Package qupath.lib.roi

Class AreaROI

java.lang.Object
qupath.lib.roi.AreaROI
All Implemented Interfaces:
Serializable, ROI
@Deprecated public class AreaROI extends Object implements Serializable
Deprecated.
since v0.6.0 (but really not used in recent versions)
Implementation of an arbitrary area ROI - which could contain disjointed or hollow regions.

It may be decomposed into one or more polygons (vertices), in which case the sign of the area is important in indicating whether the region should be considered 'positive' or a hole.

The underlying idea is based on java.awt.Area, but implemented so as to avoid a dependency on AWT.

However, because this implementation is relatively simple, it doesn't do the complicated checking and computations of AWT Areas - and so ought not be used directly. Rather, AWTAreaROI is strongly to be preferred.

The real usefulness of this class is in enabling Serialization of all ROIs to avoid a dependency on AWT, since potentially a deserialized version of this could then be used to create different kinds of Area (e.g. java.awt.Area or some JavaFX alternative.)

See Also:

  • Nested Class Summary

    Nested classes/interfaces inherited from interface qupath.lib.roi.interfaces.ROI

    ROI.RoiType

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    contains(double x, double y)
    Deprecated.
    Test is the ROI contains specified x, y coordinates.
    protected Shape
    createShape()
    Deprecated.
    Create a Shape object to represent the ROI.
    ROI
    duplicate()
    Deprecated.
    boolean
    equals(Object o)
    Deprecated.
     
    List<Point2>
    getAllPoints()
    Deprecated.
    Beware this method! This will return all polygon points (useful e.g.
    double
    getArea()
    Deprecated.
    Get the area of this ROI.
    double
    getBoundsHeight()
    Deprecated.
    Returns the height of the ROI bounding box.
    double
    getBoundsWidth()
    Deprecated.
    Returns the width of the ROI bounding box.
    double
    getBoundsX()
    Deprecated.
    Returns the x coordinate for the top left of the ROI bounding box.
    double
    getBoundsY()
    Deprecated.
    Returns the y coordinate for the top left of the ROI bounding box.
    int
    getC()
    Get channel index, or -1 if the ROI relates to all available channels.
    double
    getCentroidX()
    Deprecated.
    Get the x coordinate of the ROI centroid;
    double
    getCentroidY()
    Deprecated.
    Get the y coordinate of the ROI centroid;
    ROI
    getConvexHull()
    Default implementation using JTS.
    Geometry
    getGeometry()
    Deprecated.
    Returns a org.locationtech.jts.geom.Geometry object.
    ImagePlane
    getImagePlane()
    Get the ImagePlane, which contains the values for c, z and t in a single object.
    double
    getLength()
    Deprecated.
    Get ROI length.
    int
    getNumPoints()
    Default implementation, calls ROI.getAllPoints() and then caches the result.
    String
    getRoiName()
    Deprecated.
    Get a String representation of the kind of ROI we have, e.g.
    ROI.RoiType
    getRoiType()
    Deprecated.
    Get the RoiType, used to distinguish between points, lines and areas.
    double
    getScaledArea(double pixelWidth, double pixelHeight)
    Deprecated.
    Get scaled area of the ROI, for use with calibrated pixel sizes.
    double
    getScaledLength(double pixelWidth, double pixelHeight)
    Deprecated.
    Get the scaled length, for use with calibrated pixel sizes.
    Shape
    getShape()
    Deprecated.
    Returns a java.awt.Shape representing this ROI, if possible.
    protected Shape
    getShapeInternal()
    Get a (possibly cached) shape representation of the ROI.
    double
    getSolidity()
    Calculate the solidity, defined as ROI area / convex hull area.
    int
    getT()
    Get time point index.
    int
    getZ()
    Get z-stack slice index.
    int
    hashCode()
    Deprecated.
     
    boolean
    intersects(double x, double y, double width, double height)
    Deprecated.
    Test if the ROI intersects a specified region.
    protected boolean
    intersectsBounds(double x, double y, double width, double height)
    Quick check whether the specified rectangle intersects with the bounds of this ROI.
    boolean
    isArea()
    Returns true if this ROI encloses an area.
    boolean
    isEmpty()
    True if the bounding box has zero area
    boolean
    isLine()
    Returns true if this ROI consists of line segments and does not enclose an area.
    boolean
    isPoint()
    Returns true if this ROI represents distinct (unconnected) points.
    int
    nVertices()
    Deprecated.
    Get the number of vertices used to represent this area.
    ROI
    scale(double scaleX, double scaleY, double originX, double originY)
    Deprecated.
    Create a scaled version of this ROI.
    String
    toString()
     
    ROI
    translate(double dx, double dy)
    Deprecated.
    Create a translated version of this ROI.
    ROI
    updatePlane(ImagePlane plane)
    Deprecated.
    Create a new ROI defining the same region on a different ImagePlane.

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

    Methods inherited from interface qupath.lib.roi.interfaces.ROI

    getScaledArea, getScaledLength, intersects, scale

  • Method Details

    • nVertices

      public int nVertices()
      Deprecated.
      Get the number of vertices used to represent this area. There is some 'fuzziness' to the meaning of this, since curved regions will be flattened and the same complex areas may be represented in different ways - nevertheless it provides some measure of the 'complexity' of the area.
      Returns:

    • getArea

      public double getArea()
      Deprecated.
      Description copied from interface: ROI
      Get the area of this ROI. For lines and points this returns 0.
      Specified by:
      getArea in interface ROI
      Returns:
      See Also:

    • getLength

      public double getLength()
      Deprecated.
      Description copied from interface: ROI
      Get ROI length. This is defined as
      • perimeter in the case of area ROIs
      • total length of line segments in the case of line or polyline ROIs
      • 0 in the case of point ROIs
      Specified by:
      getLength in interface ROI
      Returns:
      See Also:

    • getRoiName

      public String getRoiName()
      Deprecated.
      Description copied from interface: ROI
      Get a String representation of the kind of ROI we have, e.g. "Rectangle", "Ellipse", "Polygon"
      Specified by:
      getRoiName in interface ROI
      Returns:

    • getCentroidX

      public double getCentroidX()
      Deprecated.
      Get the x coordinate of the ROI centroid;

      Warning: If the centroid computation was too difficult (i.e. the area is particularly elaborate), then the center of the bounding box will be used instead! (However this should not be relied upon as it is liable to change in later versions)

      Specified by:
      getCentroidX in interface ROI
      Returns:

    • getCentroidY

      public double getCentroidY()
      Deprecated.
      Get the y coordinate of the ROI centroid;

      Warning: If the centroid computation was too difficult (i.e. the area is particularly elaborate), then the center of the bounding box will be used instead! (However this should not be relied upon as it is liable to change in later versions)

      Specified by:
      getCentroidY in interface ROI
      Returns:

    • contains

      public boolean contains(double x, double y)
      Deprecated.
      Description copied from interface: ROI
      Test is the ROI contains specified x, y coordinates. Only Area ROIs can return true, i.e. where ROI.isArea() returns true. All other ROIs (points, lines) return false.
      Specified by:
      contains in interface ROI
      Parameters:
      x -
      y -
      Returns:

    • intersects

      public boolean intersects(double x, double y, double width, double height)
      Deprecated.
      Description copied from interface: ROI
      Test if the ROI intersects a specified region.

      Note that this test is intended as a fast initial filter; a more detailed test using ROI.getGeometry() is recommended when exact results are needed.

      Specified by:
      intersects in interface ROI
      Parameters:
      x - the x coordinate of the region bounding box
      y - the y coordinate of the region bounding box
      width - the width of the region bounding box
      height - the height of the region bounding box
      Returns:
      true if the ROI intersects the region, false otherwise

    • duplicate

      @Deprecated public ROI duplicate()
      Deprecated.
      Description copied from interface: ROI
      Create a duplicate of the ROI.

      This method is deprecated, since ROIs are (or are moving towards being) immutable... making it pointless to duplicate them.

      Specified by:
      duplicate in interface ROI
      Returns:

    • translate

      public ROI translate(double dx, double dy)
      Deprecated.
      Description copied from interface: ROI
      Create a translated version of this ROI. The original ROI is unchanged.
      Specified by:
      translate in interface ROI
      Parameters:
      dx - horizontal translation
      dy - vertical translation
      Returns:

    • scale

      public ROI scale(double scaleX, double scaleY, double originX, double originY)
      Deprecated.
      Description copied from interface: ROI
      Create a scaled version of this ROI. Coordinates are multiplied by the given scaling factors, while the original ROI is unchanged.
      Specified by:
      scale in interface ROI
      Parameters:
      scaleX - horizontal scale value
      scaleY - vertical scale value
      originX - value subtracted from each x-ordinate prior to scaling, and added back afterwards
      originY - value subtracted from each y-ordinate prior to scaling, and added back afterwards
      Returns:
      See Also:

    • getScaledArea

      public double getScaledArea(double pixelWidth, double pixelHeight)
      Deprecated.
      Description copied from interface: ROI
      Get scaled area of the ROI, for use with calibrated pixel sizes.
      Specified by:
      getScaledArea in interface ROI
      Parameters:
      pixelWidth -
      pixelHeight -
      Returns:
      See Also:

    • getScaledLength

      public double getScaledLength(double pixelWidth, double pixelHeight)
      Deprecated.
      Description copied from interface: ROI
      Get the scaled length, for use with calibrated pixel sizes.
      Specified by:
      getScaledLength in interface ROI
      Parameters:
      pixelWidth -
      pixelHeight -
      Returns:
      See Also:

    • getBoundsX

      public double getBoundsX()
      Deprecated.
      Description copied from interface: ROI
      Returns the x coordinate for the top left of the ROI bounding box.
      Specified by:
      getBoundsX in interface ROI
      Returns:

    • getBoundsY

      public double getBoundsY()
      Deprecated.
      Description copied from interface: ROI
      Returns the y coordinate for the top left of the ROI bounding box.
      Specified by:
      getBoundsY in interface ROI
      Returns:

    • getBoundsWidth

      public double getBoundsWidth()
      Deprecated.
      Description copied from interface: ROI
      Returns the width of the ROI bounding box.
      Specified by:
      getBoundsWidth in interface ROI
      Returns:

    • getBoundsHeight

      public double getBoundsHeight()
      Deprecated.
      Description copied from interface: ROI
      Returns the height of the ROI bounding box.
      Specified by:
      getBoundsHeight in interface ROI
      Returns:

    • getAllPoints

      public List<Point2> getAllPoints()
      Deprecated.
      Beware this method! This will return all polygon points (useful e.g. for convex hull calculations), but since the area itself isn't necessarily polygonal then tracing through the points does *not* necessarily result in the same shape as that which the area represents.
      Specified by:
      getAllPoints in interface ROI
      Returns:

    • updatePlane

      public ROI updatePlane(ImagePlane plane)
      Deprecated.
      Description copied from interface: ROI
      Create a new ROI defining the same region on a different ImagePlane. The original ROI is unchanged.
      Specified by:
      updatePlane in interface ROI
      Parameters:
      plane - the new plane to use
      Returns:
      Throws:
      UnsupportedOperationException - because AreaROI is a legacy class that is no longer supported

    • equals

      public boolean equals(Object o)
      Deprecated.
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Deprecated.
      Overrides:
      hashCode in class Object

    • getGeometry

      public Geometry getGeometry()
      Deprecated.
      Description copied from interface: ROI
      Returns a org.locationtech.jts.geom.Geometry object.
      Specified by:
      getGeometry in interface ROI
      Returns:

    • getShape

      public Shape getShape()
      Deprecated.
      Description copied from interface: ROI
      Returns a java.awt.Shape representing this ROI, if possible.

      Note that PointROI throws an UnsupportedOperationException as it cannot adequately be represented by a Shape object.

      Specified by:
      getShape in interface ROI
      Returns:

    • createShape

      protected Shape createShape()
      Deprecated.
      Create a Shape object to represent the ROI.
      Returns:
      a new Shape object

    • getRoiType

      public ROI.RoiType getRoiType()
      Deprecated.
      Description copied from interface: ROI
      Get the RoiType, used to distinguish between points, lines and areas.
      Specified by:
      getRoiType in interface ROI
      Returns:

    • getImagePlane

      public ImagePlane getImagePlane()
      Description copied from interface: ROI
      Get the ImagePlane, which contains the values for c, z and t in a single object.
      Specified by:
      getImagePlane in interface ROI
      Returns:

    • getZ

      public int getZ()
      Description copied from interface: ROI
      Get z-stack slice index.

      Default is 0 if the image it relates to is not a z-stack.

      Specified by:
      getZ in interface ROI
      Returns:

    • getT

      public int getT()
      Description copied from interface: ROI
      Get time point index.

      Default is 0 if the image it relates to is not a time series.

      Specified by:
      getT in interface ROI
      Returns:

    • getC

      public int getC()
      Description copied from interface: ROI
      Get channel index, or -1 if the ROI relates to all available channels.

      (This is not currently used, but may be in the future)

      Specified by:
      getC in interface ROI
      Returns:

    • getShapeInternal

      protected Shape getShapeInternal()
      Get a (possibly cached) shape representation of the ROI. This may be mutable, and so should not be passed outside the class.
      Returns:

    • isEmpty

      public boolean isEmpty()
      True if the bounding box has zero area
      Specified by:
      isEmpty in interface ROI
      Returns:

    • intersectsBounds

      protected boolean intersectsBounds(double x, double y, double width, double height)
      Quick check whether the specified rectangle intersects with the bounds of this ROI. This can be used to avoid a more expensive intersection check.
      Parameters:
      x - x coordinate of the rectangle to test
      y - y coordinate of the rectangle to test
      width - width of the rectangle to test
      height - height of the rectangle to test
      Returns:
      true if the bounds intersect, false otherwise

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getNumPoints

      public int getNumPoints()
      Default implementation, calls ROI.getAllPoints() and then caches the result. Subclasses may override for efficiency.
      Specified by:
      getNumPoints in interface ROI
      Returns:
      Implementation Note
      the default implementation assumes that ROIs are immutable.

    • isLine

      public boolean isLine()
      Description copied from interface: ROI
      Returns true if this ROI consists of line segments and does not enclose an area.
      Specified by:
      isLine in interface ROI
      Returns:

    • isArea

      public boolean isArea()
      Description copied from interface: ROI
      Returns true if this ROI encloses an area.
      Specified by:
      isArea in interface ROI
      Returns:

    • isPoint

      public boolean isPoint()
      Description copied from interface: ROI
      Returns true if this ROI represents distinct (unconnected) points.
      Specified by:
      isPoint in interface ROI
      Returns:

    • getConvexHull

      public ROI getConvexHull()
      Default implementation using JTS. Subclasses may replace this with a more efficient implementation.
      Specified by:
      getConvexHull in interface ROI
      Returns:

    • getSolidity

      public double getSolidity()
      Description copied from interface: ROI
      Calculate the solidity, defined as ROI area / convex hull area. Returns Double.NaN if the ROI does not represent an area.
      Specified by:
      getSolidity in interface ROI
      Returns: