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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

Direct Known Subclasses:

AgglomerativeInformationBottleneck, Algorithm4DImageCalculator, AlgorithmActiveContoursWithoutEdges, AlgorithmAdaptiveKuwaharaFilter, AlgorithmAddMargins, AlgorithmAGCIE, AlgorithmAGVF, AlgorithmAHE, AlgorithmAHElocal, AlgorithmAINDANE, AlgorithmAnisotropicDiffusion, AlgorithmAntigradient2, AlgorithmAnyTwoImagesSNR, AlgorithmArcLength, AlgorithmASM, AlgorithmAutoCorrelation, AlgorithmAutoCovariance, AlgorithmAutoSeedWatershed, AlgorithmBarrelDistortion, AlgorithmBilateralFilter, AlgorithmBoundaryAttenuation, AlgorithmBoxCount, AlgorithmBrainExtractor, AlgorithmBrainSurfaceExtractor, AlgorithmBRISK, AlgorithmBSmooth, AlgorithmBSnake, AlgorithmBSpline, AlgorithmBSplineControlPointImageFilter, AlgorithmCannyEdgeDetection, AlgorithmCenterOfMass, AlgorithmCenterOfMassRGB, AlgorithmChangeType, AlgorithmCircleGeneration, AlgorithmCircleToRectangle, AlgorithmCircularSectorToRectangle, AlgorithmCoherenceEnhancingDiffusion, AlgorithmColocalizationEM, AlgorithmColocalizationRegression, AlgorithmColorEdge, AlgorithmColorSaturation, AlgorithmComplexConcat, AlgorithmComplexToReal, AlgorithmConcat, AlgorithmConcatMult, AlgorithmConstELSUNCOpt3D, AlgorithmConstPowellOptBase, AlgorithmConstrainedELSUNCOAR3D, AlgorithmConstrainedOAR3D, AlgorithmContrastEnhancementUsingExposureFusion, AlgorithmConvergenceField, AlgorithmConvert3Dto4D, AlgorithmConvert4Dto3D, AlgorithmConvolver, AlgorithmCorrectSpacing, AlgorithmCrop, AlgorithmCropTilted, AlgorithmCubicLagrangian, AlgorithmCumulativeHistogram, AlgorithmCyclicPermutation, AlgorithmDConvolver, AlgorithmDemonsLite, AlgorithmDEMRI3, AlgorithmDicomOrder, AlgorithmDICOMtoAVI, AlgorithmDistanceFilter, AlgorithmDTI2EGFA, AlgorithmDTIColorDisplay, AlgorithmDTIColorDisplay, AlgorithmDTICreateListFile, AlgorithmDTITract, AlgorithmDualContourSearch, AlgorithmDWI2DTI, AlgorithmEdgeDetection3D, AlgorithmEdgeLaplacian, AlgorithmEdgeLaplacianSep, AlgorithmEdgeNMSuppression, AlgorithmEdgePreservingSmoothing, AlgorithmEfficientWatershed, AlgorithmEllipseGeneration, AlgorithmEllipseToCircle, AlgorithmEllipseToRectangle, AlgorithmEllipticFilter, AlgorithmEllipticFourierDescriptors, AlgorithmELSUNCOpt2D, AlgorithmELSUNCOpt3D, AlgorithmEmbeddedConfidenceEdgeDetection, AlgorithmEntropicEdgeDetection, AlgorithmEntropyMinimization, AlgorithmEvaluateMaskSegmentation, AlgorithmEvaluateSegmentation, AlgorithmExtractSlices, AlgorithmExtractSlicesVolumes, AlgorithmExtractSurface, AlgorithmExtractSurfaceCubes, AlgorithmFaceAnonymizer, AlgorithmFaceAnonymizerBET, AlgorithmFacetModel, AlgorithmFastMarching, AlgorithmFastMarching, AlgorithmFFT, AlgorithmFFT2, AlgorithmFIREEdgeExtraction, AlgorithmFlip, AlgorithmFloodFill, AlgorithmFRAP, AlgorithmFrequencyFilter, AlgorithmFrequencyFilterColor, AlgorithmFRETAcceptorPhotobleach, AlgorithmFRETBleedThrough, AlgorithmFRETEfficiency, AlgorithmFuzzMinDeAndChatterji, AlgorithmFuzzyCMeans, AlgorithmFuzzyConnectednessSegmentation, AlgorithmFuzzyMinimization, AlgorithmGaussianBlur, AlgorithmGaussianBlurSep, AlgorithmGaussianMixtureModelEM, AlgorithmGenerateIsolines, AlgorithmGradientInverseWeightedSmoothing, AlgorithmGradientMagnitude, AlgorithmGradientMagnitudeSep, AlgorithmGraphBasedSegmentation, AlgorithmGrayScaleMorphology25D, AlgorithmGrayScaleMorphology2D, AlgorithmGrayScaleMorphology3D, AlgorithmGuidedFilter, AlgorithmGVF, AlgorithmHaralickTexture, AlgorithmHarrisCornerDetector, AlgorithmHarrisLaplace, AlgorithmHeightFunction, AlgorithmHepticLagrangian, AlgorithmHessian, AlgorithmHilbertTransform, AlgorithmHillClimbingWatershed, AlgorithmHistogram, AlgorithmHistogram2Dim, AlgorithmHistogramMatch, AlgorithmHistogramSliceMatch, AlgorithmHMRF_EM, AlgorithmHoughCardioid, AlgorithmHoughCircle, AlgorithmHoughEllipse, AlgorithmHoughHyperbola, AlgorithmHoughLine, AlgorithmHoughParabola, AlgorithmHurstIndex, AlgorithmIAGCWD, AlgorithmIHN3Correction, AlgorithmImageCalculator, AlgorithmImageHessian, AlgorithmImageMath, AlgorithmIndependentComponents, AlgorithmInsertSlice, AlgorithmInsertVolume, AlgorithmIsophoteCurvature, AlgorithmIteratedBlindDeconvolution, AlgorithmKernelRegression, AlgorithmKMeans, AlgorithmLaplacian, AlgorithmLapMedianess, AlgorithmLawsTexture, AlgorithmLearnFromFailure64, AlgorithmLearnFromFailure64Knees, AlgorithmLevelSet, AlgorithmLevelSetDiffusion, AlgorithmLLE, AlgorithmLocalNormalization, AlgorithmLocalVariance, AlgorithmLogSlopeMapping, AlgorithmLowerCompletion, AlgorithmLuminanceAdaptation, AlgorithmMarkovSegment, AlgorithmMarkovSmooth, AlgorithmMask, AlgorithmMatchForReference, AlgorithmMatchImages, AlgorithmMaximumIntensityProjection, AlgorithmMaximumLikelihoodIteratedBlindDeconvolution, AlgorithmMean, AlgorithmMeanShiftClustering, AlgorithmMeanShiftSegmentation, AlgorithmMedian, AlgorithmMidsagittal, AlgorithmMinimumPerimeterPolygon, AlgorithmMixGaussEM, AlgorithmMode, AlgorithmMorphologicalFilter, AlgorithmMorphology25D, AlgorithmMorphology2D, AlgorithmMorphology3D, AlgorithmMosaicToSlices, AlgorithmMRIShadingCorrection, AlgorithmMSER, AlgorithmMSpectralFuzzyCMeans, AlgorithmMultiExponentialFitting, AlgorithmN4MRIBiasFieldCorrectionFilter, AlgorithmNearlyCircleToCircle, AlgorithmNetworkSnake, AlgorithmNLNoiseReduction, AlgorithmNMSuppression, AlgorithmNoise, AlgorithmNonlocalMeansFilter, AlgorithmNonMaxSuppts, AlgorithmNonparametricSegmentation, AlgorithmObjectExtractor, AlgorithmPbBoundaryDetection, AlgorithmPhaseCongruency, AlgorithmPointArea, AlgorithmPointSetToImageFilter, AlgorithmPowellOptBase, AlgorithmPowerWatershed, AlgorithmPrincipalComponents, AlgorithmProstateBoundaryExt, AlgorithmProstateBoundaryFeature2D, AlgorithmProstateFeatures, AlgorithmProstateFeatures2D, AlgorithmProstateFeaturesSaveAutoTrain, AlgorithmQuantify, AlgorithmQuantifyMask, AlgorithmQuinticLagrangian, AlgorithmRandSliceOrder, AlgorithmRegBSpline, AlgorithmRegChamfer, AlgorithmRegELSUNCOAR25D, AlgorithmRegELSUNCOAR2D, AlgorithmRegELSUNCOAR35D, AlgorithmRegELSUNCOAR3D, AlgorithmRegionGrow, AlgorithmRegionMergingViaBoundaryMelting, AlgorithmRegionsFromPartialBorders, AlgorithmRegLeastSquares, AlgorithmRegOAR25D2, AlgorithmRegOAR2D, AlgorithmRegOAR35D, AlgorithmRegOAR3D, AlgorithmRegPatientPos, AlgorithmRegularizedIsotropicDiffusion, AlgorithmRegValidation, AlgorithmRegVOILandmark, AlgorithmRemoveSlices, AlgorithmRemoveTSlices, AlgorithmReplaceBlankSlicesWithAverages, AlgorithmReplaceRemovedSlices, AlgorithmReplaceSlice, AlgorithmReplaceValue, AlgorithmReslice, AlgorithmRGBConcat, AlgorithmRGBtoGray, AlgorithmRGBtoGrays, AlgorithmRGBtoHSB, AlgorithmRiceWaveletTools, AlgorithmRotate, AlgorithmRuleBasedContrastEnhancement, AlgorithmScaleSaliency, AlgorithmSCDSegmentation, AlgorithmSeparableConvolver, AlgorithmSequentialScanningWatershed, AlgorithmSFTA, AlgorithmShortestPathWatershed, AlgorithmSimulatedExposureFusion, AlgorithmSingleMRIImageSNR, AlgorithmSkullRemoval, AlgorithmSliceAveraging, AlgorithmSM2, AlgorithmSnake, AlgorithmSobel, AlgorithmSpectralClustering, AlgorithmSphereGeneration, AlgorithmSplitAndMergeWatershed, AlgorithmStandardDeviationThreshold, AlgorithmSubsample, AlgorithmSubset, AlgorithmSubtractVOI, AlgorithmSwap34, AlgorithmSwapDims, AlgorithmSwapSlicesVolume, AlgorithmSWI, AlgorithmSymmetricNearestNeighbor, AlgorithmTalairachTransform, AlgorithmTamuraTexture, AlgorithmTextureAnalysis, AlgorithmTextureSegmentation, AlgorithmThinning2D, AlgorithmThresholdDual, AlgorithmThresholdDualRGB, AlgorithmTiltCorrection, AlgorithmTimeFitting, AlgorithmTProcess, AlgorithmTPSpline, AlgorithmTranscode, AlgorithmTransform, AlgorithmTransformBSpline, AlgorithmTransformVOI, AlgorithmTrilateralFilter, AlgorithmTwoMRIImagesSNR, AlgorithmUnionFindComponentLabelling, AlgorithmUnionFindWatershed, AlgorithmUnsharpMask, AlgorithmVesselEnhancement, AlgorithmVOIExtraction, AlgorithmVOIExtractionPaint, AlgorithmVOIHausdorffDistance, AlgorithmVOILogicalOperations, AlgorithmVOIProps, AlgorithmVOIShapeInterpolation, AlgorithmVOISimplexOpt, AlgorithmWatershed, AlgorithmWaveletFuse, AlgorithmWaveletThreshold, AlgorithmWSinc, Backpropagation, BiorthogonalWavelets, BlindDeblur, BM3D, ChirpZTransform, ContourPlot, CopyMoveAttackDetection, CopyMoveAttackDetection2, Covdet, DBSCANClusteringSegment, DiscreteCosineTransform, DiscreteSineTransform, DoublyConnectedSC, DTIGradTableCorrectionAfterTrans, FFTUtility, FFTUtilityEP, fMRIBlindDeconvolution, GaussianMixtureModelsIncompleteSamples, HaarTransform, HartleyTransform, HartleyTransform2, HistogramOfOrientedGradients, HornSchunk, ImageQuality, ImRegPOC, InverseLaplaceTest, JDialogLoadImage.AlgorithmLoadB, libdt, LIBSVM, LightboxGenerator, LocalIntensityOrderPattern, LSCM, LSQR, MotionDetection, MultiGuidedFilter, MultiResolutionBilateralFilter, NLMeans_filt2D, NoiseLevel, OpenCLAlgorithmBase, OpticalFlowToolbox, PhasePreservingDenoising, PseudoPolarFourierTransform, PyramidToolbox, PyWavelets, Quaternions, RectangularConformalMap, SchwarzChristoffelMapping, SchwarzChristoffelMapping2, SIFT, SIFT3D, SIFTImageSimilarity, SlantTransform, SpatialBroxOpticalFlow, StochasticForests, SVM, SymmsIntegralMapping, TemporalBroxOpticalFlow, TVL1FLOW, WalshHadamardTransform, WalshHadamardTransform2, WalshHadamardTransform3
```
public abstract class AlgorithmBase
extends java.lang.Thread
implements java.awt.event.ActionListener, java.awt.event.WindowListener
```
Base abstract class for algorithms.

Version:

0.1 Feburary 11, 1998

Author:

Matthew J. McAuliffe, Ph.D.

Nested Class Summary
- 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`	`completed`	This flag will be set to true when the algorithm has completed.
`protected boolean`	`destFlag`	Destination flag indicating if a destination (result) image is generated.
`protected ModelImage`	`destImage`	Destination image.
`private double`	`elapsedTime`	Elapsed time (in milliseconds) -- time it took for algorithm to run.
`protected boolean`	`image25D`	If true process each image of a 3D volume independently.
`private javax.swing.event.EventListenerList`	`listenerList`	A list of the ChangeListeners which are interested in the ChangeEvent.
`protected java.util.BitSet`	`mask`	Mask indicating which voxels to process.
`protected int`	`maxProgressValue`	Used to store the maximum value of the progress bar.
`protected int`	`minProgressValue`	Used to store the minimum value of the progress bar.
`protected boolean`	`multiThreadingEnabled`	Indicates if multi-threading will be used to optimize the algorithm.
`protected int`	`nthreads`	The number of threads will be used to execute the algorithm if multi-threading is enabled
`private java.util.Vector<AlgorithmInterface>`	`objectList`	Vector list of AlgorithmInterface objects.
`protected float`	`progress`	Store the progress being made.
`protected int`	`progressModulus`
`protected float`	`progressStep`
`protected boolean`	`runningInSeparateThread`	Should be set to true if NOT in a single thread - will NOT force a graphics update of the progress bar.
`protected boolean`	`separable`	If true convolution kernels are separable.
`protected ModelImage`	`srcImage`	Source image.
`private long`	`startTime`	Start time (in milliseconds) to be used to compute elapsed time.
`protected boolean`	`threadStopped`	Flag indicating whether or not the thread is stopped.

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

Constructor Summary

Constructors
Constructor	Description
`AlgorithmBase()`	Default constructor which sets thread stopped to false, source and destination images to null, and destination flag to false.
`AlgorithmBase(ModelImage destImage, ModelImage srcImage)`	Constructor which sets thread stopped to false and sets source and destination images.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent e)`	Routine to catch action events
`void`	`addListener(AlgorithmInterface obj)`	Add a listener to this class so that when when the algorithm has completed processing it can use notifyListener to notify all listeners that the algorithm has completed.
`void`	`addProgressChangeListener(ProgressChangeListener l)`	Adds the ProgressChangeListener to this FileBase object.
`static int`	`calculateImageSize(int[] dims)`	Calculate the size of the image.
`void`	`calculatePrincipleAxis(ModelImage image, boolean doColor)`	Working ...
`double`	`computeElapsedTime()`	Computes the elapased time as the difference between the start time and the current time (both of which are in milliseconds).
`static double`	`computeElapsedTime(long start)`	Computes the elapased time as the difference between the start time and the current time (both of which are in milliseconds).
`protected float[]`	`convertIntoFloat(java.lang.String[] str)`	Takes an array of strings and converts each entry into a float value.
`protected void`	`delinkProgressToAlgorithm(AlgorithmBase baseAlgo)`	Disconnect this algorithm with the progress bar which holds a reference to this algorithm.
`protected void`	`delinkProgressToAlgorithmMulti(AlgorithmBase baseAlgo)`
`void`	`displayError(java.lang.String error)`	Displays an error in a frame.
`void`	`errorCleanUp(java.lang.String strErr, boolean gcFlag)`	Display string pass into the method.
`void`	`finalize()`	Calls garbage collector to release system resources.
`protected void`	`fireProgressStateChanged(float fVal, java.lang.String title, java.lang.String message)`	Updates listeners of progress status.
`protected void`	`fireProgressStateChanged(int value)`	Notifies all listeners that have registered interest for notification on this event type.
`protected void`	`fireProgressStateChanged(int value, java.lang.String title, java.lang.String message)`	Notifies all listeners that have registered interest for notification on this event type.
`protected void`	`fireProgressStateChanged(java.lang.String message)`	Notifies listeners that have registered interest for notification on this event type.
`protected void`	`fireProgressStateChanged(java.lang.String imageName, java.lang.String message)`	Updates listeners of progress status.
`int[]`	`generateProgressValues(int currentProgress, int desiredMaxProgress)`	Helper function to determine which values to pass on to linked algorithms (that will fire progress changes to the same progress bar).
`ModelImage`	`getDestImage()`	Accessor to return the destination image
`double`	`getElapsedTime()`	Returns the elapsed time in seconds.
`java.util.BitSet`	`getMask()`	Gets the Bitset mask object.
`int`	`getMaxProgressValue()`	Returns the max progress value.
`int`	`getMinProgressValue()`	Returns the min progress value.
`int`	`getNumberOfThreads()`
`float`	`getProgress()`
`ViewJProgressBar`	`getProgressChangeListener()`	If there is a progress bar that is listening to the algorithm's progress change events, this will retrieve that progress bar.
`ProgressChangeListener[]`	`getProgressChangeListeners()`	Returns the progress change event listener list.
`int`	`getProgressModulus()`
`float`	`getProgressStep()`
`int[]`	`getProgressValues()`	Gets the current stored min and max progress values.
`ModelImage`	`getSrcImage()`	Gets the current source image for the algorithm
`boolean`	`isCompleted()`	Returns flag that indicates that the algorithm has been sucessfully completed.
`boolean`	`isImage25D()`	Returns flag that indicates if the image should be processed slice by slice.
`boolean`	`isMultiThreadingEnabled()`
`boolean`	`isRunningInSeparateThread()`	Should be set to true if NOT in a single thread (i.e., the main gui and this algo are in different threads) - will NOT force a graphics update of the progress bar.
`boolean`	`isThreadStopped()`	Returns flag that indicates that the algorithm thread has been stopped.
`protected void`	`linkProgressToAlgorithm(AlgorithmBase baseAlgo)`	Helper function to link the currently listening progress bar with an algorithm created within an algorithm.
`protected void`	`linkProgressToAlgorithm(AlgorithmBase baseAlgo, java.lang.String title, int min, int max)`	New helper function for use with the ViewJProgressBarMulti.
`void`	`makeProgress(float step)`
`void`	`notifyListeners(AlgorithmBase algorithm)`	Used to notify all listeners that the algorithm has completed.
`void`	`removeListener(AlgorithmInterface obj)`	Remove a listener from the class.
`void`	`removeProgressChangeListener(ProgressChangeListener l)`	Removes the ChangeListener from the FileBase object.
`void`	`run()`	Performs start-up and tear-down operations that should be done by all algorithms (timing, history log).
`abstract void`	`runAlgorithm()`	Actually runs the algorithm.
`void`	`setCompleted(boolean flag)`	Sets completed to flag indicating if algorithm has sucessfully completed.
`void`	`setImage25D(boolean flag)`	Sets a flag to indicate the image has dimensions of (i.e. spacial, spacial, time) and image processing routines should apply 2.5D algorithm.
`void`	`setMask(java.util.BitSet imageMask)`	Sets the mask (BitSet object).
`void`	`setMaxProgressValue(int maxProgressValue)`	Sets the max progress value.
`void`	`setMinProgressValue(int minProgressValue)`	Sets the min progress value.
`void`	`setMultiThreadingEnabled(boolean multiThreadingEnabled)`
`void`	`setNumberOfThreads(int nthreads)`
`void`	`setProgress(int progress)`
`void`	`setProgressModulus(int progressModulus)`
`void`	`setProgressStep(float progressStep)`
`void`	`setProgressValues(int[] minmax)`	Sets the min and max progress values from an array of two ints.
`void`	`setProgressValues(int min, int max)`	Sets both the min and max progress values.
`void`	`setRunningInSeparateThread(boolean separateThread)`	Sets the running in separate thread flag which controls how the progress bar is updated.
`void`	`setSrcImage(ModelImage srcImage)`	Sets the source image of the algorithm
`void`	`setStartTime()`	Sets the start time to the current time.
`void`	`setThreadStopped(boolean flag)`	Sets the thread stopped to flag indicating if algorithm has stopped.
`boolean`	`startMethod(int priority)`	Checks to see if a thread is already running on this object.
`void`	`windowActivated(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowClosed(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Sets completed to false, disposes the progress bar and notifies all listeners that the algorithm is stopped.
`void`	`windowDeactivated(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowDeiconified(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowIconified(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowOpened(java.awt.event.WindowEvent event)`	Do nothing.

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
  - destFlag
```
protected boolean destFlag
```
    Destination flag indicating if a destination (result) image is generated.
  - destImage
```
protected ModelImage destImage
```
    Destination image.
  - image25D
```
protected boolean image25D
```
    If true process each image of a 3D volume independently.
  - separable
```
protected boolean separable
```
    If true convolution kernels are separable.
  - mask
```
protected java.util.BitSet mask
```
    Mask indicating which voxels to process. If true process voxel else skip.
  - runningInSeparateThread
```
protected boolean runningInSeparateThread
```
    Should be set to true if NOT in a single thread - will NOT force a graphics update of the progress bar. Should be set to false if in a single thread - will force a graphics update of the progress bar. This defaults to false, since we can automatically set it to true when startMethod() is called. When starting the algorithm with run(), this boolean should remain false.
    
    See Also:
    
    startMethod(int), run()
  - srcImage
```
protected ModelImage srcImage
```
    Source image.
  - threadStopped
```
protected volatile boolean threadStopped
```
    Flag indicating whether or not the thread is stopped.
  - completed
```
private boolean completed
```
    This flag will be set to true when the algorithm has completed.
  - elapsedTime
```
private double elapsedTime
```
    Elapsed time (in milliseconds) -- time it took for algorithm to run.
  - listenerList
```
private javax.swing.event.EventListenerList listenerList
```
    A list of the ChangeListeners which are interested in the ChangeEvent.
  - maxProgressValue
```
protected int maxProgressValue
```
    Used to store the maximum value of the progress bar.
  - minProgressValue
```
protected int minProgressValue
```
    Used to store the minimum value of the progress bar.
  - objectList
```
private java.util.Vector<AlgorithmInterface> objectList
```
    Vector list of AlgorithmInterface objects. When the algorithm has been stopped or completed, all listeners in this list are notified.
  - startTime
```
private long startTime
```
    Start time (in milliseconds) to be used to compute elapsed time.
  - progress
```
protected float progress
```
    Store the progress being made.
  - progressStep
```
protected float progressStep
```
  - progressModulus
```
protected int progressModulus
```
  - multiThreadingEnabled
```
protected boolean multiThreadingEnabled
```
    Indicates if multi-threading will be used to optimize the algorithm.
  - nthreads
```
protected int nthreads
```
    The number of threads will be used to execute the algorithm if multi-threading is enabled
- Constructor Detail
  - AlgorithmBase
```
public AlgorithmBase()
```
    Default constructor which sets thread stopped to false, source and destination images to null, and destination flag to false.
  - AlgorithmBase
```
public AlgorithmBase(ModelImage destImage,
                     ModelImage srcImage)
```
    Constructor which sets thread stopped to false and sets source and destination images.
    
    Parameters:
    
    destImage - Destination image, can be null.
    
    srcImage - Source image, should not be null.
- Method Detail
  - runAlgorithm
```
public abstract void runAlgorithm()
```
    Actually runs the algorithm. Implemented by inheriting algorithms.
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent e)
```
    Routine to catch action events
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Parameters:
    
    e - ActionEvent
  - addListener
```
public void addListener(AlgorithmInterface obj)
```
    Add a listener to this class so that when when the algorithm has completed processing it can use notifyListener to notify all listeners that the algorithm has completed.
    
    Parameters:
    
    obj - AlgorithmInterface "object' to be added to the list
  - addProgressChangeListener
```
public void addProgressChangeListener(ProgressChangeListener l)
```
    Adds the ProgressChangeListener to this FileBase object.
    
    Parameters:
    
    l - the ProgressChangeListener object
  - calculatePrincipleAxis
```
public void calculatePrincipleAxis(ModelImage image,
                                   boolean doColor)
```
    Working ... This function is never used. It doesn't modify any parameters or data members and returns void.
    
    Parameters:
    
    image - DOCUMENT ME!
    
    doColor - DOCUMENT ME!
  - computeElapsedTime
```
public double computeElapsedTime()
```
    Computes the elapased time as the difference between the start time and the current time (both of which are in milliseconds).
    
    Returns:
    
    the elapsed time in seconds -- this is a double value
  - computeElapsedTime
```
public static double computeElapsedTime(long start)
```
    Computes the elapased time as the difference between the start time and the current time (both of which are in milliseconds).
    
    Returns:
    
    the elapsed time in seconds -- this is a double value
  - displayError
```
public void displayError(java.lang.String error)
```
    Displays an error in a frame.
    
    Parameters:
    
    error - string that is displayed
  - errorCleanUp
```
public void errorCleanUp(java.lang.String strErr,
                         boolean gcFlag)
```
    Display string pass into the method. If the string is null no message is displayed. The completed flag is set to false and the progress bar is disposed;
    
    Parameters:
    
    strErr - the string that is to be displayed. If the string is null no message is displayed.
    
    gcFlag - if true call the garbage collector.
  - finalize
```
public void finalize()
```
    Calls garbage collector to release system resources.
    
    Overrides:
    
    finalize in class java.lang.Object
  - generateProgressValues
```
public int[] generateProgressValues(int currentProgress,
                                    int desiredMaxProgress)
```
    Helper function to determine which values to pass on to linked algorithms (that will fire progress changes to the same progress bar). You pass in the current progress and then the max desired progress.... you do NOT adjust the progress yourself, you assume a 0-100 range always, so if the current progress of a certain algorithm was 50%, and you want the helper algorithm to run on an adjusted scale of 50% to 70%, then you pass 50 and 70 as current & desiredMax respectively. if the algorithm passing this in was on a scale of 0->50, then the displayed progress will range from 25% to 35% (50% of 50->70)
    
    Parameters:
    
    currentProgress - current progress of algorithm on a 0->100 scale
    
    desiredMaxProgress - max progress desired for linked algorithm
    
    Returns:
    
    array of 2 ints [current, max]
  - getDestImage
```
public ModelImage getDestImage()
```
    Accessor to return the destination image
    
    Returns:
    
    ModelImage destination image
  - getElapsedTime
```
public double getElapsedTime()
```
    Returns the elapsed time in seconds. This does not compute a new elapsed time.
    
    Returns:
    
    the elapsed time, in seconds computed earlier
    
    See Also:
    
    computeElapsedTime()
  - getMask
```
public java.util.BitSet getMask()
```
    Gets the Bitset mask object.
    
    Returns:
    
    The mask indicating which voxels of the image to process
  - getMaxProgressValue
```
public int getMaxProgressValue()
```
    Returns the max progress value.
    
    Returns:
    
    max progress value
  - getMinProgressValue
```
public int getMinProgressValue()
```
    Returns the min progress value.
    
    Returns:
    
    min progress value
  - getProgressChangeListener
```
public ViewJProgressBar getProgressChangeListener()
```
    If there is a progress bar that is listening to the algorithm's progress change events, this will retrieve that progress bar. This function is really only here to support AlgorithmExtractSurface, AlgorithmExtractSurfaceCubes, and AlgorithmHeightFunction which use ModelQuadMesh and ModelTriangle Mesh (which do not follow the standard algorithmbase setup). This function should not be used elsewhere and will probably be removed (and modelquad/trianglemesh will be changed).
    
    Returns:
    
    a progressbar if there is one listening, null otherwise.
  - getProgressChangeListeners
```
public ProgressChangeListener[] getProgressChangeListeners()
```
    Returns the progress change event listener list.
    
    Returns:
    
    the progress change event listener list.
  - getProgressValues
```
public int[] getProgressValues()
```
    Gets the current stored min and max progress values.
    
    Returns:
    
    int [] { currentMin, currentMax}
  - getSrcImage
```
public ModelImage getSrcImage()
```
    Gets the current source image for the algorithm
    
    Returns:
    
    the source image
  - isCompleted
```
public boolean isCompleted()
```
    Returns flag that indicates that the algorithm has been sucessfully completed.
    
    Returns:
    
    true if algorithm completed successfully, false if it was stopped or had an error.
  - isImage25D
```
public boolean isImage25D()
```
    Returns flag that indicates if the image should be processed slice by slice.
    
    Returns:
    
    true if image should be processed slice by slice.
  - isRunningInSeparateThread
```
public boolean isRunningInSeparateThread()
```
    Should be set to true if NOT in a single thread (i.e., the main gui and this algo are in different threads) - will NOT force a graphics update of the progress bar. Should be set to false if in a single thread - will force a graphics update of the progress bar.
    
    Returns:
    
    boolean true if this algorithm is in a different thread from the main mipav gui thread.
  - isThreadStopped
```
public boolean isThreadStopped()
```
    Returns flag that indicates that the algorithm thread has been stopped.
    
    Returns:
    
    true if thread has stopped.
  - notifyListeners
```
public void notifyListeners(AlgorithmBase algorithm)
```
    Used to notify all listeners that the algorithm has completed.
    
    Parameters:
    
    algorithm - algorithm class that has completed the function
  - removeListener
```
public void removeListener(AlgorithmInterface obj)
```
    Remove a listener from the class.
    
    Parameters:
    
    obj - the algorithm listener to be removed from the list for this algo
  - removeProgressChangeListener
```
public void removeProgressChangeListener(ProgressChangeListener l)
```
    Removes the ChangeListener from the FileBase object.
    
    Parameters:
    
    l - the ProgressChangeListener object
  - run
```
public void run()
```
    Performs start-up and tear-down operations that should be done by all algorithms (timing, history log). Since this class extends the Thread class it can be run in its own thread by invoking object.start(); It can also be invoked without a new thread by calling the the run() method directly (ie. object.run()).
    
    Specified by:
    
    run in interface java.lang.Runnable
    
    Overrides:
    
    run in class java.lang.Thread
  - setCompleted
```
public void setCompleted(boolean flag)
```
    Sets completed to flag indicating if algorithm has sucessfully completed.
    
    Parameters:
    
    flag - Flag to set to true if the algorithm has completed.
  - setImage25D
```
public void setImage25D(boolean flag)
```
    Sets a flag to indicate the image has dimensions of (i.e. spacial, spacial, time) and image processing routines should apply 2.5D algorithm.
    
    Parameters:
    
    flag - flag to set to
  - setMask
```
public void setMask(java.util.BitSet imageMask)
```
    Sets the mask (BitSet object).
    
    Parameters:
    
    imageMask - BitSet object indicating which voxels to process
  - setMaxProgressValue
```
public void setMaxProgressValue(int maxProgressValue)
```
    Sets the max progress value.
    
    Parameters:
    
    maxProgressValue - the maximum progress value
  - setMinProgressValue
```
public void setMinProgressValue(int minProgressValue)
```
    Sets the min progress value.
    
    Parameters:
    
    minProgressValue - the minimum progress value
  - setProgressValues
```
public void setProgressValues(int[] minmax)
```
    Sets the min and max progress values from an array of two ints.
    
    Parameters:
    
    minmax - array of two ints [min, max]
  - setProgressValues
```
public void setProgressValues(int min,
                              int max)
```
    Sets both the min and max progress values.
    
    Parameters:
    
    min - the min progress value
    
    max - the max progress value
  - setRunningInSeparateThread
```
public void setRunningInSeparateThread(boolean separateThread)
```
    Sets the running in separate thread flag which controls how the progress bar is updated. If true the progress bar is not forced to update.
    
    Parameters:
    
    separateThread - Should be set to true if NOT in a single thread (i.e., the main gui and this algo are in different threads) - will NOT force a graphics update of the progress bar. Should be set to false if in a single thread - will force a graphics update of the progress bar.
  - setSrcImage
```
public void setSrcImage(ModelImage srcImage)
```
    Sets the source image of the algorithm
    
    Parameters:
    
    srcImage - the source image
  - setStartTime
```
public void setStartTime()
```
    Sets the start time to the current time. This should be called at the beginning of the run() method.
  - setThreadStopped
```
public void setThreadStopped(boolean flag)
```
    Sets the thread stopped to flag indicating if algorithm has stopped.
    
    Parameters:
    
    flag - flag to set to
  - startMethod
```
public final boolean startMethod(int priority)
```
    Checks to see if a thread is already running on this object. If so, it returns false, else it starts the thread and returns true.
    
    Parameters:
    
    priority - thread priority
    
    Returns:
    
    false if a thread is already running this algorithm, true otherwise
  - windowActivated
```
public void windowActivated(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowActivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window activated event
  - windowClosed
```
public void windowClosed(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowClosed in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window closed event
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Sets completed to false, disposes the progress bar and notifies all listeners that the algorithm is stopped.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - event that triggered function
  - windowDeactivated
```
public void windowDeactivated(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowDeactivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window deactivated event
  - windowDeiconified
```
public void windowDeiconified(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowDeiconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window deiconified event
  - windowIconified
```
public void windowIconified(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowIconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window iconified event
  - windowOpened
```
public void windowOpened(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowOpened in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window opened event
  - convertIntoFloat
```
protected float[] convertIntoFloat(java.lang.String[] str)
```
    Takes an array of strings and converts each entry into a float value. Useful for updating DICOM file information.
    
    Parameters:
    
    str - Some number of strings in an array
    
    Returns:
    
    An array of floats; the same number of entries in str are returned in the array.
  - fireProgressStateChanged
```
protected void fireProgressStateChanged(java.lang.String message)
```
    Notifies listeners that have registered interest for notification on this event type.
    
    Parameters:
    
    message - the new message to display on the progress bar
  - fireProgressStateChanged
```
protected void fireProgressStateChanged(int value)
```
    Notifies all listeners that have registered interest for notification on this event type.
    
    Parameters:
    
    value - the value of the progress bar.
  - fireProgressStateChanged
```
protected void fireProgressStateChanged(java.lang.String imageName,
                                        java.lang.String message)
```
    Updates listeners of progress status. Without actually changing the numerical value
    
    Parameters:
    
    imageName - the name of the image
    
    message - the new message to display
  - fireProgressStateChanged
```
protected void fireProgressStateChanged(int value,
                                        java.lang.String title,
                                        java.lang.String message)
```
    Notifies all listeners that have registered interest for notification on this event type.
    
    Parameters:
    
    value - the value of the progress bar.
    
    title - the title of the progress dialog.
    
    message - the message for that specific progress value.
  - fireProgressStateChanged
```
protected void fireProgressStateChanged(float fVal,
                                        java.lang.String title,
                                        java.lang.String message)
```
    Updates listeners of progress status.
    
    Parameters:
    
    fVal - the percent progress of the algorithm so far
    
    title - the title to send to the listeners
    
    message - the message to send to the listeners
  - linkProgressToAlgorithm
```
protected void linkProgressToAlgorithm(AlgorithmBase baseAlgo)
```
    Helper function to link the currently listening progress bar with an algorithm created within an algorithm. This function should only be called when the other algorithm is expected to update the progress bar seamlessly. It should be called in conjuction with AlgorithmBase's setProgressValues() so that the sub-algorithm will have know the min and max progress values.
    Generally this will be called with the following lines: linkProgressToAlgorithm(theSubAlgorithm); theSubAlgorithm.setProgressValues(generateProgressValues(currentProgressOfAlgorithm, desiredMaxProgressOfSubAlgorithm));
    
    Parameters:
    
    baseAlgo - the subalgorithm created within current algorithm
  - linkProgressToAlgorithm
```
protected void linkProgressToAlgorithm(AlgorithmBase baseAlgo,
                                       java.lang.String title,
                                       int min,
                                       int max)
```
    New helper function for use with the ViewJProgressBarMulti. This allows for keeping track of multi-threaded algorithms and allow the user to better keep track of multiple processes being run. Any linked algorithms should update together in the manner specificed by min/max.
    
    Parameters:
    
    baseAlgo - the subalgorithm created within current algorithm
    
    title - the title shown in the progress bar panel
    
    min - the lower bound of the updating portion of the parent algorithm
    
    max - the upper bound of the updating portion of the parent algorithm
  - delinkProgressToAlgorithm
```
protected void delinkProgressToAlgorithm(AlgorithmBase baseAlgo)
```
    Disconnect this algorithm with the progress bar which holds a reference to this algorithm. In order to release the memory of this algorithm, this function should be called after the algorithm was finished.
    
    Parameters:
    
    baseAlgo -
  - delinkProgressToAlgorithmMulti
```
protected void delinkProgressToAlgorithmMulti(AlgorithmBase baseAlgo)
```
  - getProgress
```
public float getProgress()
```
  - setProgress
```
public void setProgress(int progress)
```
  - makeProgress
```
public void makeProgress(float step)
```
  - getProgressStep
```
public float getProgressStep()
```
  - setProgressStep
```
public void setProgressStep(float progressStep)
```
  - isMultiThreadingEnabled
```
public boolean isMultiThreadingEnabled()
```
  - setMultiThreadingEnabled
```
public void setMultiThreadingEnabled(boolean multiThreadingEnabled)
```
  - getNumberOfThreads
```
public int getNumberOfThreads()
```
  - setNumberOfThreads
```
public void setNumberOfThreads(int nthreads)
```
  - getProgressModulus
```
public int getProgressModulus()
```
  - setProgressModulus
```
public void setProgressModulus(int progressModulus)
```
  - calculateImageSize
```
public static int calculateImageSize(int[] dims)
```
    Calculate the size of the image.
    
    Parameters:
    
    dims -
    
    Returns:

Class AlgorithmBase

Nested Class Summary

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

Field Summary

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

destFlag

destImage

image25D

separable

mask

runningInSeparateThread

srcImage

threadStopped

completed

elapsedTime

listenerList

maxProgressValue

minProgressValue

objectList

startTime

progress

progressStep

progressModulus

multiThreadingEnabled

nthreads

Constructor Detail

AlgorithmBase

AlgorithmBase

Method Detail

runAlgorithm

actionPerformed

addListener

addProgressChangeListener

calculatePrincipleAxis

computeElapsedTime

computeElapsedTime

displayError

errorCleanUp

finalize

generateProgressValues

getDestImage

getElapsedTime

getMask

getMaxProgressValue

getMinProgressValue

getProgressChangeListener

getProgressChangeListeners

getProgressValues

getSrcImage

isCompleted

isImage25D

isRunningInSeparateThread

isThreadStopped

notifyListeners

removeListener

removeProgressChangeListener

run

setCompleted

setImage25D

setMask

setMaxProgressValue

setMinProgressValue

setProgressValues

setProgressValues

setRunningInSeparateThread

setSrcImage

setStartTime

setThreadStopped

startMethod

windowActivated

windowClosed

windowClosing

windowDeactivated

windowDeiconified

windowIconified