plugins.kernel.roi.roi3d

Class ROI3DArea

java.lang.Object

icy.roi.ROI

icy.roi.ROI3D

plugins.kernel.roi.roi3d.ROI3DStack<ROI2DArea>

plugins.kernel.roi.roi3d.ROI3DArea

All Implemented Interfaces:

ChangeListener, XMLPersistent, OverlayListener, ROIListener, java.lang.Iterable<ROI2DArea>, java.util.EventListener

public class ROI3DArea
extends ROI3DStack<ROI2DArea>

3D Area ROI.

Author:

Stephane

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ROI3DArea.ROI3DAreaPainter

Nested classes/interfaces inherited from class plugins.kernel.roi.roi3d.ROI3DStack

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 inherited from class plugins.kernel.roi.roi3d.ROI3DStack

PROPERTY_USECHILDCOLOR

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
ROI3DArea()
ROI3DArea(BooleanMask2D mask2d, int zMin, int zMax) Create a 3D Area ROI type from the specified BooleanMask3D.
ROI3DArea(BooleanMask3D mask) Create a 3D Area ROI type from the specified BooleanMask3D.
ROI3DArea(Point3D pt)
ROI3DArea(Point5D pt)
ROI3DArea(ROI3DArea area) Create a copy of the specified 3D Area ROI.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(BooleanMask3D mask) Add the specified BooleanMask3D content to this ROI3DArea
void	add(int z, BooleanMask2D maskSlice) Add the specified BooleanMask2D with the existing slice at given Z position.
ROI	add(ROI roi, boolean allowCreate) Adds content of specified ROI into this ROI.
void	addBrush(java.awt.geom.Point2D pos, int z) Add brush point at specified position and for specified Z slice.
void	addPoint(int x, int y, int z) Adds the specified point to this ROI
void	downscale() Fast 2x down scaling (each 2x2x2 block points become 1 point).
void	downscale(int nbPointForTrue) Fast 2x down scaling (each 2x2x2 block points become 1 point).
void	downscale2D() Fast 2x down scaling (each 2x2 block points become 1 point).
void	downscale2D(int nbPointForTrue) Fast 2x down scaling (each 2x2 block points become 1 point).
void	exclusiveAdd(BooleanMask3D mask) Exclusively add the specified BooleanMask3D content to this ROI3DArea
void	exclusiveAdd(int z, BooleanMask2D maskSlice) Exclusively add the specified BooleanMask2D with the existing slice at given Z position.
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.
java.lang.String	getDefaultName()
Point3D[]	getEdgePoints() Deprecated. Use ROI3D.getBooleanMask(boolean) and BooleanMask3D.getContourPoints() instead.
Point3D[]	getPoints() Deprecated. Use ROI3D.getBooleanMask(boolean) and BooleanMask3D.getPoints() instead.
void	intersect(BooleanMask3D mask) Intersect the specified BooleanMask3D content with this ROI3DArea
void	intersect(int z, BooleanMask2D maskSlice) Intersect the specified BooleanMask2D with the existing slice at given Z position.
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	isEmpty() Returns true if the ROI is empty (the mask does not contains any point).
boolean	isOverEdge(IcyCanvas canvas, double x, double y, double z) Returns true if specified point coordinates overlap the ROI edge.
void	onChanged(CollapsibleEvent object) roi changed
void	optimizeBounds() Optimize the bounds size to the minimum surface which still include all mask.
void	removeBrush(java.awt.geom.Point2D pos, int z) Remove brush point from the mask at specified position and for specified Z slice.
void	removePoint(int x, int y, int z) Remove a point from the mask.
void	setAsBooleanMask(BooleanMask3D mask) Set the mask from a BooleanMask3D object.
void	setAsBooleanMask(Rectangle3D.Integer rect, BooleanMask2D[] mask) Set the 3D mask from a 2D boolean mask array
void	setPoint(int x, int y, int z, boolean value) Set the value for the specified point in the mask.
void	setPosition2D(java.awt.geom.Point2D newPosition) Set all 2D slices ROI to same position.
void	setSlice(int z, BooleanMask2D maskSlice) Sets the BooleanMask2D slice at given Z position to this 3D ROI
void	setSlice(int z, ROI2D roiSlice, boolean merge) Deprecated. Use one of these methods instead : #setSlice(int, ROI2DArea), setSlice(int, BooleanMask2D), #add(int, ROI2DArea) or add(BooleanMask3D)
void	subtract(BooleanMask3D mask) Subtract the specified BooleanMask3D from this ROI3DArea
void	subtract(int z, BooleanMask2D maskSlice) Subtract the specified BooleanMask2D from the existing slice at given Z position.
ROI	subtract(ROI roi, boolean allowCreate) Subtract the specified ROI content from current ROI.
void	translate(double dx, double dy) Deprecated. Use ROI3DStack.translate(double, double, double) instead.
void	upscale() Fast up scaling by a factor of 2 (each point become a 2x2x2 block points)
void	upscale2D() Fast up scaling by a factor of 2 (each point become a 2x2 block points) 2D version (down scale is done on XY dimension only).

Methods inherited from class plugins.kernel.roi.roi3d.ROI3DStack

add, add, canTranslate, clear, computeBounds3D, computeNumberOfContourPoints, computeNumberOfPoints, computeSurfaceArea, contains, contains, exclusiveAdd, exclusiveAdd, getBooleanMask2D, getBooleanMask2D, getSizeZ, getSlice, getSlice, getUseChildColor, hasSelectedPoint, intersect, intersect, intersects, iterator, loadFromXML, overlayChanged, removeSlice, roiChanged, saveToXML, setC, setColor, setCreating, setFocused, setName, setReadOnly, setSelected, setSlice, setT, setUseChildColor, subtract, subtract, translate, translate, unselectAllPoints

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, 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, 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

Constructor Detail

ROI3DArea

public ROI3DArea()

ROI3DArea

public ROI3DArea(Point3D pt)

ROI3DArea

public ROI3DArea(Point5D pt)

ROI3DArea

public ROI3DArea(BooleanMask3D mask)

Create a 3D Area ROI type from the specified BooleanMask3D.

ROI3DArea

public ROI3DArea(ROI3DArea area)

Create a copy of the specified 3D Area ROI.

ROI3DArea

public ROI3DArea(BooleanMask2D mask2d,
         int zMin,
         int zMax)

Create a 3D Area ROI type from the specified BooleanMask3D.

Method Detail

getDefaultName

public java.lang.String getDefaultName()

Overrides:

getDefaultName in class ROI3DStack<ROI2DArea>

Returns:

the default name for this ROI class

addPoint

public void addPoint(int x,
            int y,
            int z)

Adds the specified point to this ROI

removePoint

public void removePoint(int x,
               int y,
               int z)

Remove a point from the mask.
Don't forget to call optimizeBounds() after consecutive remove operation to refresh the mask bounds.

setPoint

public void setPoint(int x,
            int y,
            int z,
            boolean value)

Set the value for the specified point in the mask. Don't forget to call optimizeBounds() after consecutive remove point operation to refresh the mask bounds.

addBrush

public void addBrush(java.awt.geom.Point2D pos,
            int z)

Add brush point at specified position and for specified Z slice.

removeBrush

public void removeBrush(java.awt.geom.Point2D pos,
               int z)

Remove brush point from the mask at specified position and for specified Z slice.
Don't forget to call optimizeBounds() after consecutive remove operation to refresh the mask bounds.

add

public void add(BooleanMask3D mask)

Add the specified BooleanMask3D content to this ROI3DArea

add

public void add(int z,
       BooleanMask2D maskSlice)

Add the specified BooleanMask2D with the existing slice at given Z position.
If there is no slice at this Z position then the method is equivalent to #setSlice(int, ROI2DArea) with new ROI2DArea(maskSlice)

Parameters:

z - the position where the slice must be added

maskSlice - the 2D boolean mask to merge

exclusiveAdd

public void exclusiveAdd(BooleanMask3D mask)

Exclusively add the specified BooleanMask3D content to this ROI3DArea

exclusiveAdd

public void exclusiveAdd(int z,
                BooleanMask2D maskSlice)

Exclusively add the specified BooleanMask2D with the existing slice at given Z position.
If there is no slice at this Z position then the method is equivalent to #setSlice(int, ROI2DArea) with new ROI2DArea(maskSlice)

Parameters:

z - the position where the slice must be exclusively added

maskSlice - the 2D boolean mask to merge

intersect

public void intersect(BooleanMask3D mask)

Intersect the specified BooleanMask3D content with this ROI3DArea

intersect

public void intersect(int z,
             BooleanMask2D maskSlice)

Intersect the specified BooleanMask2D with the existing slice at given Z position.

Parameters:

z - the position where the slice must be set

maskSlice - the 2D boolean mask to merge

subtract

public void subtract(BooleanMask3D mask)

Subtract the specified BooleanMask3D from this ROI3DArea

subtract

public void subtract(int z,
            BooleanMask2D maskSlice)

Subtract the specified BooleanMask2D from the existing slice at given Z position.

Parameters:

z - the position where the slice must be subtracted

maskSlice - the 2D boolean mask to subtract

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 ROI3DStack<ROI2DArea>

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)

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 ROI3DStack<ROI2DArea>

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)

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 ROI3DStack<ROI2DArea>

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)

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 ROI3DStack<ROI2DArea>

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)

setSlice

public void setSlice(int z,
            BooleanMask2D maskSlice)

Sets the BooleanMask2D slice at given Z position to this 3D ROI

Parameters:

z - the position where the slice must be set

maskSlice - the BooleanMask2D to set

setSlice

@Deprecated
public void setSlice(int z,
                       ROI2D roiSlice,
                       boolean merge)

Deprecated. Use one of these methods instead :
#setSlice(int, ROI2DArea), setSlice(int, BooleanMask2D), #add(int, ROI2DArea) or add(BooleanMask3D)

isEmpty

public boolean isEmpty()

Returns true if the ROI is empty (the mask does not contains any point).

Overrides:

isEmpty in class ROI3DStack<ROI2DArea>

getEdgePoints

@Deprecated
public Point3D[] getEdgePoints()

Deprecated. Use ROI3D.getBooleanMask(boolean) and BooleanMask3D.getContourPoints() instead.

getPoints

@Deprecated
public Point3D[] getPoints()

Deprecated. Use ROI3D.getBooleanMask(boolean) and BooleanMask3D.getPoints() instead.

translate

@Deprecated
public void translate(double dx,
                        double dy)

Deprecated. Use ROI3DStack.translate(double, double, double) instead.

isOverEdge

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

Description copied from class: ROI3D

Returns true if specified point coordinates overlap the ROI edge.
Use ROI3D.contains(double, double, double) to test for content overlap instead.
We provide a default implementation to not break compatibility.

Overrides:

isOverEdge in class ROI3D

setPosition2D

public void setPosition2D(java.awt.geom.Point2D newPosition)

Set all 2D slices ROI to same position.

setAsBooleanMask

public void setAsBooleanMask(BooleanMask3D mask)

Set the mask from a BooleanMask3D object.
If specified mask is null then ROI is cleared.

setAsBooleanMask

public void setAsBooleanMask(Rectangle3D.Integer rect,
                    BooleanMask2D[] mask)

Set the 3D mask from a 2D boolean mask array

Parameters:

rect - the 3D region defined by 2D boolean mask array

mask - the 3D mask data (array length should be equals to rect.sizeZ)

upscale

public void upscale()

Fast up scaling by a factor of 2 (each point become a 2x2x2 block points)

downscale

public void downscale(int nbPointForTrue)

Fast 2x down scaling (each 2x2x2 block points become 1 point).

Parameters:

nbPointForTrue - the minimum number of truepoints from a 2x2x2 block to give a true resulting point.
Accepted value: 1 to 5 (default is 5)

downscale

public void downscale()

Fast 2x down scaling (each 2x2x2 block points become 1 point).

upscale2D

public void upscale2D()

Fast up scaling by a factor of 2 (each point become a 2x2 block points) 2D version (down scale is done on XY dimension only).

downscale2D

public void downscale2D(int nbPointForTrue)

Fast 2x down scaling (each 2x2 block points become 1 point).
2D version (down scale is done on XY dimension only).

Parameters:

nbPointForTrue - the minimum number of truepoints from a 2x2 block to give a true resulting point.
Accepted value: 1 to 4

downscale2D

public void downscale2D()

Fast 2x down scaling (each 2x2 block points become 1 point).
2D version (down scale is done on XY dimension only).

optimizeBounds

public void optimizeBounds()

Optimize the bounds size to the minimum surface which still include all mask.
You should call it after consecutive remove operations if you directly addressed mask data.

onChanged

public void onChanged(CollapsibleEvent object)

roi changed

Specified by:

onChanged in interface ChangeListener

Overrides:

onChanged in class ROI