net.imglib2.algorithm.localextrema

Class LocalExtrema

java.lang.Object

net.imglib2.algorithm.localextrema.LocalExtrema

public class LocalExtrema
extends Object

Provides findLocalExtrema(net.imglib2.RandomAccessibleInterval<T>, net.imglib2.algorithm.localextrema.LocalExtrema.LocalNeighborhoodCheck<P, T>, java.util.concurrent.ExecutorService) to find pixels that are extrema in their local neighborhood.

Author:

Tobias Pietzsch, Philipp Hanslovsky

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	LocalExtrema.LocalNeighborhoodCheck<P,T> A local extremum check.
static class	LocalExtrema.MaximumCheck<T extends Comparable<T>> A LocalExtrema.LocalNeighborhoodCheck to test whether a pixel is a local maximum.
static class	LocalExtrema.MinimumCheck<T extends Comparable<T>> A LocalExtrema.LocalNeighborhoodCheck to test whether a pixel is a local minimum.

Constructor Summary

Constructors

Constructor and Description
LocalExtrema()

Method Summary

Modifier and Type	Method and Description
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessible<T> source, net.imglib2.Interval interval, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessible<T> source, net.imglib2.Interval interval, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessible<T> source, net.imglib2.Interval interval, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape, ExecutorService service, int numTasks) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessible<T> source, net.imglib2.Interval interval, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape, ExecutorService service, int numTasks, int splitDim) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessibleInterval<T> source, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck) Find pixels that are extrema in their local neighborhood.
static <P,T> ArrayList<P>	findLocalExtrema(net.imglib2.RandomAccessibleInterval<T> source, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, ExecutorService service) Deprecated.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessibleInterval<T> source, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessibleInterval<T> source, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape, ExecutorService service, int numTasks) Find pixels that are extrema in their local neighborhood.
static <P,T> List<P>	findLocalExtrema(net.imglib2.RandomAccessibleInterval<T> source, LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck, Shape shape, ExecutorService service, int numTasks, int splitDim) Find pixels that are extrema in their local neighborhood.
static int	getBiggestDimension(net.imglib2.Interval interval)
static long[]	getRequiredBorderSize(Shape shape, int nDim) Get the required border size based on the bounding box of the neighborhood specified by shape.
static <T> net.imglib2.view.IntervalView<T>	shrink(net.imglib2.RandomAccessibleInterval<T> source, long[] margin) Shrink a RandomAccessibleInterval symmetrically, i.e. the margin is applied both to min and max.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LocalExtrema

public LocalExtrema()

Method Detail

findLocalExtrema

@Deprecated
public static <P,T> ArrayList<P> findLocalExtrema(net.imglib2.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(net.imglib2.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(net.imglib2.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(net.imglib2.RandomAccessible<T> source,
                                             net.imglib2.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(net.imglib2.RandomAccessible<T> source,
                                             net.imglib2.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(net.imglib2.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(net.imglib2.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(net.imglib2.RandomAccessible<T> source,
                                             net.imglib2.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(net.imglib2.RandomAccessible<T> source,
                                             net.imglib2.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> net.imglib2.view.IntervalView<T> shrink(net.imglib2.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(net.imglib2.Interval interval)

Parameters:

interval -

Returns:

The biggest dimension of interval.