Package ij.gui

Class ShapeRoi

java.lang.Object
ij.gui.Roi
ij.gui.ShapeRoi
All Implemented Interfaces:
Serializable, Cloneable, Iterable<Point>
public class ShapeRoi
extends Roi
A subclass of ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape. A ShapeRoi is constructed from a ij.gui.Roi object, or as a result of logical operators (i.e., union, intersection, exclusive or, and subtraction) provided by this class. These operators use the package java.awt.geom as a backend.
This code is in the public domain.
Author:
Cezar M.Tigaret
See Also:
Serialized Form

  • Constructor Details

    • ShapeRoi

      public ShapeRoi​(Roi r)
      Constructs a ShapeRoi from an Roi.

    • ShapeRoi

      public ShapeRoi​(Shape s)
      Constructs a ShapeRoi from a Shape.

    • ShapeRoi

      public ShapeRoi​(int x, int y, Shape s)
      Constructs a ShapeRoi from a Shape.

    • ShapeRoi

      public ShapeRoi​(float[] shapeArray)
      Constructs a ShapeRoi from an array of variable length path segments. Each segment consists of the segment type followed by 0-6 coordintes (0-3 end points and control points). Depending on the type, a segment uses from 1 to 7 elements of the array.

  • Method Details

    • clone

      public Object clone()
      Returns a deep copy of this.
      Overrides:
      clone in class Roi

    • or

      public ShapeRoi or​(ShapeRoi sr)
      Unary union operator. The caller is set to its union with the argument.
      Returns:
      the union of this and sr

    • and

      public ShapeRoi and​(ShapeRoi sr)
      Unary intersection operator. The caller is set to its intersection with the argument (i.e., the overlapping regions between the operands).
      Returns:
      the overlapping regions between this and sr

    • xor

      public ShapeRoi xor​(ShapeRoi sr)
      Unary exclusive or operator. The caller is set to the non-overlapping regions between the operands.
      Returns:
      the union of the non-overlapping regions of this and sr

    • not

      public ShapeRoi not​(ShapeRoi sr)
      Unary subtraction operator. The caller is set to the result of the operation between the operands.
      Returns:
      this subtracted from sr

    • getRois

      public Roi[] getRois()
      Converts a Shape into Roi object(s).
      This method parses the shape into (possibly more than one) Roi objects and returns them in an array.
      A simple, "regular" path results in a single Roi following these simple rules:
      Shape type Roi class Roi type
      java.awt.geom.Rectangle2D.Double ij.gui.Roi Roi.RECTANGLE
      java.awt.geom.Ellipse2D.Double ij.gui.OvalRoi Roi.OVAL
      java.awt.geom.Line2D.Double ij.gui.Line Roi.LINE
      java.awt.Polygon ij.gui.PolygonRoi Roi.POLYGON


      Each subpath of a java.awt.geom.GeneralPath is converted following these rules:
      Segment
      types       		Number of
      segments       		Closed
      path       		Value of
      forceAngle       		Value of
      forceTrace       		Roi type
      lines only: 0 ShapeRoi.NO_TYPE
      1 ShapeRoi.NO_TYPE
      2 Y ShapeRoi.NO_TYPE
      N Roi.LINE
      3 Y N Roi.POLYGON
      N Y Roi.ANGLE
      N N Roi.POLYLINE
      4 Y Roi.RECTANGLE
      N Roi.POLYLINE
      <= MAXPOLY Y Roi.POLYGON
      N Roi.POLYLINE
      > MAXPOLY Y Y Roi.TRACED_ROI
      N Roi.FREEROI
      N Roi.FREELINE
      anything
      else:       		<= 2 ShapeRoi.NO_TYPE
      > 2 ShapeRoi.SHAPE_ROI
      Returns:
      an array of ij.gui.Roi objects.

    • shapeToRoi

      public Roi shapeToRoi()
      Attempts to convert this ShapeRoi into a single non-composite Roi.
      Returns:
      an ij.gui.Roi object or null if it cannot be simplified to become a non-composite roi.

    • trySimplify

      public Roi trySimplify()
      Attempts to convert this ShapeRoi into a single non-composite Roi. For showing as a Roi, one should apply copyAttributes
      Returns:
      an ij.gui.Roi object, which is either the non-composite roi, or this ShapeRoi (if such a conversion is not possible) or null if this is an empty roi.

    • contains

      public boolean contains​(int x, int y)
      Checks whether the center of the specified pixel inside of this ROI's shape boundaries. Note the ImageJ convention of 0.5 pixel shift between outline and pixel center, i.e., pixel (0,0) is enclosed by the rectangle spanned between (0,0) and (1,1). The value slightly below 0.5 is for rounding according to the ImageJ convention (which is opposite to that of the java.awt.Shape class): In ImageJ, points exactly at the left (right) border are considered outside (inside); points exactly on horizontal borders, are considered outside (inside) at the border with the lower (higher) y.
      Overrides:
      contains in class Roi

    • containsPoint

      public boolean containsPoint​(double x, double y)
      Returns whether coordinate (x,y) is contained in the Roi. Note that the coordinate (0,0) is the top-left corner of pixel (0,0). Use contains(int, int) to determine whether a given pixel is contained in the Roi.
      Overrides:
      containsPoint in class Roi

    • getLength

      public double getLength()
      Returns the perimeter of this ShapeRoi.
      Overrides:
      getLength in class Roi

    • getShapeAsArray

      public float[] getShapeAsArray()
      Retrieves the end points and control points of the path as a float array. The array contains a sequence of variable length segments that use from from one to seven array elements. The first element of a segment is the type as defined in the PathIterator interface. SEG_MOVETO and SEG_LINETO segments also include two coordinates (one end point), SEG_QUADTO segments include four coordinates and SEG_CUBICTO segments include six coordinates (three points). Coordinates are with respect to the image bounds, not the Roi bounds.

    • draw

      public void draw​(Graphics g)
      Non-destructively draws the shape of this object on the associated ImagePlus.
      Overrides:
      draw in class Roi

    • drawRoiBrush

      public void drawRoiBrush​(Graphics g)

    • drawPixels

      public void drawPixels​(ImageProcessor ip)
      Draws the shape of this object onto the specified ImageProcessor.
      This method will always draw a flattened version of the actual shape (i.e., all curve segments will be approximated by line segments).
      Overrides:
      drawPixels in class Roi
      See Also:
      ImageProcessor.setColor(java.awt.Color), ImageProcessor.setLineWidth(int)

    • getMask

      public ImageProcessor getMask()
      Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask set to white (255) and pixels "outside" the mask set to black (0). Takes into account the usual ImageJ convention of 0.5 pxl shift between the outline and pixel coordinates; e.g., pixel (0,0) is surrounded by the rectangle spanned between (0,0) and (1,1). Note that apart from the 0.5 pixel shift, ImageJ has different convention for the border points than the java.awt.Shape class: In ImageJ, points exactly at the left (right) border are considered outside (inside); points exactly on horizontal borders, are considered outside (inside) at the border with the lower (higher) y.
      Overrides:
      getMask in class Roi

    • getShape

      public Shape getShape()
      Returns a reference to the Shape object encapsulated by this ShapeRoi.

    • isHandle

      public int isHandle​(int sx, int sy)
      Always returns -1 since ShapeRois do not have handles.
      Overrides:
      isHandle in class Roi

    • getSelectionCoordinates

      public FloatPolygon getSelectionCoordinates()
      Used by the getSelectionCoordinates macro function

    • getFloatPolygon

      public FloatPolygon getFloatPolygon​(double flatness, boolean separateSubpaths, boolean addPointForClose, boolean absoluteCoord)
      Returns a FloatPolygon with all vertices of the flattened shape, i.e., the shape approximated by straight line segments. This method is for listing the coordinates and creating the convex hull.
      Parameters:
      flatness - Roughly the maximum allowable distance between the shape and the approximate polygon
      separateSubpaths - whether individual subpaths should be separated by NaN coordinates
      addPointForClose - whether the starting point of a closed subpath should be repeated at its end. Note that with addPointForClose = false, there is no distinction between open and closed subpaths.
      absoluteCoord - specifies whether the coordinates should be with respect to image bounds, not Roi bounds.

    • getFloatPolygon

      public FloatPolygon getFloatPolygon​(Shape shape, double flatness, boolean separateSubpaths, boolean addPointForClose, boolean absoluteCoord)

    • getFloatConvexHull

      public FloatPolygon getFloatConvexHull()
      Description copied from class: Roi
      Returns the convex hull of this Roi as a FloatPolygon. Coordinates of the convex hull are image pixel coordinates.
      Overrides:
      getFloatConvexHull in class Roi

    • getPolygon

      public Polygon getPolygon()
      Description copied from class: Roi
      Returns the outline of this selection as a Polygon, or null if this is a straight line selection.
      Overrides:
      getPolygon in class Roi
      See Also:
      ImageProcessor.setRoi(java.awt.Rectangle), ImageProcessor.drawPolygon(java.awt.Polygon), ImageProcessor.fillPolygon(java.awt.Polygon)

    • getFloatPolygon

      public FloatPolygon getFloatPolygon()
      Returns all vertex points of the shape as approximated by polygons, in image pixel coordinates
      Overrides:
      getFloatPolygon in class Roi

    • getFloatPolygon

      public FloatPolygon getFloatPolygon​(String options)
      Returns all vertex points of the shape as approximated by polygons, where options may include "close" to add points to close each subpath, and "separate" to insert NaN values between subpaths (= individual polygons)
      Overrides:
      getFloatPolygon in class Roi

    • size

      public int size()
      Retuns the number of vertices, of this shape as approximated by straight lines. Note that points might be counted twice where the shape gets closed.
      Overrides:
      size in class Roi