plugins.kernel.roi.roi2d

Class ROI2DShape

java.lang.Object

icy.roi.ROI

icy.roi.ROI2D

plugins.kernel.roi.roi2d.ROI2DShape

All Implemented Interfaces:

ChangeListener, XMLPersistent, java.awt.Shape

Direct Known Subclasses:

ROI2DLine, ROI2DPath, ROI2DPoint, ROI2DPolygon, ROI2DPolyLine, ROI2DRectShape, ROI2DShape

public abstract class ROI2DShape
extends ROI2D
implements java.awt.Shape

Author:

Stephane

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ROI2DShape.ROI2DShapePainter

Nested classes/interfaces inherited from class icy.roi.ROI2D

ROI2D.ROI2DPainter

Nested classes/interfaces inherited from class icy.roi.ROI

ROI.ROIGroupId, ROI.ROIIdComparator, ROI.ROINameComparator, ROI.ROIPainter

Field Summary

Fields inherited from class icy.roi.ROI2D

ID_C, ID_T, ID_Z

Fields inherited from class icy.roi.ROI

DEFAULT_COLOR, DEFAULT_NORMAL_COLOR, DEFAULT_OPACITY, DEFAULT_STROKE, defaultColor, defaultOpacity, defaultShowName, defaultStroke, ID_CLASSNAME, ID_COLOR, ID_GROUPID, ID_ID, ID_NAME, ID_OPACITY, ID_PROPERTIES, ID_READONLY, ID_ROI, ID_SELECTED, ID_SHOWNAME, ID_STROKE, idComparator, nameComparator, PROPERTY_COLOR, PROPERTY_CREATING, PROPERTY_GROUPID, PROPERTY_ICON, PROPERTY_NAME, PROPERTY_OPACITY, PROPERTY_READONLY, PROPERTY_SHOWNAME, PROPERTY_STROKE, ROI_CHANGED_ALL, ROI_CHANGED_POSITION

Constructor Summary

Constructors

Constructor and Description
ROI2DShape(java.awt.Shape shape)

Method Summary

Methods

Modifier and Type	Method and Description
Anchor2D	addNewPoint(java.awt.geom.Point2D pos, boolean insert) Add a new point to this shape ROI.
Anchor2D	addNewPoint(java.awt.geom.Point2D pos, boolean insert, boolean select) Add a new point to this shape ROI.
void	addPoint(Anchor2D pt, int index) Internal use only, use addNewPoint(Point2D, boolean) instead.
boolean	addPoint(java.awt.geom.Point2D pos, boolean insert) Deprecated. Use addNewPoint(Point2D, boolean) instead.
boolean	addPointAt(java.awt.geom.Point2D pos, boolean insert) Deprecated. Use addNewPoint(Point2D, boolean) instead.
boolean	canAddPoint() Return true if this ROI support adding new point
boolean	canRemovePoint() Return true if this ROI support removing point
boolean	canTranslate() Returns true if the ROI support translate operation.
java.awt.geom.Rectangle2D	computeBounds2D() Calculate and returns the 2D bounding box of the ROI.
double	computeNumberOfContourPoints() Compute and returns the number of point (pixel) composing the ROI contour.
boolean	contains(double x, double y) Tests if the specified coordinates are inside the ROI.
boolean	contains(double x, double y, double w, double h) Tests if the ROI entirely contains the specified rectangular area.
boolean	contains(java.awt.geom.Point2D p) Tests if a specified Point2D is inside the ROI.
boolean	contains(java.awt.geom.Rectangle2D r) Tests if the interior of the ROI entirely contains the specified Rectangle2D.
void	controlPointOverlayChanged(OverlayEvent event) Called when anchor overlay changed
void	controlPointPositionChanged(Anchor2D source) Called when anchor position changed
boolean[]	getBooleanMask(int x, int y, int width, int height, boolean inclusive) Get the boolean bitmap mask for the specified rectangular area of the roi.
java.util.List<Anchor2D>	getControlPoints() Return the list of control points for this ROI.
java.lang.String	getDefaultName()
ROI	getExclusiveUnion(ROI roi) Compute exclusive union with specified ROI and return result in a new ROI.
ROI	getIntersection(ROI roi) Compute intersection with specified ROI and return result in a new ROI.
double	getLength(Sequence sequence) Computes and returns the length/perimeter of the ROI in um given the pixel size informations from the specified Sequence.
java.awt.geom.PathIterator	getPathIterator(java.awt.geom.AffineTransform at)
java.awt.geom.PathIterator	getPathIterator(java.awt.geom.AffineTransform at, double flatness)
java.util.ArrayList<java.awt.geom.Point2D>	getPoints() Return the list of positions of control points for this ROI.
java.awt.Shape	getShape()
ROI	getSubtraction(ROI roi) Subtract the specified ROI and return result in a new ROI.
ROI	getUnion(ROI roi) Compute union with specified ROI and return result in a new ROI.
boolean	hasSelectedPoint() Returns true if the ROI has a (control) point which is currently focused/selected
boolean	intersects(double x, double y, double w, double h) Tests if the interior of the ROI intersects the interior of a specified rectangular area.
boolean	intersects(java.awt.geom.Rectangle2D r) Tests if the interior of the ROI intersects the interior of a specified Rectangle2D.
boolean	isOverEdge(IcyCanvas canvas, double x, double y) Returns true if specified point coordinates overlap the ROI edge.
boolean	loadFromXML(org.w3c.dom.Node node) LOAD
void	onChanged(CollapsibleEvent object) roi changed
void	painterChanged(PainterEvent event) Called when anchor painter changed, provided only for backward compatibility.
boolean	removePoint(Anchor2D pt) This method give you lower level access on point remove operation but can be unsafe.
boolean	removePointAt(IcyCanvas canvas, java.awt.geom.Point2D imagePoint) Deprecated. Use removeSelectedPoint(IcyCanvas) instead.
boolean	removeSelectedPoint(IcyCanvas canvas) Remove the current selected point.
void	translate(double dx, double dy) Translate the ROI position by the specified delta X/Y.
void	unselectAllPoints() Remove focus/selected state on all (control) points.

Methods inherited from class icy.roi.ROI2D

canSetBounds, canSetPosition, computeBounds5D, computeNumberOfPoints, computePerimeter, contains, contains, contains, getArea, getAsBooleanMask, getAsBooleanMask, getAsBooleanMask, getAsBooleanMask, getAsBooleanMask, getAsBooleanMask, getBooleanMask, getBooleanMask, getBooleanMask, getBooleanMask, getBooleanMask, getBooleanMask2D, getBooleanMask2D, getBounds, getBounds2D, getC, getDimension, getPerimeter, getPerimeter, getPosition, getPosition2D, getROI2DList, getROI2DList, getROI2DList, getSubROI, getT, getZ, intersects, intersects, isActiveFor, isActiveFor, isOver, isOver, isOverEdge, isOverEdge, isOverEdge, merge, saveToXML, setBounds2D, setBounds5D, setC, setPosition, setPosition2D, setPosition5D, setT, setZ, substract, subtract

Methods inherited from class icy.roi.ROI

add, addListener, attachTo, beginUpdate, canvasToImageDeltaX, canvasToImageDeltaY, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaY, canvasToImageLogDeltaY, canvasToImageLogDeltaY, canvasToImageLogDeltaY, contains, contains, copyFrom, create, create, create, create, createFromXML, delete, delete, detachFrom, detachFromAll, detachFromAll, endUpdate, exclusiveAdd, focusChanged, getAdjustedStroke, getAdjustedStroke, getBooleanMask2D, getBounds5D, getClassName, getColor, getCopy, getDefaultColor, getDefaultOpacity, getDefaultShowName, getDefaultStroke, getDisplayColor, getFirstSequence, getFocusedColor, getGroupId, getIcon, getId, getName, getNameSuffix, getNumberOfContourPoints, getNumberOfPoints, getOpacity, getOverlay, getPainter, getPosition5D, getProperties, getProperty, getPropertyValue, getROICount, getROIList, getROIList, getROIList, getROIsFromXML, getSelectedColor, getSequences, getShowName, getSimpleClassName, getStroke, getVolume, internalFocus, internalSelect, internalUnfocus, internalUnselect, intersect, intersects, isAttached, isCreating, isDefaultName, isEditable, isEmpty, isFocused, isReadOnly, isSelected, isUpdating, loadFromXML, loadROIsFromXML, merge, mergeWith, nameChanged, painterChanged, propertyChanged, remove, remove, removeListener, roiChanged, roiChanged, roiChanged, saveROIsToXML, selectionChanged, setColor, setCreating, setDefaultColor, setDefaultOpacity, setDefaultShowName, setDefaultStroke, setEditable, setFocused, setGroupId, setIcon, setMousePos, setName, setOpacity, setProperty, setPropertyValue, setReadOnly, setROIsFromXML, setSelected, setSelected, setSelectedColor, setShowName, setStroke, subtract

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.awt.Shape

getBounds, getBounds2D

Constructor Detail

ROI2DShape

public ROI2DShape(java.awt.Shape shape)

Method Detail

getDefaultName

public java.lang.String getDefaultName()

Overrides:

getDefaultName in class ROI2D

Returns:

the default name for this ROI class

getShape

public java.awt.Shape getShape()

Returns:

the shape

canAddPoint

public boolean canAddPoint()

Return true if this ROI support adding new point

canRemovePoint

public boolean canRemovePoint()

Return true if this ROI support removing point

addPoint

public void addPoint(Anchor2D pt,
            int index)

Internal use only, use addNewPoint(Point2D, boolean) instead.

addPoint

@Deprecated
public boolean addPoint(java.awt.geom.Point2D pos,
                          boolean insert)

Deprecated. Use addNewPoint(Point2D, boolean) instead.

addPointAt

@Deprecated
public boolean addPointAt(java.awt.geom.Point2D pos,
                            boolean insert)

Deprecated. Use addNewPoint(Point2D, boolean) instead.

addNewPoint

public Anchor2D addNewPoint(java.awt.geom.Point2D pos,
                   boolean insert,
                   boolean select)

Add a new point to this shape ROI.

Parameters:

pos - position of the new point

insert - if set to true the new point will be inserted between the 2 closest points (in pixels distance) else the new point is inserted at the end of the point list

select - select the new created point

Returns:

the new created Anchor2D point if the operation succeed or null otherwise (if the ROI does not support this operation for instance)

addNewPoint

public Anchor2D addNewPoint(java.awt.geom.Point2D pos,
                   boolean insert)

Add a new point to this shape ROI.

Parameters:

pos - position of the new point

insert - if set to true the new point will be inserted between the 2 closest points (in pixels distance) else the new point is inserted at the end of the point list

Returns:

the new created Anchor2D point if the operation succeed or null otherwise (if the ROI does not support this operation for instance)

removePoint

public boolean removePoint(Anchor2D pt)

This method give you lower level access on point remove operation but can be unsafe.
Use removeSelectedPoint(IcyCanvas) when possible.

removePointAt

@Deprecated
public boolean removePointAt(IcyCanvas canvas,
                               java.awt.geom.Point2D imagePoint)

Deprecated. Use removeSelectedPoint(IcyCanvas) instead.

removeSelectedPoint

public boolean removeSelectedPoint(IcyCanvas canvas)

Remove the current selected point.

hasSelectedPoint

public boolean hasSelectedPoint()

Description copied from class: ROI

Returns true if the ROI has a (control) point which is currently focused/selected

Specified by:

hasSelectedPoint in class ROI

unselectAllPoints

public void unselectAllPoints()

Description copied from class: ROI

Remove focus/selected state on all (control) points.
Override this method depending implementation

Overrides:

unselectAllPoints in class ROI

computeNumberOfContourPoints

public double computeNumberOfContourPoints()

Description copied from class: ROI

Compute and returns the number of point (pixel) composing the ROI contour.

Overrides:

computeNumberOfContourPoints in class ROI2D

getLength

public double getLength(Sequence sequence)
                 throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Computes and returns the length/perimeter of the ROI in um given the pixel size informations from the specified Sequence.
Generic implementation of length computation uses the number of contour point (approximation). This method should be overridden whenever possible to provide faster and accurate calculation.
Throws a UnsupportedOperationException if the operation is not supported for this ROI.

Overrides:

getLength in class ROI

Throws:

java.lang.UnsupportedOperationException

See Also:

ROI.getNumberOfContourPoints()

isOverEdge

public boolean isOverEdge(IcyCanvas canvas,
                 double x,
                 double y)

Returns true if specified point coordinates overlap the ROI edge.

Specified by:

isOverEdge in class ROI2D

getControlPoints

public java.util.List<Anchor2D> getControlPoints()

Return the list of control points for this ROI.

getPoints

public java.util.ArrayList<java.awt.geom.Point2D> getPoints()

Return the list of positions of control points for this ROI.

getPathIterator

public java.awt.geom.PathIterator getPathIterator(java.awt.geom.AffineTransform at)

Specified by:

getPathIterator in interface java.awt.Shape

getPathIterator

public java.awt.geom.PathIterator getPathIterator(java.awt.geom.AffineTransform at,
                                         double flatness)

Specified by:

getPathIterator in interface java.awt.Shape

getBooleanMask

public boolean[] getBooleanMask(int x,
                       int y,
                       int width,
                       int height,
                       boolean inclusive)

Description copied from class: ROI2D

Get the boolean bitmap mask for the specified rectangular area of the roi.
if the pixel (x,y) is contained in the roi then result[(y * width) + x] = true
if the pixel (x,y) is not contained in the roi then result[(y * width) + x] = false

Overrides:

getBooleanMask in class ROI2D

Parameters:

x - the X coordinate of the upper-left corner of the specified rectangular area

y - the Y coordinate of the upper-left corner of the specified rectangular area

width - the width of the specified rectangular area

height - the height of the specified rectangular area

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

Returns:

the boolean bitmap mask

contains

public boolean contains(java.awt.geom.Point2D p)

Description copied from class: ROI2D

Tests if a specified Point2D is inside the ROI.

Specified by:

contains in interface java.awt.Shape

Overrides:

contains in class ROI2D

Parameters:

p - the specified Point2D to be tested

Returns:

true if the specified Point2D is inside the boundary of the ROI; false otherwise.

contains

public boolean contains(java.awt.geom.Rectangle2D r)

Description copied from class: ROI2D

Tests if the interior of the ROI entirely contains the specified Rectangle2D. The ROI.contains() method allows a implementation to conservatively return false when:

• the intersect method returns true and
• the calculations to determine whether or not the ROI entirely contains the Rectangle2D are prohibitively expensive.

This means that for some ROIs this method might return false even though the ROI contains the Rectangle2D.

Specified by:

contains in interface java.awt.Shape

Overrides:

contains in class ROI2D

Parameters:

r - The specified Rectangle2D

Returns:

true if the interior of the ROI entirely contains the Rectangle2D; false otherwise or, if the ROI contains the Rectangle2D and the intersects method returns true and the containment calculations would be too expensive to perform.

See Also:

ROI2D.contains(double, double, double, double)

contains

public boolean contains(double x,
               double y)

Description copied from class: ROI2D

Tests if the specified coordinates are inside the ROI.

Specified by:

contains in interface java.awt.Shape

Specified by:

contains in class ROI2D

Parameters:

x - the specified X coordinate to be tested

y - the specified Y coordinate to be tested

Returns:

true if the specified coordinates are inside the ROI boundary; false otherwise.

contains

public boolean contains(double x,
               double y,
               double w,
               double h)

Description copied from class: ROI2D

Tests if the ROI entirely contains the specified rectangular area. All coordinates that lie inside the rectangular area must lie within the ROI for the entire rectangular area to be considered contained within the ROI.

The ROI.contains() method allows a ROI implementation to conservatively return false when:

• the intersect method returns true and
• the calculations to determine whether or not the ROI entirely contains the rectangular area are prohibitively expensive.

This means that for some ROIs this method might return false even though the ROI contains the rectangular area.

Specified by:

contains in interface java.awt.Shape

Specified by:

contains in class ROI2D

Parameters:

x - the X coordinate of the upper-left corner of the specified rectangular area

y - the Y coordinate of the upper-left corner of the specified rectangular area

w - the width of the specified rectangular area

h - the height of the specified rectangular area

Returns:

true if the interior of the ROI entirely contains the specified rectangular area; false otherwise or, if the ROI contains the rectangular area and the intersects method returns true and the containment calculations would be too expensive to perform.

intersects

public boolean intersects(java.awt.geom.Rectangle2D r)

Description copied from class: ROI2D

Tests if the interior of the ROI intersects the interior of a specified Rectangle2D. The ROI.intersects() method allows a ROI implementation to conservatively return true when:

• there is a high probability that the Rectangle2D and the ROI intersect, but
• the calculations to accurately determine this intersection are prohibitively expensive.

This means that for some ROIs this method might return true even though the Rectangle2D does not intersect the ROI.

Specified by:

intersects in interface java.awt.Shape

Overrides:

intersects in class ROI2D

Parameters:

r - the specified Rectangle2D

Returns:

true if the interior of the ROI and the interior of the specified Rectangle2D intersect, or are both highly likely to intersect and intersection calculations would be too expensive to perform; false otherwise.

See Also:

ROI2D.intersects(double, double, double, double)

intersects

public boolean intersects(double x,
                 double y,
                 double w,
                 double h)

Description copied from class: ROI2D

Tests if the interior of the ROI intersects the interior of a specified rectangular area. The rectangular area is considered to intersect the ROI if any point is contained in both the interior of the ROI and the specified rectangular area.

The ROI.intersects() method allows a ROI implementation to conservatively return true when:

• there is a high probability that the rectangular area and the ROI intersect, but
• the calculations to accurately determine this intersection are prohibitively expensive.

This means that for some ROIs this method might return true even though the rectangular area does not intersect the ROI.

Specified by:

intersects in interface java.awt.Shape

Specified by:

intersects in class ROI2D

Parameters:

x - the X coordinate of the upper-left corner of the specified rectangular area

y - the Y coordinate of the upper-left corner of the specified rectangular area

w - the width of the specified rectangular area

h - the height of the specified rectangular area

Returns:

true if the interior of the ROI and the interior of the rectangular area intersect, or are both highly likely to intersect and intersection calculations would be too expensive to perform; false otherwise.

computeBounds2D

public java.awt.geom.Rectangle2D computeBounds2D()

Description copied from class: ROI2D

Calculate and returns the 2D bounding box of the ROI.
This method is used by ROI2D.getBounds2D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.

Specified by:

computeBounds2D in class ROI2D

getUnion

public ROI getUnion(ROI roi)
             throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Compute union with specified ROI and return result in a new ROI.
The default implementation use ROIUtil.getUnion(ROI, ROI) internally but it maybe overridden.

Overrides:

getUnion in class ROI

Throws:

java.lang.UnsupportedOperationException

getIntersection

public ROI getIntersection(ROI roi)
                    throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Compute intersection with specified ROI and return result in a new ROI.
The default implementation use ROIUtil.getIntersection(ROI, ROI) internally but it maybe overridden.

Overrides:

getIntersection in class ROI

Throws:

java.lang.UnsupportedOperationException

getExclusiveUnion

public ROI getExclusiveUnion(ROI roi)
                      throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Compute exclusive union with specified ROI and return result in a new ROI.
The default implementation use ROIUtil.getExclusiveUnion(ROI, ROI) internally but it maybe overridden.

Overrides:

getExclusiveUnion in class ROI

Throws:

java.lang.UnsupportedOperationException

getSubtraction

public ROI getSubtraction(ROI roi)
                   throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Subtract the specified ROI and return result in a new ROI.
The default implementation use ROIUtil.getSubtraction(ROI, ROI) internally but it maybe overridden.

Overrides:

getSubtraction in class ROI

Throws:

java.lang.UnsupportedOperationException

canTranslate

public boolean canTranslate()

Description copied from class: ROI2D

Returns true if the ROI support translate operation.

Overrides:

canTranslate in class ROI2D

See Also:

ROI2D.translate(double, double)

translate

public void translate(double dx,
             double dy)

Description copied from class: ROI2D

Translate the ROI position by the specified delta X/Y.
Note that not all ROI support this operation so you should test it by calling ROI2D.canTranslate() first.

Overrides:

translate in class ROI2D

Parameters:

dx - translation value to apply on X dimension

dy - translation value to apply on Y dimension

See Also:

ROI2D.canTranslate(), ROI2D.setPosition2D(Point2D)

controlPointPositionChanged

public void controlPointPositionChanged(Anchor2D source)

Called when anchor position changed

controlPointOverlayChanged

public void controlPointOverlayChanged(OverlayEvent event)

Called when anchor overlay changed

painterChanged

public void painterChanged(PainterEvent event)

Called when anchor painter changed, provided only for backward compatibility.
Don't use it.

onChanged

public void onChanged(CollapsibleEvent object)

roi changed

Specified by:

onChanged in interface ChangeListener

Overrides:

onChanged in class ROI

loadFromXML

public boolean loadFromXML(org.w3c.dom.Node node)

Description copied from interface: XMLPersistent

LOAD

Specified by:

loadFromXML in interface XMLPersistent

Overrides:

loadFromXML in class ROI2D