java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmHistogram

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmHistogram
extends AlgorithmBase
```
Calculates the histogram for an image. The number of bins is determined by the extents of the histogram model. The calling algorithm can specify if the histogram is to be calculated for whole image or only over VOI regions. The Otsu and Maximum Entrophy thresholds are also automatically calculated and stored in the ModelHistogram structure. The Otsu and Max entropy can take time (minutes) to calculate for histgrams with bins larger than (10,000).

Version:

0.1 September 18, 1997

See Also:

ModelHistogram

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`AlgorithmHistogram.GrayLevelClass`	Used specifally by the Otsu threshold algorithm to define a gray level object for calculating probabilities.

Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`dataOutput`	Flag indicating whether or not histogram data is output to the data window.
`private boolean`	`displayGraph`
`private boolean`	`entireImage`	If true the histogram should be calculated for the entire image.
`private double[]`	`highValue`	DOCUMENT ME!
`private int[]`	`histoBuffer`	DOCUMENT ME!
`private ModelHistogram`	`histogram`	Reference to the histogram storage object.
`private ModelImage`	`image`	Reference to the image.
`private double[]`	`lowValue`	DOCUMENT ME!
`private int`	`processMode`
`private int`	`RGBOffset`	Indicates which channel of the RGB image the histogram should be calculated. 1 = Red channel 2 = Green channel 3 = Blue channel
`private static int`	`SEPARATE_VOIS`
`private int`	`summaryBins`	Used to indicate the number of histogram bins when using the constructors that do NOT pass in the histogram object.
`private static int`	`TOTAL_VOIS`
`private boolean`	`userLimits`
`private double`	`userMax`
`private double`	`userMin`
`private static int`	`WHOLE_IMAGE`

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmHistogram(ModelHistogram histogram, int RGBOffset, ModelImage image, boolean maskFlag)`	Constructs the histogram calculation object for an RGB image.
`AlgorithmHistogram(ModelHistogram histogram, ModelImage image, boolean maskFlag)`	Constructs the histogram calculation object.
`AlgorithmHistogram(ModelImage image, int summaryBins)`	Constructs the histogram calculation object for an image.
`AlgorithmHistogram(ModelImage image, int summaryBins, boolean maskFlag)`	Constructs the histogram calculation object for an image.
`AlgorithmHistogram(ModelImage image, int summaryBins, boolean maskFlag, boolean displayGraph, boolean userLimits, double userMin, double userMax)`	Constructs the histogram calculation object for an image.
`AlgorithmHistogram(ModelImage image, int summaryBins, int RGBOffset)`	Constructs the histogram calculation object for an RGB image.
`AlgorithmHistogram(ModelImage image, int summaryBins, int RGBOffset, boolean maskFlag)`	Constructs the histogram calculation object for an RGB image.
`AlgorithmHistogram(ModelImage image, int summaryBins, int RGBOffset, boolean maskFlag, boolean displayGraph, boolean userLimits, double userMin, double userMax)`	Constructs the histogram calculation object for an RGB image.
`AlgorithmHistogram(ModelImage image, int summaryBins, int processMode, boolean displayGraph, boolean userLimits, float userMin, float userMax)`	Constructs the histogram calculation object for an image.
`AlgorithmHistogram(ModelImage image, int summaryBins, int RGBOffset, int processMode, boolean displayGraph, boolean userLimits, float userMin, float userMax)`	Constructs the histogram calculation object for an RGB image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Dispose of local variables.
`void`	`entireImage(boolean flag)`	Sets a flag to indicate if the histogram is to be calculated for the entire image or just the VOI.
`private int`	`entropySplit(int[] hist)`	Calculate maximum entropy split of a histogram.
`void`	`finalize()`	Prepares this class for destruction.
`double[]`	`getHighValue()`	DOCUMENT ME!
`int[]`	`getHistoBuffer()`	The buffer of all histogram values.
`double[]`	`getLowValue()`	DOCUMENT ME!
`ModelHistogram`	`getModelHistogram()`	Accessor to the histogram.
`private int`	`otsuThreshold(ModelImage image, int[] histoBuffer)`	This algorithm is an implementation of Otsu thresholding technique based on the minimization of inter-class variance [otsu79].
`void`	`runAlgorithm()`	Calculates the histogram.
`void`	`runData(int bins, int VOINum)`	Calculates the histogram and outputs the number of counts per bin and area/volume information.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

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

- Field Detail
  - WHOLE_IMAGE
```
private static final int WHOLE_IMAGE
```
    See Also:
    
    Constant Field Values
  - TOTAL_VOIS
```
private static final int TOTAL_VOIS
```
    See Also:
    
    Constant Field Values
  - SEPARATE_VOIS
```
private static final int SEPARATE_VOIS
```
    See Also:
    
    Constant Field Values
  - dataOutput
```
private boolean dataOutput
```
    Flag indicating whether or not histogram data is output to the data window.
  - entireImage
```
private boolean entireImage
```
    If true the histogram should be calculated for the entire image.
  - highValue
```
private double[] highValue
```
    DOCUMENT ME!
  - histoBuffer
```
private int[] histoBuffer
```
    DOCUMENT ME!
  - histogram
```
private ModelHistogram histogram
```
    Reference to the histogram storage object.
  - image
```
private ModelImage image
```
    Reference to the image.
  - lowValue
```
private double[] lowValue
```
    DOCUMENT ME!
  - RGBOffset
```
private int RGBOffset
```
    Indicates which channel of the RGB image the histogram should be calculated. 1 = Red channel 2 = Green channel 3 = Blue channel
  - summaryBins
```
private int summaryBins
```
    Used to indicate the number of histogram bins when using the constructors that do NOT pass in the histogram object.
  - displayGraph
```
private boolean displayGraph
```
  - userLimits
```
private boolean userLimits
```
  - userMin
```
private double userMin
```
  - userMax
```
private double userMax
```
  - processMode
```
private int processMode
```
- Constructor Detail
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins)
```
    Constructs the histogram calculation object for an image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelHistogram histogram,
                          ModelImage image,
                          boolean maskFlag)
```
    Constructs the histogram calculation object.
    
    Parameters:
    
    histogram - model of a histogram
    
    image - model of the source image
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          boolean maskFlag)
```
    Constructs the histogram calculation object for an image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          int processMode,
                          boolean displayGraph,
                          boolean userLimits,
                          float userMin,
                          float userMax)
```
    Constructs the histogram calculation object for an image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    processMode - WHOLE_IMAGE, TOTAL_VOIS, or SEPARATE_VOIS
    
    displayGraph - If true, produces a graph for display
    
    userLimits - If true, histogram goes from userMin to userMax instead of image.getMin() to image.getMax()
    
    userMin -
    
    usermax -
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          boolean maskFlag,
                          boolean displayGraph,
                          boolean userLimits,
                          double userMin,
                          double userMax)
```
    Constructs the histogram calculation object for an image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
    
    displayGraph - If true, produces a graph for display
    
    userLimits - If true, histogram goes from userMin to userMax instead of image.getMin() to image.getMax()
    
    userMin -
    
    usermax -
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          int RGBOffset)
```
    Constructs the histogram calculation object for an RGB image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    RGBOffset - correct offset for RED = 1 , GREEN = 2, or BLUE = 3 component to be exported
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelHistogram histogram,
                          int RGBOffset,
                          ModelImage image,
                          boolean maskFlag)
```
    Constructs the histogram calculation object for an RGB image.
    
    Parameters:
    
    histogram - model of a histogram for a RGB component
    
    RGBOffset - correct offset for RED = 1 , GREEN = 2, or BLUE = 3 component to be exported
    
    image - model of the source image
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          int RGBOffset,
                          boolean maskFlag)
```
    Constructs the histogram calculation object for an RGB image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    RGBOffset - correct offset for RED = 1 , GREEN = 2, or BLUE = 3 component to be exported
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          int RGBOffset,
                          int processMode,
                          boolean displayGraph,
                          boolean userLimits,
                          float userMin,
                          float userMax)
```
    Constructs the histogram calculation object for an RGB image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    RGBOffset - correct offset for RED = 1 , GREEN = 2, or BLUE = 3 component to be exported
    
    processMode - WHOLE_IMAGE, TOTAL_VOIS, or SEPARATE_VOIS
    
    displayGraph - If true, produces a graph for display * @param userLimits If true, histogram goes from userMin to userMax instead of image.getMin() to image.getMax()
    
    userMin -
    
    usermax -
  - AlgorithmHistogram
```
public AlgorithmHistogram(ModelImage image,
                          int summaryBins,
                          int RGBOffset,
                          boolean maskFlag,
                          boolean displayGraph,
                          boolean userLimits,
                          double userMin,
                          double userMax)
```
    Constructs the histogram calculation object for an RGB image.
    
    Parameters:
    
    image - ModelImage the image
    
    summaryBins - number of bins in the histogram
    
    RGBOffset - correct offset for RED = 1 , GREEN = 2, or BLUE = 3 component to be exported
    
    maskFlag - Flag that indicates that the histogram will be calculated for the whole image if equal to true
    
    displayGraph - If true, produces a graph for display * @param userLimits If true, histogram goes from userMin to userMax instead of image.getMin() to image.getMax()
    
    userMin -
    
    usermax -
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    Dispose of local variables.
  - entireImage
```
public void entireImage(boolean flag)
```
    Sets a flag to indicate if the histogram is to be calculated for the entire image or just the VOI.
    
    Parameters:
    
    flag - true = histogram of entire image, false = histogram of VOI
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getHighValue
```
public double[] getHighValue()
```
    DOCUMENT ME!
    
    Returns:
    
    double[]
  - getHistoBuffer
```
public int[] getHistoBuffer()
```
    The buffer of all histogram values.
    
    Returns:
    
    int[]
  - getLowValue
```
public double[] getLowValue()
```
    DOCUMENT ME!
    
    Returns:
    
    double[]
  - getModelHistogram
```
public ModelHistogram getModelHistogram()
```
    Accessor to the histogram.
    
    Returns:
    
    returns the model of the histogram
  - runAlgorithm
```
public void runAlgorithm()
```
    Calculates the histogram.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - runData
```
public void runData(int bins,
                    int VOINum)
```
    Calculates the histogram and outputs the number of counts per bin and area/volume information.
    
    Parameters:
    
    bins - number of bins in the histogram
  - entropySplit
```
private int entropySplit(int[] hist)
```
    Calculate maximum entropy split of a histogram. This method is very similar to Otsu's method. Rather than maximising the inter-class variance, it maximizes the inter-class entropy. Entropy is a measure of the uncertainity of an event taking place. You can calculate it as: S = -(sum)p*log2(p) so it is very straightforward to do using the histogram data. (p is the probability of a pixel greyscale value in the image, and (sum) is the greek capital sigma. It is customary to use log in base 2. P.K. Sahoo, S. Soltani, K.C. Wong and, Y.C. Chen "A Survey of Thresholding Techniques", Computer Vision, Graphics, and Image Processing, Vol. 41, pp.233-260, 1988.
    
    Parameters:
    
    hist - histogram to be thresholded.
    
    Returns:
    
    index of the maximum entropy split.`
    
    Throws:
    
    java.lang.IllegalArgumentException - DOCUMENT ME!
  - otsuThreshold
```
private int otsuThreshold(ModelImage image,
                          int[] histoBuffer)
```
    This algorithm is an implementation of Otsu thresholding technique based on the minimization of inter-class variance [otsu79].
    
    Parameters:
    
    image - DOCUMENT ME!
    
    histoBuffer - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!

Class AlgorithmHistogram

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

WHOLE_IMAGE

TOTAL_VOIS

SEPARATE_VOIS

dataOutput

entireImage

highValue

histoBuffer

histogram

image

lowValue

RGBOffset

summaryBins

displayGraph

userLimits

userMin

userMax

processMode

Constructor Detail

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

AlgorithmHistogram

Method Detail

disposeLocal

entireImage

finalize

getHighValue

getHistoBuffer

getLowValue

getModelHistogram

runAlgorithm

runData

entropySplit

otsuThreshold