Class IsolatedConnectedImageFilter

java.lang.Object
org.itk.simple.ProcessObject
org.itk.simple.ImageFilter
org.itk.simple.IsolatedConnectedImageFilter

public class IsolatedConnectedImageFilter extends ImageFilter
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. See: itk::simple::IsolatedConnected for the procedural interface itk::IsolatedConnectedImageFilter for the Doxygen on the original ITK class. C++ includes: sitkIsolatedConnectedImageFilter.h
  • Constructor Details

    • IsolatedConnectedImageFilter

      protected IsolatedConnectedImageFilter(long cPtr, boolean cMemoryOwn)
    • IsolatedConnectedImageFilter

      public IsolatedConnectedImageFilter()
      itk::simple::IsolatedConnectedImageFilter::IsolatedConnectedImageFilter() Default Constructor that takes no arguments and initializes default parameters
  • Method Details

    • getCPtr

      protected static long getCPtr(IsolatedConnectedImageFilter obj)
    • swigRelease

      protected static long swigRelease(IsolatedConnectedImageFilter obj)
    • finalize

      protected void finalize()
      Overrides:
      finalize in class ImageFilter
    • delete

      public void delete()
      virtual itk::simple::IsolatedConnectedImageFilter::~IsolatedConnectedImageFilter() Destructor
      Overrides:
      delete in class ImageFilter
    • setSeed1

      public void setSeed1(VectorUInt32 Seed1)
      Self& itk::simple::IsolatedConnectedImageFilter::SetSeed1(std::vector< unsigned int > Seed1) Set a single seed point 1. This seed will be isolated from Seed2 (if possible). All pixels connected to this seed will be replaced with ReplaceValue.
    • getSeed1

      public VectorUInt32 getSeed1()
      std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::GetSeed1() const
    • setSeed2

      public void setSeed2(VectorUInt32 Seed2)
      Self& itk::simple::IsolatedConnectedImageFilter::SetSeed2(std::vector< unsigned int > Seed2) Set a single seed point 2. This seed will be isolated from Seed1 (if possible).
    • getSeed2

      public VectorUInt32 getSeed2()
      std::vector<unsigned int> itk::simple::IsolatedConnectedImageFilter::GetSeed2() const
    • setLower

      public void setLower(double Lower)
      Self& itk::simple::IsolatedConnectedImageFilter::SetLower(double Lower) Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.
    • getLower

      public double getLower()
      double itk::simple::IsolatedConnectedImageFilter::GetLower() const Set/Get the limit on the lower threshold value. The default is the NonpositiveMin() for the InputPixelType.
    • setUpper

      public void setUpper(double Upper)
      Self& itk::simple::IsolatedConnectedImageFilter::SetUpper(double Upper) Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.
    • getUpper

      public double getUpper()
      double itk::simple::IsolatedConnectedImageFilter::GetUpper() const Set/Get the limit on the upper threshold value. The default is the max() for the InputPixelType.
    • setReplaceValue

      public void setReplaceValue(short ReplaceValue)
      Self& itk::simple::IsolatedConnectedImageFilter::SetReplaceValue(uint8_t ReplaceValue) Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.
    • getReplaceValue

      public short getReplaceValue()
      uint8_t itk::simple::IsolatedConnectedImageFilter::GetReplaceValue() const Set/Get value to replace thresholded pixels. Pixels that lie within the thresholds will be replaced with this value. The default is 1.
    • setIsolatedValueTolerance

      public void setIsolatedValueTolerance(double IsolatedValueTolerance)
      Self& itk::simple::IsolatedConnectedImageFilter::SetIsolatedValueTolerance(double IsolatedValueTolerance) Set/Get the precision required for the intensity threshold value. The default is 1.
    • getIsolatedValueTolerance

      public double getIsolatedValueTolerance()
      double itk::simple::IsolatedConnectedImageFilter::GetIsolatedValueTolerance() const Set/Get the precision required for the intensity threshold value. The default is 1.
    • setFindUpperThreshold

      public void setFindUpperThreshold(boolean FindUpperThreshold)
      Self& itk::simple::IsolatedConnectedImageFilter::SetFindUpperThreshold(bool FindUpperThreshold) Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
    • findUpperThresholdOn

      public void findUpperThresholdOn()
      Self& itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOn() Set the value of FindUpperThreshold to true or false respectfully.
    • findUpperThresholdOff

      public void findUpperThresholdOff()
      Self& itk::simple::IsolatedConnectedImageFilter::FindUpperThresholdOff()
    • getFindUpperThreshold

      public boolean getFindUpperThreshold()
      bool itk::simple::IsolatedConnectedImageFilter::GetFindUpperThreshold() const Set/Get whether to find an upper threshold (separating two dark regions) or a lower threshold (separating two bright regions).
    • getThresholdingFailed

      public boolean getThresholdingFailed()
      bool itk::simple::IsolatedConnectedImageFilter::GetThresholdingFailed() const Get the flag that tells whether the algorithm failed to find a threshold. This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
    • getIsolatedValue

      public double getIsolatedValue()
      double itk::simple::IsolatedConnectedImageFilter::GetIsolatedValue() const Get value that isolates the two seeds. This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
    • getName

      public String getName()
      std::string itk::simple::IsolatedConnectedImageFilter::GetName() const Name of this class
      Overrides:
      getName in class ProcessObject
    • toString

      public String toString()
      std::string itk::simple::IsolatedConnectedImageFilter::ToString() const Print ourselves out
      Overrides:
      toString in class ProcessObject
    • execute

      public Image execute(Image image1)
      Image itk::simple::IsolatedConnectedImageFilter::Execute(const Image &image1) Execute the filter on the input image