SimpleITK  2.1.0.dev86
Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | Friends | List of all members
itk::simple::ThresholdMaximumConnectedComponentsImageFilter Class Reference

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. More...

#include <sitkThresholdMaximumConnectedComponentsImageFilter.h>

+ Inheritance diagram for itk::simple::ThresholdMaximumConnectedComponentsImageFilter:
+ Collaboration diagram for itk::simple::ThresholdMaximumConnectedComponentsImageFilter:

Public Types

using PixelIDTypeList = ScalarPixelIDTypeList
 
using Self = ThresholdMaximumConnectedComponentsImageFilter
 
- Public Types inherited from itk::simple::ImageFilter
using Self = ImageFilter
 
- Public Types inherited from itk::simple::ProcessObject
using Self = ProcessObject
 

Public Member Functions

Image Execute (const Image &image1)
 
uint8_t GetInsideValue () const
 
uint32_t GetMinimumObjectSizeInPixels () const
 
std::string GetName () const
 
uint8_t GetOutsideValue () const
 
double GetUpperBoundary () const
 
SelfSetInsideValue (uint8_t InsideValue)
 
SelfSetMinimumObjectSizeInPixels (uint32_t MinimumObjectSizeInPixels)
 
SelfSetOutsideValue (uint8_t OutsideValue)
 
SelfSetUpperBoundary (double UpperBoundary)
 
 ThresholdMaximumConnectedComponentsImageFilter ()
 
std::string ToString () const
 
virtual ~ThresholdMaximumConnectedComponentsImageFilter ()
 
- 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

uint8_t m_InsideValue {1u}
 
std::unique_ptr< detail::MemberFunctionFactory< MemberFunctionType > > m_MemberFactory
 
uint32_t m_MinimumObjectSizeInPixels {0u}
 
uint8_t m_OutsideValue {0u}
 
double m_UpperBoundary {std::numeric_limits<double>::max()}
 

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::ProcessObjectGetActiveProcess ()
 
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
 
NonCopyableoperator= (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<class TImageType >
static Image CastITKToImage (TImageType *img)
 
static const itk::EventObjectGetITKEventObject (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)
 

Detailed Description

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: https://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.
See also
itk::simple::ThresholdMaximumConnectedComponents for the procedural interface
itk::ThresholdMaximumConnectedComponentsImageFilter for the Doxygen on the original ITK class.

Definition at line 61 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

Member Typedef Documentation

◆ MemberFunctionType

Setup for member function dispatching

Definition at line 131 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ PixelIDTypeList

Define the pixels types supported by this filter

Definition at line 73 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ Self

Constructor & Destructor Documentation

◆ ~ThresholdMaximumConnectedComponentsImageFilter()

virtual itk::simple::ThresholdMaximumConnectedComponentsImageFilter::~ThresholdMaximumConnectedComponentsImageFilter ( )
virtual

Destructor

◆ ThresholdMaximumConnectedComponentsImageFilter()

itk::simple::ThresholdMaximumConnectedComponentsImageFilter::ThresholdMaximumConnectedComponentsImageFilter ( )

Default Constructor that takes no arguments and initializes default parameters

Member Function Documentation

◆ Execute()

Image itk::simple::ThresholdMaximumConnectedComponentsImageFilter::Execute ( const Image image1)

Execute the filter on the input image

◆ ExecuteInternal()

template<class TImageType >
Image itk::simple::ThresholdMaximumConnectedComponentsImageFilter::ExecuteInternal ( const Image image1)
private

◆ GetInsideValue()

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetInsideValue ( ) const
inline

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.

Definition at line 104 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetMinimumObjectSizeInPixels()

uint32_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetMinimumObjectSizeInPixels ( ) const
inline

The pixel type must support comparison operators. 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.

Definition at line 84 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetName()

std::string itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetName ( ) const
inlinevirtual

Name of this class

Implements itk::simple::ProcessObject.

Definition at line 117 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetOutsideValue()

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetOutsideValue ( ) const
inline

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.

Definition at line 114 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ GetUpperBoundary()

double itk::simple::ThresholdMaximumConnectedComponentsImageFilter::GetUpperBoundary ( ) const
inline

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.

Definition at line 94 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetInsideValue()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetInsideValue ( uint8_t  InsideValue)
inline

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.

Definition at line 99 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetMinimumObjectSizeInPixels()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetMinimumObjectSizeInPixels ( uint32_t  MinimumObjectSizeInPixels)
inline

The pixel type must support comparison operators. 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.

Definition at line 79 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetOutsideValue()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetOutsideValue ( uint8_t  OutsideValue)
inline

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.

Definition at line 109 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ SetUpperBoundary()

Self& itk::simple::ThresholdMaximumConnectedComponentsImageFilter::SetUpperBoundary ( double  UpperBoundary)
inline

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.

Definition at line 89 of file sitkThresholdMaximumConnectedComponentsImageFilter.h.

◆ ToString()

std::string itk::simple::ThresholdMaximumConnectedComponentsImageFilter::ToString ( ) const
virtual

Print ourselves out

Reimplemented from itk::simple::ProcessObject.

Friends And Related Function Documentation

◆ detail::MemberFunctionAddressor< MemberFunctionType >

Member Data Documentation

◆ m_InsideValue

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::m_InsideValue {1u}
private

◆ m_MemberFactory

std::unique_ptr<detail::MemberFunctionFactory<MemberFunctionType> > itk::simple::ThresholdMaximumConnectedComponentsImageFilter::m_MemberFactory
private

◆ m_MinimumObjectSizeInPixels

uint32_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::m_MinimumObjectSizeInPixels {0u}
private

◆ m_OutsideValue

uint8_t itk::simple::ThresholdMaximumConnectedComponentsImageFilter::m_OutsideValue {0u}
private

◆ m_UpperBoundary

double itk::simple::ThresholdMaximumConnectedComponentsImageFilter::m_UpperBoundary {std::numeric_limits<double>::max()}
private

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