Class Histogram1d<T>
- java.lang.Object
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- net.imglib2.histogram.Histogram1d<T>
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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,Typed<LongType>
public class Histogram1d<T> extends java.lang.Object implements Img<LongType>
A Histogram1d is a histogram that tracks up to four kinds of values: 1) values in the center of the distribution 2) values to the left of the center of the distribution (lower tail) 3) values to the right of the center of the distribution (upper tail) 4) values outside the other areasNote: the last three classifications may not be present depending upon the makeup of the input data.
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Field Summary
Fields Modifier and Type Field Description private DiscreteFrequencyDistributiondistribprivate TfirstValueprivate longignoredCountprivate BinMapper1d<T>mapperprivate long[]pos
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Constructor Summary
Constructors Constructor Description Histogram1d(java.lang.Iterable<T> data, BinMapper1d<T> mapper)Construct a histogram from an iterable set of data and a bin mapping algorithm.Histogram1d(BinMapper1d<T> mapper)Construct a histogram from a bin mapping algorithm.Histogram1d(Histogram1d<T> other)Construct a histogram whose bin mappings match another histogram.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private voidadd(java.lang.Iterable<T> data)voidaddData(java.lang.Iterable<T> data)Counts additional data contained in a given iterable collection.Histogram1d<T>copy()voidcountData(java.lang.Iterable<T> data)Counts the data contained in the given data source using the underlying bin distribution.Cursor<LongType>cursor()Returns aRealCursorthat iterates with optimal speed without calculating the location at each iteration step.voiddecrement(long binPos)Directly decrement a bin by position.voiddecrement(T value)Directly decrement a bin by value,DiscreteFrequencyDistributiondfd()Get the discrete frequency distribution associated with this histogram.longdimension(int d)Return the size of the given dimension of the frequency distribution of this histogram.voiddimensions(long[] dims)Fill the provided long[] with the sizes of all dimensions of the frequency distribution of this histogram.longdistributionCount()Returns the frequency count of all values in the distribution: lower tail + middle + upper tail.ImgFactory<LongType>factory()Get aImgFactorythat createsImgs of the same kind as this one.TfirstDataValue()Returns the first data value of the input iteration.LongTypefirstElement()Get the first element of thisIterableRealInterval.longfrequency(long binPos)Returns the frequency count of the values within a bin.longfrequency(T value)Returns the frequency count of values within a bin using a representative value.longgetBinCount()Returns the number of bins contained in the histogram.voidgetCenterValue(long binPos, T value)Gets the value associated with the center of a bin.voidgetLowerBound(long binPos, T value)Gets the value associated with the left edge of a bin.LongTypegetType()Get an instance ofT.voidgetUpperBound(long binPos, T value)Gets the value associated with the right edge of the bin.booleanhasTails()Returns true if the histogram has tail bins at both ends which count extreme values.longignoredCount()Returns the frequency count of values that were ignored because they could not be mapped to any bin.booleanincludesLowerBound(long binPos)Returns true if the given bin interval is closed on the leftbooleanincludesUpperBound(long binPos)Returns true if the given bin interval is closed on the rightvoidincrement(long binPos)Directly increment a bin by position.voidincrement(T value)Directly increment a bin by value.private voidinit(java.lang.Iterable<T> data)booleanisInLowerTail(T value)Returns true if a given value is mapped to the lower tail of the distribution.booleanisInMiddle(T value)Returns true if a given value is mapped to the middle of the distribution.booleanisInUpperTail(T value)Returns true if a given value is mapped to the upper tail of the distribution.booleanisOutside(T value)Returns true if a given value is outside the distribution.java.lang.ObjectiterationOrder()Returns the iteration order of thisIterableRealInterval.java.util.Iterator<LongType>iterator()Cursor<LongType>localizingCursor()Returns aRealLocalizableIteratorthat calculates its location at each iteration step.longlowerTailCount()Returns the frequency count of values in the lower tail bin (if any).longmap(T value)Returns a bin position by mapping from a representative value.longmax()longmax(int d)Get the maximum in dimension d.voidmax(long[] max)Write the maximum of each dimension into long[].voidmax(Positionable max)Sets aPositionableto the maximum of thisIntervallongmin()longmin(int d)Get the minimum in dimension d.voidmin(long[] min)Write the minimum of each dimension into long[].voidmin(Positionable min)Sets aPositionableto the minimum of thisIntervalintnumDimensions()Return the number of dimensions of the frequency distribution of this histogram.RandomAccess<LongType>randomAccess()Create a random access sampler for integer coordinates.RandomAccess<LongType>randomAccess(Interval interval)Create a random access sampler for integer coordinates.doublerealMax()voidrealMax(double[] max)Write the maximum of each dimension into double[].doublerealMax(int d)Get the maximum in dimension d.voidrealMax(RealPositionable max)Sets aRealPositionableto the maximum of thisIntervaldoublerealMin()voidrealMin(double[] min)Write the minimum of each dimension into double[].doublerealMin(int d)Get the minimum in dimension d.voidrealMin(RealPositionable min)Sets aRealPositionableto the minimum of thisIntervaldoublerelativeFrequency(long binPos, boolean includeTails)Returns the relative frequency of values within a bin.doublerelativeFrequency(T value, boolean includeTails)Returns the relative frequency of values within a bin using a representative value.private voidreset()voidresetCounters()Resets all data counts to 0.longsize()Returns the number of elements in thisFunction.private voidsubtract(java.lang.Iterable<T> data)voidsubtractData(java.lang.Iterable<T> data)Uncounts some original data contained in a given iterable collection.long[]toLongArray()Returns a bare long[] histogram with the same bin counts as this histogram.longtotalCount()Returns the total count of all values observed; both within and without the entire distribution.longupperTailCount()Returns the frequency count of values in the upper tail bin (if any).longvalueCount()Returns the frequency count of all values in the middle of the distribution.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface net.imglib2.Dimensions
dimensions, dimensionsAsLongArray, dimensionsAsPoint
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Methods inherited from interface net.imglib2.Interval
maxAsLongArray, maxAsPoint, minAsLongArray, minAsPoint
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Methods inherited from interface net.imglib2.IterableInterval
localizingSpliterator, spliterator
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Methods inherited from interface net.imglib2.IterableRealInterval
parallelStream, stream
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Methods inherited from interface net.imglib2.RandomAccessible
getAt, getAt, getAt
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Methods inherited from interface net.imglib2.RealInterval
maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint
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Field Detail
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firstValue
private T firstValue
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mapper
private BinMapper1d<T> mapper
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distrib
private DiscreteFrequencyDistribution distrib
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pos
private long[] pos
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ignoredCount
private long ignoredCount
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Constructor Detail
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Histogram1d
public Histogram1d(BinMapper1d<T> mapper)
Construct a histogram from a bin mapping algorithm. Use countData() to populate it.- Parameters:
mapper- The algorithm used to map values to bins
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Histogram1d
public Histogram1d(Histogram1d<T> other)
Construct a histogram whose bin mappings match another histogram. After this construction the histogram bins are unpopulated.- Parameters:
other- The histogram to copy.
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Histogram1d
public Histogram1d(java.lang.Iterable<T> data, BinMapper1d<T> mapper)
Construct a histogram from an iterable set of data and a bin mapping algorithm.- Parameters:
data- The iterable set of values to calculate uponmapper- The algorithm used to map values to bins
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Method Detail
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firstDataValue
public T firstDataValue()
Returns the first data value of the input iteration.
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hasTails
public boolean hasTails()
Returns true if the histogram has tail bins at both ends which count extreme values.
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lowerTailCount
public long lowerTailCount()
Returns the frequency count of values in the lower tail bin (if any).
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upperTailCount
public long upperTailCount()
Returns the frequency count of values in the upper tail bin (if any).
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valueCount
public long valueCount()
Returns the frequency count of all values in the middle of the distribution.
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distributionCount
public long distributionCount()
Returns the frequency count of all values in the distribution: lower tail + middle + upper tail. Does not include ignored values.
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ignoredCount
public long ignoredCount()
Returns the frequency count of values that were ignored because they could not be mapped to any bin.
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totalCount
public long totalCount()
Returns the total count of all values observed; both within and without the entire distribution. Thus it includes ignored values. One should decide carefully between using distributionCount() and totalCount().
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frequency
public long frequency(T value)
Returns the frequency count of values within a bin using a representative value. Note that multiple values can be mapped to one bin so this is NOT the frequency count of this exact value in the distribution.- Parameters:
value- A representative value of interest
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frequency
public long frequency(long binPos)
Returns the frequency count of the values within a bin.
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relativeFrequency
public double relativeFrequency(T value, boolean includeTails)
Returns the relative frequency of values within a bin using a representative value. Note that multiple values can be mapped to one bin so this is NOT the relative frequency of this exact value in the distribution.This calculation is of the number of values in the bin divided by either the number of values in the distribution or the number of values in the center of the distribution (tails ignored).
One can devise other ways to count relative frequencies that consider ignored values also. If needed one can use the various count methods and frequency methods to calculate any relative frequency desired.
- Parameters:
value- A representative value of interestincludeTails- Flag for determining whether to include tails in calculation.
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relativeFrequency
public double relativeFrequency(long binPos, boolean includeTails)Returns the relative frequency of values within a bin.This calculation is of the number of values in the bin divided by either the number of values in the distribution or the number of values in the center of the distribution (tails ignored).
One can devise other ways to count relative frequencies that consider ignored values also. If needed one can use the various count methods and frequency methods to calculate any relative frequency desired.
- Parameters:
binPos- The position of the bin of interestincludeTails- Flag for determining whether to include tails in calculation.
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getBinCount
public long getBinCount()
Returns the number of bins contained in the histogram.
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map
public long map(T value)
Returns a bin position by mapping from a representative value.
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getCenterValue
public void getCenterValue(long binPos, T value)Gets the value associated with the center of a bin.- Parameters:
binPos- The bin number of interestvalue- The output to fill with the center value
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getLowerBound
public void getLowerBound(long binPos, T value)Gets the value associated with the left edge of a bin.- Parameters:
binPos- The bin number of interestvalue- The output to fill with the left edge value
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getUpperBound
public void getUpperBound(long binPos, T value)Gets the value associated with the right edge of the bin.- Parameters:
binPos- The bin number of interestvalue- The output to fill with the right edge value
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includesUpperBound
public boolean includesUpperBound(long binPos)
Returns true if the given bin interval is closed on the right- Parameters:
binPos- The bin number of the interval of interest
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includesLowerBound
public boolean includesLowerBound(long binPos)
Returns true if the given bin interval is closed on the left- Parameters:
binPos- The bin number of the interval of interest
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isInLowerTail
public boolean isInLowerTail(T value)
Returns true if a given value is mapped to the lower tail of the distribution.- Parameters:
value- The value to determine the location of
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isInUpperTail
public boolean isInUpperTail(T value)
Returns true if a given value is mapped to the upper tail of the distribution.- Parameters:
value- The value to determine the location of
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isInMiddle
public boolean isInMiddle(T value)
Returns true if a given value is mapped to the middle of the distribution.- Parameters:
value- The value to determine the location of
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isOutside
public boolean isOutside(T value)
Returns true if a given value is outside the distribution.- Parameters:
value- The value to determine the location of
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dfd
public DiscreteFrequencyDistribution dfd()
Get the discrete frequency distribution associated with this histogram.
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countData
public void countData(java.lang.Iterable<T> data)
Counts the data contained in the given data source using the underlying bin distribution.- Parameters:
data- The total data to count
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addData
public void addData(java.lang.Iterable<T> data)
Counts additional data contained in a given iterable collection. One can use this to update an existing histogram with a subset of values.- Parameters:
data- The new data to count
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subtractData
public void subtractData(java.lang.Iterable<T> data)
Uncounts some original data contained in a given iterable collection. One can use this to update an existing histogram with a subset of values.- Parameters:
data- The old data to uncount
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increment
public void increment(long binPos)
Directly increment a bin by position.- Parameters:
binPos- The 1-d index of the bin
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decrement
public void decrement(long binPos)
Directly decrement a bin by position.- Parameters:
binPos- The 1-d index of the bin
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increment
public void increment(T value)
Directly increment a bin by value.- Parameters:
value- The value to map to a bin position
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decrement
public void decrement(T value)
Directly decrement a bin by value,- Parameters:
value- The value to map to a bin position
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resetCounters
public void resetCounters()
Resets all data counts to 0.
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toLongArray
public long[] toLongArray()
Returns a bare long[] histogram with the same bin counts as this histogram.
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numDimensions
public int numDimensions()
Return the number of dimensions of the frequency distribution of this histogram.- Specified by:
numDimensionsin interfaceEuclideanSpace
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dimension
public long dimension(int d)
Return the size of the given dimension of the frequency distribution of this histogram.- Specified by:
dimensionin interfaceDimensions- Specified by:
dimensionin interfaceInterval
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dimensions
public void dimensions(long[] dims)
Fill the provided long[] with the sizes of all dimensions of the frequency distribution of this histogram.- Specified by:
dimensionsin interfaceDimensions
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randomAccess
public RandomAccess<LongType> randomAccess()
Description copied from interface:RandomAccessibleCreate 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 (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();
Theaccessa1on the extended image is valid everywhere. However, somewhat counter-intuitively, theaccessa2on the extended and cropped image is only valid on the intervalimgto which the extended image was cropped. The access is only required to cover this interval, because it is the domain of the cropped image.Viewsattempts 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 theRandomAccessibleIntervalis 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:
randomAccessin interfaceRandomAccessible<T>- Returns:
- random access sampler
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randomAccess
public RandomAccess<LongType> randomAccess(Interval interval)
Description copied from interface:RandomAccessibleCreate 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:
randomAccessin interfaceRandomAccessible<T>- Parameters:
interval- in which interval you intend to use the random access.- Returns:
- random access sampler
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min
public long min()
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min
public long min(int d)
Description copied from interface:IntervalGet the minimum in dimension d.
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min
public void min(long[] min)
Description copied from interface:IntervalWrite the minimum of each dimension into long[].
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min
public void min(Positionable min)
Description copied from interface:IntervalSets aPositionableto the minimum of thisInterval
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max
public long max()
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max
public long max(int d)
Description copied from interface:IntervalGet the maximum in dimension d.
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max
public void max(long[] max)
Description copied from interface:IntervalWrite the maximum of each dimension into long[].
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max
public void max(Positionable max)
Description copied from interface:IntervalSets aPositionableto the maximum of thisInterval
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realMin
public double realMin()
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realMin
public double realMin(int d)
Description copied from interface:RealIntervalGet the minimum in dimension d.- Specified by:
realMinin interfaceInterval- Specified by:
realMinin interfaceRealInterval- Parameters:
d- dimension- Returns:
- minimum in dimension d.
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realMin
public void realMin(double[] min)
Description copied from interface:RealIntervalWrite the minimum of each dimension into double[].- Specified by:
realMinin interfaceRealInterval
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realMin
public void realMin(RealPositionable min)
Description copied from interface:RealIntervalSets aRealPositionableto the minimum of thisInterval- Specified by:
realMinin interfaceRealInterval
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realMax
public double realMax()
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realMax
public double realMax(int d)
Description copied from interface:RealIntervalGet the maximum in dimension d.- Specified by:
realMaxin interfaceInterval- Specified by:
realMaxin interfaceRealInterval- Parameters:
d- dimension- Returns:
- maximum in dimension d.
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realMax
public void realMax(double[] max)
Description copied from interface:RealIntervalWrite the maximum of each dimension into double[].- Specified by:
realMaxin interfaceRealInterval
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realMax
public void realMax(RealPositionable max)
Description copied from interface:RealIntervalSets aRealPositionableto the maximum of thisInterval- Specified by:
realMaxin interfaceRealInterval
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cursor
public Cursor<LongType> cursor()
Description copied from interface:IterableRealIntervalReturns a
RealCursorthat 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:
cursorin interfaceIterableInterval<T>- Specified by:
cursorin interfaceIterableRealInterval<T>- Specified by:
cursorin interfaceRandomAccessibleInterval<T>- Returns:
- fast iterating iterator
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localizingCursor
public Cursor<LongType> localizingCursor()
Description copied from interface:IterableRealIntervalReturns a
RealLocalizableIteratorthat 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:
localizingCursorin interfaceIterableInterval<T>- Specified by:
localizingCursorin interfaceIterableRealInterval<T>- Specified by:
localizingCursorin interfaceRandomAccessibleInterval<T>- Returns:
- fast localizing iterator
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size
public long size()
Description copied from interface:IterableRealIntervalReturns the number of elements in this
Function.- Specified by:
sizein interfaceIterableRealInterval<T>- Specified by:
sizein interfaceRandomAccessibleInterval<T>- Returns:
- number of elements
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firstElement
public LongType firstElement()
Description copied from interface:IterableRealIntervalGet the first element of thisIterableRealInterval. This is a shortcut forcursor().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 theIterableRealInterval.- Specified by:
firstElementin interfaceIterableRealInterval<T>- Returns:
- the first element in iteration order.
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iterationOrder
public java.lang.Object iterationOrder()
Description copied from interface:IterableRealIntervalReturns the iteration order of thisIterableRealInterval. If the returned object equals (Object.equals(Object)) the iteration order of anotherIterableRealIntervalf then they can be copied by synchronous iteration. That is, having anIteratoron this and anotherIteratoron 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:
iterationOrderin interfaceIterableRealInterval<T>- Specified by:
iterationOrderin interfaceRandomAccessibleInterval<T>- Returns:
- the iteration order of this
IterableRealInterval. - See Also:
FlatIterationOrder
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iterator
public java.util.Iterator<LongType> iterator()
- Specified by:
iteratorin interfacejava.lang.Iterable<T>- Specified by:
iteratorin interfaceIterableRealInterval<T>
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factory
public ImgFactory<LongType> factory()
Description copied from interface:ImgGet aImgFactorythat createsImgs 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 Histogram1d<T> copy()
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getType
public LongType getType()
Description copied from interface:TypedGet an instance ofT.It should not be assumed that the returned
Tinstance is an independent copy. In particular, repeated calls togetType()may return the same instance.
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reset
private void reset()
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init
private void init(java.lang.Iterable<T> data)
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add
private void add(java.lang.Iterable<T> data)
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subtract
private void subtract(java.lang.Iterable<T> data)
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