Module ij
Package ij.gui

Class Roi

java.lang.Object
ij.gui.Roi
All Implemented Interfaces:
Serializable, Cloneable, Iterable<Point>
Direct Known Subclasses:
ImageRoi, Line, OvalRoi, PolygonRoi, ShapeRoi, TextRoi

public class Roi extends Object implements Cloneable, Serializable, Iterable<Point>
A rectangular region of interest and superclass for the other ROI classes. This class implements Iterable<Point> and can thus be used to iterate over the contained coordinates. Usage example:
 Roi roi = ...;
 for (Point p : roi) {
   // process p
 }
 
Convention for subpixel resolution and zooming in:
  • Area ROIs: Integer coordinates refer to the top-left corner of the pixel with these coordinates. Thus, pixel (0,0) is enclosed by the rectangle spanned between points (0,0) and (1,1), i.e., a rectangle at (0,0) with width = height = 1 pixel.
  • Line and Point Rois: Integer coordinates refer to the center of a pixel. Thus, a line from (0,0) to (1,0) has its start and end points in the center of pixels (0,0) and (1,0), respectively, and drawing the line should affect both pixels. For images dispplayed at high zoom levels, this means that (open) lines and single points are displayed 0.5 pixels further to the right and bottom than the outlines of area ROIs (closed lines) with the same coordinates.
Note that rectangular and (nonrotated) oval ROIs do not support subpixel resolution. Since ImageJ 1.52t, this convention does not depend on the Prefs.subpixelResolution (previously accessible via Edit>Options>Plot) and this flag has no effect any more.
See Also:
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
     
    protected double
     
    protected boolean
     
    protected ImageProcessor
     
    protected boolean
     
    protected ImagePlus
     
    protected int
     
    protected int
     
    protected int
     
    protected int
     
    static final int
     
    protected boolean
     
    static final int
     
    protected static Color
     
    protected static Color
     
    static final int
     
    static final int
     
    protected Color
     
    protected double
     
    static final int
     
    static final int
     
    static final int
     
    protected Color
     
    protected ImageCanvas
     
    protected boolean
     
    protected ImagePlus
     
    protected Color
     
    static final int
     
    protected static int
     
    protected double
     
    static final int
     
    static final int
     
    protected boolean
     
    static final int
     
    static final int
     
    protected int
     
    protected int
     
    protected int
     
    protected int
     
    static final BasicStroke
     
    static final int
     
    protected boolean
     
    protected static int
     
    static final int
     
    static final int
     
    static final int
     
    static Roi
    Get using getPreviousRoi() and set using setPreviousRoi()
    static final int
     
    static final int
     
    protected static Color
     
    protected BasicStroke
     
    protected Color
     
    static final int
     
    protected int
     
    protected boolean
     
    protected boolean
     
    protected int
     
    protected int
     
  • Constructor Summary

    Constructors
    Constructor
    Description
    Roi(double x, double y, double width, double height)
    Creates a rectangular ROI using double arguments.
    Roi(double x, double y, double width, double height, int cornerDiameter)
    Creates a rounded rectangular ROI using double arguments.
    Roi(int x, int y, int width, int height)
    Creates a rectangular ROI.
    Roi(int x, int y, int width, int height, int cornerDiameter)
    Creates a new rounded rectangular ROI.
    Roi(int x, int y, int width, int height, ImagePlus imp)
    Deprecated. 
    Roi(int sx, int sy, ImagePlus imp)
    Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
    Roi(int sx, int sy, ImagePlus imp, int cornerDiameter)
    Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
    Creates a new rectangular Roi.
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Aborts constructing or modifying the roi (called by the ImageJ class on escape)
    void
     
    static void
     
    protected int
     
    Returns a copy of this roi.
    boolean
    contains(int x, int y)
    Returns whether the center of pixel (x,y) is contained in the Roi.
    boolean
    containsPoint(double x, double y)
    Returns whether coordinate (x,y) is contained in the Roi.
    static Roi
    Converts a line selection into an area (polygon or composite) selection.
    Author: Michael Schmid
    Deprecated. 
    void
    Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
    static Roi
    create(double x, double y, double width, double height)
    Creates a rectangular ROI.
    static Roi
    create(double x, double y, double width, double height, int cornerDiameter)
    Creates a rounded rectangular ROI.
    void
     
    void
     
    void
    Deprecated.
    replaced by drawPixels(ImageProcessor)
    void
    Draws the selection outline on the specified ImageProcessor.
    void
     
    void
     
    boolean
    Checks whether two rectangles are equal.
    double
    Overridden by PolygonRoi (angle between first two points), TextRoi (text angle) and Line (line angle).
    double
    getAngle(int x1, int y1, int x2, int y2)
    Returns the angle in degrees between the specified line and a horizontal line.
    boolean
     
    Deprecated.
    replaced by getBounds()
    Returns this selection's bounding rectangle.
    static Color
    Returns the default (global) color used for drawing ROI outlines.
    Returns the coordinates of the pixels inside this ROI as a FloatPolygon.
    Returns the coordinates of the pixels inside this ROI as an array of Points.
    double[]
     
    Returns the convex hull of this Roi as a Polygon with integer coordinates by rounding the floating-point values.
    int
    Returns the rounded rectangle corner diameter (pixels).
    final int
    Returns the channel position of this ROI, or zero if this ROI is not associated with a particular channel.
    static int
    Returns the current paste transfer mode.
     
    static Color
     
    static int
    Returns the group value assigned to newly created ROIs.
    static int
    Returns the default handle size.
    static double
    Returns the default stroke width.
    boolean
    Deprecated.
    Drawoffset is not used any more.
    double
    Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
    double[]
    Returns an array with the following values:
    [0] "Feret" (maximum caliper width)
    [1] "FeretAngle" (angle of diameter with maximum caliper width, between 0 and 180 deg)
    [2] "MinFeret" (minimum caliper width)
    [3][4] , "FeretX" and "FeretY", the X and Y coordinates of the starting point (leftmost point) of the maximum-caliper-width diameter.
    Returns the fill color used to display this ROI, or null if it is displayed transparently.
    double
    getFloatAngle(double x1, double y1, double x2, double y2)
    Returns the angle in degrees between the specified line and a horizontal line.
    Returns this selection's bounding rectangle (with subpixel accuracy).
    Returns the convex hull of this Roi as a FloatPolygon.
    double
     
    Returns the outline of this selection as a FloatPolygon
    Returns the outline in image pixel coordinates, where options may include "close" to add a point to close the outline if this is an area roi and the outline is not closed yet.
    double
     
    int
    Returns the group attribute of this ROI.
    static String
    getGroupName(int groupNumber)
    Returns the group name associtated with the specified group.
    static String
    Returns the group names as a comma-delimeted string.
    int
    Returns the current handle size.
    int
    Returns a hashcode for this Roi that typically changes if it is moved, even though it is still the same object.
    Returns the ImagePlus associated with this ROI, or null.
    int
    Returns the ID of the image associated with this ROI.
    Returns, as a FloatPolygon, an interpolated version of this selection that has points spaced 1.0 pixel apart.
    getInterpolatedPolygon(double interval, boolean smooth)
    Returns, as a FloatPolygon, an interpolated version of this selection with points spaced 'interval' pixels apart.
    protected FloatPolygon
    getInterpolatedPolygon(FloatPolygon p, double interval, boolean smooth)
    Returns, as a FloatPolygon, an interpolated version of this selection with points spaced abs('interval') pixels apart.
    Returns the inverted roi, or null if this is not an area roi or cannot be converted to a ShapeRoi.
    double
    Returns the perimeter length.
    static Vector
     
    protected double
     
    Always returns null for rectangular Roi's
    Returns the name of this ROI, or null.
    int
    Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
    Returns the outline of this selection as a Polygon.
    int
    Returns the stack position (image number) of this ROI, or zero if the ROI is not associated with a particular stack image.
    static Roi
    Returns the Roi saved by setPreviousRoi().
     
    getProperty(String property)
     
    int
     
     
     
    int
    Obsolete; replaced by getCornerDiameter().
    protected BasicStroke
     
    boolean
    Returns 'true' if the stroke width is scaled as images are zoomed.
    int
     
     
    Returns the Stroke used to draw this ROI, or null if no Stroke is used.
    Returns the the color used to draw the ROI outline or null if the default color is being used.
    float
    Returns the lineWidth.
    final int
    Returns the frame position of this ROI, or zero if this ROI is not associated with a particular frame.
    int
     
    Convenience method that converts Roi type to a human-readable form.
    double
     
    double
     
    final int
    Returns the slice position of this ROI, or zero if this ROI is not associated with a particular slice.
    protected void
    grow(int sx, int sy)
     
    protected void
    handleMouseDown(int sx, int sy)
     
    protected void
    handleMouseDrag(int sx, int sy, int flags)
     
    protected void
    handleMouseUp(int screenX, int screenY)
     
    boolean
    Returns 'true' if setPosition(C,Z,T) has been called.
    final boolean
    Returns 'true' if this ROI is displayed and is also in an overlay.
    boolean
    Returns 'true' if this is an area selection.
    boolean
     
    boolean
    Returns 'true' if this is an ROI primarily used from drawing (e.g., TextRoi or Arrow).
    int
    isHandle(int sx, int sy)
    Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
    static boolean
    isInteger(double x)
    Returns whether a number is an integer
    boolean
    Returns 'true' if this is a line selection.
    protected boolean
    Return 'true' if this is a line or point selection.
    boolean
    Returns true if this ROI is currently displayed on an image.
    Required by the Iterable interface.
    static double[]
    lineCircleIntersection(double ax, double ay, double bx, double by, double cx, double cy, double rad, boolean ignoreOutside)
    Calculates intersections of a line segment with a circle Author N.Vischer ax, ay, bx, by: points A and B of line segment cx, cy, rad: Circle center and radius.
    protected boolean
    Returns whether a roi created interactively should have subpixel resolution, (if the roi type supports it), i.e., whether the magnification is high enough
    protected static boolean
    magnificationForSubPixel(double magnification)
     
    protected void
    mouseDownInHandle(int handle, int sx, int sy)
     
    void
     
    void
     
    void
     
    protected void
    moveHandle(int sx, int sy)
     
    void
     
    void
    nudge(int key)
    Nudge ROI one pixel on arrow key press.
    void
    nudgeCorner(int key)
    Nudge lower right corner of rectangular and oval ROIs by one pixel based on arrow key press.
    protected int
    offScreenX(int sx)
    Converts image canvas screen x coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    protected double
    offScreenXD(int sx)
    Converts image canvas screen x coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    protected int
    offScreenY(int sy)
    Converts image canvas screen y coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    protected double
    offScreenYD(int sy)
    Converts image canvas screen y coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    static void
     
    static void
     
    static void
     
    protected int
    screenX(int ox)
     
    protected int
    screenXD(double ox)
    Converts an image pixel x (offscreen)coordinate to a screen x coordinate, taking the the line or area convention for coordinates into account
    protected int
    screenY(int oy)
     
    protected int
    screenYD(double oy)
    Converts an image pixel y (offscreen)coordinate to a screen y coordinate, taking the the line or area convention for coordinates into account
    void
    setAntiAlias(boolean antiAlias)
     
    void
    Sets the bounds of rectangular, oval or text selections.
    static void
    Sets the default (global) color used for ROI outlines.
    void
    setCornerDiameter(int cornerDiameter)
    Sets the rounded rectangle corner diameter (pixels).
    static void
    Sets the default stroke color.
    static void
     
    static void
    setDefaultGroup(int group)
    Sets the group value assigned to newly created ROIs, and also sets the default ROI color to the group color.
    static void
    setDefaultStrokeWidth(double width)
    Sets the default stroke width.
    void
    setDrawOffset(boolean drawOffset)
    Deprecated.
    This method was previously used to draw lines and polylines shifted by 0.5 pixels top the bottom and right, for better agreement with the position used by ProfilePlot, with the default taken from Prefs.subPixelResolution.
    void
    Sets the fill color used to display this ROI, or set to null to display it transparently.
    void
    setFlattenScale(double scale)
     
    void
    setGroup(int group)
    Sets the group of this Roi, and updates stroke color accordingly.
    static void
    setGroupName(int groupNumber, String name)
     
    static void
    Sets the group names from a comma-delimeted string.
    void
    setHandleSize(int size)
    Sets the current handle size.
    void
    setIgnoreClipRect(boolean ignoreClipRect)
     
    void
    Sets the ImagePlus associated with this ROI.
    void
    Deprecated.
    replaced by setStrokeColor()
    void
    setIsCursor(boolean isCursor)
     
    void
    setLineWidth(int width)
    Deprecated.
    replaced by setStrokeWidth(int)
    void
    setLocation(double x, double y)
    Set the location of the ROI in image coordinates.
    void
    setLocation(int x, int y)
    Set the location of the ROI in image coordinates.
    void
    Sets the name of this ROI.
    void
    setNonScalable(boolean nonScalable)
    Set 'nonScalable' true to have TextRois in a display list drawn at a fixed location and size.
    static void
    setPasteMode(int transferMode)
    Sets the Paste transfer mode.
    void
    setPosition(int n)
    Sets the stack position (image number) of this ROI.
    void
    setPosition(int channel, int slice, int frame)
    Sets the hyperstack position of this ROI.
    void
    Sets the position of this ROI based on the stack position of the specified image.
    static void
    Saves 'roi' so it can be restored later using Edit/Selection/Restore Selection.
    void
    setProperties(String properties)
     
    void
    setProperty(String key, String value)
     
    void
     
    protected void
     
    void
    setRotationCenter(double x, double y)
     
    void
    setRoundRectArcSize(int cornerDiameter)
    Obsolete; replaced by setCornerDiameter().
    void
    Sets the Stroke used to draw this ROI.
    void
    Sets the color used by this ROI to draw its outline.
    void
    setStrokeWidth(double strokeWidth)
    This is a version of setStrokeWidth() that accepts a double argument.
    void
    setStrokeWidth(float strokeWidth)
    Sets the width of the line used to draw this ROI.
    void
    setUnscalableStrokeWidth(double strokeWidth)
    Sets the width of the line used to draw this ROI and prevents the width from increasing when the image is zoomed.
    void
     
    int
    Returns the number of points in this selection; equivalent to getFloatPolygon().npoints.
    void
    startPaste(ImagePlus clipboard)
     
    boolean
    Returns true if this is a slection that supports sub-pixel resolution.
    void
    Deprecated
    static float[]
    toFloat(int[] arr)
    Converts an int array to a float array.
    static int[]
    toInt(float[] arr)
    Converts a float array to an int array using truncation.
    static int[]
    toInt(float[] arr, int[] arr2, int size)
     
    static int[]
    toIntR(float[] arr)
    Converts a float array to an int array using rounding.
     
    void
    update(boolean add, boolean subtract)
    If 'add' is true, adds this selection to the previous one.
    protected void
     
    void
    updateWideLine(float width)
     
    protected boolean
    Returns 'true' if this ROI uses for drawing the convention for line and point ROIs, where the coordinates are with respect to the pixel center.
    static Roi
    xor(Roi[] rois)
     

    Methods inherited from class java.lang.Object

    finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    Methods inherited from interface java.lang.Iterable

    forEach, spliterator
  • Field Details

    • CONSTRUCTING

      public static final int CONSTRUCTING
      See Also:
    • MOVING

      public static final int MOVING
      See Also:
    • RESIZING

      public static final int RESIZING
      See Also:
    • NORMAL

      public static final int NORMAL
      See Also:
    • MOVING_HANDLE

      public static final int MOVING_HANDLE
      See Also:
    • RECTANGLE

      public static final int RECTANGLE
      See Also:
    • OVAL

      public static final int OVAL
      See Also:
    • POLYGON

      public static final int POLYGON
      See Also:
    • FREEROI

      public static final int FREEROI
      See Also:
    • TRACED_ROI

      public static final int TRACED_ROI
      See Also:
    • LINE

      public static final int LINE
      See Also:
    • POLYLINE

      public static final int POLYLINE
      See Also:
    • FREELINE

      public static final int FREELINE
      See Also:
    • ANGLE

      public static final int ANGLE
      See Also:
    • COMPOSITE

      public static final int COMPOSITE
      See Also:
    • POINT

      public static final int POINT
      See Also:
    • HANDLE_SIZE

      public static final int HANDLE_SIZE
      See Also:
    • NOT_PASTING

      public static final int NOT_PASTING
      See Also:
    • FERET_ARRAYSIZE

      public static final int FERET_ARRAYSIZE
      See Also:
    • FERET_ARRAY_POINTOFFSET

      public static final int FERET_ARRAY_POINTOFFSET
      See Also:
    • onePixelWide

      public static final BasicStroke onePixelWide
    • ROIColor

      protected static Color ROIColor
    • pasteMode

      protected static int pasteMode
    • lineWidth

      protected static int lineWidth
    • defaultFillColor

      protected static Color defaultFillColor
    • previousRoi

      public static Roi previousRoi
      Get using getPreviousRoi() and set using setPreviousRoi()
    • type

      protected int type
    • xMax

      protected int xMax
    • yMax

      protected int yMax
    • imp

      protected ImagePlus imp
    • ic

      protected ImageCanvas ic
    • oldX

      protected int oldX
    • oldY

      protected int oldY
    • oldWidth

      protected int oldWidth
    • oldHeight

      protected int oldHeight
    • clipX

      protected int clipX
    • clipY

      protected int clipY
    • clipWidth

      protected int clipWidth
    • clipHeight

      protected int clipHeight
    • clipboard

      protected ImagePlus clipboard
    • constrain

      protected boolean constrain
    • center

      protected boolean center
    • aspect

      protected boolean aspect
    • updateFullWindow

      protected boolean updateFullWindow
    • mag

      protected double mag
    • asp_bk

      protected double asp_bk
    • cachedMask

      protected ImageProcessor cachedMask
    • handleColor

      protected Color handleColor
    • strokeColor

      protected Color strokeColor
    • instanceColor

      protected Color instanceColor
    • fillColor

      protected Color fillColor
    • stroke

      protected BasicStroke stroke
    • nonScalable

      protected boolean nonScalable
    • overlay

      protected boolean overlay
    • wideLine

      protected boolean wideLine
    • ignoreClipRect

      protected boolean ignoreClipRect
    • flattenScale

      protected double flattenScale
    • defaultColor

      protected static Color defaultColor
  • Constructor Details

    • Roi

      public Roi(int x, int y, int width, int height)
      Creates a rectangular ROI.
    • Roi

      public Roi(double x, double y, double width, double height)
      Creates a rectangular ROI using double arguments.
    • Roi

      public Roi(int x, int y, int width, int height, int cornerDiameter)
      Creates a new rounded rectangular ROI.
    • Roi

      public Roi(double x, double y, double width, double height, int cornerDiameter)
      Creates a rounded rectangular ROI using double arguments.
    • Roi

      public Roi(Rectangle r)
      Creates a new rectangular Roi.
    • Roi

      public Roi(int sx, int sy, ImagePlus imp)
      Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
    • Roi

      public Roi(int sx, int sy, ImagePlus imp, int cornerDiameter)
      Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates. For rectangular rois, also a corner diameter may be specified to make it a rounded rectangle
    • Roi

      public Roi(int x, int y, int width, int height, ImagePlus imp)
      Deprecated.
  • Method Details

    • create

      public static Roi create(double x, double y, double width, double height)
      Creates a rectangular ROI.
    • create

      public static Roi create(double x, double y, double width, double height, int cornerDiameter)
      Creates a rounded rectangular ROI.
    • setLocation

      public void setLocation(int x, int y)
      Set the location of the ROI in image coordinates.
    • setLocation

      public void setLocation(double x, double y)
      Set the location of the ROI in image coordinates.
    • setImage

      public void setImage(ImagePlus imp)
      Sets the ImagePlus associated with this ROI. imp may be null to remove the association to an image.
    • getImage

      public ImagePlus getImage()
      Returns the ImagePlus associated with this ROI, or null.
    • getImageID

      public int getImageID()
      Returns the ID of the image associated with this ROI.
    • getType

      public int getType()
    • getState

      public int getState()
    • getLength

      public double getLength()
      Returns the perimeter length.
    • getFeretsDiameter

      public double getFeretsDiameter()
      Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
    • getFeretValues

      public double[] getFeretValues()
      Returns an array with the following values:
      [0] "Feret" (maximum caliper width)
      [1] "FeretAngle" (angle of diameter with maximum caliper width, between 0 and 180 deg)
      [2] "MinFeret" (minimum caliper width)
      [3][4] , "FeretX" and "FeretY", the X and Y coordinates of the starting point (leftmost point) of the maximum-caliper-width diameter.
      [5-7] reserved
      All these values and point coordinates are in calibrated image coordinates.

      The following array elements are end points of the maximum and minimum caliper diameter, in unscaled image pixel coordinates:
      [8][9] "FeretX1", "FeretY1"; unscaled versions of "FeretX" and "FeretY" (subclasses may use any end of the diameter, not necessarily the left one)
      [10][11] "FeretX2", "FeretY2", end point of the maxium-caliper-width diameter. Both of these points are vertices of the convex hull.
      The final four array elements are the starting and end points of the minimum caliper width,
      [12],[13] "MinFeretX", "MinFeretY", and
      [14],[15] "MinFeretX2", "MinFeretY2". These two pooints are not sorted by x, but the first point point (MinFeretX, MinFeretY) is guaranteed to be a vertex of the convex hull, while second point (MinFeretX2, MinFeretY2) usually is not a vertex point but at a boundary line of the convex hull.

    • getConvexHull

      public Polygon getConvexHull()
      Returns the convex hull of this Roi as a Polygon with integer coordinates by rounding the floating-point values. Coordinates of the convex hull are image pixel coordinates.
    • getFloatConvexHull

      public FloatPolygon getFloatConvexHull()
      Returns the convex hull of this Roi as a FloatPolygon. Coordinates of the convex hull are image pixel coordinates.
    • getBounds

      public Rectangle getBounds()
      Returns this selection's bounding rectangle.
    • getFloatBounds

      public Rectangle2D.Double getFloatBounds()
      Returns this selection's bounding rectangle (with subpixel accuracy).
    • setBounds

      public void setBounds(Rectangle2D.Double b)
      Sets the bounds of rectangular, oval or text selections. Note that for these types, subpixel resolution is ignored, and the x,y values are rounded down, the width and height values rounded up. Do not use for other ROI types since their width and height are results of a calculation. For translating ROIs, use setLocation.
    • getBoundingRect

      public Rectangle getBoundingRect()
      Deprecated.
      replaced by getBounds()
    • getPolygon

      public Polygon getPolygon()
      Returns the outline of this selection as a Polygon.
      See Also:
    • getFloatPolygon

      public FloatPolygon getFloatPolygon()
      Returns the outline of this selection as a FloatPolygon
    • getFloatPolygon

      public FloatPolygon getFloatPolygon(String options)
      Returns the outline in image pixel coordinates, where options may include "close" to add a point to close the outline if this is an area roi and the outline is not closed yet. (For ShapeRois, "separate" inserts NaN values between subpaths).
    • getInterpolatedPolygon

      public FloatPolygon getInterpolatedPolygon()
      Returns, as a FloatPolygon, an interpolated version of this selection that has points spaced 1.0 pixel apart.
    • getInterpolatedPolygon

      public FloatPolygon getInterpolatedPolygon(double interval, boolean smooth)
      Returns, as a FloatPolygon, an interpolated version of this selection with points spaced 'interval' pixels apart. If 'smooth' is true, traced and freehand selections are first smoothed using a 3 point running average.
    • getInterpolatedPolygon

      protected FloatPolygon getInterpolatedPolygon(FloatPolygon p, double interval, boolean smooth)
      Returns, as a FloatPolygon, an interpolated version of this selection with points spaced abs('interval') pixels apart. If 'smooth' is true, traced and freehand selections are first smoothed using a 3 point running average. If 'interval' is negative, the program is allowed to decrease abs('interval') so that the last segment will hit the end point
    • getContainedPoints

      public Point[] getContainedPoints()
      Returns the coordinates of the pixels inside this ROI as an array of Points.
      See Also:
    • getContainedFloatPoints

      public FloatPolygon getContainedFloatPoints()
      Returns the coordinates of the pixels inside this ROI as a FloatPolygon.
      See Also:
    • lineCircleIntersection

      public static double[] lineCircleIntersection(double ax, double ay, double bx, double by, double cx, double cy, double rad, boolean ignoreOutside)
       Calculates intersections of a line segment with a circle
       Author N.Vischer
       ax, ay, bx, by: points A and B of line segment
       cx, cy, rad: Circle center and radius.
       ignoreOutside: if true, ignores intersections outside the line segment A-B
       Returns an array of 0, 2 or 4 coordinates (for 0, 1, or 2 intersection
       points). If two intersection points are returned, they are listed in travel
       direction A->B
       
    • clone

      public Object clone()
      Returns a copy of this roi. See Thinking is Java by Bruce Eckel (www.eckelobjects.com) for a good description of object cloning.
      Overrides:
      clone in class Object
    • abortModification

      public void abortModification(ImagePlus imp)
      Aborts constructing or modifying the roi (called by the ImageJ class on escape)
    • grow

      protected void grow(int sx, int sy)
    • moveHandle

      protected void moveHandle(int sx, int sy)
    • nudge

      public void nudge(int key)
      Nudge ROI one pixel on arrow key press.
    • nudgeCorner

      public void nudgeCorner(int key)
      Nudge lower right corner of rectangular and oval ROIs by one pixel based on arrow key press.
    • updateClipRect

      protected void updateClipRect()
    • clipRectMargin

      protected int clipRectMargin()
    • handleMouseDrag

      protected void handleMouseDrag(int sx, int sy, int flags)
    • draw

      public void draw(Graphics g)
    • drawOverlay

      public void drawOverlay(Graphics g)
    • getHandleSize

      public int getHandleSize()
      Returns the current handle size.
    • setHandleSize

      public void setHandleSize(int size)
      Sets the current handle size.
    • getDefaultHandleSize

      public static int getDefaultHandleSize()
      Returns the default handle size.
    • resetDefaultHandleSize

      public static void resetDefaultHandleSize()
    • drawPixels

      public void drawPixels()
      Deprecated.
      replaced by drawPixels(ImageProcessor)
    • drawPixels

      public void drawPixels(ImageProcessor ip)
      Draws the selection outline on the specified ImageProcessor.
      See Also:
    • contains

      public boolean contains(int x, int y)
      Returns whether the center of pixel (x,y) is contained in the Roi. The position of a pixel center determines whether a pixel is selected. 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. This convention is opposite to that of the java.awt.Shape class.
    • 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.
    • getInverse

      public Roi getInverse(ImagePlus imp)
      Returns the inverted roi, or null if this is not an area roi or cannot be converted to a ShapeRoi. If imp is not given, assumes a rectangle of size 2e9*2e9 for the boundary.
    • isHandle

      public int isHandle(int sx, int sy)
      Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
    • mouseDownInHandle

      protected void mouseDownInHandle(int handle, int sx, int sy)
    • handleMouseDown

      protected void handleMouseDown(int sx, int sy)
    • handleMouseUp

      protected void handleMouseUp(int screenX, int screenY)
    • update

      public void update(boolean add, boolean subtract)
      If 'add' is true, adds this selection to the previous one. If 'subtract' is true, subtracts it from the previous selection. Called by the IJ.doWand() method, and the makeRectangle(), makeOval(), makePolygon() and makeSelection() macro functions.
    • showStatus

      public void showStatus()
    • getMask

      public ImageProcessor getMask()
      Always returns null for rectangular Roi's
    • startPaste

      public void startPaste(ImagePlus clipboard)
    • endPaste

      public void endPaste()
    • abortPaste

      public void abortPaste()
    • getDefaultStrokeWidth

      public static double getDefaultStrokeWidth()
      Returns the default stroke width.
    • setDefaultStrokeWidth

      public static void setDefaultStrokeWidth(double width)
      Sets the default stroke width.
    • getDefaultGroup

      public static int getDefaultGroup()
      Returns the group value assigned to newly created ROIs.
    • setDefaultGroup

      public static void setDefaultGroup(int group)
      Sets the group value assigned to newly created ROIs, and also sets the default ROI color to the group color. Set to zero to not have a default group and to use the default ROI color.
      See Also:
    • getGroup

      public int getGroup()
      Returns the group attribute of this ROI.
    • getGroupName

      public static String getGroupName(int groupNumber)
      Returns the group name associtated with the specified group.
    • setGroupName

      public static void setGroupName(int groupNumber, String name)
    • saveGroupNames

      public static void saveGroupNames()
    • getGroupNames

      public static String getGroupNames()
      Returns the group names as a comma-delimeted string.
    • setGroupNames

      public static void setGroupNames(String names)
      Sets the group names from a comma-delimeted string.
    • setGroup

      public void setGroup(int group)
      Sets the group of this Roi, and updates stroke color accordingly.
    • getAngle

      public double getAngle(int x1, int y1, int x2, int y2)
      Returns the angle in degrees between the specified line and a horizontal line.
    • getFloatAngle

      public double getFloatAngle(double x1, double y1, double x2, double y2)
      Returns the angle in degrees between the specified line and a horizontal line.
    • setColor

      public static void setColor(Color c)
      Sets the default (global) color used for ROI outlines.
      See Also:
    • getColor

      public static Color getColor()
      Returns the default (global) color used for drawing ROI outlines.
      See Also:
    • setStrokeColor

      public void setStrokeColor(Color c)
      Sets the color used by this ROI to draw its outline. This color, if not null, overrides the global color set by the static setColor() method.
      See Also:
    • getStrokeColor

      public Color getStrokeColor()
      Returns the the color used to draw the ROI outline or null if the default color is being used.
      See Also:
    • setDefaultColor

      public static void setDefaultColor(Color color)
      Sets the default stroke color.
    • setFillColor

      public void setFillColor(Color color)
      Sets the fill color used to display this ROI, or set to null to display it transparently.
      See Also:
    • getFillColor

      public Color getFillColor()
      Returns the fill color used to display this ROI, or null if it is displayed transparently.
      See Also:
    • setDefaultFillColor

      public static void setDefaultFillColor(Color color)
    • getDefaultFillColor

      public static Color getDefaultFillColor()
    • setAntiAlias

      public void setAntiAlias(boolean antiAlias)
    • getAntiAlias

      public boolean getAntiAlias()
    • setRenderingHint

      protected void setRenderingHint(Graphics2D g2d)
    • copyAttributes

      public void copyAttributes(Roi roi2)
      Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
    • setInstanceColor

      public void setInstanceColor(Color c)
      Deprecated.
      replaced by setStrokeColor()
    • setLineWidth

      public void setLineWidth(int width)
      Deprecated.
      replaced by setStrokeWidth(int)
    • updateWideLine

      public void updateWideLine(float width)
    • setNonScalable

      public void setNonScalable(boolean nonScalable)
      Set 'nonScalable' true to have TextRois in a display list drawn at a fixed location and size.
    • setStrokeWidth

      public void setStrokeWidth(float strokeWidth)
      Sets the width of the line used to draw this ROI. Set the width to 0.0 and the ROI will be drawn using a a 1 pixel stroke width regardless of the magnification.
      See Also:
    • setStrokeWidth

      public void setStrokeWidth(double strokeWidth)
      This is a version of setStrokeWidth() that accepts a double argument.
    • setUnscalableStrokeWidth

      public void setUnscalableStrokeWidth(double strokeWidth)
      Sets the width of the line used to draw this ROI and prevents the width from increasing when the image is zoomed.
    • getStrokeWidth

      public float getStrokeWidth()
      Returns the lineWidth.
    • setStroke

      public void setStroke(BasicStroke stroke)
      Sets the Stroke used to draw this ROI.
    • getStroke

      public BasicStroke getStroke()
      Returns the Stroke used to draw this ROI, or null if no Stroke is used.
    • getScaleStrokeWidth

      public boolean getScaleStrokeWidth()
      Returns 'true' if the stroke width is scaled as images are zoomed.
    • getScaledStroke

      protected BasicStroke getScaledStroke()
    • getName

      public String getName()
      Returns the name of this ROI, or null.
    • setName

      public void setName(String name)
      Sets the name of this ROI.
    • setPasteMode

      public static void setPasteMode(int transferMode)
      Sets the Paste transfer mode.
      See Also:
    • setCornerDiameter

      public void setCornerDiameter(int cornerDiameter)
      Sets the rounded rectangle corner diameter (pixels).
    • getCornerDiameter

      public int getCornerDiameter()
      Returns the rounded rectangle corner diameter (pixels).
    • setRoundRectArcSize

      public void setRoundRectArcSize(int cornerDiameter)
      Obsolete; replaced by setCornerDiameter().
    • getRoundRectArcSize

      public int getRoundRectArcSize()
      Obsolete; replaced by getCornerDiameter().
    • setPosition

      public void setPosition(int n)
      Sets the stack position (image number) of this ROI. In an overlay, this ROI is only displayed when the stack is at the specified position. Set to zero to have the ROI displayed on all images in the stack.
      See Also:
    • getPosition

      public int getPosition()
      Returns the stack position (image number) of this ROI, or zero if the ROI is not associated with a particular stack image.
      See Also:
    • setPosition

      public void setPosition(int channel, int slice, int frame)
      Sets the hyperstack position of this ROI. In an overlay, this ROI is only displayed when the hyperstack is at the specified position.
      See Also:
    • hasHyperStackPosition

      public boolean hasHyperStackPosition()
      Returns 'true' if setPosition(C,Z,T) has been called.
    • setPosition

      public void setPosition(ImagePlus imp)
      Sets the position of this ROI based on the stack position of the specified image.
    • getCPosition

      public final int getCPosition()
      Returns the channel position of this ROI, or zero if this ROI is not associated with a particular channel.
    • getZPosition

      public final int getZPosition()
      Returns the slice position of this ROI, or zero if this ROI is not associated with a particular slice.
    • getTPosition

      public final int getTPosition()
      Returns the frame position of this ROI, or zero if this ROI is not associated with a particular frame.
    • setPrototypeOverlay

      public void setPrototypeOverlay(Overlay overlay)
    • getPrototypeOverlay

      public Overlay getPrototypeOverlay()
    • getPasteMode

      public int getPasteMode()
      Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
      See Also:
    • getCurrentPasteMode

      public static int getCurrentPasteMode()
      Returns the current paste transfer mode.
    • isArea

      public boolean isArea()
      Returns 'true' if this is an area selection.
    • isLine

      public boolean isLine()
      Returns 'true' if this is a line selection.
    • isLineOrPoint

      protected boolean isLineOrPoint()
      Return 'true' if this is a line or point selection.
    • isDrawingTool

      public boolean isDrawingTool()
      Returns 'true' if this is an ROI primarily used from drawing (e.g., TextRoi or Arrow).
    • getMagnification

      protected double getMagnification()
    • getTypeAsString

      public String getTypeAsString()
      Convenience method that converts Roi type to a human-readable form.
    • isVisible

      public boolean isVisible()
      Returns true if this ROI is currently displayed on an image.
    • subPixelResolution

      public boolean subPixelResolution()
      Returns true if this is a slection that supports sub-pixel resolution.
    • getDrawOffset

      @Deprecated public boolean getDrawOffset()
      Deprecated.
      Drawoffset is not used any more.
    • setDrawOffset

      @Deprecated public void setDrawOffset(boolean drawOffset)
      Deprecated.
      This method was previously used to draw lines and polylines shifted by 0.5 pixels top the bottom and right, for better agreement with the position used by ProfilePlot, with the default taken from Prefs.subPixelResolution. Now the shift is independent of this setting and only depends on the ROI type (area or line/point ROI).
    • setIgnoreClipRect

      public void setIgnoreClipRect(boolean ignoreClipRect)
    • isActiveOverlayRoi

      public final boolean isActiveOverlayRoi()
      Returns 'true' if this ROI is displayed and is also in an overlay.
    • equals

      public boolean equals(Object obj)
      Checks whether two rectangles are equal.
      Overrides:
      equals in class Object
    • offScreenX

      protected int offScreenX(int sx)
      Converts image canvas screen x coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    • offScreenY

      protected int offScreenY(int sy)
      Converts image canvas screen y coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    • offScreenXD

      protected double offScreenXD(int sx)
      Converts image canvas screen x coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    • offScreenYD

      protected double offScreenYD(int sy)
      Converts image canvas screen y coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
    • useLineSubpixelConvention

      protected boolean useLineSubpixelConvention()
      Returns 'true' if this ROI uses for drawing the convention for line and point ROIs, where the coordinates are with respect to the pixel center. Returns false for area rois, which have coordinates with respect to the upper left corners of the pixels
    • magnificationForSubPixel

      protected boolean magnificationForSubPixel()
      Returns whether a roi created interactively should have subpixel resolution, (if the roi type supports it), i.e., whether the magnification is high enough
    • magnificationForSubPixel

      protected static boolean magnificationForSubPixel(double magnification)
    • screenXD

      protected int screenXD(double ox)
      Converts an image pixel x (offscreen)coordinate to a screen x coordinate, taking the the line or area convention for coordinates into account
    • screenYD

      protected int screenYD(double oy)
      Converts an image pixel y (offscreen)coordinate to a screen y coordinate, taking the the line or area convention for coordinates into account
    • screenX

      protected int screenX(int ox)
    • screenY

      protected int screenY(int oy)
    • toInt

      public static int[] toInt(float[] arr)
      Converts a float array to an int array using truncation.
    • toInt

      public static int[] toInt(float[] arr, int[] arr2, int size)
    • toIntR

      public static int[] toIntR(float[] arr)
      Converts a float array to an int array using rounding.
    • toFloat

      public static float[] toFloat(int[] arr)
      Converts an int array to a float array.
    • isInteger

      public static boolean isInteger(double x)
      Returns whether a number is an integer
    • setProperty

      public void setProperty(String key, String value)
    • getProperty

      public String getProperty(String property)
    • setProperties

      public void setProperties(String properties)
    • getProperties

      public String getProperties()
    • getPropertyCount

      public int getPropertyCount()
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • temporarilyHide

      public void temporarilyHide()
      Deprecated
    • mouseDragged

      public void mouseDragged(MouseEvent e)
    • mouseMoved

      public void mouseMoved(MouseEvent e)
    • mouseReleased

      public void mouseReleased(MouseEvent e)
    • getXBase

      public double getXBase()
    • getYBase

      public double getYBase()
    • getFloatWidth

      public double getFloatWidth()
    • getFloatHeight

      public double getFloatHeight()
    • getAngle

      public double getAngle()
      Overridden by PolygonRoi (angle between first two points), TextRoi (text angle) and Line (line angle).
    • enableSubPixelResolution

      public void enableSubPixelResolution()
    • setIsCursor

      public void setIsCursor(boolean isCursor)
    • isCursor

      public boolean isCursor()
    • getDebugInfo

      public String getDebugInfo()
    • getStatistics

      public ImageStatistics getStatistics()
    • getRotationCenter

      public FloatPolygon getRotationCenter()
    • setRotationCenter

      public void setRotationCenter(double x, double y)
    • size

      public int size()
      Returns the number of points in this selection; equivalent to getFloatPolygon().npoints.
    • setPreviousRoi

      public static void setPreviousRoi(Roi roi)
      Saves 'roi' so it can be restored later using Edit/Selection/Restore Selection.
    • getPreviousRoi

      public static Roi getPreviousRoi()
      Returns the Roi saved by setPreviousRoi().
    • getContourCentroid

      public double[] getContourCentroid()
    • convertToPolygon

      public Roi convertToPolygon()
      Deprecated.
      Obsolete, replaced by Roi.convertLineToArea()
    • convertLineToArea

      public static Roi convertLineToArea(Roi line)
      Converts a line selection into an area (polygon or composite) selection.
      Author: Michael Schmid
    • getHashCode

      public int getHashCode()
      Returns a hashcode for this Roi that typically changes if it is moved, even though it is still the same object.
    • setFlattenScale

      public void setFlattenScale(double scale)
    • notifyListeners

      public void notifyListeners(int id)
    • xor

      public static Roi xor(Roi[] rois)
    • addRoiListener

      public static void addRoiListener(RoiListener listener)
    • removeRoiListener

      public static void removeRoiListener(RoiListener listener)
    • getListeners

      public static Vector getListeners()
    • iterator

      public Iterator<Point> iterator()
      Required by the Iterable interface. Use to iterate over the contained coordinates. Usage example:
       for (Point p : roi) {
         // process p
       }
       
      Author: Wilhelm Burger
      Specified by:
      iterator in interface Iterable<Point>
      See Also: