ITK
4.1.0
Insight Segmentation and Registration Toolkit
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#include <itkIsolatedConnectedImageFilter.h>
Label pixels that are connected to one set of seeds but not another.
IsolatedConnectedImageFilter finds the optimal threshold to separate two regions. It has two modes, one to separate dark regions surrounded by bright regions by automatically finding a minimum isolating upper threshold, and another to separate bright regions surrounded by dark regions by automatically finding a maximum lower isolating threshold. The mode can be chosen by setting FindUpperThresholdOn()/Off(). In both cases, the isolating threshold is retrieved with GetIsolatedValue().
The algorithm labels pixels with ReplaceValue that are connected to Seeds1 AND NOT connected to Seeds2. When finding the threshold to separate two dark regions surrounded by bright regions, given a fixed lower threshold, the filter adjusts the upper threshold until the two sets of seeds are not connected. The algorithm uses a binary search to adjust the upper threshold, starting at Upper. The reverse is true for finding the threshold to separate two bright regions. Lower defaults to the smallest possible value for the InputImagePixelType, and Upper defaults to the largest possible value for the InputImagePixelType.
The user can also supply the Lower and Upper values to restrict the search. However, if the range is too restrictive, it could happen that no isolating threshold can be found between the user specified Lower and Upper values. Therefore, unless the user is sure of the bounds to set, it is recommended that the user set these values to the lowest and highest intensity values in the image, respectively.
The user can specify more than one seed for both regions to separate. The algorithm will try find the threshold that ensures that all of the first seeds are contained in the resulting segmentation and all of the second seeds are not contained in the segmentation.
It is possible that the algorithm may not be able to find the isolating threshold because no such threshold exists. The user can check for this by querying the GetThresholdingFailed() flag.
Definition at line 71 of file itkIsolatedConnectedImageFilter.h.
typedef SmartPointer< const Self > itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::ConstPointer |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 79 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::IndexType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::IndexType |
Definition at line 93 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::ConstPointer itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputImageConstPointer |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 90 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::PixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputImagePixelType |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 92 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::Pointer itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputImagePointer |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 89 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::RegionType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputImageRegionType |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 91 of file itkIsolatedConnectedImageFilter.h.
typedef TInputImage itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputImageType |
Some convenient typedefs.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 86 of file itkIsolatedConnectedImageFilter.h.
typedef NumericTraits< InputImagePixelType >::RealType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::InputRealType |
Definition at line 104 of file itkIsolatedConnectedImageFilter.h.
typedef OutputImageType::PixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::OutputImagePixelType |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 99 of file itkIsolatedConnectedImageFilter.h.
typedef OutputImageType::Pointer itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::OutputImagePointer |
Reimplemented from itk::ImageSource< TOutputImage >.
Definition at line 97 of file itkIsolatedConnectedImageFilter.h.
typedef OutputImageType::RegionType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::OutputImageRegionType |
Superclass typedefs.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 98 of file itkIsolatedConnectedImageFilter.h.
typedef TOutputImage itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::OutputImageType |
Some convenient typedefs.
Reimplemented from itk::ImageSource< TOutputImage >.
Definition at line 96 of file itkIsolatedConnectedImageFilter.h.
typedef SmartPointer< Self > itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::Pointer |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 78 of file itkIsolatedConnectedImageFilter.h.
typedef std::vector< IndexType > itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SeedsContainerType |
Definition at line 101 of file itkIsolatedConnectedImageFilter.h.
typedef IsolatedConnectedImageFilter itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::Self |
Standard class typedefs.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 76 of file itkIsolatedConnectedImageFilter.h.
typedef InputImageType::SizeType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SizeType |
Definition at line 94 of file itkIsolatedConnectedImageFilter.h.
typedef ImageToImageFilter< TInputImage, TOutputImage > itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::Superclass |
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
Definition at line 77 of file itkIsolatedConnectedImageFilter.h.
itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::IsolatedConnectedImageFilter | ( | ) | [protected] |
End concept checking
itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::~IsolatedConnectedImageFilter | ( | ) | [inline, protected] |
End concept checking
Definition at line 195 of file itkIsolatedConnectedImageFilter.h.
itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::IsolatedConnectedImageFilter | ( | const Self & | ) | [private] |
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::AddSeed1 | ( | const IndexType & | seed | ) |
Add seed point 1.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::AddSeed2 | ( | const IndexType & | seed | ) |
Add seed point 2.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::ClearSeeds1 | ( | ) |
Clear all the seeds1.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::ClearSeeds2 | ( | ) |
Clear all the seeds2.
virtual::itk::LightObject::Pointer itk::IsolatedConnectedImageFilter< 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.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::EnlargeOutputRequestedRegion | ( | DataObject * | ) | [protected, virtual] |
Give the process object a chance to indictate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.
Reimplemented from itk::ProcessObject.
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::FindUpperThresholdOff | ( | ) | [virtual] |
Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::FindUpperThresholdOn | ( | ) | [virtual] |
Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GenerateData | ( | ) | [protected, virtual] |
A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.
Reimplemented from itk::ImageSource< TOutputImage >.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GenerateInputRequestedRegion | ( | ) | [protected, virtual] |
What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that imaging filters operate differently than the classes to this point in the class hierachy. Up till now, the base assumption has been that the largest possible region will be requested of the input.
This implementation of GenerateInputRequestedRegion() only processes the inputs that are a subclass of the ImageBase<InputImageDimension>. If an input is another type of DataObject (including an Image of a different dimension), they are skipped by this method. The subclasses of ImageToImageFilter are responsible for providing an implementation of GenerateInputRequestedRegion() when there are multiple inputs of different types.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
virtual const bool& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetFindUpperThreshold | ( | ) | [virtual] |
Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
virtual const InputImagePixelType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetIsolatedValue | ( | ) | [virtual] |
Get value that isolates the two seeds.
virtual const InputImagePixelType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetIsolatedValueTolerance | ( | ) | [virtual] |
Set/Get the precision required for the intensity threshold value. The default is 1.
virtual const InputImagePixelType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetLower | ( | ) | [virtual] |
Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.
virtual const char* itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetNameOfClass | ( | ) | const [virtual] |
Run-time type information (and related methods).
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
virtual const OutputImagePixelType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetReplaceValue | ( | ) | [virtual] |
Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.
virtual const SeedsContainerType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetSeeds1 | ( | ) | const [virtual] |
Method to access seed container
virtual const SeedsContainerType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetSeeds2 | ( | ) | const [virtual] |
Method to access seed container
virtual const bool& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetThresholdingFailed | ( | ) | [virtual] |
Get the flag that tells whether the algorithm failed to find a threshold.
virtual const InputImagePixelType& itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetUpper | ( | ) | [virtual] |
Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.
InputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::GetUpperValueLimit | ( | ) | [inline] |
Definition at line 154 of file itkIsolatedConnectedImageFilter.h.
static Pointer itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::New | ( | ) | [static] |
Method for creation through the object factory.
Reimplemented from itk::Object.
void itk::IsolatedConnectedImageFilter< 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 >.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::PrintSelf | ( | std::ostream & | os, |
Indent | indent | ||
) | const [virtual] |
Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.
Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetFindUpperThreshold | ( | bool | _arg | ) | [virtual] |
Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetIsolatedValueTolerance | ( | InputImagePixelType | _arg | ) | [virtual] |
Set/Get the precision required for the intensity threshold value. The default is 1.
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetLower | ( | InputImagePixelType | _arg | ) | [virtual] |
Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetReplaceValue | ( | OutputImagePixelType | _arg | ) | [virtual] |
Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetSeed1 | ( | const IndexType & | seed | ) |
Set seed point 1. This seed will be isolated from Seed2 (if possible). All pixels connected to this seed will be replaced with ReplaceValue. This method is deprecated, please use AddSeed()
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetSeed2 | ( | const IndexType & | seed | ) |
Set seed point 2. This seed will be isolated from Seed1 (if possible). This method is deprecated, please use AddSeed()
virtual void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetUpper | ( | InputImagePixelType | _arg | ) | [virtual] |
Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.
void itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::SetUpperValueLimit | ( | InputImagePixelType | upperValue | ) | [inline] |
Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType. These methods have been deprecated. Please use Set/Get Upper instead.
Definition at line 149 of file itkIsolatedConnectedImageFilter.h.
itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::typedef | ( | Concept::HasNumericTraits< InputImagePixelType > | ) |
Begin concept checking This class requires InputHasNumericTraitsCheck in the form of ( Concept::HasNumericTraits< InputImagePixelType > )
bool itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_FindUpperThreshold [protected] |
Definition at line 208 of file itkIsolatedConnectedImageFilter.h.
InputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_IsolatedValue [protected] |
Definition at line 205 of file itkIsolatedConnectedImageFilter.h.
InputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_IsolatedValueTolerance [protected] |
Definition at line 206 of file itkIsolatedConnectedImageFilter.h.
InputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_Lower [protected] |
Definition at line 200 of file itkIsolatedConnectedImageFilter.h.
OutputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_ReplaceValue [protected] |
Definition at line 203 of file itkIsolatedConnectedImageFilter.h.
SeedsContainerType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_Seeds1 [protected] |
End concept checking
Definition at line 196 of file itkIsolatedConnectedImageFilter.h.
SeedsContainerType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_Seeds2 [protected] |
End concept checking
Definition at line 197 of file itkIsolatedConnectedImageFilter.h.
bool itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_ThresholdingFailed [protected] |
Definition at line 209 of file itkIsolatedConnectedImageFilter.h.
InputImagePixelType itk::IsolatedConnectedImageFilter< TInputImage, TOutputImage >::m_Upper [protected] |
Definition at line 201 of file itkIsolatedConnectedImageFilter.h.