Package gov.nih.mipav.model.algorithms

Class AlgorithmBase

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
All Implemented Interfaces:
ActionListener, WindowListener, Runnable, 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, Confmap, ContourPlot, CopyMoveAttackDetection, CopyMoveAttackDetection2, Covdet, DBSCANClusteringSegment, Dijkstra, DiscreteCosineTransform, DiscreteSineTransform, DoublyConnectedSC, DTIGradTableCorrectionAfterTrans, FFTUtility, FFTUtilityEP, fMRIBlindDeconvolution, GaussianMixtureModelsIncompleteSamples, HaarTransform, HartleyTransform, HartleyTransform2, HistogramOfOrientedGradients, HornSchunk, ImageQuality, ImRegPOC, InverseLaplaceTest, JDialogLoadImage.AlgorithmLoadB, LargestCircle, 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, SphericalConformalMap, StochasticForests, SVM, SymmsIntegralMapping, TemporalBroxOpticalFlow, TVL1FLOW, Voro, WalshHadamardTransform, WalshHadamardTransform2, WalshHadamardTransform3
public abstract class AlgorithmBase extends Thread implements ActionListener, WindowListener
Base abstract class for algorithms.
Version:
0.1 Feburary 11, 1998
Author:
Matthew J. McAuliffe, Ph.D.

  • Field Details

    • 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 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:

    • 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 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 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 Details

    • 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 Details

    • runAlgorithm

      public abstract void runAlgorithm()
      Actually runs the algorithm. Implemented by inheriting algorithms.

    • actionPerformed

      public void actionPerformed(ActionEvent e)
      Routine to catch action events
      Specified by:
      actionPerformed in interface 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(String error)
      Displays an error in a frame.
      Parameters:
      error - string that is displayed

    • errorCleanUp

      public void errorCleanUp(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 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 invalid input: '&' 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:

    • getMask

      public 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 Runnable
      Overrides:
      run in class 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(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(WindowEvent event)
      Do nothing.
      Specified by:
      windowActivated in interface WindowListener
      Parameters:
      event - the window activated event

    • windowClosed

      public void windowClosed(WindowEvent event)
      Do nothing.
      Specified by:
      windowClosed in interface WindowListener
      Parameters:
      event - the window closed event

    • windowClosing

      public void windowClosing(WindowEvent event)
      Sets completed to false, disposes the progress bar and notifies all listeners that the algorithm is stopped.
      Specified by:
      windowClosing in interface WindowListener
      Parameters:
      event - event that triggered function

    • windowDeactivated

      public void windowDeactivated(WindowEvent event)
      Do nothing.
      Specified by:
      windowDeactivated in interface WindowListener
      Parameters:
      event - the window deactivated event

    • windowDeiconified

      public void windowDeiconified(WindowEvent event)
      Do nothing.
      Specified by:
      windowDeiconified in interface WindowListener
      Parameters:
      event - the window deiconified event

    • windowIconified

      public void windowIconified(WindowEvent event)
      Do nothing.
      Specified by:
      windowIconified in interface WindowListener
      Parameters:
      event - the window iconified event

    • windowOpened

      public void windowOpened(WindowEvent event)
      Do nothing.
      Specified by:
      windowOpened in interface WindowListener
      Parameters:
      event - the window opened event

    • convertIntoFloat

      protected float[] convertIntoFloat(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(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(String imageName, 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, String title, 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, String title, 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, 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: