ROI4DStack

java.lang.Object
- icy.roi.ROI
- - icy.roi.ROI4D
  - - plugins.kernel.roi.roi4d.ROI4DStack<R>

Type Parameters:
R - the type of 3D ROI for each slice of this 4D ROI

All Implemented Interfaces:

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

Direct Known Subclasses:

ROI4DArea, ROI4DStackRectangle
```
public class ROI4DStack<R extends ROI3D>
extends ROI4D
implements ROIListener, OverlayListener, java.lang.Iterable<R>
```
Abstract class defining a generic 4D ROI as a stack of individual 3D ROI slices.

Author:

Alexandre Dufour, Stephane Dallongeville

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class ROI4DStack.ROI4DStackPainter
- 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`	`ROI4DStack.ROI4DStackPainter`

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String PROPERTY_USECHILDCOLOR
- Fields inherited from class icy.roi.ROI4D
  ID_C
- 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

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`PROPERTY_USECHILDCOLOR`

Constructor Summary

Constructors
Constructor and Description

ROI4DStack(java.lang.Class<R> roiClass)
Creates a new 4D ROI based on the given 3D ROI type.

Constructors
Constructor and Description
`ROI4DStack(java.lang.Class<R> roiClass)` Creates a new 4D ROI based on the given 3D ROI type.

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`canTranslate()` Returns `true` if the ROI support translate operation.
`void`	`clear()` Removes all slices.
`Rectangle4D`	`computeBounds4D()` Calculate and returns the 4D 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.
`boolean`	`contains(double x, double y, double z, double t)` Tests if the specified coordinates are inside the `ROI`.
`boolean`	`contains(double x, double y, double z, double t, double sizeX, double sizeY, double sizeZ, double sizeT)` Tests if the `ROI` entirely contains the specified 4D rectangular area.
`BooleanMask2D`	`getBooleanMask2D(int z, int t, boolean inclusive)` Get the `BooleanMask2D` object representing the roi for the specified Z,T position.
`boolean[]`	`getBooleanMask2D(int x, int y, int width, int height, int z, int t, boolean inclusive)` Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
`java.lang.String`	`getDefaultName()`
`int`	`getSizeT()`
`R`	`getSlice(int t)` Returns the ROI slice at given T position.
`R`	`getSlice(int t, boolean createIfNull)` Returns the ROI slice at given T position.
`boolean`	`getUseChildColor()` Returns `true` if the ROI directly uses the 3D slice color draw property and `false` if it uses the global 4D ROI color draw property.
`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 t, double sizeX, double sizeY, double sizeZ, double sizeT)` Tests if the interior of the `ROI` intersects the interior of a specified 4D 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 t)` Removes slice at the given T 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 4D ROI.
`void`	`setColor(java.awt.Color value)` Set the ROI painter base color.
`void`	`setColor(int t, 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`	`setOpacity(float value)` Sets the ROI painter content opacity factor (0 = transparent while 1 means opaque).
`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 t, R roi3d)` Sets the slice for the given T position.
`void`	`setStroke(double value)` Set ROI painter stroke.
`void`	`setUseChildColor(boolean value)` Set to `true` if you want to directly use the 3D slice color draw property and `false` to keep the global 4D ROI color draw property.
`void`	`translate(double dx, double dy, double dz, double dt)` Translate the ROI position by the specified delta X/Y/Z/T.
`void`	`translate(int t)` Translate the stack of specified T position.
`void`	`unselectAllPoints()` Remove focus/selected state on all (control) points.

Methods inherited from class icy.roi.ROI4D
canSetBounds, canSetPosition, computeBounds5D, contains, contains, contains, contains, contains, getBooleanMask, getBooleanMask2D, getBooleanMask2D, getBooleanMask2D, getBooleanMask3D, getBooleanMask3D, getBooleanMask4D, getBounds, getBounds4D, getC, getDimension, getPosition, getPosition4D, getROI4DList, getROI4DList, intersects, intersects, intersects, isActiveFor, isActiveFor, setBounds4D, setBounds5D, setPosition4D, setPosition5D

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, getLength, 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, getVolume, internalFocus, internalSelect, internalUnfocus, internalUnselect, intersect, 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, setDefaultColor, setDefaultOpacity, setDefaultShowName, setDefaultStroke, setEditable, setGroupId, setIcon, setMousePos, setName, setProperty, setPropertyValue, setROIsFromXML, setSelected, setSelectedColor, setShowName, subtract

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - PROPERTY_USECHILDCOLOR
```
public static final java.lang.String PROPERTY_USECHILDCOLOR
```
    See Also:
    Constant Field Values
- Constructor Detail
  - ROI4DStack
```
public ROI4DStack(java.lang.Class<R> roiClass)
```
    Creates a new 4D ROI based on the given 3D ROI type.
- Method Detail
  - getDefaultName
```
public java.lang.String getDefaultName()
```
    Overrides:
    
    getDefaultName in class ROI4D
    
    Returns:
    the default name for this ROI class
  - getUseChildColor
```
public boolean getUseChildColor()
```
    Returns true if the ROI directly uses the 3D slice color draw property and false if it uses the global 4D ROI color draw property.
  - setUseChildColor
```
public void setUseChildColor(boolean value)
```
    Set to true if you want to directly use the 3D slice color draw property and false to keep the global 4D ROI color draw property.
    
    See Also:
    setColor(int, Color)
  - setColor
```
public void setColor(int t,
            java.awt.Color value)
```
    Set the painter color for the specified ROI slice.
    
    See Also:
    setUseChildColor(boolean)
  - setColor
```
public void setColor(java.awt.Color value)
```
    Description copied from class: ROI
    
    Set the ROI painter base color.
    
    Overrides:
    
    setColor in class ROI
  - setOpacity
```
public void setOpacity(float value)
```
    Description copied from class: ROI
    
    Sets the ROI painter content opacity factor (0 = transparent while 1 means opaque).
    
    Overrides:
    
    setOpacity in class ROI
  - setStroke
```
public void setStroke(double value)
```
    Description copied from class: ROI
    
    Set ROI painter stroke.
    
    Overrides:
    
    setStroke in class ROI
  - 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
  - setC
```
public void setC(int value)
```
    Description copied from class: ROI4D
    
    Sets C position of this 4D 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 ROI4D
  - isEmpty
```
public boolean isEmpty()
```
    Returns true if the ROI stack is empty.
    
    Overrides:
    
    isEmpty in class ROI
  - getSizeT
```
public int getSizeT()
```
    Returns:
    The size of this ROI stack along T.
    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 t)
```
    Returns the ROI slice at given T position.
  - getSlice
```
public R getSlice(int t,
         boolean createIfNull)
```
    Returns the ROI slice at given T position.
  - setSlice
```
public void setSlice(int t,
            R roi3d)
```
    Sets the slice for the given T position.
  - removeSlice
```
public R removeSlice(int t)
```
    Removes slice at the given T position and returns it.
  - clear
```
public void clear()
```
    Removes all slices.
  - computeBounds4D
```
public Rectangle4D computeBounds4D()
```
    Description copied from class: ROI4D
    
    Calculate and returns the 4D bounding box of the ROI.
    This method is used by ROI4D.getBounds4D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.
    
    Specified by:
    
    computeBounds4D in class ROI4D
  - contains
```
public boolean contains(double x,
               double y,
               double z,
               double t)
```
    Description copied from class: ROI4D
    
    Tests if the specified coordinates are inside the ROI.
    
    Specified by:
    
    contains in class ROI4D
    
    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
    t - the specified T coordinate to be tested
    
    Returns:
    true if the specified 4D coordinates are inside the ROI boundary; false otherwise.
  - contains
```
public boolean contains(double x,
               double y,
               double z,
               double t,
               double sizeX,
               double sizeY,
               double sizeZ,
               double sizeT)
```
    Description copied from class: ROI4D
    Tests if the ROI entirely contains the specified 4D 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 ROI4D
    
    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
    t - the T 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
    sizeT - size for T dimension of the specified rectangular area
    
    Returns:
    true if the interior of the ROI entirely contains the specified 4D rectangular area; false otherwise or, if the ROI contains the 4D 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 t,
                 double sizeX,
                 double sizeY,
                 double sizeZ,
                 double sizeT)
```
    Description copied from class: ROI4D
    Tests if the interior of the ROI intersects the interior of a specified 4D rectangular area. The 4D 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 4D 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 4D rectangular area does not intersect the ROI.
    Specified by:
    
    intersects in class ROI4D
    
    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
    t - the T 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
    sizeT - size for T 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
  - 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 ROI4D
  - 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 ROI4D
  - canTranslate
```
public boolean canTranslate()
```
    Description copied from class: ROI4D
    
    Returns true if the ROI support translate operation.
    
    Overrides:
    
    canTranslate in class ROI4D
    
    See Also:
    ROI4D.translate(double, double, double, double)
  - translate
```
public void translate(int t)
```
    Translate the stack of specified T position.
  - translate
```
public void translate(double dx,
             double dy,
             double dz,
             double dt)
```
    Description copied from class: ROI4D
    
    Translate the ROI position by the specified delta X/Y/Z/T.
    Note that not all ROI support this operation so you should test it by calling ROI4D.canTranslate() first.
    
    Overrides:
    
    translate in class ROI4D
    
    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
    dt - translation value to apply on T dimension
    See Also:
    ROI4D.canTranslate(), ROI4D.setPosition4D(Point4D)
  - getBooleanMask2D
```
public boolean[] getBooleanMask2D(int x,
                         int y,
                         int width,
                         int height,
                         int z,
                         int t,
                         boolean inclusive)
```
    Description copied from class: ROI4D
    
    Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
    if the pixel (x,y) is contained in the roi Z,T position then result[(y * width) + x] = true
    if the pixel (x,y) is not contained in the roi Z,T position then result[(y * width) + x] =
    
    Overrides:
    
    getBooleanMask2D in class ROI4D
    
    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
    t - T 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,
                             int t,
                             boolean inclusive)
```
    Description copied from class: ROI4D
    
    Get the BooleanMask2D object representing the roi for the specified Z,T position.
    It contains the rectangle mask bounds and the associated boolean array mask.
    if the pixel (x,y) is contained in the roi Z,T position then result.mask[(y * w) + x] = true
    if the pixel (x,y) is not contained in the roi Z,T position then result.mask[(y * w) + x] = false
    
    Overrides:
    
    getBooleanMask2D in class ROI4D
    
    Parameters:
    z - Z position we want to retrieve the boolean mask
    t - T 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 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 ROI4D
  - 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 ROI4D

Class ROI4DStack<R extends ROI3D>

Nested Class Summary

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

Field Summary

Fields inherited from class icy.roi.ROI4D

Fields inherited from class icy.roi.ROI

Constructor Summary

Method Summary

Methods inherited from class icy.roi.ROI4D

Methods inherited from class icy.roi.ROI

Methods inherited from class java.lang.Object

Field Detail

PROPERTY_USECHILDCOLOR

Constructor Detail

ROI4DStack

Method Detail

getDefaultName

getUseChildColor

setUseChildColor

setColor

setColor

setOpacity

setStroke

setCreating

setReadOnly

setFocused

setSelected

setC

isEmpty

getSizeT

getSlice

getSlice

setSlice

removeSlice

clear

computeBounds4D

contains

contains

intersects

hasSelectedPoint

unselectAllPoints

computeNumberOfContourPoints

computeNumberOfPoints

canTranslate

translate

translate

getBooleanMask2D

getBooleanMask2D

roiChanged

overlayChanged

iterator

loadFromXML

saveToXML