Class DiscreteFrequencyDistribution
- java.lang.Object
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- net.imglib2.histogram.DiscreteFrequencyDistribution
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- All Implemented Interfaces:
java.lang.Iterable<LongType>
,Dimensions
,EuclideanSpace
,Img<LongType>
,Interval
,IterableInterval<LongType>
,IterableRealInterval<LongType>
,RandomAccessible<LongType>
,RandomAccessibleInterval<LongType>
,RealInterval
public class DiscreteFrequencyDistribution extends java.lang.Object implements Img<LongType>
This class represents an n-dimensional set of counters. Histogram implementations use these for tracking value counts.- Author:
- Barry DeZonia
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Constructor Summary
Constructors Constructor Description DiscreteFrequencyDistribution(long[] binCounts)
Construct an n-dimensional counter with the given number of binsDiscreteFrequencyDistribution(Img<LongType> img)
Construct an n-dimensional counter using a providedImg<LongType>
to store counts.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DiscreteFrequencyDistribution
copy()
Cursor<LongType>
cursor()
Returns aRealCursor
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)
Get the number of pixels in a given dimension d.void
dimensions(long[] dimensions)
Write the number of pixels in each dimension into long[].ImgFactory<LongType>
factory()
Get aImgFactory
that createsImg
s of the same kind as this one.LongType
firstElement()
Get the first element of thisIterableRealInterval
.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.java.lang.Object
iterationOrder()
Returns the iteration order of thisIterableRealInterval
.java.util.Iterator<LongType>
iterator()
Cursor<LongType>
localizingCursor()
Returns aRealLocalizable
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 aPositionable
to the maximum of thisInterval
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 aPositionable
to the minimum of thisInterval
long
modeCount()
Returns the highest frequency count found within the bins.java.util.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)
Get the maximum in dimension d.void
realMax(RealPositionable max)
Sets aRealPositionable
to the maximum of thisInterval
void
realMin(double[] min)
Write the minimum of each dimension into double[].double
realMin(int d)
Get the minimum in dimension d.void
realMin(RealPositionable min)
Sets aRealPositionable
to the minimum of thisInterval
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 thisFunction
.long
totalValues()
Returns the total number of values counted by this distribution.
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Method Detail
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resetCounters
public void resetCounters()
Resets all frequency counts to zero.
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frequency
public long frequency(long[] binPos)
Returns the frequency count associated with a given bin.
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setFrequency
public void setFrequency(long[] binPos, long value)
Sets the frequency count associated with a given bin.
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relativeFrequency
public double relativeFrequency(long[] binPos)
Returns the relative frequency(0 <= f <= 1)
associated with a given bin.
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increment
public void increment(long[] binPos)
Increments the frequency count of a specified bin.
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decrement
public void decrement(long[] binPos)
Decrements the frequency count of a specified bin.
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totalValues
public long totalValues()
Returns the total number of values counted by this distribution.
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modeCount
public long modeCount()
Returns the highest frequency count found within the bins.
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modePositions
public java.util.List<long[]> modePositions()
Returns a list of bin positions of the highest frequency bins.
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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:RandomAccessibleInterval
s have a finite domain (theirInterval
), soRandomAccessible.randomAccess()
is only guaranteed to cover this finite domain. This may lead to unexpected results when usingViews
. In the following codeRandomAccessible<T> extended = Views.extendBorder( img ) RandomAccessibleInterval<T> cropped = Views.interval( extended, img ); RandomAccess<T> a1 = extended.randomAccess(); RandomAccess<T> a2 = cropped.randomAccess();
Theaccess
a1
on the extended image is valid everywhere. However, somewhat counter-intuitively, theaccess
a2
on the extended and cropped image is only valid on the intervalimg
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 theRandomAccessibleInterval
, and you know that theRandomAccessibleInterval
is actually defined beyond its interval boundaries, then use theRandomAccessible.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 interfaceRandomAccessible<LongType>
- Returns:
- random access sampler
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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 interfaceRandomAccessible<LongType>
- Parameters:
interval
- in which interval you intend to use the random access.- Returns:
- random access sampler
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numDimensions
public int numDimensions()
Description copied from interface:EuclideanSpace
Gets the space's number of dimensions.- Specified by:
numDimensions
in interfaceEuclideanSpace
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min
public long min(int d)
Description copied from interface:Interval
Get the minimum in dimension d.
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min
public void min(long[] min)
Description copied from interface:Interval
Write the minimum of each dimension into long[].
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min
public void min(Positionable min)
Description copied from interface:Interval
Sets aPositionable
to the minimum of thisInterval
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max
public long max(int d)
Description copied from interface:Interval
Get the maximum in dimension d.
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max
public void max(long[] max)
Description copied from interface:Interval
Write the maximum of each dimension into long[].
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max
public void max(Positionable max)
Description copied from interface:Interval
Sets aPositionable
to the maximum of thisInterval
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realMin
public double realMin(int d)
Description copied from interface:RealInterval
Get the minimum in dimension d.- Specified by:
realMin
in interfaceRealInterval
- Parameters:
d
- dimension- Returns:
- minimum in dimension d.
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realMin
public void realMin(double[] min)
Description copied from interface:RealInterval
Write the minimum of each dimension into double[].- Specified by:
realMin
in interfaceRealInterval
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realMin
public void realMin(RealPositionable min)
Description copied from interface:RealInterval
Sets aRealPositionable
to the minimum of thisInterval
- Specified by:
realMin
in interfaceRealInterval
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realMax
public double realMax(int d)
Description copied from interface:RealInterval
Get the maximum in dimension d.- Specified by:
realMax
in interfaceRealInterval
- Parameters:
d
- dimension- Returns:
- maximum in dimension d.
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realMax
public void realMax(double[] max)
Description copied from interface:RealInterval
Write the maximum of each dimension into double[].- Specified by:
realMax
in interfaceRealInterval
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realMax
public void realMax(RealPositionable max)
Description copied from interface:RealInterval
Sets aRealPositionable
to the maximum of thisInterval
- Specified by:
realMax
in interfaceRealInterval
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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 interfaceDimensions
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dimension
public long dimension(int d)
Description copied from interface:Dimensions
Get the number of pixels in a given dimension d.- Specified by:
dimension
in interfaceDimensions
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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 interfaceIterableInterval<LongType>
- Specified by:
cursor
in interfaceIterableRealInterval<LongType>
- Returns:
- fast iterating iterator
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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 interfaceIterableInterval<LongType>
- Specified by:
localizingCursor
in interfaceIterableRealInterval<LongType>
- Returns:
- fast localizing iterator
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size
public long size()
Description copied from interface:IterableRealInterval
Returns the number of elements in this
Function
.- Specified by:
size
in interfaceIterableRealInterval<LongType>
- Returns:
- number of elements
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firstElement
public LongType firstElement()
Description copied from interface:IterableRealInterval
Get the first element of thisIterableRealInterval
. This is a shortcut forcursor().next()
. This can be used to create a new variable of type T usingfirstElement().createVariable()
, which is useful in generic methods to store temporary results, e.g., a running sum over pixels in theIterableRealInterval
.- Specified by:
firstElement
in interfaceIterableRealInterval<LongType>
- Returns:
- the first element in iteration order.
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iterationOrder
public java.lang.Object iterationOrder()
Description copied from interface:IterableRealInterval
Returns the iteration order of thisIterableRealInterval
. If the returned object equals (Object.equals(Object)
) the iteration order of anotherIterableRealInterval
f then they can be copied by synchronous iteration. That is, having anIterator
on this and anotherIterator
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 interfaceIterableRealInterval<LongType>
- Returns:
- the iteration order of this
IterableRealInterval
. - See Also:
FlatIterationOrder
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iterator
public java.util.Iterator<LongType> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<LongType>
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factory
public ImgFactory<LongType> factory()
Description copied from interface:Img
Get aImgFactory
that createsImg
s 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.
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copy
public DiscreteFrequencyDistribution copy()
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