Package gov.nih.mipav.model.algorithms

Class AlgorithmVOIProps

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
gov.nih.mipav.model.algorithms.AlgorithmVOIProps
All Implemented Interfaces:
VOIStatisticList, ActionListener, WindowListener, Runnable, 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 invalid input: '&' 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.

  • Field Details

    • 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:

    • 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:

    • PROCESS_PER_SLICE

      public static final int PROCESS_PER_SLICE
      Algorithm sums all statistics from each contour on the same slice
      See Also:

    • PROCESS_PER_CONTOUR

      public static final int PROCESS_PER_CONTOUR
      Algorithm maintains separate statistics per contour
      See Also:

    • activeVOI

      private VOI activeVOI
      The VOI on which to perform the calculations.

    • nf

      protected DecimalFormat nf
      Formatting for float values into strings.

    • nfe

      protected DecimalFormat nfe

    • processType

      protected int processType
      How the VOI calculations should be performed (entire, contour, slice).

    • propertyList

      protected 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 ThreadGroup calcGroup
      The top-level group of threads used for calculating.

    • statsList

      protected boolean[] statsList

  • Constructor Details

    • 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 Details

    • 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 String getCenterOfMass()
      Gets the the center of mass of the VOI ; return center of mass defined by the VOI.
      Returns:
      DOCUMENT ME!

    • getCenterOfMassB

      public 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 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 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 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 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 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 String getPerimeter()
      Gets the perimeter of the VOI (in terms of res).
      Returns:
      String perimeter string

    • getCircularity

      public String getCircularity()
      Gets the circularity of the VOI.
      Returns:
      String circularity string

    • getSolidity

      public String getSolidity()
      Gets the solidity of the VOI.
      Returns:
      String solidity string

    • getNumberOfIndentationsCurvture

      public String getNumberOfIndentationsCurvture()

    • getNumberOfIndentationsHull

      public String getNumberOfIndentationsHull()

    • getMeanCurvature

      public String getMeanCurvature()
      Returns:

    • getStdDevCurvature

      public String getStdDevCurvature()
      Returns:

    • getMeanNegativeCurvature

      public String getMeanNegativeCurvature()
      Returns:

    • getAsymmetryIndex

      public 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 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:
      position - (x,y,z(slice)) position in FileCoordinates
      image - The image the point lies within.
      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 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(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 String addScannerLabels(String baseString, WildMagic.LibFoundation.Mathematics.Vector3f currentPt)
      DOCUMENT ME!
      Parameters:
      leadBase - DOCUMENT ME!

    • indexOf

      protected int indexOf(String statistic)

    • initialiseDataHolders

      private void initialiseDataHolders(int numberOfVOIs)
      DOCUMENT ME!
      Parameters:
      numberOfVOIs - DOCUMENT ME!