ITK  4.1.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Types | Private Member Functions | Private Attributes | Static Private Attributes
itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage > Class Template Reference

#include <itkThresholdMaximumConnectedComponentsImageFilter.h>

+ Inheritance diagram for itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >:
+ Collaboration diagram for itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >:

List of all members.

Public Types

typedef SmartPointer< const SelfConstPointer
typedef InputImageType::PixelType InputImagePixelType
typedef
InputImageType::ConstPointer 
InputImagePointer
typedef InputImageType::RegionType InputImageRegionType
typedef TInputImage InputImageType
typedef TInputImage::PixelType PixelType
typedef SmartPointer< SelfPointer
typedef
ThresholdMaximumConnectedComponentsImageFilter 
Self
typedef ImageToImageFilter
< TInputImage, TOutputImage > 
Superclass

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
virtual const char * GetNameOfClass () const
virtual SizeValueType GetNumberOfObjects () const
virtual PixelType GetThresholdValue () const
 typedef (Concept::Comparable< PixelType >) PixelTypeComparable
virtual void SetMinimumObjectSizeInPixels (unsigned int _arg)
virtual unsigned int GetMinimumObjectSizeInPixels () const
virtual void SetInsideValue (PixelType _arg)
virtual void SetOutsideValue (PixelType _arg)
virtual void SetUpperBoundary (PixelType _arg)
virtual PixelType GetInsideValue () const
virtual PixelType GetOutsideValue () const
virtual PixelType GetUpperBoundary () const

Static Public Member Functions

static Pointer New ()

Protected Member Functions

SizeValueType ComputeConnectedComponents (void)
void GenerateData (void)

Private Types

typedef
ConnectedComponentImageFilter
< OutputImageType,
FilterImageType
ConnectedFilterType
typedef FilterImageType::Pointer FilterImagePointer
typedef itk::Image
< FilterPixelType,
itkGetStaticConstMacro(ImageDimension) > 
FilterImageType
typedef unsigned int FilterPixelType
typedef
MinimumMaximumImageCalculator
< InputImageType
MinMaxCalculatorType
typedef
RelabelComponentImageFilter
< FilterImageType,
FilterImageType
RelabelFilterType
typedef
BinaryThresholdImageFilter
< InputImageType,
OutputImageType
ThresholdFilterType

Private Member Functions

void operator= (const Self &)
 ThresholdMaximumConnectedComponentsImageFilter (const Self &)

Private Attributes

ConnectedFilterType::Pointer m_ConnectedComponent
PixelType m_InsideValue
RelabelFilterType::Pointer m_LabeledComponent
PixelType m_LowerBoundary
unsigned int m_MinimumObjectSizeInPixels
MinMaxCalculatorType::Pointer m_MinMaxCalculator
SizeValueType m_NumberOfObjects
PixelType m_OutsideValue
ThresholdFilterType::Pointer m_ThresholdFilter
PixelType m_ThresholdValue
PixelType m_UpperBoundary

Static Private Attributes

static const unsigned int ImageDimension = TInputImage::ImageDimension
typedef TOutputImage OutputImageType
typedef OutputImageType::Pointer OutputImagePointer
typedef OutputImageType::RegionType OutputImageRegionType
typedef OutputImageType::PixelType OutputImagePixelType
 ThresholdMaximumConnectedComponentsImageFilter ()
 ~ThresholdMaximumConnectedComponentsImageFilter ()
void PrintSelf (std::ostream &os, Indent indent) const

Detailed Description

template<class TInputImage, class TOutputImage = TInputImage>
class itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >

Finds the threshold value of an image based on maximizing the number of objects in the image that are larger than a given minimal size.

This method is based on Topological Stable State Thresholding to calculate the threshold set point. This method is particularly effective when there are a large number of objects in a microscopy image. Compiling in Debug mode and enable the debug flag for this filter to print debug information to see how the filter focuses in on a threshold value. Please see the Insight Journal's MICCAI 2005 workshop for a complete description. References are below.
Parameters
The MinimumObjectSizeInPixels parameter is controlled through the class Get/SetMinimumObjectSizeInPixels() method. Similar to the standard itk::BinaryThresholdImageFilter the Get/SetInside and Get/SetOutside values of the threshold can be set. The GetNumberOfObjects() and GetThresholdValue() methods return the number of objects above the minimum pixel size and the calculated threshold value.
Automatic Thresholding in ITK
There are multiple methods to automatically calculate the threshold intensity value of an image. As of version 4.0, ITK has a Thresholding ( ITKThresholding ) module which contains numerous automatic thresholding methods.implements two of these. Topological Stable State Thresholding works well on images with a large number of objects to be counted.
References:
1) Urish KL, August J, Huard J. "Unsupervised segmentation for myofiber counting in immunoflourescent images". Insight Journal. ISC/NA-MIC/MICCAI Workshop on Open-Source Software (2005) Dspace handle: http://hdl.handle.net/1926/48 2) Pikaz A, Averbuch, A. "Digital image thresholding based on topological stable-state". Pattern Recognition, 29(5): 829-843, 1996.
Questions: email Ken Urish at ken.urish(at)gmail.com Please cc the itk list serve for archival purposes.

Definition at line 74 of file itkThresholdMaximumConnectedComponentsImageFilter.h.


Member Typedef Documentation

template<class TInputImage , class TOutputImage = TInputImage>
typedef ConnectedComponentImageFilter< OutputImageType, FilterImageType > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ConnectedFilterType [private]
template<class TInputImage , class TOutputImage = TInputImage>
typedef SmartPointer< const Self > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ConstPointer
template<class TInputImage , class TOutputImage = TInputImage>
typedef FilterImageType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::FilterImagePointer [private]
template<class TInputImage , class TOutputImage = TInputImage>
typedef itk::Image< FilterPixelType, itkGetStaticConstMacro(ImageDimension) > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::FilterImageType [private]
template<class TInputImage , class TOutputImage = TInputImage>
typedef unsigned int itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::FilterPixelType [private]

Typedef for filter pixel type.

Definition at line 170 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef InputImageType::PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::InputImagePixelType
template<class TInputImage , class TOutputImage = TInputImage>
typedef InputImageType::ConstPointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::InputImagePointer
template<class TInputImage , class TOutputImage = TInputImage>
typedef InputImageType::RegionType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::InputImageRegionType
template<class TInputImage , class TOutputImage = TInputImage>
typedef TInputImage itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::InputImageType

Some additional typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 138 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef MinimumMaximumImageCalculator< InputImageType > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::MinMaxCalculatorType [private]
template<class TInputImage , class TOutputImage = TInputImage>
typedef OutputImageType::PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::OutputImagePixelType

Some additional typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 150 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef OutputImageType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::OutputImagePointer

Some additional typedefs.

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 148 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef OutputImageType::RegionType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::OutputImageRegionType

Some additional typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 149 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef TOutputImage itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::OutputImageType

Some additional typedefs.

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 147 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef TInputImage::PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::PixelType

Typedef to describe the type of pixel.

Definition at line 89 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef SmartPointer< Self > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::Pointer
template<class TInputImage , class TOutputImage = TInputImage>
typedef RelabelComponentImageFilter< FilterImageType, FilterImageType > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::RelabelFilterType [private]
template<class TInputImage , class TOutputImage = TInputImage>
typedef ThresholdMaximumConnectedComponentsImageFilter itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::Self

Standard class typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 79 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
typedef ImageToImageFilter< TInputImage, TOutputImage > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::Superclass
template<class TInputImage , class TOutputImage = TInputImage>
typedef BinaryThresholdImageFilter< InputImageType, OutputImageType > itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ThresholdFilterType [private]

Constructor & Destructor Documentation

template<class TInputImage , class TOutputImage = TInputImage>
itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ThresholdMaximumConnectedComponentsImageFilter ( ) [protected]

Some additional typedefs.

template<class TInputImage , class TOutputImage = TInputImage>
itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::~ThresholdMaximumConnectedComponentsImageFilter ( ) [inline, protected]

Some additional typedefs.

Definition at line 153 of file itkThresholdMaximumConnectedComponentsImageFilter.h.

template<class TInputImage , class TOutputImage = TInputImage>
itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ThresholdMaximumConnectedComponentsImageFilter ( const Self ) [private]

Member Function Documentation

template<class TInputImage , class TOutputImage = TInputImage>
SizeValueType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ComputeConnectedComponents ( void  ) [protected]

Runs a series of filters that thresholds the image, dilates/erodes for edge enhancement, and counts the number of relabeled connected components

template<class TInputImage , class TOutputImage = TInputImage>
virtual::itk::LightObject::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::CreateAnother ( void  ) const [virtual]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<class TInputImage , class TOutputImage = TInputImage>
void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GenerateData ( void  ) [protected, virtual]
template<class TInputImage , class TOutputImage = TInputImage>
virtual PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetInsideValue ( ) const [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
virtual unsigned int itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetMinimumObjectSizeInPixels ( ) const [virtual]

Set the minimum pixel area used to count objects on the image. Thus, only objects that have a pixel area greater than the minimum pixel area will be counted as an object in the optimization portion of this filter. Essentially, it eliminates noise from being counted as an object. The default value is zero.

template<class TInputImage , class TOutputImage = TInputImage>
virtual const char* itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods).

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage = TInputImage>
virtual SizeValueType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetNumberOfObjects ( ) const [virtual]

Returns the number of objects in the image. This information is only valid after the filter has executed. Useful if your counting something

template<class TInputImage , class TOutputImage = TInputImage>
virtual PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetOutsideValue ( ) const [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
virtual PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetThresholdValue ( ) const [virtual]

Returns the automatic threshold setpoint. This information is only valid after the filter has executed.

template<class TInputImage , class TOutputImage = TInputImage>
virtual PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::GetUpperBoundary ( ) const [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
static Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage , class TOutputImage = TInputImage>
void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::operator= ( const Self ) [private]

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage = TInputImage>
void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const [protected, virtual]

Some additional typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage = TInputImage>
virtual void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::SetInsideValue ( PixelType  _arg) [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
virtual void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::SetMinimumObjectSizeInPixels ( unsigned int  _arg) [virtual]

Set the minimum pixel area used to count objects on the image. Thus, only objects that have a pixel area greater than the minimum pixel area will be counted as an object in the optimization portion of this filter. Essentially, it eliminates noise from being counted as an object. The default value is zero.

template<class TInputImage , class TOutputImage = TInputImage>
virtual void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::SetOutsideValue ( PixelType  _arg) [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
virtual void itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::SetUpperBoundary ( PixelType  _arg) [virtual]

The following Set/Get methods are for the binary threshold function. This class automatically calculates the lower threshold boundary. The upper threshold boundary, inside value, and outside value can be defined by the user, however the standard values are used as default if not set by the user. The default value of the: Inside value is the maximum pixel type intensity. Outside value is the minimum pixel type intensity. Upper threshold boundary is the maximum pixel type intensity.

template<class TInputImage , class TOutputImage = TInputImage>
itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::typedef ( Concept::Comparable< PixelType )

The pixel type must support comparison operators. This class requires PixelTypeComparable in the form of ( Concept::Comparable< PixelType > )


Member Data Documentation

template<class TInputImage , class TOutputImage = TInputImage>
const unsigned int itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::ImageDimension = TInputImage::ImageDimension [static, private]
template<class TInputImage , class TOutputImage = TInputImage>
ConnectedFilterType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_ConnectedComponent [private]
template<class TInputImage , class TOutputImage = TInputImage>
PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_InsideValue [private]
template<class TInputImage , class TOutputImage = TInputImage>
RelabelFilterType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_LabeledComponent [private]
template<class TInputImage , class TOutputImage = TInputImage>
PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_LowerBoundary [private]
template<class TInputImage , class TOutputImage = TInputImage>
unsigned int itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_MinimumObjectSizeInPixels [private]
template<class TInputImage , class TOutputImage = TInputImage>
MinMaxCalculatorType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_MinMaxCalculator [private]
template<class TInputImage , class TOutputImage = TInputImage>
SizeValueType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_NumberOfObjects [private]
template<class TInputImage , class TOutputImage = TInputImage>
PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_OutsideValue [private]
template<class TInputImage , class TOutputImage = TInputImage>
ThresholdFilterType::Pointer itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_ThresholdFilter [private]
template<class TInputImage , class TOutputImage = TInputImage>
PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_ThresholdValue [private]
template<class TInputImage , class TOutputImage = TInputImage>
PixelType itk::ThresholdMaximumConnectedComponentsImageFilter< TInputImage, TOutputImage >::m_UpperBoundary [private]

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