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

All Implemented Interfaces:

VOIStatisticList, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmVOIProps
extends AlgorithmBase
implements VOIStatisticList
```
This class calculates a properties of an image defined by a VOI. Attributes include: volume, area, number of pixels, center of mass, average pixel intensity, standard deviation of intensity, eccentricity, principalAxis, coefficient of skewness, and coefficient of kurtosis.

Version:

0.1 Feb 11, 1998

Author:

Matthew J. McAuliffe, Ph.D. Calculates and prepares for display image statistics generated on closed VOI Contours. The contours can exist on any of the three orthogonal image slices. The user can select to display the contour statistics sorted by contour, contour and slice, slice (contours are summed over a slice), or by a total sum. Depending on the type of output selected by the user the contours are displayed with the following information tags: By contour : Name, ID By contour & slice: Name, orientation, slice, ID By slice only: Name, orientation; slice By total VOI: Name Most of the statistics are generated by iterating through the set of voxels that are contained within the closed contour. These statistic calculations take advantage of the information that is generated with the VOIBase.getMask() function and stored inside the VOIBase class. Because the information is generated once at the start of the calculation and stored, the performance for all statistic calculations is improved. When the VOIBase.getMask() function is called the following information is stored in the VOIBase class: BitSet mask of voxels inside the closed contour Vector list of voxel positions inside the closed contour Geometric Center of the contour. The following statistics can be derived directly from the stored information: -- number of voxels -- area -- volume -- min, max, sum, average intensity -- median, mode, mode count -- standard deviation, coefficient of skewness, coefficient of kurtosis, center of mass -- geometric center When the AlgorithmVOIProps is instantiated from a dialog, the user is able to select the statistics to calculate. The list of selected statistics is passed to the AlgorithmVOIProps and only the statistics requested by the user are calculated. When AlgorithmVOIProps is accessed through another algorithm, all statistics are automatically calculated. Median statistics (median, mode, mode count) are calculated in a function that takes the list of voxels as input, can be used on a single contour or on a group of contours. Standard deviation statistics are calculated in a function that takes the list of voxel positions, can be used on a single contour or on a group of contours.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmVOIProps.Calc34D
- 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 VOI`	`activeVOI`	The VOI on which to perform the calculations.
`private java.lang.ThreadGroup`	`calcGroup`	The top-level group of threads used for calculating.
`private int`	`consecutiveNegativeNeeded`
`protected boolean`	`distanceFlag`	Whether or not to calculate largest distance (only 3D), true by default
`protected boolean`	`doOnlyActiveContours`	Boolean for if the algorithm should ONLY check active contours
`private double`	`negativeCurvatureNeeded`
`private double`	`negativeHysteresisFraction`
`protected java.text.DecimalFormat`	`nf`	Formatting for float values into strings.
`protected java.text.DecimalFormat`	`nfe`
`private double`	`positiveHysteresisFraction`
`static int`	`PROCESS_PER_CONTOUR`	Algorithm maintains separate statistics per contour
`static int`	`PROCESS_PER_SLICE`	Algorithm sums all statistics from each contour on the same slice
`static int`	`PROCESS_PER_SLICE_AND_CONTOUR`	Algorithm maintains separate statistics per contour and denotes the slice of each contour
`static int`	`PROCESS_PER_VOI`	Algorithm sums all statistics for the entire VOI
`protected int`	`processType`	How the VOI calculations should be performed (entire, contour, slice).
`protected java.util.Vector<VOIStatisticalProperties>`	`propertyList`	Vector to hold all properties calculated within the algorithm for later access.
`protected JPanelPixelExclusionSelector.RangeType`	`rangeFlag`	Specifies how a range of pixels is excluded from VOI calculations.
`protected ViewVOIVector`	`selectedVOIset`	Vector of all VOIs that will have calculations performed.
`protected boolean`	`showTotals`	Whether or not to show totals for each calculation.
`protected boolean`	`sliceDistanceFlag`	Whether or not to calculate largest slice distance, true by default
`private boolean`	`smoothCurvature`
`protected boolean[]`	`statsList`

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

Fields inherited from interface gov.nih.mipav.model.structures.VOIStatisticList
areaDescription, asymmetryIndexDescription, avgIntensity, axisDescription, circularityDescription, deviationDescription, eccentricityDescription, fractalDimensionBoxCountDescription, fractalDimensionEuclideanDistanceDescription, geometricCenterDescription, invariantMoment1Description, invariantMoment2Description, invariantMoment3Description, invariantMoment4Description, invariantMoment5Description, invariantMoment6Description, invariantMoment7Description, kurtosisDescription, largestDistanceDescription, largestSliceDistanceDescription, majorAxisDescription, massCenterDescription, maxIntensity, maxWidthDescription, meanCurvatureDescription, meanNegativeCurvatureDescription, median, minIntensity, minorAxisDescription, mode, modeCount, numberOfIndentationsCurvatureDescription, numberOfIndentationsHullDescription, numberOfStatistics, perimeterDescription, quantityDescription, skewnessDescription, solidityDescription, statisticDescription, stdDevCurvatureDescription, sumIntensities, surfaceAreaDescription, volumeDescription

Constructor Summary

Constructors
Constructor	Description
`AlgorithmVOIProps(ModelImage srcImg, int pType, JPanelPixelExclusionSelector.RangeType rangeFlag, ViewVOIVector voiSet)`	constructor. note that if there are no VOIs to act on, this constructor returns quietly.
`AlgorithmVOIProps(ModelImage srcImg, int processType, ViewVOIVector voiSet)`	constructor.
`AlgorithmVOIProps(ModelImage srcImg, ViewVOIVector voiSet)`	constructor. sets the source image of the algorithm, and presets the algorithm to calculate properties of 3D images as a volume of interest, rather than by slice.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected java.lang.String`	`addScannerLabels(java.lang.String baseString, WildMagic.LibFoundation.Mathematics.Vector3f currentPt)`	DOCUMENT ME!
`void`	`finalize()`	Prepares this class for destruction.
`float`	`getArea()`	Gets the area of the VOI; return area defined by the VOI.
`java.lang.String`	`getAsymmetryIndex()`
`float`	`getAvgInten()`	Gets the average intensity of the VOI return average intensity of image defined by the VOI.
`float`	`getAvgIntenB()`	Gets the average intensity of the Blue channel of VOI return average intensity of the Blue channel of image defined by the VOI.
`float`	`getAvgIntenG()`	Gets the average intensity of the Green channel of VOI return average intensity of the Green channel of image defined by the VOI.
`float`	`getAvgIntenR()`	Gets the average intensity of the Red channel of VOI return average intensity of the Red channel of image defined by the VOI.
`java.lang.String`	`getCenterOfMass()`	Gets the the center of mass of the VOI ; return center of mass defined by the VOI.
`java.lang.String`	`getCenterOfMassB()`	Gets the the blue center of mass of the VOI ; return blue center of mass defined by the VOI.
`java.lang.String`	`getCenterOfMassG()`	Gets the the green center of mass of the VOI ; return green center of mass defined by the VOI.
`java.lang.String`	`getCenterOfMassR()`	Gets the the red center of mass of the VOI ; return red center of mass defined by the VOI.
`java.lang.String`	`getCircularity()`	Gets the circularity of the VOI.
`float`	`getEccentricity()`	Gets the eccentricity of the VOI: 1 = line, 0 = circle; return eccentricity of the VOI.
`double`	`getFractalDimensionBoxCount()`
`double`	`getFractalDimensionEuclideanDistance()`
`java.lang.String`	`getGeometricCenter()`	Gets the the geometric center of the VOI ; return geometric center defined by the VOI.
`float`	`getKurtosis()`	Gets the coefficient of kurtosis of the pixel values in the VOI
`float`	`getKurtosisB()`	Gets the coefficient of kurtosis of the blue pixel values in the VOI
`float`	`getKurtosisG()`	Gets the coefficient of kurtosis of the green pixel values in the VOI
`float`	`getKurtosisR()`	Gets the coefficient of kurtosis of the red pixel values in the VOI
`java.lang.String`	`getLargestDistance()`	Gets the largest line segment totally contained within a 3D VOI (in terms of res).
`java.lang.String`	`getLargestSliceDistance()`	Gets the largest line segment totally contained within a VOI slice (in terms of res).
`float`	`getMajorAxis()`	Gets the major axis of VOI (only valid for 2D object); return major axis length of the VOI.
`float`	`getMaxIntensity()`	Gets the maximum intensity of the VOI return average intensity of image defined by the VOI.
`float`	`getMaxIntensityBlue()`	Gets the maximum intensity of the Blue channel for the VOI return average intensity of image defined by the VOI.
`float`	`getMaxIntensityGreen()`	Gets the maximum intensity of the Green channel for the VOI return average intensity of image defined by the VOI.
`float`	`getMaxIntensityRed()`	Gets the maximum intensity of the Red channel for the VOI return average intensity of image defined by the VOI.
`java.lang.String`	`getMeanCurvature()`
`java.lang.String`	`getMeanNegativeCurvature()`
`float`	`getMedian()`	Gets the median
`float`	`getMedianB()`	Gets the median of the Blue channel of image defined by the VOI.
`float`	`getMedianG()`	Gets the median of the Green channel of image defined by the VOI.
`float`	`getMedianR()`	Gets the median of the Red channel of image defined by the VOI.
`float`	`getMinIntensity()`	Gets the minimum intensity of the VOI return average intensity of image defined by the VOI.
`float`	`getMinIntensityBlue()`	Gets the minimum intensity of the Blue channel for the VOI return average intensity of image defined by the VOI.
`float`	`getMinIntensityGreen()`	Gets the minimum intensity of the Green channel for the VOI return average intensity of image defined by the VOI.
`float`	`getMinIntensityRed()`	Gets the minimum intensity of the Red channel for the VOI return average intensity of image defined by the VOI.
`float`	`getMinorAxis()`	Gets the minor axis of VOI (only valid for 2D object); return minor axis length of the VOI.
`float`	`getMode()`	Gets the mode
`float`	`getModeB()`	Gets the mode of the Blue channel of image defined by the VOI.
`int`	`getModeCount()`	Gets the mode
`int`	`getModeCountB()`	Gets the mode of the Blue channel of image defined by the VOI.
`int`	`getModeCountG()`	Gets the mode of the Green channel of image defined by the VOI.
`int`	`getModeCountR()`	Gets the mode of the Red channel of image defined by the VOI.
`float`	`getModeG()`	Gets the mode of the Green channel of image defined by the VOI.
`float`	`getModeR()`	Gets the mode of the Red channel of image defined by the VOI.
`java.lang.String`	`getNumberOfIndentationsCurvture()`
`java.lang.String`	`getNumberOfIndentationsHull()`
`int`	`getNVoxels()`	Gets the the number of pixels return number of pixels defined by the VOI.
`java.lang.String`	`getPerimeter()`	Gets the perimeter of the VOI (in terms of res).
`float`	`getPrincipalAxis()`	Gets the principle axis of VOI (only valid for 2D object); return pricipal axis angle of the VOI.
`int`	`getProcessType()`	Reports if algorithm is performing calcs per slice, per contour, or for entire VOI.
`java.lang.String[]`	`getScannerPositionLabels(WildMagic.LibFoundation.Mathematics.Vector3f position)`	Gets position data to display in message bar - for DICOM and MINC images, gives patient position as well.
`float`	`getSkewness()`	Gets the coefficient of skewness of the pixel values in the VOI
`float`	`getSkewnessB()`	Gets the coefficient of skewness of the blue pixel values in the VOI
`float`	`getSkewnessG()`	Gets the coefficient of skewness of the green pixel values in the VOI
`float`	`getSkewnessR()`	Gets the coefficient of skewness of the red pixel values in the VOI
`java.lang.String`	`getSolidity()`	Gets the solidity of the VOI.
`float`	`getStdDev()`	Gets the standard deviation of image intensities return standard deviation of image intensities defined by the VOI.
`float`	`getStdDevB()`	Gets the get standard deviation of image intensities (blue channel) return standard deviation of image intensities defined by the VOI.
`java.lang.String`	`getStdDevCurvature()`
`float`	`getStdDevG()`	Gets the standard deviation of image intensities (green channel) return standard deviation of image intensities defined by the VOI.
`float`	`getStdDevR()`	Gets the standard deviation of image intensities (red channel) return standard deviation of image intensities defined by the VOI.
`float`	`getSumIntensities()`	Gets the sum of image intensities defined by the VOI
`float`	`getSumIntensitiesB()`	Gets the sum of blue channel mage intensities defined by the VOI
`float`	`getSumIntensitiesG()`	Gets the sum of green channel image intensities defined by the VOI
`float`	`getSumIntensitiesR()`	Gets the sum of red channel image intensities defined by the VOI
`float`	`getSurfaceArea()`	Gets the surfaceArea of the VOI; return surfaceArea defined by the VOI.
`ViewVOIVector`	`getVOIList()`	gets the selected VOIset
`VOIStatisticalProperties`	`getVOIProperties(VOI aVOI)`	DOCUMENT ME!
`float`	`getVolume()`	Gets the volume of the VOI; return volume defined by the VOI.
`protected int`	`indexOf(java.lang.String statistic)`
`private void`	`initialiseDataHolders(int numberOfVOIs)`	DOCUMENT ME!
`boolean`	`isColor()`	Accessor that indicates if the source image is a color image.
`java.lang.String[]`	`makeStatisticListDescriptions()`	Creates the list of labels to use in the checkboxes.
`void`	`runAlgorithm()`	Begins execution of the software.
`void`	`setConsecutiveNegativeNeeded(int consecutiveNegativeNeeded)`
`void`	`setDistanceFlag(boolean distanceFlag)`	Sets whether the largest distance is calculated.
`void`	`setDoOnlyActiveContours(boolean doActive)`	Sets the flag for calculating totals ONLY for active contours
`void`	`setNegativeCurvatureNeeded(double negativeCurvatureNeeded)`
`void`	`setNegativeHysteresisFraction(double negativeHysteresisFraction)`
`void`	`setPositiveHysteresisFraction(double positiveHysteresisFraction)`
`void`	`setPrecisionDisplay(int numDecimal, boolean doForce)`	Sets the String float formatter to trim to numDecimal number of decimals.
`void`	`setSelectedStatistics(boolean[] checkList)`	Sets the list of selected statistics to calculate.
`void`	`setSelectedVOI(VOI aVOI)`	DOCUMENT ME!
`void`	`setShowTotals(boolean totals)`	tells the algorithm to total the property calculations.
`void`	`setSliceDistanceFlag(boolean sliceDistanceFlag)`	Sets whether the largest slice distance is calculated.
`void`	`setSmoothCurvature(boolean smoothCurvature)`
`void`	`setVOIList(ViewVOIVector vvv)`	sets the selected VOIset and the data set data storage sizes based on the number of curves in the Vector.
`void`	`setVOIList(javax.swing.ListModel list)`	DOCUMENT ME!

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
  - smoothCurvature
```
private boolean smoothCurvature
```
  - negativeHysteresisFraction
```
private double negativeHysteresisFraction
```
  - positiveHysteresisFraction
```
private double positiveHysteresisFraction
```
  - consecutiveNegativeNeeded
```
private int consecutiveNegativeNeeded
```
  - negativeCurvatureNeeded
```
private double negativeCurvatureNeeded
```
  - PROCESS_PER_VOI
```
public static final int PROCESS_PER_VOI
```
    Algorithm sums all statistics for the entire VOI
    
    See Also:
    
    Constant Field Values
  - PROCESS_PER_SLICE_AND_CONTOUR
```
public static final int PROCESS_PER_SLICE_AND_CONTOUR
```
    Algorithm maintains separate statistics per contour and denotes the slice of each contour
    
    See Also:
    
    Constant Field Values
  - PROCESS_PER_SLICE
```
public static final int PROCESS_PER_SLICE
```
    Algorithm sums all statistics from each contour on the same slice
    
    See Also:
    
    Constant Field Values
  - PROCESS_PER_CONTOUR
```
public static final int PROCESS_PER_CONTOUR
```
    Algorithm maintains separate statistics per contour
    
    See Also:
    
    Constant Field Values
  - activeVOI
```
private VOI activeVOI
```
    The VOI on which to perform the calculations.
  - nf
```
protected java.text.DecimalFormat nf
```
    Formatting for float values into strings.
  - nfe
```
protected java.text.DecimalFormat nfe
```
  - processType
```
protected int processType
```
    How the VOI calculations should be performed (entire, contour, slice).
  - propertyList
```
protected java.util.Vector<VOIStatisticalProperties> propertyList
```
    Vector to hold all properties calculated within the algorithm for later access.
  - rangeFlag
```
protected JPanelPixelExclusionSelector.RangeType rangeFlag
```
    Specifies how a range of pixels is excluded from VOI calculations.
  - sliceDistanceFlag
```
protected boolean sliceDistanceFlag
```
    Whether or not to calculate largest slice distance, true by default
  - distanceFlag
```
protected boolean distanceFlag
```
    Whether or not to calculate largest distance (only 3D), true by default
  - selectedVOIset
```
protected ViewVOIVector selectedVOIset
```
    Vector of all VOIs that will have calculations performed.
  - showTotals
```
protected boolean showTotals
```
    Whether or not to show totals for each calculation.
  - doOnlyActiveContours
```
protected boolean doOnlyActiveContours
```
    Boolean for if the algorithm should ONLY check active contours
  - calcGroup
```
private java.lang.ThreadGroup calcGroup
```
    The top-level group of threads used for calculating.
  - statsList
```
protected boolean[] statsList
```
- Constructor Detail
  - AlgorithmVOIProps
```
public AlgorithmVOIProps(ModelImage srcImg,
                         int pType,
                         JPanelPixelExclusionSelector.RangeType rangeFlag,
                         ViewVOIVector voiSet)
```
    constructor. note that if there are no VOIs to act on, this constructor returns quietly.
    
    Parameters:
    
    srcImg - image model that contain the VOI
    
    pType - list of items to perform the statistics operations on
    
    rangeFlag - Whether the range of values specified by the statistics generator should be ignored
    
    voiSet - The VOIs that will be calculated
  - AlgorithmVOIProps
```
public AlgorithmVOIProps(ModelImage srcImg,
                         int processType,
                         ViewVOIVector voiSet)
```
    constructor.
    
    Parameters:
    
    srcImg - image model that contain the VOI
    
    processType - perform the property calculations for each slice, rather than for whole volume of interest
    
    voiSet - The VOIs that will be calculated
  - AlgorithmVOIProps
```
public AlgorithmVOIProps(ModelImage srcImg,
                         ViewVOIVector voiSet)
```
    constructor. sets the source image of the algorithm, and presets the algorithm to calculate properties of 3D images as a volume of interest, rather than by slice.
    
    Parameters:
    
    srcImg - image model that contain the VOI
    
    voiSet - The VOIs that will be calculated
- Method Detail
  - setSmoothCurvature
```
public void setSmoothCurvature(boolean smoothCurvature)
```
  - setNegativeHysteresisFraction
```
public void setNegativeHysteresisFraction(double negativeHysteresisFraction)
```
  - setPositiveHysteresisFraction
```
public void setPositiveHysteresisFraction(double positiveHysteresisFraction)
```
  - setConsecutiveNegativeNeeded
```
public void setConsecutiveNegativeNeeded(int consecutiveNegativeNeeded)
```
  - setNegativeCurvatureNeeded
```
public void setNegativeCurvatureNeeded(double negativeCurvatureNeeded)
```
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getArea
```
public float getArea()
```
    Gets the area of the VOI; return area defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getSurfaceArea
```
public float getSurfaceArea()
```
    Gets the surfaceArea of the VOI; return surfaceArea defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getAvgInten
```
public float getAvgInten()
```
    Gets the average intensity of the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getAvgIntenB
```
public float getAvgIntenB()
```
    Gets the average intensity of the Blue channel of VOI return average intensity of the Blue channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getAvgIntenG
```
public float getAvgIntenG()
```
    Gets the average intensity of the Green channel of VOI return average intensity of the Green channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getAvgIntenR
```
public float getAvgIntenR()
```
    Gets the average intensity of the Red channel of VOI return average intensity of the Red channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getCenterOfMass
```
public java.lang.String getCenterOfMass()
```
    Gets the the center of mass of the VOI ; return center of mass defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getCenterOfMassB
```
public java.lang.String getCenterOfMassB()
```
    Gets the the blue center of mass of the VOI ; return blue center of mass defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getCenterOfMassG
```
public java.lang.String getCenterOfMassG()
```
    Gets the the green center of mass of the VOI ; return green center of mass defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getCenterOfMassR
```
public java.lang.String getCenterOfMassR()
```
    Gets the the red center of mass of the VOI ; return red center of mass defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getEccentricity
```
public float getEccentricity()
```
    Gets the eccentricity of the VOI: 1 = line, 0 = circle; return eccentricity of the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getGeometricCenter
```
public java.lang.String getGeometricCenter()
```
    Gets the the geometric center of the VOI ; return geometric center defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getKurtosis
```
public float getKurtosis()
```
    Gets the coefficient of kurtosis of the pixel values in the VOI
    
    Returns:
  - getKurtosisB
```
public float getKurtosisB()
```
    Gets the coefficient of kurtosis of the blue pixel values in the VOI
    
    Returns:
  - getKurtosisG
```
public float getKurtosisG()
```
    Gets the coefficient of kurtosis of the green pixel values in the VOI
    
    Returns:
  - getKurtosisR
```
public float getKurtosisR()
```
    Gets the coefficient of kurtosis of the red pixel values in the VOI
    
    Returns:
  - getLargestDistance
```
public java.lang.String getLargestDistance()
```
    Gets the largest line segment totally contained within a 3D VOI (in terms of res). If this unexpectedly returns zero, make sure you have not inadvertently set distanceFlag to false.
    
    Returns:
    
    String largest distance string
  - getLargestSliceDistance
```
public java.lang.String getLargestSliceDistance()
```
    Gets the largest line segment totally contained within a VOI slice (in terms of res). If this unexpectedly returns zero, make sure you have not inadvertently set sliceDistanceFlag to false.
    
    Returns:
    
    String largest slice distance string
  - getMajorAxis
```
public float getMajorAxis()
```
    Gets the major axis of VOI (only valid for 2D object); return major axis length of the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMaxIntensity
```
public float getMaxIntensity()
```
    Gets the maximum intensity of the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMaxIntensityBlue
```
public float getMaxIntensityBlue()
```
    Gets the maximum intensity of the Blue channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMaxIntensityGreen
```
public float getMaxIntensityGreen()
```
    Gets the maximum intensity of the Green channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMaxIntensityRed
```
public float getMaxIntensityRed()
```
    Gets the maximum intensity of the Red channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMedian
```
public float getMedian()
```
    Gets the median
    
    Returns:
    
    DOCUMENT ME!
  - getMedianB
```
public float getMedianB()
```
    Gets the median of the Blue channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMedianG
```
public float getMedianG()
```
    Gets the median of the Green channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMedianR
```
public float getMedianR()
```
    Gets the median of the Red channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMinIntensity
```
public float getMinIntensity()
```
    Gets the minimum intensity of the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMinIntensityBlue
```
public float getMinIntensityBlue()
```
    Gets the minimum intensity of the Blue channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMinIntensityGreen
```
public float getMinIntensityGreen()
```
    Gets the minimum intensity of the Green channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMinIntensityRed
```
public float getMinIntensityRed()
```
    Gets the minimum intensity of the Red channel for the VOI return average intensity of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMinorAxis
```
public float getMinorAxis()
```
    Gets the minor axis of VOI (only valid for 2D object); return minor axis length of the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getMode
```
public float getMode()
```
    Gets the mode
    
    Returns:
    
    DOCUMENT ME!
  - getModeB
```
public float getModeB()
```
    Gets the mode of the Blue channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getModeCount
```
public int getModeCount()
```
    Gets the mode
    
    Returns:
    
    DOCUMENT ME!
  - getModeCountB
```
public int getModeCountB()
```
    Gets the mode of the Blue channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getModeCountG
```
public int getModeCountG()
```
    Gets the mode of the Green channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getModeCountR
```
public int getModeCountR()
```
    Gets the mode of the Red channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getModeG
```
public float getModeG()
```
    Gets the mode of the Green channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getModeR
```
public float getModeR()
```
    Gets the mode of the Red channel of image defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getNVoxels
```
public int getNVoxels()
```
    Gets the the number of pixels return number of pixels defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getPerimeter
```
public java.lang.String getPerimeter()
```
    Gets the perimeter of the VOI (in terms of res).
    
    Returns:
    
    String perimeter string
  - getCircularity
```
public java.lang.String getCircularity()
```
    Gets the circularity of the VOI.
    
    Returns:
    
    String circularity string
  - getSolidity
```
public java.lang.String getSolidity()
```
    Gets the solidity of the VOI.
    
    Returns:
    
    String solidity string
  - getNumberOfIndentationsCurvture
```
public java.lang.String getNumberOfIndentationsCurvture()
```
  - getNumberOfIndentationsHull
```
public java.lang.String getNumberOfIndentationsHull()
```
  - getMeanCurvature
```
public java.lang.String getMeanCurvature()
```
    Returns:
  - getStdDevCurvature
```
public java.lang.String getStdDevCurvature()
```
    Returns:
  - getMeanNegativeCurvature
```
public java.lang.String getMeanNegativeCurvature()
```
    Returns:
  - getAsymmetryIndex
```
public java.lang.String getAsymmetryIndex()
```
  - getPrincipalAxis
```
public float getPrincipalAxis()
```
    Gets the principle axis of VOI (only valid for 2D object); return pricipal axis angle of the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getFractalDimensionBoxCount
```
public double getFractalDimensionBoxCount()
```
  - getFractalDimensionEuclideanDistance
```
public double getFractalDimensionEuclideanDistance()
```
  - getProcessType
```
public int getProcessType()
```
    Reports if algorithm is performing calcs per slice, per contour, or for entire VOI.
    
    Returns:
    
    processType (int for process type)
  - getScannerPositionLabels
```
public java.lang.String[] getScannerPositionLabels(WildMagic.LibFoundation.Mathematics.Vector3f position)
```
    Gets position data to display in message bar - for DICOM and MINC images, gives patient position as well. The image's associated transformation must be FileInfoBase.TRANSFORM_SCANNER_ANATOMICAL, or the orientations must be set up correctly, or else the function returns null.
    
    Parameters:
    
    image - The image the point lies within.
    
    position - (x,y,z(slice)) position in FileCoordinates
    
    Returns:
    
    An array of strings that represent patient position.
  - getSkewness
```
public float getSkewness()
```
    Gets the coefficient of skewness of the pixel values in the VOI
    
    Returns:
  - getSkewnessB
```
public float getSkewnessB()
```
    Gets the coefficient of skewness of the blue pixel values in the VOI
    
    Returns:
  - getSkewnessG
```
public float getSkewnessG()
```
    Gets the coefficient of skewness of the green pixel values in the VOI
    
    Returns:
  - getSkewnessR
```
public float getSkewnessR()
```
    Gets the coefficient of skewness of the red pixel values in the VOI
    
    Returns:
  - getStdDev
```
public float getStdDev()
```
    Gets the standard deviation of image intensities return standard deviation of image intensities defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getStdDevB
```
public float getStdDevB()
```
    Gets the get standard deviation of image intensities (blue channel) return standard deviation of image intensities defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getStdDevG
```
public float getStdDevG()
```
    Gets the standard deviation of image intensities (green channel) return standard deviation of image intensities defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getStdDevR
```
public float getStdDevR()
```
    Gets the standard deviation of image intensities (red channel) return standard deviation of image intensities defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - getSumIntensities
```
public float getSumIntensities()
```
    Gets the sum of image intensities defined by the VOI
    
    Returns:
  - getSumIntensitiesB
```
public float getSumIntensitiesB()
```
    Gets the sum of blue channel mage intensities defined by the VOI
    
    Returns:
  - getSumIntensitiesG
```
public float getSumIntensitiesG()
```
    Gets the sum of green channel image intensities defined by the VOI
    
    Returns:
  - getSumIntensitiesR
```
public float getSumIntensitiesR()
```
    Gets the sum of red channel image intensities defined by the VOI
    
    Returns:
  - getVOIProperties
```
public VOIStatisticalProperties getVOIProperties(VOI aVOI)
```
    DOCUMENT ME!
    
    Parameters:
    
    aVOI - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getVolume
```
public float getVolume()
```
    Gets the volume of the VOI; return volume defined by the VOI.
    
    Returns:
    
    DOCUMENT ME!
  - isColor
```
public boolean isColor()
```
    Accessor that indicates if the source image is a color image.
    
    Returns:
    
    true if the image is a color image.
  - makeStatisticListDescriptions
```
public java.lang.String[] makeStatisticListDescriptions()
```
    Creates the list of labels to use in the checkboxes.
    
    Returns:
    
    DOCUMENT ME!
  - runAlgorithm
```
public void runAlgorithm()
```
    Begins execution of the software.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setDistanceFlag
```
public void setDistanceFlag(boolean distanceFlag)
```
    Sets whether the largest distance is calculated. Defaults to true, set to false if VOI will not complete.
    
    Parameters:
    
    distanceFlag -
  - setDoOnlyActiveContours
```
public void setDoOnlyActiveContours(boolean doActive)
```
    Sets the flag for calculating totals ONLY for active contours
    
    Parameters:
    
    doActive -
  - setPrecisionDisplay
```
public void setPrecisionDisplay(int numDecimal,
                                boolean doForce)
```
    Sets the String float formatter to trim to numDecimal number of decimals.
    
    Parameters:
    
    numDecimal - int number of decimals
    
    doForce - boolean force numDecimal or allow zero
  - setSelectedStatistics
```
public void setSelectedStatistics(boolean[] checkList)
```
    Sets the list of selected statistics to calculate. Default is to calculate all statistics.
    
    Parameters:
    
    checkList -
  - setSelectedVOI
```
public void setSelectedVOI(VOI aVOI)
```
    DOCUMENT ME!
    
    Parameters:
    
    aVOI - DOCUMENT ME!
  - setShowTotals
```
public void setShowTotals(boolean totals)
```
    tells the algorithm to total the property calculations.
    
    Parameters:
    
    totals - DOCUMENT ME!
  - setSliceDistanceFlag
```
public void setSliceDistanceFlag(boolean sliceDistanceFlag)
```
    Sets whether the largest slice distance is calculated. Defaults to true, set to false if VOI will not complete.
    
    Parameters:
    
    sliceDistanceFlag -
  - setVOIList
```
public void setVOIList(javax.swing.ListModel list)
```
    DOCUMENT ME!
    
    Parameters:
    
    list - DOCUMENT ME!
  - setVOIList
```
public void setVOIList(ViewVOIVector vvv)
```
    sets the selected VOIset and the data set data storage sizes based on the number of curves in the Vector.
    
    Parameters:
    
    vvv - DOCUMENT ME!
  - getVOIList
```
public ViewVOIVector getVOIList()
```
    gets the selected VOIset
    
    Parameters:
    
    vvv - DOCUMENT ME!
  - addScannerLabels
```
protected java.lang.String addScannerLabels(java.lang.String baseString,
                                            WildMagic.LibFoundation.Mathematics.Vector3f currentPt)
```
    DOCUMENT ME!
    
    Parameters:
    
    leadBase - DOCUMENT ME!
  - indexOf
```
protected int indexOf(java.lang.String statistic)
```
  - initialiseDataHolders
```
private void initialiseDataHolders(int numberOfVOIs)
```
    DOCUMENT ME!
    
    Parameters:
    
    numberOfVOIs - DOCUMENT ME!

Class AlgorithmVOIProps

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

Fields inherited from interface gov.nih.mipav.model.structures.VOIStatisticList

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

smoothCurvature

negativeHysteresisFraction

positiveHysteresisFraction

consecutiveNegativeNeeded

negativeCurvatureNeeded

PROCESS_PER_VOI

PROCESS_PER_SLICE_AND_CONTOUR

PROCESS_PER_SLICE

PROCESS_PER_CONTOUR

activeVOI

nf

nfe

processType

propertyList

rangeFlag

sliceDistanceFlag

distanceFlag

selectedVOIset

showTotals

doOnlyActiveContours

calcGroup

statsList

Constructor Detail

AlgorithmVOIProps

AlgorithmVOIProps

AlgorithmVOIProps

Method Detail

setSmoothCurvature

setNegativeHysteresisFraction

setPositiveHysteresisFraction

setConsecutiveNegativeNeeded

setNegativeCurvatureNeeded

finalize

getArea

getSurfaceArea

getAvgInten

getAvgIntenB

getAvgIntenG

getAvgIntenR

getCenterOfMass

getCenterOfMassB

getCenterOfMassG

getCenterOfMassR

getEccentricity

getGeometricCenter

getKurtosis

getKurtosisB

getKurtosisG

getKurtosisR

getLargestDistance

getLargestSliceDistance

getMajorAxis

getMaxIntensity

getMaxIntensityBlue

getMaxIntensityGreen

getMaxIntensityRed

getMedian

getMedianB

getMedianG

getMedianR

getMinIntensity

getMinIntensityBlue

getMinIntensityGreen

getMinIntensityRed

getMinorAxis

getMode

getModeB