Package com.xinapse.multisliceimage.roi

Class IrregularROI

java.lang.Object
com.xinapse.multisliceimage.roi.ROI
com.xinapse.multisliceimage.roi.IrregularROI
All Implemented Interfaces:
EditableOutlineROI, RotatableROI, StretchableROI, Cloneable
Direct Known Subclasses:
ContourROI, CurvedLineROI, IrregularROIInProgress
public class IrregularROI extends ROI implements Cloneable, StretchableROI, RotatableROI, EditableOutlineROI
A Class representing an irregularly-shaped closed region on an image.

  • Field Details

    • POINTSTOKEN

      public static final String POINTSTOKEN
      The token written to ROI output files to indicate that a list of points is to follow.
      See Also:

    • xpts

      protected double[] xpts
      The x-coordinates of points forming the outline of this Irregular ROI in real-space (mm) coordinates.

    • ypts

      protected double[] ypts
      The y-coordinates of points forming the outline of this Irregular ROI in real-space (mm) coordinates.

    • nPoints

      protected int nPoints
      The number of points forming the outline.

  • Constructor Details

    • IrregularROI

      public IrregularROI(double[] x, double[] y, int n, ROIState state) throws ROIException
      Creates a new IrregularROI with the specified shape in mm coordinates.
      Parameters:
      x - an array of x-coordinates for the points forming the outline.
      y - an array of y-coordinates for the points forming the outline.
      n - the number points to be taken from the x and y arrays - must be less than or equal to then length of the smallest array.
      state - the ROIState of the newly-created ROI.
      Throws:
      ROIException - if the ROI cannot be created as specified.

    • IrregularROI

      public IrregularROI(List<? extends Point2D> pointsList, ROIState state) throws ROIException
      Creates a new IrregularROI with the specified shape in mm coordinates.
      Parameters:
      pointsList - a List of Point2D, in real-space (mm) coordinates, forming the outline.
      state - the ROIState of the newly-created ROI.
      Throws:
      ROIException - if the ROI cannot be created as specified.

  • Method Details

    • getVertices

      public Point2D[] getVertices()
      Returns the vertex locations for this IrregularROI.
      Returns:
      the vertex locations as an array of Point2D.

    • getVertex

      public Point2D getVertex(int index)
      Returns a vertex location for this IrregularROI.
      Parameters:
      index - the index of the vertex to return.
      Returns:
      the vertex location as a Point2D.

    • getNormal

      public org.jogamp.vecmath.Vector2d getNormal(int index) throws ROIException
      Returns the outward normal vector at a vertex.
      Parameters:
      index - the index to the vertex.
      Returns:
      the outward unit normal vector.
      Throws:
      ROIException - if the vertex index is invalid.

    • containsVertex

      public boolean containsVertex(Point2D vertex)
      Tests whether the supplied vertex location is one of the vertex locations for this ROI.
      Parameters:
      vertex - the vertex location to test.
      Returns:
      true if the supplied vertex location is one of the vertex locations for this ROI; false otherwise.

    • getCreateInteractionType

      public static InteractionType getCreateInteractionType()
      Returns the type of interaction needed to create an IrregularROI.
      Returns:
      type of interaction needed to create an IrregularROI - InteractionType.CLICK_OUTLINE.

    • 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.

    • move

      public void move(double dx, double dy, double stretchX, double stretchY)
      Description copied from interface: StretchableROI
      Moves and stretches an ROI. A stretch value is a scaling factor for dimensions in either the horizontal or vertical directions. A stretch of 1.0 means no stretch.
      Specified by:
      move in interface StretchableROI
      Parameters:
      dx - the distance (in mm) to move the centre of the StretchableROI in the horizontal direction.
      dy - the distance (in mm) to move the centre of the StretchableROI in the vertical direction.
      stretchX - the stretch in the horizontal direction.
      stretchY - the stretch in the vertical 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.

    • moveVertex

      public void moveVertex(Point2D newPos, Handle handle, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean pixelSnap) throws ROIException
      Description copied from interface: EditableOutlineROI
      Move a point on the outline of this EditableOutlineROI to a new position.
      Specified by:
      moveVertex in interface EditableOutlineROI
      Parameters:
      newPos - the new location of the vertex in real-space coordinates.
      handle - the Handle that the user has grabbed, used to identify the vertex to be moved.
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the pixel width in mm.
      pixelYSize - the pixel height in mm.
      pixelSnap - whether pixel snap is turned on.
      Throws:
      ROIException - if the vertex cannot be moved to the requested position.

    • deleteVertex

      public boolean deleteVertex(Handle handle) throws ROIException
      Description copied from interface: EditableOutlineROI
      Delete a point on the outline of this EditableOutlineROI that is under a handle.
      Specified by:
      deleteVertex in interface EditableOutlineROI
      Parameters:
      handle - the Handle that the user has grabbed, used to identify the vertex to be deleted.
      Returns:
      true if a point is successfully deleted.
      Throws:
      ROIException - if the point cannot be deleted from this ROI.

    • insertTwoVertices

      public boolean insertTwoVertices(Handle handle)
      Description copied from interface: EditableOutlineROI
      Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.
      Specified by:
      insertTwoVertices in interface EditableOutlineROI
      Parameters:
      handle - the Handle that the user has grabbed, used to identify the vertex around which the new vertices are to be placed.
      Returns:
      true if a point is successfully inserted.

    • setVertex

      public void setVertex(Point2D pos, int idx) throws ROIException
      Sets one vertex position for this ROI.
      Parameters:
      pos - the coordinates of the new position.
      idx - an index to the corordinate position.
      Throws:
      ArrayIndexOutOfBoundsException - if the index is invalid.
      ROIException - if the moving the vertex would result in an invalid IrregularROI.

    • setVertices

      public void setVertices(Point2D[] vertices) throws ROIException
      Sets the vertex positions for this ROI.
      Parameters:
      vertices - an array of new vertex positions.
      Throws:
      ROIException - if the setting the vertex positions would result in an invalid IrregularROI.

    • setVertices

      public void setVertices(List<? extends Point2D> vertices) throws ROIException
      Sets the vertex positions for this ROI.
      Parameters:
      vertices - a java.util.List<? extends Point2D> of new vertex positions.
      Throws:
      ROIException - if the setting the vertex positions would result in an invalid IrregularROI.

    • setVertices

      public void setVertices(double[] x, double[] y) throws ROIException
      Sets the vertex positions for this ROI.
      Parameters:
      x - an array of x-coordinates for the new vertex positions.
      y - an array of y-coordinates for the new vertex positions.
      Throws:
      ROIException - if the vertices cannot be set as specified.

    • setVertices

      public void setVertices(double[] x, double[] y, int n) throws ROIException
      Sets the vertex positions for this ROI.
      Parameters:
      x - an array of x-coordinates for the new vertex positions.
      y - an array of y-coordinates for the new vertex positions.
      n - the number of points to copy from the arrays, starting at index 0.
      Throws:
      ROIException - if the vertices cannot be set as specified.
      ROIException - if the setting the vertex positions would result in an invalid IrregularROI.

    • 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.

    • 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.

    • 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.

    • getNPoints

      public int getNPoints()
      Returns the number of vertices that define the outline.
      Returns:
      the number of vertices that define the outline.

    • erasePoints

      public List<IrregularROI> erasePoints(List<Point2D> erasePoints, float size, int nCols, int nRows, float pixelXSize, float pixelYSize)
      Erase points from this IrregularROI. erasePoints may edit this IrregularROI by deleting points, or it may split this IrregularROI into two or more new IrregularROIs. If more than one IrregularROI is returned, then the (edited) original IrregularROI will be in the list of returned IrregularROIs, and will be the remaining IrregularROI which is biggest (has the most points).
      Parameters:
      erasePoints - a List of points through which the erasing pen has passed.
      size - the size of the erasing pen in mm.
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the pixel width in mm.
      pixelYSize - the pixel height in mm.
      Returns:
      a List of IrregularROIs resulting from the points erasure.

    • simplify

      public void simplify(double minDistanceBetweenPoints) throws ROIException
      Simplifies the outline shape of this IrregularROI such that none of the vertex points is less than the specified minimum distance apart.
      Parameters:
      minDistanceBetweenPoints - the minimum distance betwen vertex points.
      Throws:
      ROIException - if the outline simplification results in an invalid ROI.

    • join

      public IrregularROI join(IrregularROI roi) throws ROIException
      Joins this ROI to another IrregularROI with a waisted join - a join at the nearest point. If the two ROIs overlap, then the resulting ROI is just the union of the two ROIs.
      Parameters:
      roi - the roi to which this is to be joined.
      Returns:
      the original ROI joined to the ROI supplied as an argument.
      Throws:
      ROIException - if the two ROIs cannot be joined.

    • closestPoints

      public Line2D closestPoints(IrregularROI roi)
      Returns the line that represents the line that joins the two points that are closest together (in space) between this IrregularROI and another IrregularROI.
      Parameters:
      roi - the IrregularROI against which this IrregularROI will be tested.
      Returns:
      a Line2D representing the line that joins the two closest points. The first end of the line will be on this IrregularROI, and the second will be on the supplied argument IrregularROI.

    • orderPoints

      public void orderPoints(IrregularROI toROI) throws ROIException
      Sets the order of the outline points of this ROI so that they are in the closest possible correspondence (spatially) with the outline points of the supplied IrregularROI.
      Parameters:
      toROI - the IrregularROI to which the order of the outline points is to me matched.
      Throws:
      ROIException - if the number of outline points is different between this IrregularROI and the supplied IrregularROI.

    • toSpline

      public SplineROI toSpline()
      Converts this IrregularROI to a SplineROI. The number of knot points will be set automatically so that the SplineROI is a good approximation to this IrregularROI. The knot points will be evenly spaced around the outline of the SplineROI.
      Returns:
      a SplineROI that is an approximation to this IrregularROI.

    • toSpline

      public SplineROI toSpline(int nKnotPoints) throws ROIException
      Converts this IrregularROI to a SplineROI with the specified number of knot points. The knot points will be evenly spaced around the outline of this IrregularROI.
      Parameters:
      nKnotPoints - the number of knot points in the SplineROI.
      Returns:
      a SplineROI that is an approximation to this IrregularROI.
      Throws:
      ROIException - if the specified number of knot points is less than 3.

    • makeConvex

      public void makeConvex(float pixelXSize, float pixelYSize, float minConcaveRadius) throws CancelledException
      Make this IrregularROI convex, or at least less concave. The supplied pixel sizes are used to decide on the separation between data points around the IrregularROI. A minimum radius of curvature for concave radii of curvature is given.
      Parameters:
      pixelXSize - the width of an image pixel in mm.
      pixelYSize - the height of an image pixel in mm.
      minConcaveRadius - the minimum radius of curvature for concave parts of this ROI.
      Throws:
      CancelledException - if the operation is cancelled by the user.

    • makeConvex

      public void makeConvex(CanAddROIToFrame canAddROIToFrame, float pixelXSize, float pixelYSize, float minConcaveRadius)
      Make this IrregularROI convex, or at least less concave. The supplied pixel sizes are used to decide on the separation between data points around the IrregularROI. A minimum radius of curvature for concave radii of curvature is given. The action of making the ROI convex will be executed asynchronously using a SwingWorker that will update the ImageDisplayer when finished.
      Parameters:
      canAddROIToFrame - the CanAddROIToFrame to be updated when the operation is complete.
      pixelXSize - the width of an image pixel in mm.
      pixelYSize - the height of an image pixel in mm.
      minConcaveRadius - the minimum radius of curvature for concave parts of this ROI.

    • 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).

    • 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()
      Description copied from class: ROI
      Returns the perimeter length of this ROI.
      Specified by:
      getPerimeter in class ROI
      Returns:
      the perimeter length of this 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.
      Returns:
      the main principal axis angle of this ROI.

    • getVertexHandles

      public Handle[] getVertexHandles()
      Description copied from interface: EditableOutlineROI
      Returns an array of VertexHandles.
      Specified by:
      getVertexHandles in interface EditableOutlineROI
      Returns:
      an array of VertexHandles, or null if this ROI is not having its outline edited.

    • getPrecedingVisibleHandle

      public Handle getPrecedingVisibleHandle(Handle handle)
      Description copied from interface: EditableOutlineROI
      Returns the visible Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.
      Specified by:
      getPrecedingVisibleHandle in interface EditableOutlineROI
      Parameters:
      handle - the handle for which to get the preceding handle.
      Returns:
      the preceding visible Handle, or null if there is no preceding visible handle.

    • getFollowingVisibleHandle

      public Handle getFollowingVisibleHandle(Handle handle)
      Description copied from interface: EditableOutlineROI
      Returns the visible Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.
      Specified by:
      getFollowingVisibleHandle in interface EditableOutlineROI
      Parameters:
      handle - the handle for which to get the following handle.
      Returns:
      the following visible Handle, or null if there is no following visible handle.

    • selfIntersects

      public boolean selfIntersects()
      Returns true if this ROI has line segments that cross.
      Returns:
      true if this ROI has line segments that cross; false otherwise.

    • removeSelfIntersections

      public void removeSelfIntersections() throws ROIException
      Modifies this IrregularROI, converting any self-intersecting segments so that after this method call, the ROI does not self-intersect. Any "internal" hollows that result from self-intersections are removed.
      Throws:
      ROIException - if the operation cannot be completed.

    • contains

      public boolean contains(ROI roi)
      Indicates whether this IrregularROI 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 IrregularROI contains the specified ROI; false otherwise.

    • intersect

      public List<ROI> intersect(ROI roi, IndeterminateProgressMonitor progressMonitor) throws ROIException, CancelledException
      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.
      Throws:
      ROIException - if the operation cannot be performed.
      CancelledException - if the operation is cancelled by the user.

    • 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 IrregularROI.
      Overrides:
      hashCode in class ROI
      Returns:
      a hash code value for this IrregularROI.

    • 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 IrregularROI 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.

    • main

      public static void main(String[] args)
      Run the self-test on this class.
      Parameters:
      args - ignored.