Constructor Detail

• LocalExtrema

  public LocalExtrema()

Method Detail

• findLocalExtrema

  @Deprecated
  public static <P,T> ArrayList<P> findLocalExtrema(RandomAccessibleInterval<T> source,
                                                                LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                                                ExecutorService service)

  Deprecated. 
  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. The task is parallelized along the last dimension of source. The number of tasks for parallelization is determined as: Math.max( Math.min( maxSizeDim, numThreads * 20 ), 1 ) where maxSizeDim is the longest dimension of img after adjusting for the bounding box of a RectangleShape with span 1, and numThreads is Runtime.getRuntime().availableProcessors() RectangleShape is used as local neighborhood. Note: Pixels within 1 point of the source border will be ignored as local extrema candidates because the complete neighborhood would not be included in source. To include those pixel, expand source accordingly. The returned coordinate list is valid for the original source.

  Parameters:

  source - Find local extrema within this RandomAccessibleInterval

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum.

  service - ExecutorService handles parallel tasks

  Returns:

  ArrayList of extrema

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessibleInterval<T> source,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape,
                                               ExecutorService service,
                                               int numTasks)
                                        throws InterruptedException,
                                               ExecutionException

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. The task is parallelized along the longest dimension of source after adjusting for size based on shape. Note: Pixels within a margin of source border as determined by getRequiredBorderSize(Shape, int) will be ignored as local extrema candidates because the complete neighborhood would not be included in source. To include those pixel, expand source accordingly. The returned coordinate list is valid for the original source.

  Parameters:

  source - Find local extrema within this RandomAccessibleInterval

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood.

  service - ExecutorService handles parallel tasks

  numTasks - Number of tasks for parallel execution

  Returns:

  List of extrema

  Throws:

  ExecutionException

  InterruptedException

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessibleInterval<T> source,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape,
                                               ExecutorService service,
                                               int numTasks,
                                               int splitDim)
                                        throws InterruptedException,
                                               ExecutionException

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. Note: Pixels within a margin of source border as determined by getRequiredBorderSize(Shape, int) will be ignored as local extrema candidates because the complete neighborhood would not be included in source. To include those pixel, expand source accordingly. The returned coordinate list is valid for the original source.

  Parameters:

  source - Find local extrema within this RandomAccessibleInterval

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood.

  service - ExecutorService handles parallel tasks

  numTasks - Number of tasks for parallel execution

  splitDim - Dimension along which input should be split for parallization

  Returns:

  List of extrema

  Throws:

  ExecutionException

  InterruptedException

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessible<T> source,
                                               Interval interval,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape,
                                               ExecutorService service,
                                               int numTasks)
                                        throws InterruptedException,
                                               ExecutionException

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. The task is parallelized along the longest dimension of interval

  Parameters:

  source - Find local extrema of the function defined by this RandomAccessible

  interval - Domain in which to look for local extrema. It is the callers responsibility to ensure that source is defined in all neighborhoods of interval.

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood.

  service - ExecutorService handles parallel tasks

  numTasks - Number of tasks for parallel execution

  Returns:

  List of extrema

  Throws:

  ExecutionException

  InterruptedException

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessible<T> source,
                                               Interval interval,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape,
                                               ExecutorService service,
                                               int numTasks,
                                               int splitDim)
                                        throws InterruptedException,
                                               ExecutionException

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface.

  Parameters:

  source - Find local extrema of the function defined by this RandomAccessible

  interval - Domain in which to look for local extrema. It is the callers responsibility to ensure that source is defined in all neighborhoods of {code interval}.

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood.

  service - ExecutorService handles parallel tasks

  numTasks - Number of tasks for parallel execution

  splitDim - Dimension along which input should be split for parallization

  Returns:

  List of extrema

  Throws:

  ExecutionException

  InterruptedException

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessibleInterval<T> source,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck)

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. RectangleShape is used as local neighborhood. Note: Pixels within 1 point of the source border will be ignored as local extrema candidates because the complete neighborhood would not be included in source. To include those pixel, expand source accordingly. The returned coordinate list is valid for the original source.

  Parameters:

  source - Find local extrema within this RandomAccessibleInterval

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum.

  Returns:

  List of extrema

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessibleInterval<T> source,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape)

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. Note: Pixels within a margin of source border as determined by getRequiredBorderSize(Shape, int) will be ignored as local extrema candidates because the complete neighborhood would not be included in source. To include those pixel, expand source accordingly. The returned coordinate list is valid for the original source.

  Parameters:

  source - Find local extrema within this RandomAccessibleInterval

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood

  Returns:

  List of extrema

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessible<T> source,
                                               Interval interval,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck)

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface. The local neighborhood is defined as RectangleShape with span 1.

  Parameters:

  source - Find local extrema within this RandomAccessible

  interval - Specifies the domain within which to look for extrema

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  Returns:

  List of extrema

• findLocalExtrema

  public static <P,T> List<P> findLocalExtrema(RandomAccessible<T> source,
                                               Interval interval,
                                               LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
                                               Shape shape)

  Find pixels that are extrema in their local neighborhood. The specific test for being an extremum can be specified as an implementation of the LocalExtrema.LocalNeighborhoodCheck interface.

  Parameters:

  source - Find local extrema within this RandomAccessible

  interval - Specifies the domain within which to look for extrema

  localNeighborhoodCheck - Check if current pixel qualifies as local maximum. It is the callers responsibility to pass a LocalExtrema.LocalNeighborhoodCheck that avoids the center pixel if shape does not skip the center pixel.

  shape - Defines the local neighborhood

  Returns:

  List of extrema

• getRequiredBorderSize

  public static long[] getRequiredBorderSize(Shape shape,
                                             int nDim)

  Get the required border size based on the bounding box of the neighborhood specified by shape. This is useful for determining by how much a RandomAccessibleInterval should be expanded to include min and max positions in the local extrema search.

  Parameters:

  shape - Defines the local neighborhood

  nDim - Number of dimensions.

  Returns:

  The required border size for the local neighborhood specified by shape

• shrink

  public static <T> IntervalView<T> shrink(RandomAccessibleInterval<T> source,
                                           long[] margin)

  Shrink a RandomAccessibleInterval symmetrically, i.e. the margin is applied both to min and max.

  Parameters:

  source -

  margin -

  Returns:

• getBiggestDimension

  public static int getBiggestDimension(Interval interval)

  Parameters:

  interval -

  Returns:

  The biggest dimension of interval.