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, java.lang.Cloneable

Direct Known Subclasses:

ContourROI, CurvedLineROI, IrregularROIInProgress

public class IrregularROI
extends ROI
implements java.lang.Cloneable, StretchableROI, RotatableROI, EditableOutlineROI

A Class representing an irregularly-shaped closed region on an image.

Field Summary

protected int	nPoints The number of points forming the outline.
static java.lang.String	POINTSTOKEN The token written to ROI output files to indicate that a list of points is to follow.
protected double[]	xpts The x-coodinates of points forming the outline of this Irregular ROI in real-space (mm) cooordinates.
protected double[]	ypts The y-coodinates of points forming the outline of this Irregular ROI in real-space (mm) cooordinates.

Fields inherited from class com.xinapse.multisliceimage.roi.ROI

handles, PREFERENCES_NODE_NAME, XTOKEN, YTOKEN

Constructor Summary

IrregularROI(double[] x, double[] y, int n, ROIState state)
Creates a new IrregularROI with the specified shape in mm coordinates.

IrregularROI(java.util.List<java.awt.geom.Point2D.Double> pointsList, ROIState state)
Creates a new IrregularROI with the specified shape in mm coordinates.

Method Summary

IrregularROI	clone() Returns a clone of this ROI.
java.awt.geom.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.
boolean	contains(ROI roi) Indicates whether this IrregularROI contains another ROI entirely within its borders.
boolean	deleteVertex(Handle handle) Delete a point on the outline of this EditableOutlineROI that is under a handle.
java.util.List<ROI>	dilate(double radius, java.util.concurrent.atomic.AtomicInteger opCounter, CancellableThread.Flag cancelFlag) Dilates this ROI by the specified distance.
boolean	draw(java.awt.Graphics g, java.awt.Rectangle visibleRectangle, int imageDrawCols, int imageDrawRows, int xOffset, int yOffset, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean drawAnnotation) Draws this ROI if it needs to be be drawn on screen.
void	drawInOrthoView(java.awt.Image orthoView, javax.vecmath.Point3f orthoViewPosition, javax.media.j3d.Transform3D imageToViewTx, int nCols, int nRows, int nSlices, float pixelXSize, float pixelYSize, boolean filled) Draws this ROI on top of an orthogonal view of an image.
boolean	equals(java.lang.Object o) Indicates whether some Object is equal to this ROI.
java.util.List<ROI>	erasePoints(java.util.List<java.awt.geom.Point2D> erasePoints, float size, int nCols, int nRows, float pixelXSize, float pixelYSize) Erase points from this ROI.
void	flipHorizontal(java.awt.geom.Point2D flipPoint) Flip this ROI horizontally about a given location.
void	flipVertical(java.awt.geom.Point2D flipPoint) Flip this ROI vertically about a given location.
static javax.swing.Icon	getButtonIcon() Returns an Icon that can be used for a button to create this type of ROI.
java.awt.geom.Point2D	getCentre() Gets the centre (about which rotation will occur) of this RotatableROI in mm.
ROI	getCopy() Returns a copy of this ROI.
static InteractionType	getCreateInteractionType() Returns the type of interaction needed to create an IrregularROI.
java.lang.String	getDescription() Return a description of this type of ROI.
Feret	getFeret() Returns the minimum and maximum Feret's diameter for this ROI, in mm.
Handle	getFollowingHandle(Handle handle) Returns the Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.
static java.lang.String	getName() Returns a descriptive name for this type of ROI.
int	getNPoints() Returns the number of vertices that define the outline.
double	getPerimeter() Returns the perimeter length of this ROI.
Handle	getPrecedingHandle(Handle handle) Returns the Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.
double	getTheta() Returns the current rotation angle for this RotatableROI.
java.awt.geom.Point2D	getVertex(int index) Returns a vertex location for this IrregularROI.
Handle[]	getVertexHandles() Returns an array of VertexHandles.
java.awt.geom.Point2D[]	getVertices() Returns the vertex locations for this IrregularROI.
int	hashCode() Returns a hash code value for this IrregularROI.
boolean	insertTwoVertices(Handle handle) Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.
boolean	intersects(ROI roi) Tests whether this ROI intersects another ROI.
IrregularROI	join(IrregularROI roi) Joins this ROI to another IrregularROI with a waisted join - a join at the nearest point.
void	makeConvex(CanAddROIToFrame canAddROIToFrame, float pixelXSize, float pixelYSize, float minConcaveRadius) Make this Irregular ROI convex, or at least less concave.
void	move(double dx, double dy) Move this ROI by specified distances (in mm) in the x and y directions.
void	move(double dx, double dy, double stretchX, double stretchY) Moves and stretches an ROI.
void	moveVertex(java.awt.geom.Point2D newPos, Handle handle, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean pixelSnap) Move a point on the outline of this EditableOutlineROI to a new position.
boolean	selfIntersects() Returns true if this ROI has line segments that cross.
void	set(ROI roi) Sets the shape of this ROI to the shape of the supplied argument ROI.
void	setTheta(double theta) Sets the rotation angle for this RotatableROI.
void	setVertex(java.awt.geom.Point2D pos, int idx) Sets one vertex position for this ROI.
void	setVertices(double[] x, double[] y) Sets the vertex positions for this ROI.
void	setVertices(double[] x, double[] y, int n) Sets the vertex positions for this ROI.
void	setVertices(java.util.List<? extends java.awt.geom.Point2D> vertices) Sets the vertex positions for this ROI.
void	setVertices(java.awt.geom.Point2D[] vertices) Sets the vertex positions for this ROI.
java.lang.String	toString() Returns a String describing this ROI.

Methods inherited from class com.xinapse.multisliceimage.roi.ROI

add, add, addMorphological, clearDeletionHistory, clearStats, dilate, exclusiveOr, getAnnotation, getBoundingRectangle, getBoundingRectangle, getCachedStatistics, getClasses, getColor, getDisplayedBounds2D, getDisplayedBounds2D, getDisplayedRoiArea, getFeret, getHandles, getHandleUnderPoint, getImageSource, getPixelValue, getROIs, getROIs, getROIs, getSlice, getState, getStats, getStats, getStats, getTextColor, getTextFontSize, getUserColour, intersect, isDeleted, isEditable, isReloaded, isSelected, join, main, markDeleted, mmPosToPix, moveROIs, pixPosToMm, printStats, selectDeselect, setAnnotation, setCreationHistory, setSlice, setState, setTextColor, setTextSize, setUserColour, subtract, subtract, write, write

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.xinapse.multisliceimage.roi.StretchableROI

getDisplayedBounds2D

Field Detail

POINTSTOKEN

public static final java.lang.String POINTSTOKEN

The token written to ROI output files to indicate that a list of points is to follow.

See Also:

Constant Field Values

xpts

protected double[] xpts

The x-coodinates of points forming the outline of this Irregular ROI in real-space (mm) cooordinates.

ypts

protected double[] ypts

The y-coodinates of points forming the outline of this Irregular ROI in real-space (mm) cooordinates.

nPoints

protected int nPoints

The number of points forming the outline.

Constructor Detail

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 that 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(java.util.List<java.awt.geom.Point2D.Double> pointsList,
                    ROIState state)
             throws ROIException

Creates a new IrregularROI with the specified shape in mm coordinates.

Parameters:

pointsList - a List of Point2D.Double, 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 Detail

getVertices

public java.awt.geom.Point2D[] getVertices()

Returns the vertex locations for this IrregularROI.

Returns:

the vertex locations as an array of Point2D.

getVertex

public java.awt.geom.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.

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(java.awt.geom.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(java.awt.geom.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(java.awt.geom.Point2D newPos,
                       Handle handle,
                       int nCols,
                       int nRows,
                       float pixelXSize,
                       float pixelYSize,
                       boolean pixelSnap)

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.

deleteVertex

public boolean deleteVertex(Handle handle)

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.

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(java.awt.geom.Point2D pos,
                      int idx)

Sets one vertex position for this ROI.

Parameters:

pos - the coordinates of the new position.

idx - an index to the corordinate position.

Throws:

java.lang.ArrayIndexOutOfBoundsException - if the index is invalid.

setVertices

public void setVertices(double[] x,
                        double[] y)
                 throws ROIException

Sets the vertex positions for this ROI.

Parameters:

x - a list of x-coordinates for the new vertex positions.

y - a list 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.

setVertices

public void setVertices(java.awt.geom.Point2D[] vertices)

Sets the vertex positions for this ROI.

Parameters:

vertices - an array of new vertex positions.

setVertices

public void setVertices(java.util.List<? extends java.awt.geom.Point2D> vertices)

Sets the vertex positions for this ROI.

Parameters:

vertices - a java.util.List of new vertex positions.

getCentre

public java.awt.geom.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 java.util.List<ROI> erasePoints(java.util.List<java.awt.geom.Point2D> erasePoints,
                                       float size,
                                       int nCols,
                                       int nRows,
                                       float pixelXSize,
                                       float pixelYSize)

Description copied from interface: EditableOutlineROI

Erase points from this ROI. erasePoints may edit this ROI by deleting points, or it may split this ROI into two or more new ROIs. If more than one ROI is returned, then the (edited) original ROI will be in the list of returned ROIs, and will be the remaining ROI which is biggest (has the most points).

Specified by:

erasePoints in interface EditableOutlineROI

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 ROIs resulting from the points erasure.

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 java.awt.geom.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.

makeConvex

public void makeConvex(CanAddROIToFrame canAddROIToFrame,
                       float pixelXSize,
                       float pixelYSize,
                       float minConcaveRadius)

Description copied from interface: EditableOutlineROI

Make this Irregular ROI convex, or at least less concave. The supplied pixel sizes are used to decide on the separation between data points around the ROI. 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 javax.swing.SwingWorker that will update the ImageDisplayer when finished.

Specified by:

makeConvex in interface EditableOutlineROI

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.

dilate

public java.util.List<ROI> dilate(double radius,
                                  java.util.concurrent.atomic.AtomicInteger opCounter,
                                  CancellableThread.Flag cancelFlag)
                           throws CancelledException

Description copied from class: ROI

Dilates this ROI by the specified distance.

Parameters:

radius - the radius of dilation.

opCounter - a counter for the number of sub-operations that was performed to execute the dilation operations.

cancelFlag - a flag that, if set externally, cancels the operation.

Returns:

a List of ROIs that result from the operation.

Throws:

CancelledException

draw

public boolean draw(java.awt.Graphics g,
                    java.awt.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(java.awt.Image orthoView,
                            javax.vecmath.Point3f orthoViewPosition,
                            javax.media.j3d.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 java.awt.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.

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 ouline edited.

getPrecedingHandle

public Handle getPrecedingHandle(Handle handle)

Description copied from interface: EditableOutlineROI

Returns the Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.

Specified by:

getPrecedingHandle in interface EditableOutlineROI

Parameters:

handle - the handle for which to get the preceding handle.

Returns:

the preceding Handle, or null if there is no preceding handle.

getFollowingHandle

public Handle getFollowingHandle(Handle handle)

Description copied from interface: EditableOutlineROI

Returns the Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.

Specified by:

getFollowingHandle in interface EditableOutlineROI

Parameters:

handle - the handle for which to get the following handle.

Returns:

the following Handle, or null if there is no following 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.

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.

intersects

public boolean intersects(ROI roi)

Description copied from class: ROI

Tests whether this ROI intersects another ROI.

Note that the area of intersection may be zero if one or other of the ROIs (or both) contains no area.

Specified by:

intersects in class ROI

Parameters:

roi - the ROI to be tested for intersection.

Returns:

true in the two ROIs intersect; false otherwise.

equals

public boolean equals(java.lang.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 java.lang.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

Throws:

java.lang.ClassCastException - of 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, cast to an Object.

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 java.lang.String toString()

Description copied from class: ROI

Returns a String describing this ROI.

Specified by:

toString in class ROI

Returns:

a java.lang.String describing this ROI.

getDescription

public java.lang.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 java.lang.String getName()

Returns a descriptive name for this type of ROI.

Returns:

a String describing this type of ROI.

getButtonIcon

public static javax.swing.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.