Class HistogramNd<T>

    • Constructor Summary

      Constructors 
      Constructor Description
      HistogramNd​(java.lang.Iterable<java.util.List<T>> data, java.util.List<BinMapper1d<T>> mappers)
      Construct a histogram from an iterable set of data and a list of bin mapping algorithms.
      HistogramNd​(java.util.List<java.lang.Iterable<T>> data, java.util.List<BinMapper1d<T>> mappers)
      Construct a histogram from an iterable set of data and a list of bin mapping algorithms.
      HistogramNd​(java.util.List<BinMapper1d<T>> mappers)
      Construct a histogram from a list of bin mapping algorithms.
      HistogramNd​(HistogramNd<T> other)
      Construct a histogram whose bin mappings match another histogram.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addData​(java.lang.Iterable<java.util.List<T>> data)
      Counts additional data contained in a given iterable collection.
      void addData​(java.util.List<java.lang.Iterable<T>> data)
      Counts additional data contained in a given iterable collection.
      HistogramNd<T> copy()  
      void countData​(java.lang.Iterable<java.util.List<T>> data)
      Counts the data contained in the given data source using the underlying bin distribution.
      void countData​(java.util.List<java.lang.Iterable<T>> data)
      Counts the data contained in the given data source using the underlying bin distribution.
      Cursor<LongType> cursor()
      Returns a RealCursor that iterates with optimal speed without calculating the location at each iteration step.
      void decrement​(long[] binPos)
      Directly decrement a bin by position.
      void decrement​(java.util.List<T> values)
      Directly decrement a bin by value,
      DiscreteFrequencyDistribution dfd()
      Get the discrete frequency distribution associated with this histogram.
      long dimension​(int d)
      Return the size of the given dimension of the frequency distribution of this histogram.
      void dimensions​(long[] dims)
      Fill the provided long[] with the sizes of all dimensions of the frequency distribution of this histogram.
      long distributionCount()
      Returns the frequency count of all values in the distribution: lower tail + middle + upper tail.
      long distributionCount​(int dim, long dimVal)
      Returns the frequency count of all values in the specified dimension of the distribution: lower tail + middle + upper tail.
      ImgFactory<LongType> factory()
      Get a ImgFactory that creates Imgs of the same kind as this one.
      LongType firstElement()
      Get the first element of this IterableRealInterval.
      long frequency​(long[] binPos)
      Returns the frequency count of the values within a bin.
      long frequency​(java.util.List<T> values)
      Returns the frequency count of values within a bin using a set of representative values.
      long getBinCount()
      Returns the number of bins contained in the histogram.
      void getCenterValues​(long[] binPos, java.util.List<T> values)
      Gets the values associated with the center of a bin.
      void getLowerBounds​(long[] binPos, java.util.List<T> values)
      Gets the values associated with the left edge of a bin.
      void getUpperBounds​(long[] binPos, java.util.List<T> values)
      Gets the values associated with the right edge of a bin.
      boolean hasTails()
      Returns true if the histogram has tail bins which count extreme values for one or more dimensions
      boolean hasTails​(int dim)
      Returns true if the histogram has tail bins which count extreme values for the given dimension.
      long ignoredCount()
      Returns the frequency count of values that were ignored because they could not be mapped to any bin.
      boolean includesLowerBound​(int dim, long binPos)
      Returns true if the given bin interval is closed on the left for the given dimension.
      boolean includesLowerBounds​(long[] binPos)
      Returns true if the given bin interval is closed on the left
      boolean includesUpperBound​(int dim, long binPos)
      Returns true if the given bin interval is closed on the right for the given dimension.
      boolean includesUpperBounds​(long[] binPos)
      Returns true if the given bin interval is closed on the right
      void increment​(long[] binPos)
      Directly increment a bin by position.
      void increment​(java.util.List<T> values)
      Directly increment a bin by value.
      boolean isInLowerTail​(int dim, T value)
      Returns true if a given value for a given dimension is mapped to the lower tail of the distribution.
      boolean isInLowerTail​(java.util.List<T> values)
      Returns true if a given set of values are mapped to the lower tail of the distribution.
      boolean isInMiddle​(int dim, T value)
      Returns true if a given value for a given dimension is mapped to the middle of the distribution.
      boolean isInMiddle​(java.util.List<T> values)
      Returns true if a given set of values are mapped to the middle of the distribution.
      boolean isInUpperTail​(int dim, T value)
      Returns true if a given value for a given dimension is mapped to the upper tail of the distribution.
      boolean isInUpperTail​(java.util.List<T> values)
      Returns true if a given set of values are mapped to the upper tail of the distribution.
      boolean isOutside​(int dim, T value)
      Returns true if a given value for a given dimension is outside the distribution.
      boolean isOutside​(java.util.List<T> values)
      Returns true if a given set of values are outside the distribution.
      java.lang.Object iterationOrder()
      Returns the iteration order of this IterableRealInterval.
      java.util.Iterator<LongType> iterator()  
      Cursor<LongType> localizingCursor()
      Returns a RealLocalizable Iterator that calculates its location at each iteration step.
      long lowerTailCount()
      Returns the frequency count of values in all lower tail bins (if any).
      long lowerTailCount​(int dim)
      Returns the frequency count of values in the lower tail bin (if any) for the given dimension.
      void map​(java.util.List<T> values, long[] binPos)
      Fills a bin position by mapping from a set of representative values.
      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
      int numDimensions()
      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.
      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 a RealPositionable to the maximum of this Interval
      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 a RealPositionable to the minimum of this Interval
      double relativeFrequency​(long[] binPos, boolean includeTails)
      Returns the relative frequency of values within a bin.
      double relativeFrequency​(java.util.List<T> values, boolean includeTails)
      Returns the relative frequency of values within a bin using a set of representative values.
      void resetCounters()
      Resets all data counts to 0.
      long size()
      Returns the number of elements in this Function.
      void subtractData​(java.lang.Iterable<java.util.List<T>> data)
      Uncounts some original data contained in a given iterable collection.
      void subtractData​(java.util.List<java.lang.Iterable<T>> data)
      Uncounts some original data contained in a given iterable collection.
      long totalCount()
      Returns the total count of all values observed; both within and without the entire distribution.
      long upperTailCount()
      Returns the frequency count of values in all upper tail bins (if any).
      long upperTailCount​(int dim)
      Returns the frequency count of values in the upper tail bin (if any) for the given dimension.
      long valueCount()
      Returns the frequency count of all values in the middle of the distribution.
      long valueCount​(int dim)
      Returns the frequency count of all values in the middle of the distribution for a given dimension.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator
    • Constructor Detail

      • HistogramNd

        public HistogramNd​(java.util.List<BinMapper1d<T>> mappers)
        Construct a histogram from a list of bin mapping algorithms. Use countData() to populate it.
        Parameters:
        mappers - The algorithms used to map values to bins
      • HistogramNd

        public HistogramNd​(HistogramNd<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.
      • HistogramNd

        public HistogramNd​(java.lang.Iterable<java.util.List<T>> data,
                           java.util.List<BinMapper1d<T>> mappers)
        Construct a histogram from an iterable set of data and a list of bin mapping algorithms. Must be given one iterable data source that returns multiple data values at each point.
        Parameters:
        data - The iterable set of values to calculate upon
        mappers - The algorithms used to map values to bins
      • HistogramNd

        public HistogramNd​(java.util.List<java.lang.Iterable<T>> data,
                           java.util.List<BinMapper1d<T>> mappers)
        Construct a histogram from an iterable set of data and a list of bin mapping algorithms. Must be given multiple iterable data sources that each return a single data value at each point.
        Parameters:
        data - The iterable set of values to calculate upon
        mappers - The algorithms used to map values to bins
    • Method Detail

      • hasTails

        public boolean hasTails​(int dim)
        Returns true if the histogram has tail bins which count extreme values for the given dimension.
      • hasTails

        public boolean hasTails()
        Returns true if the histogram has tail bins which count extreme values for one or more dimensions
      • lowerTailCount

        public long lowerTailCount​(int dim)
        Returns the frequency count of values in the lower tail bin (if any) for the given dimension.
      • lowerTailCount

        public long lowerTailCount()
        Returns the frequency count of values in all lower tail bins (if any).
      • upperTailCount

        public long upperTailCount​(int dim)
        Returns the frequency count of values in the upper tail bin (if any) for the given dimension.
      • upperTailCount

        public long upperTailCount()
        Returns the frequency count of values in all upper tail bins (if any).
      • valueCount

        public long valueCount​(int dim)
        Returns the frequency count of all values in the middle of the distribution for a given dimension.
      • valueCount

        public long valueCount()
        Returns the frequency count of all values in the middle of the distribution.
      • distributionCount

        public long distributionCount​(int dim,
                                      long dimVal)
        Returns the frequency count of all values in the specified dimension of the distribution: lower tail + middle + upper tail. Does not include ignored values.
      • distributionCount

        public long distributionCount()
        Returns the frequency count of all values in the distribution: lower tail + middle + upper tail. Does not include ignored values.
      • ignoredCount

        public long ignoredCount()
        Returns the frequency count of values that were ignored because they could not be mapped to any bin.
      • 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().
      • frequency

        public long frequency​(java.util.List<T> values)
        Returns the frequency count of values within a bin using a set of representative values. Note that multiple values can be mapped to one bin so this is NOT the frequency count of this exact set of values in the distribution.
        Parameters:
        values - A set of representative values of interest
      • frequency

        public long frequency​(long[] binPos)
        Returns the frequency count of the values within a bin.
      • relativeFrequency

        public double relativeFrequency​(java.util.List<T> values,
                                        boolean includeTails)
        Returns the relative frequency of values within a bin using a set of representative values. Note that multiple values can be mapped to one bin so this is NOT the relative frequency of this exact set of values 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:
        values - A representative set of values of interest
        includeTails - Flag for determining whether to include tails in calculation.
      • 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 interest
        includeTails - Flag for determining whether to include tails in calculation.
      • getBinCount

        public long getBinCount()
        Returns the number of bins contained in the histogram.
      • map

        public void map​(java.util.List<T> values,
                        long[] binPos)
        Fills a bin position by mapping from a set of representative values.
      • getCenterValues

        public void getCenterValues​(long[] binPos,
                                    java.util.List<T> values)
        Gets the values associated with the center of a bin.
        Parameters:
        binPos - The bin index of interest
        values - The outputs to fill with the center values
      • getLowerBounds

        public void getLowerBounds​(long[] binPos,
                                   java.util.List<T> values)
        Gets the values associated with the left edge of a bin.
        Parameters:
        binPos - The bin index of interest
        values - The outputs to fill with the left edge values
      • getUpperBounds

        public void getUpperBounds​(long[] binPos,
                                   java.util.List<T> values)
        Gets the values associated with the right edge of a bin.
        Parameters:
        binPos - The bin index of interest
        values - The outputs to fill with the right edge values
      • includesUpperBounds

        public boolean includesUpperBounds​(long[] binPos)
        Returns true if the given bin interval is closed on the right
        Parameters:
        binPos - The bin number of the interval of interest
      • includesLowerBounds

        public boolean includesLowerBounds​(long[] binPos)
        Returns true if the given bin interval is closed on the left
        Parameters:
        binPos - The bin number of the interval of interest
      • includesUpperBound

        public boolean includesUpperBound​(int dim,
                                          long binPos)
        Returns true if the given bin interval is closed on the right for the given dimension.
        Parameters:
        dim - The dimension of interest
        binPos - The bin number of the interval of interest
      • includesLowerBound

        public boolean includesLowerBound​(int dim,
                                          long binPos)
        Returns true if the given bin interval is closed on the left for the given dimension.
        Parameters:
        dim - The dimension of interest
        binPos - The bin number of the interval of interest
      • isInLowerTail

        public boolean isInLowerTail​(java.util.List<T> values)
        Returns true if a given set of values are mapped to the lower tail of the distribution.
        Parameters:
        values - The set of values to determine the location of
      • isInLowerTail

        public boolean isInLowerTail​(int dim,
                                     T value)
        Returns true if a given value for a given dimension is mapped to the lower tail of the distribution.
        Parameters:
        dim - The dimension number of the axis of interest
        value - The value to determine the location of
      • isInUpperTail

        public boolean isInUpperTail​(java.util.List<T> values)
        Returns true if a given set of values are mapped to the upper tail of the distribution.
        Parameters:
        values - The set of values to determine the location of
      • isInUpperTail

        public boolean isInUpperTail​(int dim,
                                     T value)
        Returns true if a given value for a given dimension is mapped to the upper tail of the distribution.
        Parameters:
        dim - The dimension number of the axis of interest
        value - The value to determine the location of
      • isInMiddle

        public boolean isInMiddle​(java.util.List<T> values)
        Returns true if a given set of values are mapped to the middle of the distribution.
        Parameters:
        values - The set of values to determine the location of
      • isInMiddle

        public boolean isInMiddle​(int dim,
                                  T value)
        Returns true if a given value for a given dimension is mapped to the middle of the distribution.
        Parameters:
        dim - The dimension number of the axis of interest
        value - The value to determine the location of
      • isOutside

        public boolean isOutside​(java.util.List<T> values)
        Returns true if a given set of values are outside the distribution.
        Parameters:
        values - The set of values to determine the location of
      • isOutside

        public boolean isOutside​(int dim,
                                 T value)
        Returns true if a given value for a given dimension is outside the distribution.
        Parameters:
        value - The value to determine the location of
      • countData

        public void countData​(java.lang.Iterable<java.util.List<T>> data)
        Counts the data contained in the given data source using the underlying bin distribution.
        Parameters:
        data - The total data to count
      • countData

        public void countData​(java.util.List<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
      • addData

        public void addData​(java.lang.Iterable<java.util.List<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
      • addData

        public void addData​(java.util.List<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
      • subtractData

        public void subtractData​(java.lang.Iterable<java.util.List<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
      • subtractData

        public void subtractData​(java.util.List<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
      • increment

        public void increment​(long[] binPos)
        Directly increment a bin by position.
        Parameters:
        binPos - The 1-d index of the bin
      • decrement

        public void decrement​(long[] binPos)
        Directly decrement a bin by position.
        Parameters:
        binPos - The 1-d index of the bin
      • increment

        public void increment​(java.util.List<T> values)
        Directly increment a bin by value.
        Parameters:
        values - The values to map to a bin position
      • decrement

        public void decrement​(java.util.List<T> values)
        Directly decrement a bin by value,
        Parameters:
        values - The values to map to a bin position
      • resetCounters

        public void resetCounters()
        Resets all data counts to 0.
      • numDimensions

        public int numDimensions()
        Return the number of dimensions of the frequency distribution of this histogram.
        Specified by:
        numDimensions in interface EuclideanSpace
      • dimension

        public long dimension​(int d)
        Return the size of the given dimension of the frequency distribution of this histogram.
        Specified by:
        dimension in interface Dimensions
      • 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:
        dimensions in interface Dimensions
      • 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<T>
        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<T>
        Parameters:
        interval - in which interval you intend to use the random access.
        Returns:
        random access sampler
      • 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
      • 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
      • realMin

        public double realMin​(int d)
        Description copied from interface: RealInterval
        Get the minimum in dimension d.
        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
      • realMax

        public double realMax​(int d)
        Description copied from interface: RealInterval
        Get the maximum in dimension d.
        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
      • 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<T>
        Returns:
        the first element in iteration order.
      • iterationOrder

        public java.lang.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<T>
        Returns:
        the iteration order of this IterableRealInterval.
        See Also:
        FlatIterationOrder
      • iterator

        public java.util.Iterator<LongType> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<T>
      • 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<T>
        Returns:
        a factory for Imgs of the same kind as this one.
      • copy

        public HistogramNd<T> copy()
        Specified by:
        copy in interface Img<T>
        Returns:
        - A copy of the current Img instance, all pixels are duplicated