DiscreteFrequencyDistribution (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.histogram.DiscreteFrequencyDistribution

All Implemented Interfaces:

Iterable<LongType>, Dimensions, EuclideanSpace, Img<LongType>, Interval, IterableInterval<LongType>, IterableRealInterval<LongType>, RandomAccessible<LongType>, RandomAccessibleInterval<LongType>, RealInterval
```
public class DiscreteFrequencyDistribution
extends Object
implements Img<LongType>
```
This class represents an n-dimensional set of counters. Histogram implementations use these for tracking value counts.

Author:

Barry DeZonia

Constructor Summary

Constructors
Constructor and Description
`DiscreteFrequencyDistribution(Img<LongType> img)` Construct an n-dimensional counter using a provided `Img<LongType>` to store counts.
`DiscreteFrequencyDistribution(long[] binCounts)` Construct an n-dimensional counter with the given number of bins

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`DiscreteFrequencyDistribution`	`copy()`
`Cursor<LongType>`	`cursor()` Returns a `RealCursor` that iterates with optimal speed without calculating the location at each iteration step.
`void`	`decrement(long[] binPos)` Decrements the frequency count of a specified bin.
`long`	`dimension(int d)` Default implementation of `Dimensions.dimension(int)`.
`void`	`dimensions(long[] dimensions)` Write the number of pixels in each dimension into long[].
`ImgFactory<LongType>`	`factory()` Get a `ImgFactory` that creates `Img`s of the same kind as this one.
`LongType`	`firstElement()` Get the first element of this `IterableRealInterval`.
`long`	`frequency(long[] binPos)` Returns the frequency count associated with a given bin.
`void`	`increment(long[] binPos)` Increments the frequency count of a specified bin.
`Object`	`iterationOrder()` Returns the iteration order of this `IterableRealInterval`.
`Iterator<LongType>`	`iterator()`
`Cursor<LongType>`	`localizingCursor()` Returns a `RealLocalizable` `Iterator` that calculates its location at each iteration step.
`long`	`max(int d)` Get the maximum in dimension d.
`void`	`max(long[] max)` Write the maximum of each dimension into long[].
`void`	`max(Positionable max)` Sets a `Positionable` to the maximum of this `Interval`
`long`	`min(int d)` Get the minimum in dimension d.
`void`	`min(long[] min)` Write the minimum of each dimension into long[].
`void`	`min(Positionable min)` Sets a `Positionable` to the minimum of this `Interval`
`long`	`modeCount()` Returns the highest frequency count found within the bins.
`List<long[]>`	`modePositions()` Returns a list of bin positions of the highest frequency bins.
`int`	`numDimensions()` Gets the space's number of dimensions.
`RandomAccess<LongType>`	`randomAccess()` Create a random access sampler for integer coordinates.
`RandomAccess<LongType>`	`randomAccess(Interval interval)` Create a random access sampler for integer coordinates.
`void`	`realMax(double[] max)` Write the maximum of each dimension into double[].
`double`	`realMax(int d)` Default implementation of `RealInterval.realMax(int)`.
`void`	`realMax(RealPositionable max)` Sets a `RealPositionable` to the maximum of this `Interval`
`void`	`realMin(double[] min)` Write the minimum of each dimension into double[].
`double`	`realMin(int d)` Default implementation of `RealInterval.realMin(int)`.
`void`	`realMin(RealPositionable min)` Sets a `RealPositionable` to the minimum of this `Interval`
`double`	`relativeFrequency(long[] binPos)` Returns the relative frequency `(0 <= f <= 1)` associated with a given bin.
`void`	`resetCounters()` Resets all frequency counts to zero.
`void`	`setFrequency(long[] binPos, long value)` Sets the frequency count associated with a given bin.
`long`	`size()` Returns the number of elements in this `Function`.
`long`	`totalValues()` Returns the total number of values counted by this distribution.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.imglib2.RandomAccessible
getAt, getAt, getAt

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface net.imglib2.Interval
maxAsLongArray, maxAsPoint, minAsLongArray, minAsPoint

Methods inherited from interface net.imglib2.RealInterval
maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint

Methods inherited from interface net.imglib2.Dimensions
allPositive, allPositive, dimensions, dimensionsAsLongArray, dimensionsAsPoint, verify, verify, verifyAllPositive, verifyAllPositive

- Constructor Detail
  - DiscreteFrequencyDistribution
```
public DiscreteFrequencyDistribution(long[] binCounts)
```
    Construct an n-dimensional counter with the given number of bins
  - DiscreteFrequencyDistribution
```
public DiscreteFrequencyDistribution(Img<LongType> img)
```
    Construct an n-dimensional counter using a provided Img<LongType> to store counts.
- Method Detail
  - resetCounters
```
public void resetCounters()
```
    Resets all frequency counts to zero.
  - frequency
```
public long frequency(long[] binPos)
```
    Returns the frequency count associated with a given bin.
  - setFrequency
```
public void setFrequency(long[] binPos,
                         long value)
```
    Sets the frequency count associated with a given bin.
  - relativeFrequency
```
public double relativeFrequency(long[] binPos)
```
    Returns the relative frequency (0 <= f <= 1) associated with a given bin.
  - increment
```
public void increment(long[] binPos)
```
    Increments the frequency count of a specified bin.
  - decrement
```
public void decrement(long[] binPos)
```
    Decrements the frequency count of a specified bin.
  - totalValues
```
public long totalValues()
```
    Returns the total number of values counted by this distribution.
  - modeCount
```
public long modeCount()
```
    Returns the highest frequency count found within the bins.
  - modePositions
```
public List<long[]> modePositions()
```
    Returns a list of bin positions of the highest frequency bins.
  - randomAccess
```
public RandomAccess<LongType> randomAccess()
```
    Description copied from interface: RandomAccessible
    Create a random access sampler for integer coordinates.
    The returned random access covers as much of the domain as possible.
    Please note: RandomAccessibleIntervals have a finite domain (their Interval), so RandomAccessible.randomAccess() is only guaranteed to cover this finite domain. This may lead to unexpected results when using Views. In the following code
```
 RandomAccessible<T> extended = Views.extendBorder( img )
 RandomAccessibleInterval<T> cropped = Views.interval( extended, img );
 RandomAccess<T> a1 = extended.randomAccess();
 RandomAccess<T> a2 = cropped.randomAccess();
 
```
    The access a1 on the extended image is valid everywhere. However, somewhat counter-intuitively, the access a2 on the extended and cropped image is only valid on the interval img to which the extended image was cropped. The access is only required to cover this interval, because it is the domain of the cropped image. Views attempts to provide the fastest possible access that meets this requirement, and will therefore strip the extension. To deal with this, if you know that you need to access pixels outside the domain of the RandomAccessibleInterval, and you know that the RandomAccessibleInterval is actually defined beyond its interval boundaries, then use the RandomAccessible.randomAccess(Interval) variant and specify which interval you actually want to access. In the above example,
```
 RandomAccess<T> a2 = cropped.randomAccess( Intervals.expand( img, 10 ) );
 
```
    will provide the extended access as expected.
    Specified by:
    
    randomAccess in interface RandomAccessible<LongType>
    
    Returns:
    
    random access sampler
  - randomAccess
```
public RandomAccess<LongType> randomAccess(Interval interval)
```
    Description copied from interface: RandomAccessible
    
    Create a random access sampler for integer coordinates.
    The returned random access is intended to be used in the specified interval only. Thus, the RandomAccessible may provide optimized versions. If the interval is completely contained in the domain, the random access is guaranteed to provide the same values as that obtained by RandomAccessible.randomAccess() within the interval.
    
    Specified by:
    
    randomAccess in interface RandomAccessible<LongType>
    
    Parameters:
    
    interval - in which interval you intend to use the random access.
    
    Returns:
    
    random access sampler
  - numDimensions
```
public int numDimensions()
```
    Description copied from interface: EuclideanSpace
    
    Gets the space's number of dimensions.
    
    Specified by:
    
    numDimensions in interface EuclideanSpace
  - min
```
public long min(int d)
```
    Description copied from interface: Interval
    
    Get the minimum in dimension d.
    
    Specified by:
    
    min in interface Interval
    
    Parameters:
    
    d - dimension
    
    Returns:
    
    minimum in dimension d.
  - min
```
public void min(long[] min)
```
    Description copied from interface: Interval
    
    Write the minimum of each dimension into long[].
    
    Specified by:
    
    min in interface Interval
  - min
```
public void min(Positionable min)
```
    Description copied from interface: Interval
    
    Sets a Positionable to the minimum of this Interval
    
    Specified by:
    
    min in interface Interval
  - max
```
public long max(int d)
```
    Description copied from interface: Interval
    
    Get the maximum in dimension d.
    
    Specified by:
    
    max in interface Interval
    
    Parameters:
    
    d - dimension
    
    Returns:
    
    maximum in dimension d.
  - max
```
public void max(long[] max)
```
    Description copied from interface: Interval
    
    Write the maximum of each dimension into long[].
    
    Specified by:
    
    max in interface Interval
  - max
```
public void max(Positionable max)
```
    Description copied from interface: Interval
    
    Sets a Positionable to the maximum of this Interval
    
    Specified by:
    
    max in interface Interval
  - realMin
```
public double realMin(int d)
```
    Description copied from interface: Interval
    
    Default implementation of RealInterval.realMin(int).
    
    Specified by:
    
    realMin in interface Interval
    
    Specified by:
    
    realMin in interface RealInterval
    
    Parameters:
    
    d - dimension
    
    Returns:
    
    minimum in dimension d.
  - realMin
```
public void realMin(double[] min)
```
    Description copied from interface: RealInterval
    
    Write the minimum of each dimension into double[].
    
    Specified by:
    
    realMin in interface RealInterval
  - realMin
```
public void realMin(RealPositionable min)
```
    Description copied from interface: RealInterval
    
    Sets a RealPositionable to the minimum of this Interval
    
    Specified by:
    
    realMin in interface RealInterval
  - realMax
```
public double realMax(int d)
```
    Description copied from interface: Interval
    
    Default implementation of RealInterval.realMax(int).
    
    Specified by:
    
    realMax in interface Interval
    
    Specified by:
    
    realMax in interface RealInterval
    
    Parameters:
    
    d - dimension
    
    Returns:
    
    maximum in dimension d.
  - realMax
```
public void realMax(double[] max)
```
    Description copied from interface: RealInterval
    
    Write the maximum of each dimension into double[].
    
    Specified by:
    
    realMax in interface RealInterval
  - realMax
```
public void realMax(RealPositionable max)
```
    Description copied from interface: RealInterval
    
    Sets a RealPositionable to the maximum of this Interval
    
    Specified by:
    
    realMax in interface RealInterval
  - dimensions
```
public void dimensions(long[] dimensions)
```
    Description copied from interface: Dimensions
    
    Write the number of pixels in each dimension into long[].
    
    Specified by:
    
    dimensions in interface Dimensions
  - dimension
```
public long dimension(int d)
```
    Description copied from interface: Interval
    
    Default implementation of Dimensions.dimension(int).
    
    Specified by:
    
    dimension in interface Dimensions
    
    Specified by:
    
    dimension in interface Interval
  - cursor
```
public Cursor<LongType> cursor()
```
    Description copied from interface: IterableRealInterval
    
    Returns a RealCursor that iterates with optimal speed without calculating the location at each iteration step. Localization is performed on demand.
    
    Use this where localization is required rarely/ not for each iteration.
    
    Specified by:
    
    cursor in interface IterableInterval<LongType>
    
    Specified by:
    
    cursor in interface IterableRealInterval<LongType>
    
    Returns:
    
    fast iterating iterator
  - localizingCursor
```
public Cursor<LongType> localizingCursor()
```
    Description copied from interface: IterableRealInterval
    
    Returns a RealLocalizable Iterator that calculates its location at each iteration step. That is, localization is performed with optimal speed.
    
    Use this where localization is required often/ for each iteration.
    
    Specified by:
    
    localizingCursor in interface IterableInterval<LongType>
    
    Specified by:
    
    localizingCursor in interface IterableRealInterval<LongType>
    
    Returns:
    
    fast localizing iterator
  - size
```
public long size()
```
    Description copied from interface: IterableRealInterval
    
    Returns the number of elements in this Function.
    
    Specified by:
    
    size in interface IterableRealInterval<LongType>
    
    Returns:
    
    number of elements
  - firstElement
```
public LongType firstElement()
```
    Description copied from interface: IterableRealInterval
    
    Get the first element of this IterableRealInterval. This is a shortcut for cursor().next(). This can be used to create a new variable of type T using firstElement().createVariable(), which is useful in generic methods to store temporary results, e.g., a running sum over pixels in the IterableRealInterval.
    
    Specified by:
    
    firstElement in interface IterableRealInterval<LongType>
    
    Returns:
    
    the first element in iteration order.
  - iterationOrder
```
public Object iterationOrder()
```
    Description copied from interface: IterableRealInterval
    
    Returns the iteration order of this IterableRealInterval. If the returned object equals (Object.equals(Object)) the iteration order of another IterableRealInterval f then they can be copied by synchronous iteration. That is, having an Iterator on this and another Iterator on f, moving both in synchrony will point both of them to corresponding locations in their source domain. In other words, this and f have the same iteration order and means and the same number of elements.
    
    Specified by:
    
    iterationOrder in interface IterableRealInterval<LongType>
    
    Returns:
    
    the iteration order of this IterableRealInterval.
    
    See Also:
    
    FlatIterationOrder
  - iterator
```
public Iterator<LongType> iterator()
```
    Specified by:
    
    iterator in interface Iterable<LongType>
  - factory
```
public ImgFactory<LongType> factory()
```
    Description copied from interface: Img
    
    Get a ImgFactory that creates Imgs of the same kind as this one. This is useful to create Imgs for temporary storage in generic methods where the specific Img type is unknown. Note, that the factory can be used even if all references to this Img have been invalidated.
    
    Specified by:
    
    factory in interface Img<LongType>
    
    Returns:
    
    a factory for Imgs of the same kind as this one.
  - copy
```
public DiscreteFrequencyDistribution copy()
```
    Specified by:
    
    copy in interface Img<LongType>
    
    Returns:
    
    - A copy of the current Img instance, all pixels are duplicated

Class DiscreteFrequencyDistribution

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface net.imglib2.RandomAccessible

Methods inherited from interface java.lang.Iterable

Methods inherited from interface net.imglib2.Interval

Methods inherited from interface net.imglib2.RealInterval

Methods inherited from interface net.imglib2.Dimensions

Constructor Detail

DiscreteFrequencyDistribution

DiscreteFrequencyDistribution

Method Detail

resetCounters

frequency

setFrequency

relativeFrequency

increment

decrement

totalValues

modeCount

modePositions

randomAccess

randomAccess

numDimensions

min

min

min

max

max

max

realMin

realMin

realMin

realMax

realMax

realMax

dimensions

dimension

cursor

localizingCursor

size

firstElement

iterationOrder

iterator

factory

copy