plugins.kernel.roi.roi3d

Class ROI3DShape

java.lang.Object

icy.roi.ROI

icy.roi.ROI3D

plugins.kernel.roi.roi3d.ROI3DShape

All Implemented Interfaces:

ChangeListener, XMLPersistent, Shape3D

Direct Known Subclasses:

ROI3DLine, ROI3DPoint, ROI3DPolyLine

public class ROI3DShape
extends ROI3D
implements Shape3D

Base class for 3D shape ROI (working from 3D control points).

Author:

Stephane Dallongeville

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ROI3DShape.ROI3DShapePainter

Nested classes/interfaces inherited from class icy.roi.ROI3D

ROI3D.ROI3DPainter

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

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

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ID_POINT
static java.lang.String	ID_POINTS

Fields inherited from class icy.roi.ROI3D

ID_C, ID_T

Fields inherited from class icy.roi.ROI

DEFAULT_COLOR, DEFAULT_NORMAL_COLOR, DEFAULT_OPACITY, DEFAULT_STROKE, ID_CLASSNAME, ID_COLOR, ID_GROUPID, ID_ID, ID_NAME, ID_OPACITY, 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
ROI3DShape(Shape3D shape)

Method Summary

Methods

Modifier and Type	Method and Description
Anchor3D	addNewPoint(Point3D pos, boolean insert) Add a new point to the Polyline 3D ROI.
void	addPoint(Anchor3D pt, int index) Internal use only, use addNewPoint(Point3D, 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.
Rectangle3D	computeBounds3D() Calculate and returns the 3D bounding box of the ROI.
double	computeNumberOfContourPoints() Compute and returns the number of point (pixel) composing the ROI contour.
double	computeNumberOfPoints() Compute and returns the number of point (pixel) contained in the ROI.
double	computeSurfaceArea(Sequence sequence) Compute the surface area in um2 given the pixel size informations from the specified Sequence.
boolean	contains(double x, double y, double z) Tests if the specified coordinates are inside the ROI.
boolean	contains(double x, double y, double z, double sizeX, double sizeY, double sizeZ) Tests if the ROI entirely contains the specified 3D rectangular area.
boolean	contains(Point3D p) Tests if a specified Point3D is inside the ROI.
boolean	contains(Rectangle3D r) Tests if the interior of the ROI entirely contains the specified Rectangle3D.
void	controlPointOverlayChanged(OverlayEvent event) Called when anchor overlay changed
void	controlPointPositionChanged(Anchor3D source) Called when anchor position changed
java.util.List<Anchor3D>	getControlPoints() Return the list of control points for this ROI.
java.lang.String	getDefaultName()
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.util.List<Point3D>	getPoints() Return the list of position for all control points of the ROI.
Shape3D	getShape()
boolean	hasSelectedPoint() Returns true if the ROI has a (control) point which is currently focused/selected
boolean	intersects(double x, double y, double z, double sizeX, double sizeY, double sizeZ) Tests if the interior of the ROI intersects the interior of a specified 3D rectangular area.
boolean	intersects(Rectangle3D r) Tests if the interior of the ROI intersects the interior of a specified Rectangle3D.
boolean	isOverEdge(IcyCanvas canvas, double x, double y, double z) Returns true if specified point coordinates overlap the ROI edge.
boolean	loadFromXML(org.w3c.dom.Node node) LOAD
void	onChanged(CollapsibleEvent object) roi changed
boolean	removePoint(Anchor3D pt) This method give you lower level access on point remove operation but can be unsafe.
boolean	removeSelectedPoint(IcyCanvas canvas) Remove the current selected point.
void	translate(double dx, double dy, double dz) Translate the ROI position by the specified delta X/Y/Z.
void	unselectAllPoints() Remove focus/selected state on all (control) points.

Methods inherited from class icy.roi.ROI3D

canSetBounds, canSetPosition, computeBounds5D, contains, contains, contains, getBooleanMask, getBooleanMask2D, getBooleanMask2D, getBooleanMask2D, getBooleanMask2D, getBooleanMask2D, getBooleanMask3D, getBounds, getBounds3D, getC, getDimension, getPosition, getPosition3D, getROI3DList, getROI3DList, getSurfaceArea, getSurfaceArea, getT, getVolume, intersects, intersects, isActiveFor, isActiveFor, isOverEdge, isOverEdge, isOverEdge, saveToXML, setBounds3D, setBounds5D, setC, setPosition3D, setPosition5D, setT

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, getExclusiveUnion, getFirstSequence, getFocusedColor, getGroupId, getIcon, getId, getIntersection, getName, getNameSuffix, getNumberOfContourPoints, getNumberOfPoints, getOpacity, getOverlay, getPainter, getPerimeter, getPosition5D, getPropertyValue, getROICount, getROIList, getROIList, getROIList, getROIsFromXML, getSelectedColor, getSequences, getShowName, getSimpleClassName, getStroke, getSubROI, getSubtraction, getUnion, 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, 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 icy.type.geom.Shape3D

getBounds

Field Detail

ID_POINTS

public static final java.lang.String ID_POINTS

See Also:

Constant Field Values

ID_POINT

public static final java.lang.String ID_POINT

See Also:

Constant Field Values

Constructor Detail

ROI3DShape

public ROI3DShape(Shape3D shape)

Method Detail

getDefaultName

public java.lang.String getDefaultName()

Overrides:

getDefaultName in class ROI3D

Returns:

the default name for this ROI class

getShape

public Shape3D 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(Anchor3D pt,
            int index)

Internal use only, use addNewPoint(Point3D, boolean) instead.

addNewPoint

public Anchor3D addNewPoint(Point3D pos,
                   boolean insert)

Add a new point to the Polyline 3D 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 Anchor3D point

removePoint

public boolean removePoint(Anchor3D pt)

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

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

getLength

public double getLength(Sequence sequence)

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 ROI3D

See Also:

ROI.getNumberOfContourPoints()

computeSurfaceArea

public double computeSurfaceArea(Sequence sequence)

Description copied from class: ROI3D

Compute the surface area in um2 given the pixel size informations from the specified Sequence.
Generic implementation of surface area computation using the number of contour point (approximation).
This method should be overridden whenever possible to provide faster and accurate calculation.

Overrides:

computeSurfaceArea in class ROI3D

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 ROI3D

getControlPoints

public java.util.List<Anchor3D> getControlPoints()

Return the list of control points for this ROI.

getPoints

public java.util.List<Point3D> getPoints()

Return the list of position for all control points of the ROI.

isOverEdge

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

Returns true if specified point coordinates overlap the ROI edge.

Overrides:

isOverEdge in class ROI3D

contains

public boolean contains(Point3D p)

Description copied from class: ROI3D

Tests if a specified Point3D is inside the ROI.

Specified by:

contains in interface Shape3D

Overrides:

contains in class ROI3D

Parameters:

p - the specified Point3D to be tested

Returns:

true if the specified Point3D is inside the boundary of the ROI; false otherwise.

contains

public boolean contains(Rectangle3D r)

Description copied from class: ROI3D

Tests if the interior of the ROI entirely contains the specified Rectangle3D. 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 Rectangle3D are prohibitively expensive.

This means that for some ROIs this method might return false even though the ROI contains the Rectangle3D.

Specified by:

contains in interface Shape3D

Overrides:

contains in class ROI3D

Parameters:

r - The specified Rectangle3D

Returns:

true if the interior of the ROI entirely contains the Rectangle3D; false otherwise or, if the ROI contains the Rectangle3D and the intersects method returns true and the containment calculations would be too expensive to perform.

See Also:

ROI3D.contains(double, double, double, double, double, double)

contains

public boolean contains(double x,
               double y,
               double z)

Description copied from class: ROI3D

Tests if the specified coordinates are inside the ROI.

Specified by:

contains in interface Shape3D

Specified by:

contains in class ROI3D

Parameters:

x - the specified X coordinate to be tested

y - the specified Y coordinate to be tested

z - the specified Z coordinate to be tested

Returns:

true if the specified 3D coordinates are inside the ROI boundary; false otherwise.

contains

public boolean contains(double x,
               double y,
               double z,
               double sizeX,
               double sizeY,
               double sizeZ)

Description copied from class: ROI3D

Tests if the ROI entirely contains the specified 3D 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 Shape3D

Specified by:

contains in class ROI3D

Parameters:

x - the X coordinate of the minimum corner position of the specified rectangular area

y - the Y coordinate of the minimum corner position of the specified rectangular area

z - the Z coordinate of the minimum corner position of the specified rectangular area

sizeX - size for X dimension of the specified rectangular area

sizeY - size for Y dimension of the specified rectangular area

sizeZ - size for Z dimension of the specified rectangular area

Returns:

true if the interior of the ROI entirely contains the specified 3D rectangular area; false otherwise or, if the ROI contains the 3D rectangular area and the intersects method returns true and the containment calculations would be too expensive to perform.

intersects

public boolean intersects(Rectangle3D r)

Description copied from class: ROI3D

Tests if the interior of the ROI intersects the interior of a specified Rectangle3D. The ROI.intersects() method allows a ROI implementation to conservatively return true when:

• there is a high probability that the Rectangle3D 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 Rectangle3D does not intersect the ROI.

Specified by:

intersects in interface Shape3D

Overrides:

intersects in class ROI3D

Parameters:

r - the specified Rectangle3D

Returns:

true if the interior of the ROI and the interior of the specified Rectangle3D intersect, or are both highly likely to intersect and intersection calculations would be too expensive to perform; false otherwise.

See Also:

ROI3D.intersects(double, double, double,double, double, double)

intersects

public boolean intersects(double x,
                 double y,
                 double z,
                 double sizeX,
                 double sizeY,
                 double sizeZ)

Description copied from class: ROI3D

Tests if the interior of the ROI intersects the interior of a specified 3D rectangular area. The 3D 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 3D 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 3D rectangular area does not intersect the ROI.

Specified by:

intersects in interface Shape3D

Specified by:

intersects in class ROI3D

Parameters:

x - the X coordinate of the minimum corner position of the specified rectangular area

y - the Y coordinate of the minimum corner position of the specified rectangular area

z - the Z coordinate of the minimum corner position of the specified rectangular area

sizeX - size for X dimension of the specified rectangular area

sizeY - size for Y dimension of the specified rectangular area

sizeZ - size for Z dimension 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.

computeBounds3D

public Rectangle3D computeBounds3D()

Description copied from class: ROI3D

Calculate and returns the 3D bounding box of the ROI.
This method is used by ROI3D.getBounds3D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.

Specified by:

computeBounds3D in class ROI3D

canTranslate

public boolean canTranslate()

Description copied from class: ROI3D

Returns true if the ROI support translate operation.

Overrides:

canTranslate in class ROI3D

See Also:

ROI3D.translate(double, double, double)

translate

public void translate(double dx,
             double dy,
             double dz)

Description copied from class: ROI3D

Translate the ROI position by the specified delta X/Y/Z.
Note that not all ROI support this operation so you should test it by calling ROI3D.canTranslate() first.

Overrides:

translate in class ROI3D

Parameters:

dx - translation value to apply on X dimension

dy - translation value to apply on Y dimension

dz - translation value to apply on Z dimension

See Also:

ROI3D.canTranslate(), ROI3D.setPosition3D(Point3D)

controlPointPositionChanged

public void controlPointPositionChanged(Anchor3D source)

Called when anchor position changed

controlPointOverlayChanged

public void controlPointOverlayChanged(OverlayEvent event)

Called when anchor overlay changed

onChanged

public void onChanged(CollapsibleEvent object)

roi changed

Specified by:

onChanged in interface ChangeListener

Overrides:

onChanged in class ROI

computeNumberOfPoints

public double computeNumberOfPoints()

Description copied from class: ROI

Compute and returns the number of point (pixel) contained in the ROI.

Overrides:

computeNumberOfPoints in class ROI3D

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 ROI3D