Field Detail

• calcSelectedVOI

  private VOI calcSelectedVOI

  The VOI being used just for this calculation (may be a single curve of a single slice or entire VOI

Constructor Detail

• Calc34D

  public Calc34D​(VOI selectedVOI)

Method Detail

• getMedianStatistics

  public void getMedianStatistics​(AlgorithmVOIProps.Calc34D.ContourStats stats)

  Calculates the median statistics for a grayscale image. The image data is stored in the input stats.values. This function can be used for a single contour or a group of contours.

  Parameters:

  stats - contains the Vector of voxels inside the contour(s) used to calculate the median, mode and mode count.

• getMedianStatisticsRGB

  public void getMedianStatisticsRGB​(AlgorithmVOIProps.Calc34D.ContourStats stats)

  Calculates the median statistics for a color image. The image data is stored in the input stats.valuesRGB. This function can be used for a single contour or a group of contours.

  Parameters:

  stats - contains the Vector of voxels inside the contour(s) used to calculate the median, mode and mode count.

• getStdSkewStatistics

  public void getStdSkewStatistics​(AlgorithmVOIProps.Calc34D.ContourStats stats,
                                   java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kPositions,
                                   java.lang.String unit2DStr,
                                   java.lang.String unit3DStr,
                                   float ignoreMin,
                                   float ignoreMax)

  Calculates the standard deviation, coefficient of skewness, coefficient of kurtosis and center of mass for a grayscale image.

  Parameters:

  stats - output values are written into stats.

  kPositions - list of positions of voxels inside the contour (or multiple contours).

  unit2DStr - , 2D label string

  unit3DStr - , 3D label string

  ignoreMin - , threshold minimum

  ignoreMax - , threshold maximum

• getStdSkewStatisticsRGB

  public void getStdSkewStatisticsRGB​(AlgorithmVOIProps.Calc34D.ContourStats stats,
                                      java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kPositions,
                                      java.lang.String unit2DStr,
                                      java.lang.String unit3DStr,
                                      float ignoreMinR,
                                      float ignoreMaxR,
                                      float ignoreMinG,
                                      float ignoreMaxG,
                                      float ignoreMinB,
                                      float ignoreMaxB)

  Calculates the standard deviation, coefficient of skewness, coefficient of kurtosis and center of mass for a color image.

  Parameters:

  stats - output values are written into stats.

  kPositions - list of positions of voxels inside the contour (or multiple contours).

  unit2DStr - , 2D label string

  unit3DStr - , 3D label string

  ignoreMinR - , threshold minimum red

  ignoreMaxR - , threshold maximum red

  ignoreMinG - , threshold minimum green

  ignoreMaxG - , threshold maximum green

  ignoreMinB - , threshold minimum blue

  ignoreMaxB - , threshold maximum blue

• run

  public void run()

  Specified by:

  run in interface java.lang.Runnable

• calcStatsPerContour

  private AlgorithmVOIProps.Calc34D.ContourStats calcStatsPerContour​(FileInfoBase fileInfo,
                                                                     VOIBase contour,
                                                                     int orientation,
                                                                     java.lang.String unit2DStr,
                                                                     java.lang.String unit3DStr,
                                                                     float ignoreMin,
                                                                     float ignoreMax,
                                                                     VOIStatisticalProperties statProperty,
                                                                     int iSlice,
                                                                     int iID)

  Calculates statistics for a single contour. Calculations are done on an as-needed basis for faster performance.

  Parameters:

  fileInfo - information on image resolutions and dimensions

  contour - input contour

  orientation - the image plane the contour is on

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  ignoreMin - threshold minimum

  ignoreMax - threshold maximum

  statProperty - output labels are written to statProperty

  iSlice - contour slice

  iID - contour iD

  Returns:

  ContourStats data structure contains the statistic values.

• calcStatsPerContourRGB

  private AlgorithmVOIProps.Calc34D.ContourStats calcStatsPerContourRGB​(FileInfoBase fileInfo,
                                                                        VOIBase contour,
                                                                        int orientation,
                                                                        java.lang.String unit2DStr,
                                                                        java.lang.String unit3DStr,
                                                                        float ignoreMinR,
                                                                        float ignoreMaxR,
                                                                        float ignoreMinG,
                                                                        float ignoreMaxG,
                                                                        float ignoreMinB,
                                                                        float ignoreMaxB,
                                                                        VOIStatisticalProperties statProperty,
                                                                        int iSlice,
                                                                        int iID)

  Calculates statistics for a single contour. Calculations are done on an as-needed basis for faster performance.

  Parameters:

  fileInfo - information on image resolutions and dimensions

  contour - input contour

  orientation - the image plane the contour is on

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  ignoreMinR - threshold minimum red

  ignoreMaxR - threshold maximum red

  ignoreMinG - threshold minimum green

  ignoreMaxG - threshold maximum green

  ignoreMinB - threshold minimum blue

  ignoreMaxB - threshold maximum blue

  statProperty - output labels are written to statProperty

  iSlice - contour slice

  iID - contour iD

  Returns:

  ContourStats data structure contains the statistic values.

• calcStatsTotal

  private void calcStatsTotal​(VOI kVOI,
                              VOIStatisticalProperties statProperty,
                              FileInfoBase fileInfo,
                              java.lang.String unit2DStr,
                              java.lang.String unit3DStr,
                              float ignoreMin,
                              float ignoreMax)

  Calculates the statistics for the VOI as a whole (across all contours within the VOI). Calculations are done on an as-needed basis for faster performance.

  Parameters:

  contours - list of contours in the VOI

  statProperty - stores the calculated output

  fileInfo - information for image resolutions

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  ignoreMin - threshold minimum

  ignoreMax - threshold maximum

  largestDistance - largest Distance in the VOI. private void calcStatsTotal( Vector contours, VOIStatisticalProperties statProperty, FileInfoBase fileInfo, String unit2DStr, String unit3DStr, float ignoreMin, float ignoreMax, double largestDistance ) { ContourStats stats = new ContourStats(); // The following depend on each other: quantityDescription, volumeDescription, areaDescription, // circularityDescription, solidityDescription // If one is selected, all are calculated. if ( statsList[ indexOf( quantityDescription ) ] || statsList[ indexOf( volumeDescription ) ] || statsList[ indexOf( areaDescription ) ] || statsList[ indexOf( circularityDescription)] || statsList[ indexOf( solidityDescription)]) { stats.nVox = 0; stats.area = 0; stats.volume = 0; for ( int i = 0; i = 0; i = convexMask.nextSetBit(i+1)) { fVal = srcImage.getFloat(i); if (MipavUtil.inRange(ignoreMin, ignoreMax, fVal, rangeFlag)) { convexMask.set(i, false); } } } convexStats.nVox = convexMask.cardinality(); convexStats.area = convexStats.nVox * (fileInfo.getResolutions()[0] * fileInfo.getResolutions()[1]); stats.solidity = stats.area/convexStats.area; statProperty.setProperty(VOIStatisticList.solidityDescription, nf.format(stats.solidity)); } if (statsList[indexOf(numberOfIndentationsDescription)]) { stats.numberOfIndentations = contour.findVOIIndentations2D(srcImage, iSlice, null, false); statProperty.setProperty(VOIStatisticList.numberOfIndentationsDescription + end, nf.format(stats.numberOfIndentations)); } if (statsList[indexOf(meanCurvatureDescription)] || statsList[indexOf(stdDevCurvatureDescription)] || statsList[indexOf(meanNegativeCurvatureDescription)]) { Vector positions = new Vector(); Vector curvature = new Vector(); double meanCurvature[] = new double[1]; double stdDevCurvature[] = new double[1]; double meanNegativeCurvature[] = new double[1]; boolean smooth = true; VOIBase convexContour = new VOIContour((VOIContour)contour); convexContour.findPositionAndCurvature( srcImage, positions, curvature, smooth, meanCurvature, stdDevCurvature, meanNegativeCurvature); if (statsList[indexOf(meanCurvatureDescription)]) { stats.meanCurvature = meanCurvature[0]; statProperty.setProperty(VOIStatisticList.meanCurvatureDescription + end, nf.format(stats.meanCurvature)); } if (statsList[indexOf(stdDevCurvatureDescription)]) { stats.stdDevCurvature = stdDevCurvature[0]; statProperty.setProperty(VOIStatisticList.stdDevCurvatureDescription + end, nf.format(stats.stdDevCurvature)); } if (statsList[indexOf(meanNegativeCurvatureDescription)]) { stats.meanNegativeCurvature = meanNegativeCurvature[0]; statProperty.setProperty(VOIStatisticList.meanNegativeCurvatureDescription + end, nf.format(stats.meanNegativeCurvature)); } } // The following statistics are derived from the minIntensity, maxIntensity, avgIntensity, and sumIntensity: // median, mode, modeCount // deviationDescription, skewnessDescription, kurtosisDescription, massCenterDescription if ( statsList[ indexOf( minIntensity ) ] || statsList[ indexOf( maxIntensity ) ] || statsList[ indexOf( avgIntensity ) ] || statsList[ indexOf( sumIntensities ) ] || statsList[ indexOf( median ) ] || statsList[ indexOf( mode ) ] || statsList[ indexOf( modeCount ) ] || statsList[ indexOf( deviationDescription ) ] || statsList[ indexOf( skewnessDescription ) ] || statsList[ indexOf( kurtosisDescription ) ] || statsList[ indexOf( massCenterDescription ) ] ) { stats.nVox = 0; stats.values = new Vector(); stats.valuesRGB = new Vector(); for ( int i = 0; i kPositions = new Vector(); for ( int i = 0; i 2) { selectedCOM.Z *= srcImage.getFileInfo(0).getResolutions()[2]; unitStr = unit3DStr; } String comStr = unitStr + "\n\t\t" + nf.format(selectedCOM.X) + "\t" + nf.format(selectedCOM.Y) + "\t" + nf.format(selectedCOM.Z); comStr = addScannerLabels(comStr, selectedCOM); stats.gCenterString = new String(comStr); statProperty.setProperty(VOIStatisticList.geometricCenterDescription, stats.gCenterString); } // If user selects largestSliceDistanceDescription: if ( statsList[ indexOf( largestSliceDistanceDescription ) ] ) { for ( int i = 0; i

• calcStatsTotalRGB

  private void calcStatsTotalRGB​(VOI kVOI,
                                 VOIStatisticalProperties statProperty,
                                 FileInfoBase fileInfo,
                                 java.lang.String unit2DStr,
                                 java.lang.String unit3DStr,
                                 float ignoreMinR,
                                 float ignoreMaxR,
                                 float ignoreMinG,
                                 float ignoreMaxG,
                                 float ignoreMinB,
                                 float ignoreMaxB)

• printTotals

  private void printTotals​(AlgorithmVOIProps.Calc34D.ContourStats[] stats,
                           VOIStatisticalProperties statProperty,
                           java.lang.String unit2DStr,
                           java.lang.String unit3DStr,
                           java.lang.String end,
                           float ignoreMin,
                           float ignoreMax,
                           double largestDistance)

  Sums the statistics for a group of contours, where the statistics are first calculated per-contour.

  Parameters:

  stats - array of per-contour statistics

  statProperty - output is written to the statProperty

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  end - tag for statProperty labels

  ignoreMin - threshold minimum

  ignoreMax - threshold maximum

  largestDistance - VOI largest distance.

• printTotalsRGB

  private void printTotalsRGB​(AlgorithmVOIProps.Calc34D.ContourStats[] stats,
                              VOIStatisticalProperties statProperty,
                              java.lang.String unit2DStr,
                              java.lang.String unit3DStr,
                              java.lang.String end,
                              float ignoreMinR,
                              float ignoreMaxR,
                              float ignoreMinG,
                              float ignoreMaxG,
                              float ignoreMinB,
                              float ignoreMaxB,
                              double largestDistance)

  Sums the statistics for a group of contours, where the statistics are first calculated per-contour.

  Parameters:

  stats - array of per-contour statistics

  statProperty - output is written to the statProperty

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  end - tag for statProperty labels

  ignoreMinR - threshold minimum red

  ignoreMaxR - threshold maximum red

  ignoreMinG - threshold minimum green

  ignoreMaxG - threshold maximum green

  ignoreMinB - threshold minimum blue

  ignoreMaxB - threshold maximum blue

  largestDistance - VOI largest distance.

• printTotals

  private void printTotals​(java.util.Vector<AlgorithmVOIProps.Calc34D.ContourStats> allStats,
                           VOIStatisticalProperties statProperty,
                           java.lang.String unit2DStr,
                           java.lang.String unit3DStr,
                           java.lang.String end,
                           float ignoreMin,
                           float ignoreMax,
                           double largestDistance)

  Sums the statistics for a group of contours, where the statistics are first calculated per-contour.

  Parameters:

  allStats - list of per-contour statistics

  statProperty - output is written to the statProperty

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  end - tag for statProperty labels

  ignoreMin - threshold minimum

  ignoreMax - threshold maximum

  largestDistance - VOI largest distance.

• printTotalsRGB

  private void printTotalsRGB​(java.util.Vector<AlgorithmVOIProps.Calc34D.ContourStats> allStats,
                              VOIStatisticalProperties statProperty,
                              java.lang.String unit2DStr,
                              java.lang.String unit3DStr,
                              java.lang.String end,
                              float ignoreMinR,
                              float ignoreMaxR,
                              float ignoreMinG,
                              float ignoreMaxG,
                              float ignoreMinB,
                              float ignoreMaxB,
                              double largestDistance)

  Sums the statistics for a group of contours, where the statistics are first calculated per-contour.

  Parameters:

  allStats - list of per-contour statistics

  statProperty - output is written to the statProperty

  unit2DStr - 2D label string

  unit3DStr - 3D label string

  end - tag for statProperty labels

  ignoreMinR - threshold minimum red

  ignoreMaxR - threshold maximum red

  ignoreMinG - threshold minimum green

  ignoreMaxG - threshold maximum green

  ignoreMinB - threshold minimum blue

  ignoreMaxB - threshold maximum blue

  largestDistance - VOI largest distance.