'y'.
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The origin to use for oriented BIFs.
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DarkBlob region response.
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DarkLine region response.
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Flat region response.
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LightBlob region response.
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LightLine region response.
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Saddle region response.
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Slope-like region response.
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Zero order smoothed image.
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First derivative in 'y'.
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Second derivative in 'yy'.
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First derivative in 'x'.
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Second derivative in 'xy'.
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Second derivative in 'xx'.
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Scale.