Field Detail

• SampleLimit

  protected static final int SampleLimit

  See Also:

  Constant Field Values

• imageA

  protected ModelImage imageA

• imageDims

  private WildMagic.LibFoundation.Mathematics.Vector3f imageDims

• outputDirectory

  private java.lang.String outputDirectory

• sharedOutputDir

  private java.lang.String sharedOutputDir

• lattice

  protected VOIVector lattice

• left

  protected VOI left

• leftContour

  protected VOI leftContour

• right

  protected VOI right

• rightContour

  protected VOI rightContour

• latticeGrid

  private VOIVector latticeGrid

• center

  protected VOIContour center

• latticeSlices

  protected int[] latticeSlices

• afTimeC

  protected float[] afTimeC

• allTimes

  protected float[] allTimes

• splineRangeIndex

  protected int[] splineRangeIndex

• centerSpline

  protected WildMagic.LibFoundation.Curves.NaturalSpline3 centerSpline

• centerPositions

  protected VOIContour centerPositions

• leftPositions

  protected VOIContour leftPositions

• rightPositions

  protected VOIContour rightPositions

• leftLine

  private VOI leftLine

• rightLine

  private VOI rightLine

• centerLine

  private VOI centerLine

• wormDiameters

  protected java.util.Vector<java.lang.Float> wormDiameters

• extent

  protected int extent

• rightVectors

  protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> rightVectors

• normalVectors

  protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> normalVectors

• upVectors

  protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> upVectors

• curvatureNormals

  java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> curvatureNormals

• curvature

  java.util.Vector<java.lang.Float> curvature

• boxBounds

  protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Box3f> boxBounds

• ellipseBounds

  protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Ellipsoid3f> ellipseBounds

• latticeInterpolationInit

  private boolean latticeInterpolationInit

• samplingPlanes

  protected VOI samplingPlanes

• maxSplineLength

  private int maxSplineLength

• displayContours

  private VOI[] displayContours

• displayContours2

  private VOI displayContours2

• ellipseCurvesVOI

  private VOI ellipseCurvesVOI

• ellipseCurves

  protected VOIContour[] ellipseCurves

• displayInterpolatedContours

  protected VOI displayInterpolatedContours

• pickedPoint

  private WildMagic.LibFoundation.Mathematics.Vector3f pickedPoint

• showSelectedVOI

  private VOI showSelectedVOI

• showSelected

  private VOIContour[] showSelected

• DiameterBuffer

  protected final int DiameterBuffer

  See Also:

  Constant Field Values

• minRange

  protected final float minRange

  See Also:

  Constant Field Values

• leftMarker

  private VOI leftMarker

• rightMarker

  private VOI rightMarker

• annotationVOIs

  protected VOI annotationVOIs

• wormOrigin

  protected WildMagic.LibFoundation.Mathematics.Vector3f wormOrigin

• transformedOrigin

  protected WildMagic.LibFoundation.Mathematics.Vector3f transformedOrigin

• neuriteData

  private java.util.Vector<VOI> neuriteData

• voiID

  protected java.lang.Short voiID

• seamCellIDs

  private int[][] seamCellIDs

• allSeamCellIDs

  private int[][] allSeamCellIDs

• colorAnnotations

  private boolean colorAnnotations

• annotationListeners

  private java.util.Vector<AnnotationListener> annotationListeners

• curveListeners

  private java.util.Vector<CurveListener> curveListeners

• latticeListeners

  private java.util.Vector<LatticeListener> latticeListeners

• annotationPrefix

  private java.lang.String annotationPrefix

• paddingFactor

  private int paddingFactor

• numEllipsePts

  private int numEllipsePts

• latticeContours

  private VOI latticeContours

• markerNames

  private java.util.Vector<java.lang.String> markerNames

• markerCenters

  private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> markerCenters

• markerLatticeSegments

  private java.util.Vector<java.lang.Integer> markerLatticeSegments

• markerSlices

  private java.util.Vector<java.lang.Integer> markerSlices

• annotationsStraight

  private VOI annotationsStraight

• latticeStraight

  private VOIVector latticeStraight

• previewMode

  private boolean previewMode

• clipMask

  private java.util.Vector<boolean[]> clipMask

• splineControlPtsList

  protected java.util.Vector<LatticeModel.AnnotationSplineControlPts> splineControlPtsList

• numSurfaceSegments

  private int numSurfaceSegments

• currentMesh

  private WildMagic.LibGraphics.SceneGraph.TriMesh currentMesh

• latticepositionMarker

  private VOIWormAnnotation latticepositionMarker

• modelDisplayed

  private boolean modelDisplayed

  Enables the user to visualize the simple ellipse-based model of the worm during lattice construction.

• splineModel

  private boolean splineModel

• ellipseCross

  private boolean ellipseCross

• ellipseScale

  private float ellipseScale

• displayLatticeLabels

  private boolean displayLatticeLabels

Constructor Detail

• LatticeModel

  public LatticeModel​(ModelImage image)

  Creates a new LatticeModel

  Parameters:

  imageA -

• LatticeModel

  public LatticeModel​(ModelImage image,
                      VOIVector lattice)

  Creats a new LatticeModel with the given input lattice.

  Parameters:

  imageA -

  lattice -

Method Detail

• checkParentDir

  public static void checkParentDir​(java.lang.String parentDir)

• getImageName

  private static java.lang.String getImageName​(ModelImage image)

• match

  public static boolean match​(java.awt.Color c1,
                              java.awt.Color c2)

• checkName

  public static boolean checkName​(java.lang.String name,
                                  VOI annotationVOIs)

• readAnnotationsCSV

  public static VOI readAnnotationsCSV​(java.lang.String fileName)

  Read a list of annotations from a CSV file: name,x,y,z,radius (optional)

  Parameters:

  fileName -

  Returns:

  VOI containing list of annotations.

• readLatticeCSV

  public static VOIVector readLatticeCSV​(java.lang.String fileName)

• readLatticeCSV

  public static VOIVector readLatticeCSV​(java.lang.String fileName,
                                         boolean saveSeamCells)

• saveAllVOIsTo

  public static void saveAllVOIsTo​(java.lang.String voiDir,
                                   ModelImage image)

  Saves all VOIs to the specified file.

  Parameters:

  voiDir -

  image -

• saveAnnotationsAsCSV

  public static void saveAnnotationsAsCSV​(java.lang.String dir,
                                          java.lang.String fileName,
                                          VOI annotations)

• saveAnnotationsAsCSV

  public static void saveAnnotationsAsCSV​(java.lang.String dir,
                                          java.lang.String fileName,
                                          VOI annotations,
                                          boolean isCurve)

  Saves the input annotations to the CSV file in the following format: name,x,y,z

  Parameters:

  dir -

  fileName -

  annotations -

• inverseDiagonal

  private static WildMagic.LibFoundation.Mathematics.Vector3f inverseDiagonal​(ModelImage image,
                                                                              int slice,
                                                                              int extent,
                                                                              WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
                                                                              WildMagic.LibFoundation.Mathematics.Vector3f target)

• addAnnotation

  public void addAnnotation​(VOI textVOI,
                            boolean multiSelect)

  Add an annotation to the annotation list.

  Parameters:

  textVOI -

• addAnnotation

  public void addAnnotation​(VOIWormAnnotation newText,
                            boolean multiSelect)

• removeListeners

  public void removeListeners()

• addAnnotationListener

  public void addAnnotationListener​(AnnotationListener listener)

  Adds an annotation listener. The annotation listeners are updated when the annotations change in any way.

  Parameters:

  listener -

• addSplineControlPts

  public void addSplineControlPts​(java.util.Vector<VOIWormAnnotation> controlPts)

  Add a curve to the list.

  Parameters:

  textVOI -

• addCurveListener

  public void addCurveListener​(CurveListener listener)

• addLatticeListener

  public void addLatticeListener​(LatticeListener listener)

• addLeftRightMarker

  public void addLeftRightMarker​(WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                 boolean isSeam)

  Adds a new left/right marker to the worm image.

  Parameters:

  pt -

• addNeurite

  public void addNeurite​(VOI annotionVOI,
                         java.lang.String name)

  Generates a natural spline curve to fit the input set of annotation points to model a neurite.

• clear3DSelection

  public void clear3DSelection()

  Clears the selected VOI or Annotation point.

• clearAddLeftRightMarkers

  public void clearAddLeftRightMarkers()

  Enables user to start editing the lattice.

• colorAnnotations

  public void colorAnnotations​(boolean setColor)

• deleteAnnotations

  public void deleteAnnotations()

• deleteSelectedPoint

  public void deleteSelectedPoint​(boolean doAnnotation)

  Deletes the selected annotation or lattice point.

  Parameters:

  doAnnotation -

• displayAnnotation

  public void displayAnnotation​(java.lang.String name,
                                boolean display)

• dispose

  public void dispose()

  Deletes this LatticeModel

• flipLattice

  public void flipLattice()

• flipLattice

  public static void flipLattice​(VOI left,
                                 VOI right)

• generateTriMesh

  public WildMagic.LibGraphics.SceneGraph.TriMesh generateTriMesh​(boolean returnMesh,
                                                                  boolean saveMesh)

• generateTriMesh2

  public WildMagic.LibGraphics.SceneGraph.TriMesh generateTriMesh2​(boolean returnMesh,
                                                                   boolean saveMesh,
                                                                   int stepSize)

• getAnnotationPrefix

  public java.lang.String getAnnotationPrefix()

• getAnnotations

  public VOI getAnnotations()

• getAnnotationsStraight

  public VOI getAnnotationsStraight()

• getSplineCurves

  public java.util.Vector<java.lang.String> getSplineCurves()

• deleteSelectedCurve

  public void deleteSelectedCurve()

• isCurveSelected

  public boolean isCurveSelected​(java.lang.String name)

• setCurveName

  public void setCurveName​(java.lang.String oldName,
                           java.lang.String newName)

• setCurveSelected

  public void setCurveSelected​(java.lang.String name,
                               boolean selected)

• setCurveVisible

  public void setCurveVisible​(java.lang.String name,
                              boolean visible)

• getCurrentIndex

  public int getCurrentIndex()

• getLattice

  public VOIVector getLattice()

• getLatticeStraight

  public VOIVector getLatticeStraight()

• getCenter

  public VOIContour getCenter()

• getPlanes

  public VOI getPlanes()

• getEllipseCurves

  public VOIContour[] getEllipseCurves()

• getLatticeCurveLength

  public int getLatticeCurveLength()

• getCenter

  public WildMagic.LibFoundation.Mathematics.Vector3f getCenter​(int i)

• showMarker

  public void showMarker​(int i)

• getDiameter

  public int getDiameter​(int i)

• getBasisVectors

  public WildMagic.LibFoundation.Mathematics.Vector3f[] getBasisVectors​(int i)

• getLeftCurve

  public VOIContour getLeftCurve()

• getRightCurve

  public VOIContour getRightCurve()

• getCenterControlPoints

  public VOIContour getCenterControlPoints()

• getNormalVectors

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> getNormalVectors()

• getRightVectors

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> getRightVectors()

• getUpVectors

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> getUpVectors()

• getPicked

  public WildMagic.LibFoundation.Mathematics.Vector3f getPicked()

  Returns the currently selected point, either on the lattice or from the annotation list.

  Returns:

• getPicked

  public WildMagic.LibFoundation.Mathematics.Vector3f getPicked​(WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                                                boolean doAnnotation)

  Finds the closest point to the input point and sets it as the currently selected lattice or annotation point.

  Parameters:

  pt -

  doAnnotation -

  Returns:

• getPickedAnnotation

  public java.util.Vector<VOIWormAnnotation> getPickedAnnotation()

• getSamplingPlanes

  public VOI getSamplingPlanes​(boolean scale)

• hasPicked

  public boolean hasPicked()

• initializeInterpolation

  public void initializeInterpolation​(boolean saveStats)

• interpolateLattice

  public void interpolateLattice​(boolean displayResult,
                                 boolean useModel,
                                 boolean untwistImage,
                                 boolean untwistMarkers)

  Entry point in the lattice-based straightening algorithm. At this point a lattice must be defined, outlining how the worm curves in 3D. A lattice is defined ad a VOI with two curves of equal length marking the left-hand and right-hand sides or the worm.

  Parameters:

  displayResult - , when true intermediate volumes and results are displayed as well as the final straightened image.

• modifyAnnotation

  public boolean modifyAnnotation​(WildMagic.LibFoundation.Mathematics.Vector3f pt)

  Enables the user to move an annotation point with the mouse.

  Parameters:

  startPt - 3D start point of a ray intersecting the volume.

  endPt - 3D end point of a ray intersecting the volume.

  pt - point along the ray with the maximum intensity value.

• modifyLattice

  public boolean modifyLattice​(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f pt)

  Enables the user to modify the lattice point with the mouse.

  Parameters:

  startPt - 3D start point of a ray intersecting the volume.

  endPt - 3D end point of a ray intersecting the volume.

  pt - point along the ray with the maximum intensity value.

• modifyLeftRightMarker

  public void modifyLeftRightMarker​(WildMagic.LibFoundation.Mathematics.Vector3f pt)

  Sets the currently selected point (lattice or annotation).

  Parameters:

  pt -

  doAnnotation -

• moveSelectedPoint

  public void moveSelectedPoint​(WildMagic.LibFoundation.Mathematics.Vector3f direction,
                                boolean doAnnotation)

  Enables the user to move the selected point (lattice or annotation) with the arrow keys.

  Parameters:

  direction -

  doAnnotation -

• redo

  public void redo()

  VOI operation redo

• retwistAnnotations

  public VOI retwistAnnotations​(VOIVector lattice)

• retwistLattice

  public VOIVector retwistLattice​(VOIVector lattice)

• saveLattice

  public void saveLattice()

  Enables the user to save the lattice to a user-selected file.

• saveLattice

  public void saveLattice​(java.lang.String directory,
                          java.lang.String fileName)

  Saves the lattice to the specified file and directory.

  Parameters:

  directory -

  fileName -

• getContourFile

  private boolean getContourFile()

• saveMeshContoursCSV

  private void saveMeshContoursCSV()

• readMeshContoursCSV

  private void readMeshContoursCSV()

• openNeuriteCurves

  public void openNeuriteCurves​(java.lang.String outputDirectory)

• saveNeuriteCurves

  public void saveNeuriteCurves()

• untwistNeuriteCurves

  public void untwistNeuriteCurves​(boolean useLatticeModel)

• openStraightNeuriteCurves

  public static void openStraightNeuriteCurves​(ModelImage image,
                                               java.lang.String outputDirectory)

• segmentLattice

  public ModelImage segmentLattice​(ModelImage image,
                                   boolean saveContourImage,
                                   int paddingFactor,
                                   boolean segmentLattice)

• segmentLattice

  public void segmentLattice​(ModelImage image,
                             ModelImage contourImageBlur)

• selectAnnotation

  public boolean selectAnnotation​(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                                  WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                                  WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                  boolean rightMouse,
                                  boolean multiSelect)

• selectLattice

  public boolean selectLattice​(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                               WildMagic.LibFoundation.Mathematics.Vector3f pt,
                               boolean isSeam)

• setAnnotationPrefix

  public void setAnnotationPrefix​(java.lang.String s)

• setAnnotations

  public void setAnnotations​(VOI newAnnotations)

  Called when new annotations are loaded from file, replaces current annotations.

  Parameters:

  newAnnotations -

• addAnnotations

  public void addAnnotations​(VOI newAnnotations)

  Called when new annotations are loaded from file, replaces current annotations.

  Parameters:

  newAnnotations -

• setImage

  public void setImage​(ModelImage image)

  Change the underlying image for the latticeModel. Update the output directories.

  Parameters:

  image -

• setSharedDirectory

  public void setSharedDirectory​(java.lang.String dir)

• setLattice

  public void setLattice​(VOIVector newLattice)

  Called when a new lattice is loaded from file, replaces the current lattice.

  Parameters:

  newLattice -

• setMarkers

  public void setMarkers​(VOI markerVOIs)

• setPaddingFactor

  public void setPaddingFactor​(int padding)

• isPreview

  public boolean isPreview()

• setPreviewMode

  public void setPreviewMode​(boolean preview,
                             VOIVector lattice,
                             VOI annotations)

• showModel

  public void showModel​(boolean display)

• isModelDisplayed

  public boolean isModelDisplayed()

• updateCrossSection

  public void updateCrossSection​(boolean useSpline,
                                 boolean ellipse,
                                 float percent)

• showLatticeLabels

  public void showLatticeLabels​(boolean display)

• showLattice

  public void showLattice​(boolean display)

  Turns on/off lattice display:

• undo

  public void undo()

  VOI operation undo.

• untwistImage

  public void untwistImage​(boolean mainImage)

  Entry point in the lattice-based straightening algorithm. At this point a lattice must be defined, outlining how the worm curves in 3D. A lattice is defined ad a VOI with two curves of equal length marking the left-hand and right-hand sides or the worm.

  Parameters:

  displayResult - , when true intermediate volumes and results are displayed as well as the final straightened image.

• untwistMarkers

  public void untwistMarkers​(boolean untwistAll)

  Entry point in the lattice-based straightening algorithm. At this point a lattice must be defined, outlining how the worm curves in 3D. A lattice is defined ad a VOI with two curves of equal length marking the left-hand and right-hand sides or the worm.

  Parameters:

  displayResult - , when true intermediate volumes and results are displayed as well as the final straightened image.

• untwistTest

  public ModelImage[] untwistTest​(VolumeImage[] stack)

  Untwists the worm image quickly for the preview mode - without saving any images or statistics

  Returns:

  untwisted image.

• updateLattice

  public void updateLattice​(boolean isLeft,
                            VOIWormAnnotation text,
                            VOIWormAnnotation newText)

• updateAnnotation

  public void updateAnnotation​(VOIWormAnnotation annotation)

• updateSelectedPoint

  public void updateSelectedPoint​(java.awt.Color color)

• generateCurves

  protected boolean generateCurves​(float stepSize)

  Generates the set of natural spline curves to fit the current lattice.

• updateEllipseModel

  private void updateEllipseModel​(float stepSize)

• GetSquared

  protected double GetSquared​(WildMagic.LibFoundation.Mathematics.Vector3f point,
                              WildMagic.LibFoundation.Mathematics.Ellipsoid3f ellipsoid)

• interpolateContour

  protected void interpolateContour​(VOIContour contour)

  Interpolates the input contour so that the spacing between contour points is

  Parameters:

  contour -

  • loadDiameters

    protected java.util.Vector<java.lang.Float> loadDiameters​(java.lang.String imageDir)

  • loadPositions

    protected VOIContour loadPositions​(java.lang.String imageDir,
                                       java.lang.String name)

  • loadSamplePlanes

    protected VOI loadSamplePlanes​(java.lang.String imageDir)

  • makeEllipse

    protected WildMagic.LibFoundation.Mathematics.Ellipsoid3f makeEllipse​(WildMagic.LibFoundation.Mathematics.Vector3f right,
                                                                          WildMagic.LibFoundation.Mathematics.Vector3f up,
                                                                          WildMagic.LibFoundation.Mathematics.Vector3f center,
                                                                          float diameterA,
                                                                          float diameterB,
                                                                          VOIContour ellipse)

    Generates the 3D 1-voxel thick ellipsoids used in the intial worm model.

    Parameters:

    right -

    up -

    center -

    diameterA -

    diameterB -

    ellipse -

    Returns:

  • makeEllipse2DA

    protected void makeEllipse2DA​(WildMagic.LibFoundation.Mathematics.Vector3f right,
                                  WildMagic.LibFoundation.Mathematics.Vector3f up,
                                  WildMagic.LibFoundation.Mathematics.Vector3f center,
                                  float radius,
                                  VOIContour ellipse)

  • makeEllipse2DA

    protected void makeEllipse2DA​(WildMagic.LibFoundation.Mathematics.Vector3f right,
                                  WildMagic.LibFoundation.Mathematics.Vector3f up,
                                  WildMagic.LibFoundation.Mathematics.Vector3f center,
                                  float radius,
                                  WildMagic.LibFoundation.Mathematics.Vector3f normal,
                                  float curvature,
                                  VOIContour ellipse,
                                  boolean ellipseCross,
                                  float scale)

  • originToStraight

    protected WildMagic.LibFoundation.Mathematics.Vector3f originToStraight​(ModelImage model,
                                                                            ModelImage originToStraight,
                                                                            WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                                                            java.lang.String text)

    Given a point in the twisted volume, calculates and returns the corresponding point in the straightened image.

    Parameters:

    model -

    originToStraight -

    pt -

    text -

    Returns:

  • saveAnnotationStatistics

    protected VOI saveAnnotationStatistics​(java.lang.String imageDir,
                                           ModelImage model,
                                           ModelImage originToStraight,
                                           int[] outputDim,
                                           java.lang.String postFix)

    Saves the annotation statistics to a file.

    Parameters:

    image -

    model -

    originToStraight -

    outputDim -

    postFix -

    Returns:

  • saveDiameters

    protected void saveDiameters​(java.util.Vector<java.lang.Float> diameters,
                                 java.lang.String imageDir)

  • saveLatticeStatistics

    protected void saveLatticeStatistics​(java.lang.String imageDir,
                                         float length,
                                         VOI left,
                                         VOI right,
                                         float[] leftPairs,
                                         float[] rightPairs,
                                         java.lang.String postFix)

    Saves the lattice statistics to a file.

    Parameters:

    image -

    length -

    left -

    right -

    leftPairs -

    rightPairs -

    postFix -

  • savePositions

    protected void savePositions​(VOIContour contour,
                                 java.lang.String imageDir,
                                 java.lang.String name)

  • saveSamplePlanes

    protected void saveSamplePlanes​(VOI planes,
                                    java.lang.String imageDir)

  • smoothCurve

    protected WildMagic.LibFoundation.Curves.NaturalSpline3 smoothCurve​(VOIContour curve,
                                                                        float[] time)

    Generates the Natural Spline for the lattice center-line curve. Sets the time values for each point on the curve.

    Parameters:

    curve -

    time -

    Returns:

  • smoothCurve

    public static WildMagic.LibFoundation.Curves.NaturalSpline3 smoothCurve​(java.util.Vector<VOIWormAnnotation> controlPts)

  • straightenFrame

    protected WildMagic.LibFoundation.Mathematics.Vector3f[] straightenFrame​(ModelImage image,
                                                                             int slice,
                                                                             int[] extents,
                                                                             WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
                                                                             WildMagic.LibFoundation.Mathematics.Vector3f centerPos,
                                                                             WildMagic.LibFoundation.Mathematics.Vector3f leftPos,
                                                                             WildMagic.LibFoundation.Mathematics.Vector3f rightPos)

  • writeDiagonal

    protected WildMagic.LibFoundation.Mathematics.Vector3f writeDiagonal​(ModelImage image,
                                                                         int slice,
                                                                         int[] extents,
                                                                         WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
                                                                         WildMagic.LibFoundation.Mathematics.Vector3f target,
                                                                         float[] minDistance)

  • writeDiagonal

    protected void writeDiagonal​(ModelImage image,
                                 ModelImage result,
                                 int tSlice,
                                 int slice,
                                 int[] extents,
                                 WildMagic.LibFoundation.Mathematics.Vector3f[] verts)

  • writeDiagonalSampleCount

    protected void writeDiagonalSampleCount​(ModelImage image,
                                            ModelImage result,
                                            int tSlice,
                                            int slice,
                                            int[] extents,
                                            WildMagic.LibFoundation.Mathematics.Vector3f[] verts)

  • writeDiagonalTest

    protected void writeDiagonalTest​(ModelImage image,
                                     ModelImage result,
                                     int tSlice,
                                     int slice,
                                     int[] extents,
                                     WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
                                     float radiusSq)

  • addInsertionPoint

    private boolean addInsertionPoint​(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                                      WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                                      WildMagic.LibFoundation.Mathematics.Vector3f maxPt,
                                      boolean isSeam)

    Adds a point to the lattice.

    Parameters:

    startPt -

    endPt -

    maxPt -

  • clearCurves

    private void clearCurves​(boolean clearGrid)

    Resets the natural spline curves when the lattice changes.

  • colorAnnotations

    private void colorAnnotations()

    Counts the annotations and colors them based on the number of annotations. This is only used when the user is labeling seam-cells as an aid in determining if 20 pairs of seam cells have been found.

  • generateEllipses

    private void generateEllipses​(int extent)

  • makeSelectionFrame

    private void makeSelectionFrame​(WildMagic.LibFoundation.Mathematics.Vector3f right,
                                    WildMagic.LibFoundation.Mathematics.Vector3f up,
                                    WildMagic.LibFoundation.Mathematics.Vector3f center,
                                    float diameter,
                                    VOIContour ellipse)

    Generates the VOI that highlights which point (lattice or annotation) is currently selected by the user.

    Parameters:

    right -

    up -

    center -

    diameter -

    ellipse -

  • retwistAnnotation

    private WildMagic.LibFoundation.Mathematics.Vector3f retwistAnnotation​(VOIWormAnnotation annotation)

  • saveImage

    private void saveImage​(java.lang.String imageName,
                           ModelImage image,
                           boolean saveAsTif)

  • saveImage

    public static void saveImage​(ModelImage originalImage,
                                 ModelImage image,
                                 java.lang.String subDir,
                                 java.lang.String postScript)

  • saveLatticeStatistics

    private void saveLatticeStatistics()

  • saveContourAsCSV

    public static void saveContourAsCSV​(ModelImage image,
                                        java.lang.String subDir,
                                        java.lang.String postScript,
                                        VOIContour contour)

  • saveBasisVectorsAsCSV

    public static void saveBasisVectorsAsCSV​(ModelImage image,
                                             java.lang.String subDir,
                                             java.lang.String postScript,
                                             VOIContour positions,
                                             java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> normals,
                                             java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> rightVectors,
                                             java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> upVectors)

  • saveContours

    private void saveContours​(ModelImage image,
                              WildMagic.LibFoundation.Mathematics.Box3f[] contours)

  • readContours

    public static WildMagic.LibFoundation.Mathematics.Box3f[] readContours​(ModelImage image,
                                                                           java.lang.String subDir,
                                                                           java.lang.String postScript)

  • saveTriMesh

    public static void saveTriMesh​(ModelImage image,
                                   java.lang.String outputDirectory,
                                   java.lang.String subDir,
                                   java.lang.String postScript,
                                   WildMagic.LibGraphics.SceneGraph.TriMesh mesh)

  • saveSpline

    private void saveSpline​(java.lang.String outputDirectory,
                            VOI data,
                            WildMagic.LibFoundation.Mathematics.Vector3f transformedOrigin,
                            java.lang.String postFix)

  • untwist

    private void untwist​(ModelImage image,
                         int[] resultExtents,
                         boolean saveTif)

    Straightens the worm image based on the input lattice positions. The image is straightened without first building a worm model. The image is segmented after clipping based on surface markers or the lattice shape.

    Parameters:

    image -

    resultExtents -

  • untwistSampleCount

    private void untwistSampleCount​(ModelImage image,
                                    int[] resultExtents,
                                    boolean saveTif)

  • untwistLattice

    private void untwistLattice​(ModelImage image,
                                int[] resultExtents)

    Untwists the lattice and lattice interpolation curves, writing the straightened data to spreadsheet format .csv files and the straightened lattice to a VOI file. The target slices for the lattice and curve data is generated from the distance along the curve. No segmentation or interpolation is necessary:

    Parameters:

    image -

    resultExtents -

  • untwistMarkers

    private void untwistMarkers​(ModelImage image,
                                int[] resultExtents)

  • untwistAnnotations

    public ModelImage untwistAnnotations​(java.lang.String dir,
                                         ModelImage contourImage)

  • untwistTest

    private ModelImage[] untwistTest​(VolumeImage[] stack,
                                     int[] resultExtents)

    Untwists the worm image quickly for the preview mode - without saving any images or statistics Straightens the worm image based on the input lattice positions. The image is straightened without first building a worm model. The image is segmented after clipping based on surface markers or the lattice shape.

    Parameters:

    image -

    resultExtents -

  • getPrefix

    private static java.lang.String getPrefix​(java.lang.String name)

  • containsAnnotation

    private boolean containsAnnotation​(VOI annotationsList,
                                       VOIWormAnnotation text)

  • updateSplineControlPoints

    private void updateSplineControlPoints()

  • updateAnnotationListeners

    private void updateAnnotationListeners()

    Updates the list of listeners that the annotations have changed. This is how the latticeModel communicates changes to the different plugins that display lists of annotations, etc.

  • updateCurveListeners

    private void updateCurveListeners()

  • updateLatticeListeners

    private void updateLatticeListeners()

  • makeLatticeContours

    private void makeLatticeContours()

  • updateLattice

    private void updateLattice​(boolean rebuild)

    Updates the lattice data structures for rendering whenever the user changes the lattice.

    Parameters:

    rebuild -

  • updateLinks

    private void updateLinks()

    Updates the lattice data structures on undo/redo.

  • updateSelected

    private void updateSelected()

    Updates the VOI displaying which point (lattice or annotation) is currently selected when the selection changes.

  • findPoint

    private int findPoint​(VOI left,
                          WildMagic.LibFoundation.Mathematics.Vector3f pickedPoint)

  • updateSeamCount

    private void updateSeamCount()

  • renameLatticeOnLoad

    public static boolean renameLatticeOnLoad​(ModelImage image,
                                              VOIVector latticeVector)

  • saveLattice

    public static void saveLattice​(java.lang.String directory,
                                   java.lang.String fileName,
                                   VOIVector latticeVector)

  • saveLattice

    public static void saveLattice​(java.lang.String directory,
                                   java.lang.String fileName,
                                   java.lang.String latticeFileName,
                                   VOIVector latticeVector)

  • annotationChanged

    private static VOI annotationChanged​(VOI annotationsNew,
                                         VOI annotationOld)

  • latticeChanged

    private boolean latticeChanged()

  • testLatticeMeshIntersection

    private void testLatticeMeshIntersection()

  • getInsideMeshImage

    private ModelImage getInsideMeshImage​(java.util.BitSet surfaceMask)

  • getInsideMeshImage

    private ModelImage getInsideMeshImage​(WildMagic.LibGraphics.SceneGraph.TriMesh mesh)

  • blur

    private static ModelImage blur​(ModelImage image,
                                   int sigma)

    Returns a blurred image of the input image.

    Parameters:

    image -

    sigma -

    Returns:

  • getCorrectionFactor

    private static float getCorrectionFactor​(ModelImage image)

    Returns the amount of correction which should be applied to the z-direction sigma (assuming that correction is requested).

    Returns:

    the amount to multiply the z-sigma by to correct for resolution differences

  • fill

    private static int fill​(java.util.BitSet surfaceMask,
                            java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> seedList,
                            java.util.BitSet visited,
                            WildMagic.LibFoundation.Mathematics.Vector3f min,
                            WildMagic.LibFoundation.Mathematics.Vector3f max,
                            int dimX,
                            int dimY,
                            int dimZ)