plugins.kernel.roi.roi3d

Class ROI3DStack<R extends ROI2D>

java.lang.Object

icy.roi.ROI

icy.roi.ROI3D

plugins.kernel.roi.roi3d.ROI3DStack<R>

Type Parameters:

R - the type of 2D ROI for each slice of this 3D ROI

All Implemented Interfaces:

ChangeListener, XMLPersistent, OverlayListener, ROIListener, java.lang.Iterable<R>, java.util.EventListener

Direct Known Subclasses:

ROI3DArea, ROI3DStackShape

public class ROI3DStack<R extends ROI2D>
extends ROI3D
implements ROIListener, OverlayListener, java.lang.Iterable<R>

Base class defining a generic 3D ROI as a stack of individual 2D ROI slices.

Author:

Alexandre Dufour, Stephane Dallongeville

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ROI3DStack.ROI3DStackPainter

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	PROPERTY_USECHILDCOLOR Deprecated. this property does not exist anymore

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, 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
ROI3DStack(java.lang.Class<? extends R> roiClass) Creates a new 3D ROI based on the given 2D ROI type.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(int z, R roiSlice) Adds content of specified ROI slice into the ROI slice at given Z position.
void	add(ROI3DStack<R> roi) Add the specified ROI3DStack content to this ROI3DStack
ROI	add(ROI roi, boolean allowCreate) Adds content of specified ROI into this ROI.
boolean	canTranslate() Returns true if the ROI support translate operation.
void	clear() Removes all slices.
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.
void	exclusiveAdd(int z, R roiSlice) Sets the content of the ROI slice at given Z position to be the union of its current content and the content of the specified ROI, minus their intersection.
void	exclusiveAdd(ROI3DStack<R> roi) Exclusively add the specified ROI3DStack content to this ROI3DStack
ROI	exclusiveAdd(ROI roi, boolean allowCreate) Sets the content of this ROI to be the union of its current content and the content of the specified ROI, minus their intersection.
BooleanMask2D	getBooleanMask2D(int z, boolean inclusive) Get the BooleanMask2D object representing the roi for the specified Z position.
boolean[]	getBooleanMask2D(int x, int y, int width, int height, int z, boolean inclusive) Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z position.
java.lang.String	getDefaultName()
int	getSizeZ()
R	getSlice(int z) Returns the ROI slice at given Z position.
R	getSlice(int z, boolean createIfNull) Returns the ROI slice at given Z position.
boolean	getUseChildColor() Returns true if the ROI directly uses the 2D slice color draw property and false if it uses the global 3D ROI color draw property.
boolean	hasSelectedPoint() Returns true if the ROI has a (control) point which is currently focused/selected
void	intersect(int z, R roiSlice) Sets the content of the ROI slice at given Z position to the intersection of its current content and the content of the specified ROI.
void	intersect(ROI3DStack<R> roi) Process intersection of the specified ROI3DStack with this ROI3DStack.
ROI	intersect(ROI roi, boolean allowCreate) Sets the content of this ROI to the intersection of its current content and the content of the specified ROI.
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	isEmpty() Returns true if the ROI stack is empty.
java.util.Iterator<R>	iterator()
boolean	loadFromXML(org.w3c.dom.Node node) LOAD
void	overlayChanged(OverlayEvent event)
R	removeSlice(int z) Removes slice at the given Z position and returns it.
void	roiChanged(ROIEvent event)
boolean	saveToXML(org.w3c.dom.Node node) SAVE
void	setC(int value) Sets C position of this 3D ROI.
void	setColor(int z, java.awt.Color value) Set the painter color for the specified ROI slice.
void	setCreating(boolean value) Set the internal creation mode state.
void	setFocused(boolean value)
void	setName(java.lang.String value)
void	setReadOnly(boolean value) Set the read only state of ROI.
void	setSelected(boolean value) Set the selected state of this ROI.
void	setSlice(int z, R roi2d) Sets the ROI slice for the given Z position.
void	setT(int value) Sets T position of this 3D ROI.
void	setUseChildColor(boolean value) Set to true if you want to directly use the 2D slice color draw property and false to keep the global 3D ROI color draw property.
void	subtract(int z, R roiSlice) Subtract the specified ROI content from the ROI slice at given Z position.
void	subtract(ROI3DStack<R> roi) Remove the specified ROI3DStack from this ROI3DStack
ROI	subtract(ROI roi, boolean allowCreate) Subtract the specified ROI content from current ROI.
void	translate(double dx, double dy, double dz) Translate the ROI position by the specified delta X/Y/Z.
void	translate(int z) Translate the stack of specified Z position.
void	unselectAllPoints() Remove focus/selected state on all (control) points.

Methods inherited from class icy.roi.ROI3D

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

Methods inherited from class icy.roi.ROI

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, 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, getProperties, getProperty, getPropertyValue, getROICount, getROIList, getROIList, getROIList, getROIsFromXML, getSelectedColor, getSequences, getShowName, getSimpleClassName, getStroke, getSubROI, getSubtraction, getUnion, internalFocus, internalSelect, internalUnfocus, internalUnselect, intersects, isAttached, isCreating, isDefaultName, isEditable, isFocused, isReadOnly, isSelected, isUpdating, loadFromXML, loadROIsFromXML, merge, mergeWith, nameChanged, onChanged, painterChanged, propertyChanged, remove, remove, removeListener, roiChanged, roiChanged, roiChanged, saveROIsToXML, selectionChanged, setColor, setDefaultColor, setDefaultOpacity, setDefaultShowName, setDefaultStroke, setEditable, setGroupId, setIcon, setMousePos, setOpacity, setProperty, setPropertyValue, setROIsFromXML, setSelected, setSelectedColor, setShowName, setStroke

Methods inherited from class java.lang.Object

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

Field Detail

PROPERTY_USECHILDCOLOR

@Deprecated
public static final java.lang.String PROPERTY_USECHILDCOLOR

Deprecated. this property does not exist anymore

See Also:

Constant Field Values

Constructor Detail

ROI3DStack

public ROI3DStack(java.lang.Class<? extends R> roiClass)

Creates a new 3D ROI based on the given 2D ROI type.

Method Detail

getDefaultName

public java.lang.String getDefaultName()

Overrides:

getDefaultName in class ROI3D

Returns:

the default name for this ROI class

getUseChildColor

public boolean getUseChildColor()

Returns true if the ROI directly uses the 2D slice color draw property and false if it uses the global 3D ROI color draw property.

setUseChildColor

public void setUseChildColor(boolean value)

Set to true if you want to directly use the 2D slice color draw property and false to keep the global 3D ROI color draw property.

See Also:

setColor(int, Color)

setColor

public void setColor(int z,
            java.awt.Color value)

Set the painter color for the specified ROI slice.

See Also:

setUseChildColor(boolean)

setCreating

public void setCreating(boolean value)

Description copied from class: ROI

Set the internal creation mode state.
The ROI interaction behave differently when in creation mode.
You should not set this state when you create an ROI from the code.

Overrides:

setCreating in class ROI

setReadOnly

public void setReadOnly(boolean value)

Description copied from class: ROI

Set the read only state of ROI.

Overrides:

setReadOnly in class ROI

setFocused

public void setFocused(boolean value)

Overrides:

setFocused in class ROI

Parameters:

value - the focused to set

setSelected

public void setSelected(boolean value)

Description copied from class: ROI

Set the selected state of this ROI.
Use Sequence.setSelectedROI(ROI) for exclusive ROI selection.

Overrides:

setSelected in class ROI

Parameters:

value - the selected to set

setName

public void setName(java.lang.String value)

Overrides:

setName in class ROI

Parameters:

value - the name to set

setT

public void setT(int value)

Description copied from class: ROI3D

Sets T position of this 3D ROI.
You cannot set the ROI on a negative T position as -1 is a special value meaning the ROI is set on all T frames (infinite T dimension).

Overrides:

setT in class ROI3D

setC

public void setC(int value)

Description copied from class: ROI3D

Sets C position of this 3D ROI.
You cannot set the ROI on a negative C position as -1 is a special value meaning the ROI is set on all C channels (infinite C dimension).

Overrides:

setC in class ROI3D

isEmpty

public boolean isEmpty()

Returns true if the ROI stack is empty.

Overrides:

isEmpty in class ROI

getSizeZ

public int getSizeZ()

Returns:

The size of this ROI stack along Z.
Note that the returned value indicates the difference between upper and lower bounds of this ROI, but doesn't guarantee that all slices in-between exist ( getSlice(int) may still return null.

getSlice

public R getSlice(int z)

Returns the ROI slice at given Z position.

getSlice

public R getSlice(int z,
         boolean createIfNull)

Returns the ROI slice at given Z position.

setSlice

public void setSlice(int z,
            R roi2d)

Sets the ROI slice for the given Z position.

removeSlice

public R removeSlice(int z)

Removes slice at the given Z position and returns it.

clear

public void clear()

Removes all slices.

add

public void add(ROI3DStack<R> roi)
         throws java.lang.UnsupportedOperationException

Add the specified ROI3DStack content to this ROI3DStack

Throws:

java.lang.UnsupportedOperationException

exclusiveAdd

public void exclusiveAdd(ROI3DStack<R> roi)
                  throws java.lang.UnsupportedOperationException

Exclusively add the specified ROI3DStack content to this ROI3DStack

Throws:

java.lang.UnsupportedOperationException

intersect

public void intersect(ROI3DStack<R> roi)
               throws java.lang.UnsupportedOperationException

Process intersection of the specified ROI3DStack with this ROI3DStack.

Throws:

java.lang.UnsupportedOperationException

subtract

public void subtract(ROI3DStack<R> roi)
              throws java.lang.UnsupportedOperationException

Remove the specified ROI3DStack from this ROI3DStack

Throws:

java.lang.UnsupportedOperationException

add

public ROI add(ROI roi,
      boolean allowCreate)
        throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Adds content of specified ROI into this ROI. The resulting content of this ROI will include the union of both ROI's contents.
Note that this operation work only if the 2 ROIs are compatible for that type of operation. If that is not the case a UnsupportedOperationException is thrown if allowCreate parameter is set to false, if the parameter is set to true the result may be returned in a new created ROI.

     // Example:
      roi1 (before)     +         roi2       =    roi1 (after)
 
     ################     ################     ################
     ##############         ##############     ################
     ############             ############     ################
     ##########                 ##########     ################
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 

Overrides:

add in class ROI

Parameters:

roi - the ROI to be added to the current ROI

allowCreate - if set to true the method will create a new ROI to return the result of the operation if it cannot be directly processed on the current ROI

Returns:

the modified ROI or a new created ROI if the operation cannot be directly processed on the current ROI and allowCreate parameter was set to true

Throws:

java.lang.UnsupportedOperationException - if the two ROI cannot be added together.

See Also:

ROI.getUnion(ROI)

intersect

public ROI intersect(ROI roi,
            boolean allowCreate)
              throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Sets the content of this ROI to the intersection of its current content and the content of the specified ROI. The resulting ROI will include only contents that were contained in both ROI.
Note that this operation work only if the 2 ROIs are compatible for that type of operation. If that is not the case a UnsupportedOperationException is thrown if allowCreate parameter is set to false, if the parameter is set to true the result may be returned in a new created ROI.

     // Example:
     roi1 (before) intersect    roi2        =   roi1 (after)
 
     ################     ################     ################
     ##############         ##############       ############
     ############             ############         ########
     ##########                 ##########           ####
     ########                     ########
     ######                         ######
     ####                             ####
     ##                                 ##
 

Overrides:

intersect in class ROI

Parameters:

roi - the ROI to be intersected to the current ROI

allowCreate - if set to true the method will create a new ROI to return the result of the operation if it cannot be directly processed on the current ROI

Returns:

the modified ROI or a new created ROI if the operation cannot be directly processed on the current ROI and allowCreate parameter was set to true

Throws:

java.lang.UnsupportedOperationException - if the two ROI cannot be intersected together.

See Also:

ROI.getIntersection(ROI)

exclusiveAdd

public ROI exclusiveAdd(ROI roi,
               boolean allowCreate)
                 throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Sets the content of this ROI to be the union of its current content and the content of the specified ROI, minus their intersection. The resulting ROI will include only content that were contained in either this ROI or in the specified ROI, but not in both.
Note that this operation work only if the 2 ROIs are compatible for that type of operation. If that is not the case a UnsupportedOperationException is thrown if allowCreate parameter is set to false, if the parameter is set to true the result may be returned in a new created ROI.

     // Example:
      roi1 (before)   xor      roi2         =    roi1 (after)
 
     ################     ################
     ##############         ##############     ##            ##
     ############             ############     ####        ####
     ##########                 ##########     ######    ######
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 

Overrides:

exclusiveAdd in class ROI

Parameters:

roi - the ROI to be exclusively added to the current ROI

allowCreate - if set to true the method will create a new ROI to return the result of the operation if it cannot be directly processed on the current ROI

Returns:

the modified ROI or a new created ROI if the operation cannot be directly processed on the current ROI and allowCreate parameter was set to true

Throws:

java.lang.UnsupportedOperationException - if the two ROI cannot be exclusively added together.

See Also:

ROI.getExclusiveUnion(ROI)

subtract

public ROI subtract(ROI roi,
           boolean allowCreate)
             throws java.lang.UnsupportedOperationException

Description copied from class: ROI

Subtract the specified ROI content from current ROI.
Note that this operation work only if the 2 ROIs are compatible for that type of operation. If that is not the case a UnsupportedOperationException is thrown if allowCreate parameter is set to false, if the parameter is set to true the result may be returned in a new created ROI.

Overrides:

subtract in class ROI

Parameters:

roi - the ROI to subtract from the current ROI

allowCreate - if set to true the method will create a new ROI to return the result of the operation if it cannot be directly processed on the current ROI

Returns:

the modified ROI or a new created ROI if the operation cannot be directly processed on the current ROI and allowCreate parameter was set to true

Throws:

java.lang.UnsupportedOperationException - if we can't subtract the specified ROI from this ROI

See Also:

ROI.getSubtraction(ROI)

add

public void add(int z,
       R roiSlice)

Adds content of specified ROI slice into the ROI slice at given Z position. The resulting content of this ROI will include the union of both ROI's contents.
If no slice was present at the specified Z position then the method is equivalent to setSlice(int, ROI2D)

Parameters:

z - the position where the slice must be merged

roiSlice - the 2D ROI to merge

Throws:

java.lang.UnsupportedOperationException - if the given ROI slice cannot be added to this ROI

exclusiveAdd

public void exclusiveAdd(int z,
                R roiSlice)

Sets the content of the ROI slice at given Z position to be the union of its current content and the content of the specified ROI, minus their intersection. The resulting ROI will include only content that were contained in either this ROI or in the specified ROI, but not in both.
If no slice was present at the specified Z position then the method is equivalent to setSlice(int, ROI2D)

Parameters:

z - the position where the slice must be merged

roiSlice - the 2D ROI to merge

Throws:

java.lang.UnsupportedOperationException - if the given ROI slice cannot be exclusively added to this ROI

intersect

public void intersect(int z,
             R roiSlice)

Sets the content of the ROI slice at given Z position to the intersection of its current content and the content of the specified ROI. The resulting ROI will include only contents that were contained in both ROI.
If no slice was present at the specified Z position then the method does nothing.

Parameters:

z - the position where the slice must be merged

roiSlice - the 2D ROI to merge

Throws:

java.lang.UnsupportedOperationException - if the given ROI slice cannot be intersected with this ROI

subtract

public void subtract(int z,
            R roiSlice)
              throws java.lang.UnsupportedOperationException

Subtract the specified ROI content from the ROI slice at given Z position.
If no slice was present at the specified Z position then the method does nothing.

Parameters:

z - the position where the subtraction should be done

roiSlice - the 2D ROI to subtract from Z slice

Throws:

java.lang.UnsupportedOperationException - if the given ROI slice cannot be subtracted from this ROI

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

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 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 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(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 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.

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

computeSurfaceArea

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

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

Throws:

java.lang.UnsupportedOperationException

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

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

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(int z)

Translate the stack of specified Z position.

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)

getBooleanMask2D

public boolean[] getBooleanMask2D(int x,
                         int y,
                         int width,
                         int height,
                         int z,
                         boolean inclusive)

Description copied from class: ROI3D

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

Overrides:

getBooleanMask2D in class ROI3D

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

z - Z position we want to retrieve the boolean mask

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

Returns:

the boolean bitmap mask

getBooleanMask2D

public BooleanMask2D getBooleanMask2D(int z,
                             boolean inclusive)

Description copied from class: ROI3D

Get the BooleanMask2D object representing the roi for the specified Z position.
It contains the rectangle mask bounds and the associated boolean array mask.
if the pixel (x,y) is contained in the roi Z position then result.mask[(y * w) + x] = true
if the pixel (x,y) is not contained in the roi Z position then result.mask[(y * w) + x] = false

Overrides:

getBooleanMask2D in class ROI3D

Parameters:

z - Z position we want to retrieve the boolean mask

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

roiChanged

public void roiChanged(ROIEvent event)

Specified by:

roiChanged in interface ROIListener

overlayChanged

public void overlayChanged(OverlayEvent event)

Specified by:

overlayChanged in interface OverlayListener

iterator

public java.util.Iterator<R> iterator()

Specified by:

iterator in interface java.lang.Iterable<R extends ROI2D>

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

saveToXML

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

Description copied from interface: XMLPersistent

SAVE

Specified by:

saveToXML in interface XMLPersistent

Overrides:

saveToXML in class ROI3D