ROI3DStack

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

Nested Classes
Modifier and Type	Class and Description
`class`	`ROI3DStack.ROI3DStackPainter`

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, 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

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`PROPERTY_USECHILDCOLOR` Deprecated. this property does not exist anymore

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.

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, 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, 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

Icy Developer Documentation

Class ROI3DStack<R extends ROI2D>

Nested Class Summary

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

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

Field Summary

Fields inherited from class icy.roi.ROI3D

Fields inherited from class icy.roi.ROI

Constructor Summary

Method Summary

Methods inherited from class icy.roi.ROI3D

Methods inherited from class icy.roi.ROI

Methods inherited from class java.lang.Object

Field Detail

PROPERTY_USECHILDCOLOR

Constructor Detail

ROI3DStack

Method Detail

getDefaultName

getUseChildColor

setUseChildColor

setColor

setCreating

setReadOnly

setFocused

setSelected

setName

setT

setC

isEmpty

getSizeZ

getSlice

getSlice

setSlice

removeSlice

clear

add

exclusiveAdd

intersect

subtract

add

intersect

exclusiveAdd

subtract

add

exclusiveAdd

intersect

subtract

computeBounds3D

contains

contains

intersects

hasSelectedPoint

unselectAllPoints

computeSurfaceArea

computeNumberOfContourPoints

computeNumberOfPoints

canTranslate

translate

translate

getBooleanMask2D

getBooleanMask2D

roiChanged

overlayChanged

iterator

loadFromXML

saveToXML

Icy Developer Documentation