ROI5DStack

java.lang.Object
- icy.roi.ROI
- - icy.roi.ROI5D
  - - plugins.kernel.roi.roi5d.ROI5DStack<R>

Type Parameters:
R - the type of 4D ROI for each slice of this 5D ROI

All Implemented Interfaces:

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

Direct Known Subclasses:

ROI5DArea, ROI5DStackRectangle
```
public class ROI5DStack<R extends ROI4D>
extends ROI5D
implements ROIListener, OverlayListener, java.lang.Iterable<R>
```
Abstract class defining a generic 5D ROI as a stack of individual 4D ROI slices.

Author:

Alexandre Dufour, Stephane Dallongeville

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class ROI5DStack.ROI5DStackPainter
- 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`	`ROI5DStack.ROI5DStackPainter`

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String PROPERTY_USECHILDCOLOR
- 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

ROI5DStack(java.lang.Class<R> roiClass)
Creates a new 5D ROI based on the given 4D ROI type.

Constructors
Constructor and Description
`ROI5DStack(java.lang.Class<R> roiClass)` Creates a new 5D ROI based on the given 4D 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.
`Rectangle5D`	`computeBounds5D()` Calculate and returns the 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, double c)` Tests if a specified 5D point is inside the ROI.
`boolean`	`contains(double x, double y, double z, double t, double c, double sizeX, double sizeY, double sizeZ, double sizeT, double sizeC)` Tests if the `ROI` entirely contains the specified 5D rectangular area.
`BooleanMask2D`	`getBooleanMask2D(int z, int t, int c, boolean inclusive)` Returns the `BooleanMask2D` object representing the XY plan content at specified Z, T, C position.
`boolean[]`	`getBooleanMask2D(int x, int y, int width, int height, int z, int t, int c, boolean inclusive)` Returns the boolean array mask for the specified rectangular region at specified C, Z, T position.
`java.lang.String`	`getDefaultName()`
`int`	`getSizeC()`
`R`	`getSlice(int c)` Returns the ROI slice at given C position.
`R`	`getSlice(int c, boolean createIfNull)` Returns the ROI slice at given C position.
`boolean`	`getUseChildColor()` Returns `true` if the ROI directly uses the 4D slice color draw property and `false` if it uses the global 5D 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 c, double sizeX, double sizeY, double sizeZ, double sizeT, double sizeC)` Tests if the interior of the `ROI` intersects the interior of a specified 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 c)` Removes slice at the given C position and returns it.
`void`	`roiChanged(ROIEvent event)`
`boolean`	`saveToXML(org.w3c.dom.Node node)` SAVE
`void`	`setColor(java.awt.Color value)` Set the ROI painter base color.
`void`	`setColor(int c, 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 c, R roi4d)` Sets the slice for the given C position.
`void`	`setStroke(double value)` Set ROI painter stroke.
`void`	`setUseChildColor(boolean value)` Set to `true` if you want to directly use the 4D slice color draw property and `false` to keep the global 5D ROI color draw property.
`void`	`translate(double dx, double dy, double dz, double dt, double dc)` Translate the ROI position by the specified delta X/Y/Z/T.
`void`	`translate(int c)` Translate the stack of specified C position.
`void`	`unselectAllPoints()` Remove focus/selected state on all (control) points.

Methods inherited from class icy.roi.ROI5D
canSetBounds, canSetPosition, contains, getBooleanMask, getBooleanMask3D, getBooleanMask3D, getBooleanMask4D, getBooleanMask4D, getBooleanMask5D, getBounds, getDimension, getPosition, getROI5DList, getROI5DList, intersects, isActiveFor, setBounds5D, 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
  - ROI5DStack
```
public ROI5DStack(java.lang.Class<R> roiClass)
```
    Creates a new 5D ROI based on the given 4D ROI type.
- Method Detail
  - getDefaultName
```
public java.lang.String getDefaultName()
```
    Overrides:
    
    getDefaultName in class ROI5D
    
    Returns:
    the default name for this ROI class
  - getUseChildColor
```
public boolean getUseChildColor()
```
    Returns true if the ROI directly uses the 4D slice color draw property and false if it uses the global 5D ROI color draw property.
  - setUseChildColor
```
public void setUseChildColor(boolean value)
```
    Set to true if you want to directly use the 4D slice color draw property and false to keep the global 5D ROI color draw property.
    
    See Also:
    setColor(int, Color)
  - setColor
```
public void setColor(int c,
            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
  - isEmpty
```
public boolean isEmpty()
```
    Returns true if the ROI stack is empty.
    
    Overrides:
    
    isEmpty in class ROI
  - getSizeC
```
public int getSizeC()
```
    Returns:
    The size of this ROI stack along C.
    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 c)
```
    Returns the ROI slice at given C position.
  - getSlice
```
public R getSlice(int c,
         boolean createIfNull)
```
    Returns the ROI slice at given C position.
  - setSlice
```
public void setSlice(int c,
            R roi4d)
```
    Sets the slice for the given C position.
  - removeSlice
```
public R removeSlice(int c)
```
    Removes slice at the given C position and returns it.
  - clear
```
public void clear()
```
    Removes all slices.
  - computeBounds5D
```
public Rectangle5D computeBounds5D()
```
    Description copied from class: ROI
    
    Calculate and returns the bounding box of the ROI.
    This method is used by ROI.getBounds5D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.
    
    Specified by:
    
    computeBounds5D in class ROI
  - contains
```
public boolean contains(double x,
               double y,
               double z,
               double t,
               double c)
```
    Description copied from class: ROI
    
    Tests if a specified 5D point is inside the ROI.
    
    Specified by:
    
    contains in class ROI
    
    Returns:
    true if the specified Point5D is inside the boundary of the ROI; false otherwise.
  - contains
```
public boolean contains(double x,
               double y,
               double z,
               double t,
               double c,
               double sizeX,
               double sizeY,
               double sizeZ,
               double sizeT,
               double sizeC)
```
    Description copied from class: ROI
    Tests if the ROI entirely contains the specified 5D 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 ROI
    
    Parameters:
    x - the X coordinate of the start corner of the specified rectangular area
    y - the Y coordinate of the start corner of the specified rectangular area
    z - the Z coordinate of the start corner of the specified rectangular area
    t - the T coordinate of the start corner of the specified rectangular area
    c - the C coordinate of the start corner of the specified rectangular area
    sizeX - the X size of the specified rectangular area
    sizeY - the Y size of the specified rectangular area
    sizeZ - the Z size of the specified rectangular area
    sizeT - the T size of the specified rectangular area
    sizeC - the C size of the specified rectangular area
    
    Returns:
    true if the interior of the ROI entirely contains the specified rectangular area; false otherwise or, if the ROI contains the 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 c,
                 double sizeX,
                 double sizeY,
                 double sizeZ,
                 double sizeT,
                 double sizeC)
```
    Description copied from class: ROI
    Tests if the interior of the ROI intersects the interior of a specified rectangular area. The 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 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 rectangular area does not intersect the ROI.
    Specified by:
    
    intersects in class ROI
    
    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 ROI5D
  - 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 ROI5D
  - canTranslate
```
public boolean canTranslate()
```
    Description copied from class: ROI5D
    
    Returns true if the ROI support translate operation.
    
    Overrides:
    
    canTranslate in class ROI5D
    
    See Also:
    ROI5D.translate(double, double, double, double, double)
  - translate
```
public void translate(int c)
```
    Translate the stack of specified C position.
  - translate
```
public void translate(double dx,
             double dy,
             double dz,
             double dt,
             double dc)
```
    Description copied from class: ROI5D
    
    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 ROI5D.canTranslate() first.
    
    Overrides:
    
    translate in class ROI5D
    
    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
    dc - translation value to apply on C dimension
    See Also:
    ROI5D.canTranslate(), ROI5D.setPosition5D(Point5D)
  - getBooleanMask2D
```
public boolean[] getBooleanMask2D(int x,
                         int y,
                         int width,
                         int height,
                         int z,
                         int t,
                         int c,
                         boolean inclusive)
```
    Description copied from class: ROI
    
    Returns the boolean array mask for the specified rectangular region at specified C, Z, T position.
    
    If pixel (x1, y1, c, z, t) is contained in the roi:
    result[((y1 - y) * width) + (x1 - x)] = true
    If pixel (x1, y1, c, z, t) is not contained in the roi:
    result[((y1 - y) * width) + (x1 - x)] = false
    
    Overrides:
    
    getBooleanMask2D in class ROI
    
    Parameters:
    x - the X coordinate of the upper-left corner of the specified rectangular region
    y - the Y coordinate of the upper-left corner of the specified rectangular region
    width - the width of the specified rectangular region
    height - the height of the specified rectangular region
    z - Z position we want to retrieve the boolean mask
    t - T position we want to retrieve the boolean mask
    c - C 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,
                             int c,
                             boolean inclusive)
```
    Description copied from class: ROI
    
    Returns the BooleanMask2D object representing the XY plan content at specified Z, T, C position.
    
    If pixel (x, y, c, z, t) is contained in the roi:
    mask[(y - bounds.y) * bounds.width) + (x - bounds.x)] = true
    If pixel (x, y, c, z, t) is not contained in the roi:
    mask[(y - bounds.y) * bounds.width) + (x - bounds.x)] = false
    
    Overrides:
    
    getBooleanMask2D in class ROI5D
    
    Parameters:
    z - Z position we want to retrieve the boolean mask.
    Set it to -1 to retrieve the mask whatever is the Z position of ROI2D.
    t - T position we want to retrieve the boolean mask.
    Set it to -1 to retrieve the mask whatever is the T position of ROI2D/ROI3D.
    c - C position we want to retrieve the boolean mask.
    Set it to -1 to retrieve the mask whatever is the C position of ROI2D/ROI3D/ROI4D.
    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 ROI4D>
  - 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 ROI
  - 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 ROI

Class ROI5DStack<R extends ROI4D>

Nested Class Summary

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

Field Summary

Fields inherited from class icy.roi.ROI

Constructor Summary

Method Summary

Methods inherited from class icy.roi.ROI5D

Methods inherited from class icy.roi.ROI

Methods inherited from class java.lang.Object

Field Detail

PROPERTY_USECHILDCOLOR

Constructor Detail

ROI5DStack

Method Detail

getDefaultName

getUseChildColor

setUseChildColor

setColor

setColor

setOpacity

setStroke

setCreating

setReadOnly

setFocused

setSelected

isEmpty

getSizeC

getSlice

getSlice

setSlice

removeSlice

clear

computeBounds5D

contains

contains

intersects

hasSelectedPoint

unselectAllPoints

computeNumberOfContourPoints

computeNumberOfPoints

canTranslate

translate

translate

getBooleanMask2D

getBooleanMask2D

roiChanged

overlayChanged

iterator

loadFromXML

saveToXML