Class EllipticalROI

java.lang.Object
com.xinapse.multisliceimage.roi.ROI
com.xinapse.multisliceimage.roi.EllipticalROI
All Implemented Interfaces:
RegularROI, RotatableROI, Cloneable

public class EllipticalROI extends ROI implements Cloneable, RotatableROI, RegularROI
A Class representing an elliptical region of an image.
  • Field Details

    • ATOKEN

      public static final String ATOKEN
      The token written to ROI output files to represent the first semi-major axis length.
      See Also:
    • BTOKEN

      public static final String BTOKEN
      The token written to ROI output files to represent the second semi-major axis length.
      See Also:
    • THETATOKEN

      public static final String THETATOKEN
      The token written to ROI output files to represent the rotation angle.
      See Also:
  • Constructor Details

    • EllipticalROI

      public EllipticalROI(Point2D.Double centre, double a, double b, double theta) throws ROIException
      Creates a new EllipticalROI with the specified shape in mm coordinates. The ROI state will be ROIState.NORMAL.
      Parameters:
      centre - the location of the centre of the ellipse in mm coordinates.
      a - the first semi-axis length in mm.
      b - the second semi-axis length in mm.
      theta - the angle between the first axis and the x-direction. Theta is positive clockwise.
      Throws:
      ROIException - if either the major or the minor axis length is not positive.
    • EllipticalROI

      public EllipticalROI(double centreX, double centreY, double a, double b, double theta, ROIState state) throws ROIException
      Creates a new EllipticalROI with the specified shape in mm coordinates.
      Parameters:
      centreX - the x-location of the centre of the ellipse in mm.
      centreY - the y-location of the centre of the ellipse in mm.
      a - the first semi-axis length in mm.
      b - the second semi-axis length in mm.
      theta - the angle between the first axis and the x-direction. Theta is positive clockwise.
      state - the selection state of the EllipticalROI.
      Throws:
      ROIException - if either the major or the minor semi-axis length is not positive.
    • EllipticalROI

      public EllipticalROI(double centreX, double centreY, double a, double b, double theta, byte userColour, ROIState state) throws ROIException
      Creates a new EllipticalROI with the specified shape in mm coordinates.
      Parameters:
      centreX - the x-location of the centre of the ellipse in mm.
      centreY - the y-location of the centre of the ellipse in mm.
      a - the first semi-axis length in mm.
      b - the second semi-axis length in mm.
      theta - the angle between the first axis and the x-direction. Theta is positive clockwise.
      userColour - the colour of this ROI. A value of 0 indicates that the ROI will be drawn with the default colour for normal ROIs if unselected.
      state - the selection state of the EllipticalROI.
      Throws:
      ROIException - if either the major or the minor semi-axis length is not positive.
  • Method Details

    • getCentre

      public Point2D getCentre()
      Description copied from interface: RotatableROI
      Gets the centre (about which rotation will occur) of this RotatableROI in mm.
      Specified by:
      getCentre in interface RotatableROI
      Returns:
      the centre of this ROI, about which rotation will occur.
    • getA

      public double getA()
      Returns the first semi-major axis length in mm.
      Returns:
      the first semi-major axis length in mm.
    • getB

      public double getB()
      Returns the second semi-major axis length in mm.
      Returns:
      the second semi-major axis length in mm.
    • getCentrePix

      public Point2D.Double getCentrePix(int nCols, int nRows, float pixelXSize, float pixelYSize)
      Gets the centre of this ROI in pixel coordinates.
      Parameters:
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the image pixel width, in mm.
      pixelYSize - the image pixel height, in mm.
      Returns:
      the centre of this ROI in pixel coordinates.
    • getTheta

      public double getTheta()
      Description copied from interface: RotatableROI
      Returns the current rotation angle for this RotatableROI.
      Specified by:
      getTheta in interface RotatableROI
      Returns:
      theta the current rotation angle.
    • setTheta

      public void setTheta(double theta)
      Description copied from interface: RotatableROI
      Sets the rotation angle for this RotatableROI.
      Specified by:
      setTheta in interface RotatableROI
      Parameters:
      theta - the rotation angle.
    • getCreateInteractionType

      public static InteractionType getCreateInteractionType()
      Returns the type of interaction needed to create an EllipticalROI.
      Returns:
      type of interaction needed to create an EllipticalROI - InteractionType.NONE.
    • getSquareArea

      public double getSquareArea()
      Description copied from interface: RegularROI
      Returns the area of this regular ROI in square mm.
      Specified by:
      getSquareArea in interface RegularROI
      Returns:
      the area of this ROI in square mm.
    • move

      public void move(double dx, double dy)
      Description copied from class: ROI
      Move this ROI by specified distances (in mm) in the x and y directions.
      Specified by:
      move in class ROI
      Parameters:
      dx - the distance to move in the x-direction.
      dy - the distance to move in the y-direction.
    • flipVertical

      public void flipVertical(Point2D flipPoint)
      Description copied from class: ROI
      Flip this ROI vertically about a given location.
      Specified by:
      flipVertical in class ROI
      Parameters:
      flipPoint - the point about which the ROI will be flipped.
    • flipHorizontal

      public void flipHorizontal(Point2D flipPoint)
      Description copied from class: ROI
      Flip this ROI horizontally about a given location.
      Specified by:
      flipHorizontal in class ROI
      Parameters:
      flipPoint - the point about which the ROI will be flipped.
    • move

      public void move(EllipticalROI newEllipse, boolean pixelSnap)
      Moves and rehapes this EllipticalROI so that the size and location are the same as the given EllipticalROI.
      Parameters:
      newEllipse - the EllipticalROI from which to take the location, size and rotation angle.
      pixelSnap - indicates whether pixel snap is turned on.
    • getInstance

      public static EllipticalROI getInstance(Rectangle boundingRectangle, int nCols, int nRows, float pixelXSize, float pixelYSize, byte userColour, ROIState state) throws ROIException
      Creates an instance of a EllipticalROI suitable for drawing on a window. Bounding rectangle determines the maximum size of the ROI (in image pixels).
      Parameters:
      boundingRectangle - the area of screen into which the ROI must fit.
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the size of image pixels in the horizontal direction.
      pixelYSize - the size of image pixels in the vertical direction.
      userColour - the colour of this ROI. A value of 0 indicates that the ROI will be drawn with the default colour for normal ROIs if unselected.
      state - the initial state of this newly-created ROI.
      Returns:
      a new EllipticalROI that can be displayed inside the specified region of image pixels.
      Throws:
      ROIException - if the ROI cannot be created as requested.
    • draw

      public boolean draw(Graphics g, Rectangle visibleRectangle, int imageDrawCols, int imageDrawRows, int xOffset, int yOffset, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean drawAnnotation)
      Description copied from class: ROI
      Draws this ROI if it needs to be be drawn on screen.
      Overrides:
      draw in class ROI
      Parameters:
      g - the graphics context for the drawing operation.
      visibleRectangle - the part of the image that can be seen on-screen.
      imageDrawCols - width of the area in which this portion of the image is to be drawn.
      imageDrawRows - height of the area in which this portion of the image is to be drawn.
      xOffset - a horizontal offset for drawing operations.
      yOffset - a vertical offset for drawing operations.
      nCols - the number of columns in the image on which this ROI is defined.
      nRows - the number of rows in the image on which this ROI is defined.
      pixelXSize - pixel width for the image on which this ROI is defined.
      pixelYSize - pixel height for the image on which this ROI is defined.
      drawAnnotation - a flag to indicate whether annotation should be drawn.
      Returns:
      true if the ROI is visible and been drawn on screen; false otherwise.
    • drawInOrthoView

      public void drawInOrthoView(Image orthoView, org.jogamp.vecmath.Point3f orthoViewPosition, org.jogamp.java3d.Transform3D imageToViewTx, int nCols, int nRows, int nSlices, float pixelXSize, float pixelYSize, boolean filled)
      Description copied from class: ROI
      Draws this ROI on top of an orthogonal view of an image.
      Specified by:
      drawInOrthoView in class ROI
      Parameters:
      orthoView - the Image into which the ROI is to be drawn.
      orthoViewPosition - the coordinates (col, row, slice position) of the orthogonal view in the original image.
      imageToViewTx - the Transform3D that maps original image pixel coordinates to pixel coordinates in the orthogonal view.
      nCols - the number of columns in the original image.
      nRows - the number of rows in the original image.
      nSlices - the number of slices in the original image.
      pixelXSize - the pixel width in the original image.
      pixelYSize - the pixel height in the original image.
      filled - whether the ROI should be drawn filled (effective only for ROIs that enclose an area).
    • toSpline

      public SplineROI toSpline()
      Returns a SplineROI that closely approximates to this EllipticalROI.
      Returns:
      a SplineROI that closely approximates to this EllipticalROI.
    • getFeret

      public Feret getFeret()
      Description copied from class: ROI
      Returns the minimum and maximum Feret's diameter for this ROI, in mm.
      Specified by:
      getFeret in class ROI
      Returns:
      the minimum and maximum Feret's diameter (in mm) as a Feret object.
    • getPerimeter

      public double getPerimeter()
      Returns the perimeter length of this EllipticalROI. The returned perimeter is computed using the YNOT approximation formula, which gives a maximum error of 0.362%. The maximum error occurs when the eccentricity is slightly above 5.
      Specified by:
      getPerimeter in class ROI
      Returns:
      the (approximate) perimeter length of this Elliptical ROI.
    • getCentroid

      public org.jogamp.vecmath.Point2d getCentroid()
      Description copied from class: ROI
      Returns the centroid (centre of area) of this ROI.
      Specified by:
      getCentroid in class ROI
      Returns:
      the centroid of this ROI.
    • getPrincipalAxisAngle

      public double getPrincipalAxisAngle()
      Returns the angle between the major principal axis of this ROI and the x-axis. For an EllipticalROI, this is the angle between the largest ellipse axis and the x-axis.
      Returns:
      the main principal axis angle of this ROI.
    • getCreateDialog

      public static ROICreateDialog getCreateDialog(CanAddROIToFrame listener)
      Returns a JDialog that can be used to create Elliptical ROIs.
      Parameters:
      listener - the CanAddROIToFrame to which the ROI will be added when the Add button of the Dialog is clicked.
      Returns:
      a ROICreateDialog that is used to create an EllipticalROI.
    • contains

      public boolean contains(ROI roi)
      Indicates whether this EllipticalROI contains another ROI entirely within its borders.
      Specified by:
      contains in class ROI
      Parameters:
      roi - the ROI to be tested for containment within this ROI.
      Returns:
      true if this EllipticalROI contains the specified ROI; false otherwise.
    • intersect

      public List<ROI> intersect(ROI roi, IndeterminateProgressMonitor progressMonitor)
      Description copied from class: ROI
      Performs an intersection operation on the shape of this ROI with another ROI.
      Overrides:
      intersect in class ROI
      Parameters:
      roi - the ROI with which to perform the intersection operation.
      progressMonitor - if non-null, the IndeterminateProgressMonitor that can be used to cancel the operation.
      Returns:
      a List<ROI> of ROIs that result from the operation.
    • equals

      public boolean equals(Object o)
      Description copied from class: ROI
      Indicates whether some Object is equal to this ROI. To be equal, the Object must be an ROI of the same type, and of the same shape and location as this ROI.
      Specified by:
      equals in class ROI
      Parameters:
      o - the Object to be tested for equality to this ROI.
      Returns:
      true if the supplied Object is an ROI of the same type, shape and location as this ROI; false otherwise.
    • hashCode

      public int hashCode()
      Returns a hash code value for this EllipticalROI.
      Overrides:
      hashCode in class ROI
      Returns:
      a hash code value for this EllipticalROI.
    • set

      public void set(ROI roi) throws ClassCastException
      Description copied from class: ROI
      Sets the shape of this ROI to the shape of the supplied argument ROI.
      Specified by:
      set in class ROI
      Parameters:
      roi - the ROI from which the shape is set.
      Throws:
      ClassCastException - if the sub-class of the argument ROI is not the same as this ROI.
    • getCopy

      public ROI getCopy()
      Description copied from class: ROI
      Returns a copy of this ROI. The copy will be identical in shape and annotation as the original ROI, but with a history of that of a newly-created ROI.
      Specified by:
      getCopy in class ROI
      Returns:
      a copy of this ROI.
    • clone

      public EllipticalROI clone()
      Description copied from class: ROI
      Returns a clone of this ROI. The copy will be identical in shape and annotation as the original ROI, and with a history identical to the cloned ROI.
      Overrides:
      clone in class ROI
      Returns:
      a clone of this ROI, cast to an Object.
    • toString

      public String toString()
      Description copied from class: ROI
      Returns a String describing this ROI.
      Specified by:
      toString in class ROI
      Returns:
      a String describing this ROI.
    • getDescription

      public String getDescription()
      Description copied from class: ROI
      Return a description of this type of ROI.
      Specified by:
      getDescription in class ROI
      Returns:
      a String describing the type of this ROI.
    • getName

      public static String getName()
      Returns a descriptive name for this type of ROI.
      Returns:
      a String describing this type of ROI.
    • getButtonIcon

      public static Icon getButtonIcon()
      Returns an Icon that can be used for a button to create this type of ROI.
      Returns:
      an Icon that can be used to represent this type of ROI.